From moessing at uni-muenster.de Fri Jan 1 16:20:53 2016 From: moessing at uni-muenster.de (=?utf-8?Q?Wanja_M=C3=B6ssing?=) Date: Fri, 1 Jan 2016 16:20:53 +0100 Subject: [FieldTrip] =?utf-8?q?Vacant_Postdoc_Position_in_Visual_Cognition?= =?utf-8?q?/Cognitive_Neuroscience_at_the_University_of_M=C3=BCnster=2C_Ge?= =?utf-8?q?rmany?= Message-ID: <20160101152051.CE178BF402@SECMAIL.UNI-MUENSTER.DE> Our lab at the Institute of Psychology/University of Muenster, Germany, is currently looking for a postdoctoral researcher (TVL13 Mitarbeiterstelle). The initial appointment is for 3 years (extension possible). In brief, the successful applicant will contribute to the group's research projects and teaching in the Bachelor in Psychology program. Research in the lab focuses on visual cognition and cognitive neuroscience. Our research topics include visual masking, scene perception, and the role of brain oscillations in perception, attention and visual memory. Our arsenal of research methods includes psychophysics, EEG, and eye tracking (fMRI, MEG, and brain stimulation are available at other institutions in Muenster). Applicants should have strong interest in our research topics and solid experience with any of these research methods. Most of the teaching at our institute is in German; thus, good command of German is also a requirement. Application deadline is January 31 2016; we would like to fill this position until April 1. The detailed job ad is available (only in German; see requirement above) here: http://www.uni-muenster.de/Rektorat/Stellen/ausschreibungen/st_20150412_sk19.html If you are potentially interested in this position, I would be glad to answer any informal questions about the position, research, or application requirements (niko.busch at uni-muenster.de). Furthermore, I would be grateful if you could pass this information on to potentially interested colleagues. -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Sun Jan 3 00:49:25 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Sun, 3 Jan 2016 01:49:25 +0200 Subject: [FieldTrip] Fieldtrip compatibility Message-ID: Dear Fieldtrip team, Hope you are well and in good health, I am a PhD student in Compiegne University, working on "source localization and connectivity study of the sources of uterine activity for the prediction of the preterm labor''. The uterine electrical activity, measured noninvasively on the woman's abdomen by means of surface electrodes is referred to as the electrohysterogram (EHG= uterine electromyogram). We have the meshes of the uterus layers segmented from MRI, and we have a database for real pregnancy and labor signal. My question is does Fieldtrip toolbox able to deal with my data? Best regards, Saeed Zahran -------------- next part -------------- An HTML attachment was scrubbed... URL: From senakahks at gmail.com Sun Jan 3 04:38:49 2016 From: senakahks at gmail.com (Senaka Amarakeerthi) Date: Sun, 3 Jan 2016 09:08:49 +0530 Subject: [FieldTrip] Ft_databrowser layout error Message-ID: I am trying to visualise data from databrowser. But I end up with following error message. reading layout from file horizontal.lay Attempted to access laysels(14); index out of bounds because numel(laysels)=13. Error in ft_databrowser>redraw_cb (line 1821) laysel = laysels(i); Error in ft_databrowser (line 725) redraw_cb(h); Error in main (line 29) fg = ft_databrowser(cfg,data); script: cfg = []; cfg.dataset = 'Thilina.edf'; cfg.trl = [4 10 0; 12 20 0; 18 20 0; 22 110 0]; cfg.continuous = 'yes'; cfg.channel = {'all', '-COUNTER', '-INTERPOLATED', '-RAW_CQ', '-GYROX', '-GYROY', '-MARKER', '-SYNC', '-TIME_STAMP_s', '-TIME_STAMP_ms', '-CQ_AF3', '-CQ_F7', '-CQ_F3', '-CQ_FC5', '-CQ_T7', '-CQ_P7', '-CQ_O1', '-CQ_O2', '-CQ_P8', '-CQ_T8', '-CQ_FC6', '-CQ_F4', '-CQ_F8', '-CQ_AF4', '-CQ_CMS', '-CQ_DRL'}; data = ft_preprocessing(cfg); cfg.viewmode = 'horizontal'; fg = ft_databrowser(cfg,data); horizontal.lay file: 1 -0.545830 1.170536 0.290000 0.230000 AF3 2 -0.659023 0.813825 0.290000 0.230000 F3 3 -1.299041 0.943808 0.290000 0.230000 F7 4 -1.173172 0.450338 0.290000 0.230000 FC5 5 -1.299041 -0.943808 0.290000 0.230000 P7 6 -1.605703 -0.000000 0.290000 0.230000 T7 7 -0.496189 -1.527114 0.290000 0.230000 O1 8 0.545830 1.170536 0.290000 0.230000 AF4 9 0.659023 0.813825 0.290000 0.230000 F4 10 1.299041 0.943808 0.290000 0.230000 F8 11 1.173172 0.450338 0.290000 0.230000 FC6 12 1.299041 -0.943808 0.290000 0.230000 P8 13 1.527114 -0.496189 0.290000 0.230000 TP8 14 0.496189 -1.527114 0.290000 0.230000 O2 Your support to get this error fixed is highly appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Sun Jan 3 20:20:12 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Sun, 3 Jan 2016 19:20:12 +0000 Subject: [FieldTrip] (no subject) Message-ID: Dear Fieldtrip team, I am currently working on data acquired from an elektra system (neuromag). I have done all the preprocessing and the ft_freqanalysis with the gradiometers only. I combined the gradiometers to create planar gradients.However , later when doing the statistics problems occur when i want to specify the channels. The error tells me that no degrees of freedom are found for the analysis. However, when i remove the cfg.channel form the script it runs through without an error. (please see code below). My question is whether the output of the stastistic is correct without specifying the channels? If not, does anybody have suggestions how to fix the problem? I have run into similar problems when wanting to plot the time frequency data from the planar gradients after having used ft_combineplanar. Here i cannot find a layout file that suits the output of ft_combineplanar. Thus, i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, however, the layouts provided by fieldtrip does not fit that number. Has anybody run into similar problems? Or does anybody know a possible solution? Thank you very much for any suggestions Victoria %combine planar cfg = []; cfg.method ='sum'; %ComCon = ft_combineplanar(cfg,FreqCon); ComIncon = ft_combineplanar(cfg, FreqIncon); cfg = []; %cfg.channel = {'MEG'}; cfg.latency = 'all'; cfg.frequency = [14.5 16]; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; cfg_neighb.method = 'distance'; cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); design = zeros(1,size(ComGrad_con.powspctrm,1) + size(ComGrad_incon.powspctrm,1)); design(1,1:size(ComGrad_con.powspctrm,1)) = 1; design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... size(ComGrad_incon.powspctrm,1))) = 2; -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Sun Jan 3 21:18:22 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 3 Jan 2016 21:18:22 +0100 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: Dear Victoria, the system you are working with is already equipped with two orthogonal planar gradiometer sensors. Thus you should not try to create planar gradients on the basis of the planar gradients. Yet you might want to use the magnetometers only. There you can represent the activity as if it was picked up by planar gradients. Could you please skip the planar transformation bit and redo your analysis? FieldTrip provides three types of layouts for the Neuromag system: NM306all.lay NM306mag.lay NM306grad.lay. For example if you want to plot magnetometers only you’d specify cfg.layout = 'neuromag306mag.lay’; cfg.channel = 'MEG*1’; Here MEG*1 refers to magnetometers and MEG*2 and MEG*3 would be the two orthogonal planar gradients respectively. Also the neighbours are provided as neuromag306cmb_neighb.mat; neuromag306mag_neighb.mat; neuromag306planar_neighb.mat;. You might consider loading the structure of your choice directly. Here is an example tutorial that might help: http://www.fieldtriptoolbox.org/tutorial/natmeg/timefrequency Good luck, tzvetan > Dear Fieldtrip team, > > I am currently working on data acquired from an elektra system (neuromag). I have done all the preprocessing and the ft_freqanalysis with the gradiometers only. I combined the gradiometers to create planar gradients.However , later when doing the statistics problems occur when i want to specify the channels. The error tells me that no degrees of freedom are found for the analysis. However, when i remove the cfg.channel form the script it runs through without an error. (please see code below). > My question is whether the output of the stastistic is correct without specifying the channels? If not, does anybody have suggestions how to fix the problem? > > I have run into similar problems when wanting to plot the time frequency data from the planar gradients after having used ft_combineplanar. Here i cannot find a layout file that suits the output of ft_combineplanar. Thus, i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, however, the layouts provided by fieldtrip does not fit that number. > Has anybody run into similar problems? Or does anybody know a possible solution? > > Thank you very much for any suggestions > Victoria > > %combine planar > cfg = []; > cfg.method ='sum'; > %ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > cfg = []; > %cfg.channel = {'MEG'}; > cfg.latency = 'all'; > cfg.frequency = [14.5 16]; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); > > design = zeros(1,size(ComGrad_con.powspctrm,1) + size(ComGrad_incon.powspctrm,1)); > design(1,1:size(ComGrad_con.powspctrm,1)) = 1; > design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... > size(ComGrad_incon.powspctrm,1))) = 2; > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From slama at berkeley.edu Mon Jan 4 02:22:43 2016 From: slama at berkeley.edu (Katarina Slama) Date: Sun, 3 Jan 2016 17:22:43 -0800 Subject: [FieldTrip] Inferential statistics on connectivity data? Message-ID: Dear Fieldtrip community, My name is Katarina Slama. I’m a graduate student in the Knight lab at UC Berkeley, and I use ECoG to study visual attention. I am currently examining connectivity in ECoG data using ft_connectivityanalysis (cfg and data structures below). I have computed partial coherence values for a network of electrodes. Now I would like to assess the statistical significance of each of the edges by computing a non-parametric equivalent of a one-sample t-test on the coherence values over trials. I have two questions: 1. Is there a way to obtain a separate partial coherence value for each trial? At present, the partial coherence structure that ft_connectivityanalysis creates has the dimord “chan_chan_freq”. 2. Is there a fieldtrip function that is designed for computing statistics on connectivity metrics? I have been advised to look into ft_freqstatistics, but this function does not seem to be designed for the output of ft_connectivityanalysis. — input structure (freq): label: {'34' '35' '36' '37' '38' '39' '44' '45' '47' '48' '49' '50' '51' '52' '53' '54' '55' '56' '57' '62' '63' '64' '76' '77' '80' '99' '100' '101'} dimord: 'rpttap_chan_freq' freq: [2.0000 3.0000 4.0000] fourierspctrm: [220x28x3 double] cumsumcnt: [220x1 double] cumtapcnt: [220x1 double] trialinfo: [220x1 double] cfg: [1x1 struct] configuration (cfg): cfg = []; cfg.method = 'coh'; cfg.partchannel = freq.label(1); cfg.keeptrials = 'yes'; partcoh = ft_connectivityanalysis(cfg,freq); output structure (partcoh) label: {27x1 cell} dimord: 'chan_chan_freq' cohspctrm: [27x27x3 double] freq: [2.0000 3.0000 4.0000] cfg: [1x1 struct] — Thank you and best wishes, Kata -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Jan 4 09:16:28 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 4 Jan 2016 09:16:28 +0100 Subject: [FieldTrip] Fieldtrip compatibility In-Reply-To: References: Message-ID: <5E6A3CD3-4736-4AD6-B815-78713B323FC6@donders.ru.nl> Dear Saeed, Happy New Year. FieldTrip can be used for channel level time series analysis and forward and inverse volume conduction modelling of ExG. The typical application (besides MEG, i.e. magnetic measurements of brain activity) is EEG, but we also use if for intracranial EEG and for EMG. I see no reason why EHG would not work. The way you have your data represented in files on disk might be different than what is common for EEG, but see here http://www.fieldtriptoolbox.org/dataformat. This should not be too hard to deal with. The more important difference might be in the assumptions on the sources that are required for the inverse modelling. In EHG I presume you will be interested in localizing the contractions of the uterus. That is muscle activity which propagates (i.e. changes spatially over time), which may have different characteristics than the activity that we model in the brain. Also this is something that can be dealt with, but it is not merely a technical detail and it requires careful consideration of the inverse model assumptions. I know that Ahmad Diab (who I suppose is a colleague of yours) used FieldTrip for his thesis https://tel.archives-ouvertes.fr/tel-01237525/document. I suggest you look at details there and consult Ahmad. best regards, Robert On 03 Jan 2016, at 00:49, saeed zahran wrote: > Dear Fieldtrip team, > > Hope you are well and in good health, > > I am a PhD student in Compiegne University, working on "source localization and connectivity study of the sources of uterine activity for the prediction of the preterm labor''. > > The uterine electrical activity, measured noninvasively on the woman's abdomen by means of surface electrodes is referred to as the electrohysterogram (EHG= uterine electromyogram). > > We have the meshes of the uterus layers segmented from MRI, and we have a database for real pregnancy and labor signal. My question is does Fieldtrip toolbox able to deal with my data? > > Best regards, > Saeed Zahran > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Mon Jan 4 10:27:31 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 4 Jan 2016 10:27:31 +0100 Subject: [FieldTrip] clarification on beam forming evoked fields in MEG In-Reply-To: <7E884835-8D6B-47E6-987E-7C174A828C07@gmail.com> References: <7E884835-8D6B-47E6-987E-7C174A828C07@gmail.com> Message-ID: Hi Russ, The units that are used by FieldTrip in data processing are not always consistent. The problem already starts at the level of reading (where we sometimes use our own FT code, and sometimes code from other projects). MEG data might be represented in T or fT, but for Eleka there are also gradiometers that have their data expressed as T/m or fT/cm or T/mm or … Then the anatomical MRi is read in, coregistered and used to construct a volume conduction model. In that volume conduction model there is again geometrical units (m, cm, mm) but also units of conductivity. You can imagine that combining data (in algorithms) that has different units will lead to unexpected results. Hence I usually play it safe and report on the results of computations as “arbitrary units”. Mostly in statistics and interpretation it does not matter anyway. If you use SI units throughout, then the low-level FieldTrip code will work as expected and also represent the output of all computations in SI units. For anatomical models you can use ft_convert_units to scale it to meters. For electrode and gradiometer arrays you should use the distance and amplitude option in ft_datatype_sens (see the code, it is not mentioned in the help) and for Elekta the scaling should be specified as ‘amplitude/distance’. The unit handling is a known issue and we have a number of ideas on http://bugzilla.fieldtriptoolbox.org to improve it, but to little resources to actually get it resolved. best regards, Robert PS Note that for spectral analysis it is again different, since spectral power or density can be differently normalized. Also in that aspect the FT code is not 100% consistent. But since you mention ERFs that does not apply. On 31 Dec 2015, at 22:51, russ port wrote: > Dear Robert and Jan-Mathijs > > I was hoping for someone to help me with a point of clarification concerning the fieldtrip wiki. I have followed Fieldtrip’s example of creating virtual sensor ERFs for MEG data using LMCV beamforming (e.g. http://www.fieldtriptoolbox.org/tutorial/aarhus/beamformingerf). I get great ERFs for auditory responses that I’m happy with. There is a point on contention left between my lab mates and I though. Following what was discuss previously (http://mailman.science.ru.nl/pipermail/fieldtrip/2015-September/009609.html), I think that the ERF are in a “unit-less” unit. They suggest however, that these (as mentioned in the wiki) are related to equivalent current dipoles for the chosen sources (and so the unit would be A/m [or since we used cm in the head model, A/cm]). Please can you help clear up this point of contention? > > Thanks > Russ -------------- next part -------------- An HTML attachment was scrubbed... URL: From marta.bortoletto at cognitiveneuroscience.it Mon Jan 4 14:33:44 2016 From: marta.bortoletto at cognitiveneuroscience.it (Marta Bortoletto) Date: Mon, 4 Jan 2016 13:33:44 +0000 (UTC) Subject: [FieldTrip] Applying wPLI to sLORETA-derived sources? References: <1782756321.10177641.1451914424709.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <1782756321.10177641.1451914424709.JavaMail.yahoo@mail.yahoo.com> Dear Community,I have resting-state data obtained by 70-channel EEGrecording. I have calculated EEG sources and obtained estimated signal in 88 Brodmannareas (BAs) by means of sLORETA. Now I would like to measure connectivitybetween these BAs. I have seen that many connectivity measures have beendeveloped in fieldtrip, including the weighted Phase Lag Index (wPLI). Giventhat wPLI estimates time-lagged interdependences, is it appropriate to apply wPLIto sLORETA estimated sources? Thank you for your help! Marta Marta Bortoletto, PhD Cognitive Neuroscience Section, IRCCS Centro San Giovanni di Dio Fatebenefratelli Via Pilastroni 4, 25125 Brescia, Italy Phone number: (+39) 0303501594 E-mail: marta.bortoletto at cognitiveneuroscience.it web: http://www.cognitiveneuroscience.it/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon Jan 4 17:02:49 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 4 Jan 2016 17:02:49 +0100 Subject: [FieldTrip] Applying wPLI to sLORETA-derived sources? In-Reply-To: <1782756321.10177641.1451914424709.JavaMail.yahoo@mail.yahoo.com> References: <1782756321.10177641.1451914424709.JavaMail.yahoo.ref@mail.yahoo.com> <1782756321.10177641.1451914424709.JavaMail.yahoo@mail.yahoo.com> Message-ID: <269EB91B-FE42-4B47-A470-8AD7A5C71EC0@uni-konstanz.de> Dear Marta, the applicability of connectivity metrics in FieldTrip (including wPLI) is independent of the inverse operator. So the answer is yes and no. It is appropriate if you have the single observations (i.e. epochs that you cut the data into) kept in the output of your source reconstruction analysis. I guess you have 88 source waveforms and not 88 x Ntrials time series. If this is correct wPLI or any phase metric is rather inappropriate. Good luck, tzvetan > Dear Community, > I have resting-state data obtained by 70-channel EEG recording. I have calculated EEG sources and obtained estimated signal in 88 Brodmann areas (BAs) by means of sLORETA. Now I would like to measure connectivity between these BAs. I have seen that many connectivity measures have been developed in fieldtrip, including the weighted Phase Lag Index (wPLI). Given that wPLI estimates time-lagged interdependences, is it appropriate to apply wPLI to sLORETA estimated sources? > > Thank you for your help! > > Marta > > Marta Bortoletto, PhD > Cognitive Neuroscience Section, > IRCCS Centro San Giovanni di Dio Fatebenefratelli > Via Pilastroni 4, 25125 Brescia, Italy > Phone number: (+39) 0303501594 > E-mail: marta.bortoletto at cognitiveneuroscience.it > web: http://www.cognitiveneuroscience.it/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tmadsen at emory.edu Mon Jan 4 21:29:55 2016 From: tmadsen at emory.edu (Teresa Madsen) Date: Mon, 4 Jan 2016 15:29:55 -0500 Subject: [FieldTrip] How are bugs triaged? Message-ID: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 -------------- next part -------------- An HTML attachment was scrubbed... URL: From slama at berkeley.edu Tue Jan 5 01:14:42 2016 From: slama at berkeley.edu (Katarina Slama) Date: Mon, 4 Jan 2016 16:14:42 -0800 Subject: [FieldTrip] How to interpret content of partial PLV-spectrum when dimensionality is inconsistent with dimord? Message-ID: Dear Fieldtrip community, Happy new year! I have a question about computing partial PLV-values using ft_connectivityanalysis: When I try to compute PLV-values, and request that one channel be partialized, the resulting PLV-spectrum has the dimensionality 27 x 27 x 28 x 3, while dimord reports it to be: chan_chan_freq. Why this inconsistency, and how should I interpret the contents of this PLV-spectrum? I provide information about my input and output structures below. — input structure (freq): label: {'34' '35' '36' '37' '38' '39' '44' '45' '47' '48' '49' '50' '51' '52' '53' '54' '55' '56' '57' '62' '63' '64' '76' '77' '80' '99' '100' '101'} dimord: 'rpttap_chan_freq' freq: [2.0000 3.0000 4.0000] fourierspctrm: [220x28x3 double] cumsumcnt: [220x1 double] cumtapcnt: [220x1 double] trialinfo: [220x1 double] cfg: [1x1 struct] configuration structure (cfg): method: 'plv' partchannel: {'34'} plv_struct = ft_connectivityanalysis(cfg,freq); output structure (plv_struct): label: {27x1 cell} dimord: 'chan_chan_freq' plvspctrm: [4-D double] freq: [2.0000 3.0000 4.0000] dof: 220 cfg: [1x1 struct] — Thank you very much for your help! Best, Kata -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jan 5 09:10:21 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 5 Jan 2016 08:10:21 +0000 Subject: [FieldTrip] How to interpret content of partial PLV-spectrum when dimensionality is inconsistent with dimord? In-Reply-To: References: Message-ID: <0AE94B5A-16C1-40C1-8FD3-4523B25FC6FF@fcdonders.ru.nl> Hi Katarina, Good question. Could be a bug. Could you file this on bugzilla.fieldtriptoolbox.org, and upload the necessary data so that we can try and reproduce it? Thanks and best, Jan-Mathijs On Jan 5, 2016, at 1:14 AM, Katarina Slama wrote: > Dear Fieldtrip community, > > Happy new year! > > I have a question about computing partial PLV-values using ft_connectivityanalysis: > > When I try to compute PLV-values, and request that one channel be partialized, the resulting PLV-spectrum has the dimensionality 27 x 27 x 28 x 3, while dimord reports it to be: chan_chan_freq. Why this inconsistency, and how should I interpret the contents of this PLV-spectrum? > > I provide information about my input and output structures below. > > — > input structure (freq): > label: {'34' '35' '36' '37' '38' '39' '44' '45' '47' '48' '49' '50' '51' '52' '53' '54' '55' '56' '57' '62' '63' '64' '76' '77' '80' '99' '100' '101'} > dimord: 'rpttap_chan_freq' > freq: [2.0000 3.0000 4.0000] > fourierspctrm: [220x28x3 double] > cumsumcnt: [220x1 double] > cumtapcnt: [220x1 double] > trialinfo: [220x1 double] > cfg: [1x1 struct] > > configuration structure (cfg): > method: 'plv' > partchannel: {'34'} > > plv_struct = ft_connectivityanalysis(cfg,freq); > > output structure (plv_struct): > label: {27x1 cell} > dimord: 'chan_chan_freq' > plvspctrm: [4-D double] > freq: [2.0000 3.0000 4.0000] > dof: 220 > cfg: [1x1 struct] > — > > Thank you very much for your help! > > Best, > Kata > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Tue Jan 5 09:27:18 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 5 Jan 2016 08:27:18 +0000 Subject: [FieldTrip] How are bugs triaged? In-Reply-To: References: Message-ID: Hi Teresa, Generally, we don’t have an ‘official’ triage system for the bugs that are filed. The speed with which a bug is considered/resolved depends on a combination of things: 1) the quality of the bug report. 2) the perceived urgency by the people who would be able to resolve it. 3) the estimated cost-benefit relationship for the people who would be able to resolve it. 4) the amount of other piled-up work for the people who would be able to resolve it. 5) the level of serotonin. 6) the prospect of compensation in kind (beer/chocolate/formal involvement in projects etc). Thus, in general, there may be things that the bug filer can do to increase the probability for consideration/resolution, including adding code snippets and data that allow for a reproduction of a genuine bug, or by including code snippets that implement a new feature. Note that in general feature requests that are not a priority for the daily scientific work of the development/fixing team will get a low priority. In addition it should be noted that anybody who is on the list is allowed to contribute fixes/patches/features, and that it is not the responsibility of the core development team (which nowadays extends far beyond the people at the Donders Centre). Also, it should be noted that nobody has a formal requirement to provide fieldtrip/bugzilla support, it’s all pro bono. This means that we have to squeeze it in besides our daily scientific work and additional chores. Anyway, the problem is that we are just short-handed, which indeed sometimes results in bugs already being ‘open’ for a long time. Our oldest one still open dates from 2010, so the 2013 you mention is not that bad :o). With regard to the NEX file reader error you mentioned, if you think your workaround might be of benefit of other users, don’t hesitate to contribute! Best wishes, Jan-Mathijs On Jan 4, 2016, at 9:29 PM, Teresa Madsen > wrote: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tmadsen at emory.edu Tue Jan 5 18:39:14 2016 From: tmadsen at emory.edu (Teresa Madsen) Date: Tue, 5 Jan 2016 12:39:14 -0500 Subject: [FieldTrip] How are bugs triaged? (Schoffelen, J.M. (Jan Mathijs)) Message-ID: Thanks for the insight, Jan-Mathijs. I'm not exactly sure how to contribute... I'm not familiar with SVN or GIT, and it would likely be small improvements that I would suggest, not whole new functions or anything. So could I just post the applicable snippets of code as a comment on the bug report? Will anyone see it there? When I update a previously posted bug, I see this message: Changes submitted for bug 2093 Email sent to:no oneExcluding:fieldtrip-bugs at donders.ru.nl, braingirl at gmail.com So I'm assuming no one knows. Is there a way to send it back to the bug listserv? Or should I really just learn how to use GIT (which seems more straightforward than SVN - is that true?)? ;-) Thanks again, Teresa ------------------------------ > > Message: 6 > Date: Tue, 5 Jan 2016 08:27:18 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] How are bugs triaged? > Message-ID: > Content-Type: text/plain; charset="windows-1252" > > Hi Teresa, > > Generally, we don?t have an ?official? triage system for the bugs that are > filed. The speed with which a bug is considered/resolved depends on a > combination of things: > > 1) the quality of the bug report. > 2) the perceived urgency by the people who would be able to resolve it. > 3) the estimated cost-benefit relationship for the people who would be > able to resolve it. > 4) the amount of other piled-up work for the people who would be able to > resolve it. > 5) the level of serotonin. > 6) the prospect of compensation in kind (beer/chocolate/formal involvement > in projects etc). > > Thus, in general, there may be things that the bug filer can do to > increase the probability for consideration/resolution, including adding > code snippets and data that allow for a reproduction of a genuine bug, or > by including code snippets that implement a new feature. Note that in > general feature requests that are not a priority for the daily scientific > work of the development/fixing team will get a low priority. > > In addition it should be noted that anybody who is on the list is allowed > to contribute fixes/patches/features, and that it is not the responsibility > of the core development team (which nowadays extends far beyond the people > at the Donders Centre). Also, it should be noted that nobody has a formal > requirement to provide fieldtrip/bugzilla support, it?s all pro bono. > This means that we have to squeeze it in besides our daily scientific work > and additional chores. > > Anyway, the problem is that we are just short-handed, which indeed > sometimes results in bugs already being ?open? for a long time. Our oldest > one still open dates from 2010, so the 2013 you mention is not that bad > :o). With regard to the NEX file reader error you mentioned, if you think > your workaround might be of benefit of other users, don?t hesitate to > contribute! > > Best wishes, > Jan-Mathijs > > > > > On Jan 4, 2016, at 9:29 PM, Teresa Madsen tmadsen at emory.edu>> wrote: > > I'm just curious because I've gotten such quick responses and fixes on > some bugs, while others sit around for long periods of time without any > feedback. Luckily, they're not anything stopping me from doing my work, > but I was just curious if they've been seen and determined to be of low > priority, or simply overlooked. > > Examples: > http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" > button on GUI for ft_rejectvisual (summary mode) plots average of all > trials instead of the single trial requested - first posted in October > http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file > reader errors - posted in 2013 - Obviously, I've worked around it, but it's > still there with a status of "new"! > > Hope I'm not being a pest. > Thanks, > Teresa > > -- > Teresa E. Madsen, PhD > Division of Behavioral Neuroscience and Psychiatric Disorders > Yerkes National Primate Research Center > Emory University > Rainnie Lab, NSB 5233 > 954 Gatewood Rd. NE > Atlanta, GA 30329 > (770) 296-9119 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160105/9b0ab1ac/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 4 > **************************************** > -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Jan 6 09:09:12 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 6 Jan 2016 08:09:12 +0000 Subject: [FieldTrip] How are bugs triaged? In-Reply-To: References: Message-ID: <9670C70F-D4E8-4445-865C-5B41FAF81D3E@fcdonders.ru.nl> Hi Teresa, Yes, one way of contributing would be to add snippets of code to the bug. In order to attract other people’s attention, you could add (judiciously) people to the CC-list of the bug. That way you ensure that these people receive an e-mail message once the bug is updated. Note, that people then can remove themselves again if they don’t like to be updated, which is a thing that needs to be respected. Note also, that adding a group e-mail address, such as fieldtrip-bugs at donders.ru.nl is likely less efficient than adding named persons, because members of the group may feel less inclined to be actively involved if addressed as a group, rather than as an individual. Best, Jan-Mathijs On Jan 5, 2016, at 6:39 PM, Teresa Madsen > wrote: Thanks for the insight, Jan-Mathijs. I'm not exactly sure how to contribute... I'm not familiar with SVN or GIT, and it would likely be small improvements that I would suggest, not whole new functions or anything. So could I just post the applicable snippets of code as a comment on the bug report? Will anyone see it there? When I update a previously posted bug, I see this message: Changes submitted for bug 2093 Email sent to: no one Excluding: fieldtrip-bugs at donders.ru.nl, braingirl at gmail.com So I'm assuming no one knows. Is there a way to send it back to the bug listserv? Or should I really just learn how to use GIT (which seems more straightforward than SVN - is that true?)? ;-) Thanks again, Teresa ------------------------------ Message: 6 Date: Tue, 5 Jan 2016 08:27:18 +0000 From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] How are bugs triaged? Message-ID: > Content-Type: text/plain; charset="windows-1252" Hi Teresa, Generally, we don?t have an ?official? triage system for the bugs that are filed. The speed with which a bug is considered/resolved depends on a combination of things: 1) the quality of the bug report. 2) the perceived urgency by the people who would be able to resolve it. 3) the estimated cost-benefit relationship for the people who would be able to resolve it. 4) the amount of other piled-up work for the people who would be able to resolve it. 5) the level of serotonin. 6) the prospect of compensation in kind (beer/chocolate/formal involvement in projects etc). Thus, in general, there may be things that the bug filer can do to increase the probability for consideration/resolution, including adding code snippets and data that allow for a reproduction of a genuine bug, or by including code snippets that implement a new feature. Note that in general feature requests that are not a priority for the daily scientific work of the development/fixing team will get a low priority. In addition it should be noted that anybody who is on the list is allowed to contribute fixes/patches/features, and that it is not the responsibility of the core development team (which nowadays extends far beyond the people at the Donders Centre). Also, it should be noted that nobody has a formal requirement to provide fieldtrip/bugzilla support, it?s all pro bono. This means that we have to squeeze it in besides our daily scientific work and additional chores. Anyway, the problem is that we are just short-handed, which indeed sometimes results in bugs already being ?open? for a long time. Our oldest one still open dates from 2010, so the 2013 you mention is not that bad :o). With regard to the NEX file reader error you mentioned, if you think your workaround might be of benefit of other users, don?t hesitate to contribute! Best wishes, Jan-Mathijs On Jan 4, 2016, at 9:29 PM, Teresa Madsen >> wrote: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 62, Issue 4 **************************************** -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jorn at artinis.com Wed Jan 6 09:28:16 2016 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 Jan 2016 09:28:16 +0100 Subject: [FieldTrip] How are bugs triaged? In-Reply-To: <9670C70F-D4E8-4445-865C-5B41FAF81D3E@fcdonders.ru.nl> References: <9670C70F-D4E8-4445-865C-5B41FAF81D3E@fcdonders.ru.nl> Message-ID: <001d01d1485c$3128bec0$937a3c40$@artinis.com> Hi Teresa, Adding to JM’s last mail, it might be important to note that every new bug is automatically sent out to fieldtrip-bugs at donders.ru.nl , so that the core dev team will get notified, so the dev team is aware of new bugs being posted. But as JM said, depending on subjective prioritization, it might get ignored anyhow. Best, Jörn -- Jörn M. Horschig, PhD, Software Engineer Artinis Medical Systems | +31 481 350 980 From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Schoffelen, J.M. (Jan Mathijs) Sent: Wednesday, January 6, 2016 9:09 To: FieldTrip discussion list Subject: Re: [FieldTrip] How are bugs triaged? Hi Teresa, Yes, one way of contributing would be to add snippets of code to the bug. In order to attract other people’s attention, you could add (judiciously) people to the CC-list of the bug. That way you ensure that these people receive an e-mail message once the bug is updated. Note, that people then can remove themselves again if they don’t like to be updated, which is a thing that needs to be respected. Note also, that adding a group e-mail address, such as fieldtrip-bugs at donders.ru.nl is likely less efficient than adding named persons, because members of the group may feel less inclined to be actively involved if addressed as a group, rather than as an individual. Best, Jan-Mathijs On Jan 5, 2016, at 6:39 PM, Teresa Madsen > wrote: Thanks for the insight, Jan-Mathijs. I'm not exactly sure how to contribute... I'm not familiar with SVN or GIT, and it would likely be small improvements that I would suggest, not whole new functions or anything. So could I just post the applicable snippets of code as a comment on the bug report? Will anyone see it there? When I update a previously posted bug, I see this message: Changes submitted for bug 2093 Email sent to: no one Excluding: fieldtrip-bugs at donders.ru.nl , braingirl at gmail.com So I'm assuming no one knows. Is there a way to send it back to the bug listserv? Or should I really just learn how to use GIT (which seems more straightforward than SVN - is that true?)? ;-) Thanks again, Teresa ------------------------------ Message: 6 Date: Tue, 5 Jan 2016 08:27:18 +0000 From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] How are bugs triaged? Message-ID: > Content-Type: text/plain; charset="windows-1252" Hi Teresa, Generally, we don?t have an ?official? triage system for the bugs that are filed. The speed with which a bug is considered/resolved depends on a combination of things: 1) the quality of the bug report. 2) the perceived urgency by the people who would be able to resolve it. 3) the estimated cost-benefit relationship for the people who would be able to resolve it. 4) the amount of other piled-up work for the people who would be able to resolve it. 5) the level of serotonin. 6) the prospect of compensation in kind (beer/chocolate/formal involvement in projects etc). Thus, in general, there may be things that the bug filer can do to increase the probability for consideration/resolution, including adding code snippets and data that allow for a reproduction of a genuine bug, or by including code snippets that implement a new feature. Note that in general feature requests that are not a priority for the daily scientific work of the development/fixing team will get a low priority. In addition it should be noted that anybody who is on the list is allowed to contribute fixes/patches/features, and that it is not the responsibility of the core development team (which nowadays extends far beyond the people at the Donders Centre). Also, it should be noted that nobody has a formal requirement to provide fieldtrip/bugzilla support, it?s all pro bono. This means that we have to squeeze it in besides our daily scientific work and additional chores. Anyway, the problem is that we are just short-handed, which indeed sometimes results in bugs already being ?open? for a long time. Our oldest one still open dates from 2010, so the 2013 you mention is not that bad :o). With regard to the NEX file reader error you mentioned, if you think your workaround might be of benefit of other users, don?t hesitate to contribute! Best wishes, Jan-Mathijs On Jan 4, 2016, at 9:29 PM, Teresa Madsen >> wrote: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 62, Issue 4 **************************************** -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Wed Jan 6 19:57:31 2016 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Wed, 6 Jan 2016 18:57:31 +0000 Subject: [FieldTrip] =?windows-1252?q?3rd_ESCAN_Porto_CONFERENCE_=96_EXTEN?= =?windows-1252?q?DED_SUBMISSION_DEADLINE_=96_22nd_January_2016?= Message-ID: <2BAB036A9BAEA44984A131DFCE446108010BFDAB11@SRVMBX01.fpceup.psi.up.pt> Dear colleagues, In order to allow for a full recovery from the holiday season the submission deadline for the 3rd International Conference of the European Society for Cognitive and Affective Neuroscience (ESCAN) in Porto has been extended to the 22nd of January, 2016. To submit your abstract for a symposium or oral/poster presentation and for all details on the conference please visit the website: www.escan2016.eu We would appreciate it if you could pass this information along to other colleagues and students. We are looking forward to seeing you in Porto in 2016! ESCAN 2016 Porto Local Organizing Committee -------------- next part -------------- An HTML attachment was scrubbed... URL: From mbj0310 at gmail.com Thu Jan 7 14:23:03 2016 From: mbj0310 at gmail.com (Beom Jun Min) Date: Thu, 7 Jan 2016 22:23:03 +0900 Subject: [FieldTrip] Using loreta2fieldtrip Message-ID: Dear community, I tried to load sLORETA data into the fieldtrip. My experiment is a kind of ERP experiment. And currently I have 5 subjects' data with 6 different conditions. With the related instructions ( http://www.fieldtriptoolbox.org/integrating_with/integrating_with_loreta), I made the volume structures of each condition (averaged over trials) for each subject (30 files). My converted volume structures have the following contents. dim [37,44,36] transform <44 double> inside <6239x1 double> outside <52369x1 double> {mom} <37x44x36 cell> cfg <1x1 struct> Is this structure is compatible with the up-to-date version of fieldtrip? It seems the ft_sourcegrandaverage function requires parameters such as pow, nai or coh. Best regards -- BeomJun Min, M.D. Department of Medical System Engineering (DMSE) Gwangju Institute of Science and Technology (GIST) 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 500-712, Republic of Korea (South) Phone: +82-62-715-3266 / Fax: +82-62-715-3244 E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Jan 7 17:58:09 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 7 Jan 2016 17:58:09 +0100 Subject: [FieldTrip] Job vacancies MRI/MEG physicists/engineers in Oldenburg References: <568E815B.7080205@uni-oldenburg.de> Message-ID: On 07 Jan 2016, at 16:16, Stefan Debener wrote: > The European Medical School is a cooperation project between the Universities of Oldenburg and Groningen and three local hospitals. > The newly founded Neuroimaging Center at the University of Oldenburg, Germany, offers the following two positions > > 1. MEG-Physicist/Engineer (E13/TV-L, initially 3 years) > > 2. MRI-Physicist/Engineer (E13/TV-L, initially 3 years) > > The positions are suitable for part-time work. > > The Neuroimaging Center hosts a state of the art magnetoencephalograph (ElektaTriux) and a magnetic resonance tomograph (Siemens Prisma 3T) and is embedded in an excellent interdisciplinary scientific environment with a strong research focus on neurosensory, neurocognitive, and medicalresearch. > > We seek for highly motivated post-doctoral candidates (with PhD) with an academic university degree in physics, engineering or related fields, with documented research experience in magnetoencephalography (position 1) or magnetic resonance imaging (position 2). For both positions, fluency in English is necessary. German and experience in the design of neurocognitive experiments are desirable. > > Successful candidates will be responsible for the operation and administration of the MEG system and MRI system respectively, their infrastructure, the development and improvement of measurement and analyses techniques and user consultancy. > > The University of Oldenburg is rapidly growing and offers a vibrant scientific environment with strong foci on cognitive and sensory neuroscience and a new medical school. Oldenburg is an attractive city in Germany's northwest with excellent quality of life. It is close to Bremen, Hamburg, Groningen, and approx. 1 h from the north sea. > > The University of Oldenburg is dedicated to increasing the percentage of women in science. Therefore, female candidates are particularly encouraged to apply and will be given preference in cases of equal qualification. Handicapped applicants will be given preference if equally qualified. > > Electronic applications (one pdf file) are preferred and can be send to: > Professor Dr. JochemRieger: Jochem.rieger at uni-oldenburg.de > Applications by mail should be sent to > Prof. Jochem Rieger > Universität Oldenburg > Kuepkersweg 74 (W30) > 26129 Oldenburg > Germany > > The application process is open until January 31st 2016. Applications should include your CV, a list of most recent publications, and a statement (max. 3 pages). > From RICHARDS at mailbox.sc.edu Fri Jan 8 18:15:01 2016 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Fri, 8 Jan 2016 17:15:01 +0000 Subject: [FieldTrip] Using loreta2fieldtrip (Beom Jun Min) Message-ID: <2215ED56-32F8-491B-9CD4-87B8D820A719@mailbox.sc.edu> Beom Jun Min: I am not sure of the exact answer, but…. Many of FT procedures require a pos (position) matrix, which is the s/c/a x/y/z positions of each dipole, and some other position information (e.g., mm; name of space; ft volume realign). This may not be necessary for a specific proc (ft_sourcegrandaverage) but is for other (ft_sourceinterpolate). pow can be calculated from mom, either with 3-dipole-moment or single-dipole-moment. Alternatively. I have been using the Nutmeg sLORETA procedure from the FT structures and data. If you have all your data in the FT format (head model, electrodes, lf), there is a routine that “almost” works to translate your FT LF to Nutmeg, and the sLORETA and dSPM routines from Nutmeg seem to work well. One advantage of FT/Nutmeg over LORETA or sLORETA packages is the FT is oriented to single participant head models. John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: richards-john at sc.edu HTTP: jerlab.psych.sc.edu *********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From zjyao at bu.edu Fri Jan 8 20:31:15 2016 From: zjyao at bu.edu (Zhaojie Yao) Date: Fri, 8 Jan 2016 14:31:15 -0500 Subject: [FieldTrip] Question about least-square FIR filter Message-ID: <247430E1-5A73-4DAD-8A8A-8FE5A8C430F3@bu.edu> Hi I am trying to process my data through Hilbert transform. I am used to the EEGLAB package, so I tried to use the same filter recommended by EEGLAB, which is least-square FIR filter in fieldtrip. However, I got a warning, when running the function ft_specest_hilbert, that least-square FIR 'is not recommended for neural signals, only proceed if you know what you are doing’. I am curious why least-square FIR is not appropriate for neural signals? Zhaojie Yao From tokimoto at mejiro.ac.jp Sun Jan 10 12:30:14 2016 From: tokimoto at mejiro.ac.jp (Shingo Tokimoto) Date: Sun, 10 Jan 2016 20:30:14 +0900 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB Message-ID: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> Dear Fieldtrip users, I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. -------------- EEGLAB error in function ft_checkconfig() at line 147: Error: ft_checkconfig (line 147) The field cfg.neighbours is required This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. ------------ I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. ************************************************ Shingo Tokimoto, Ph.D. in Linguistics and Psychology Department of Foreign Languages Mejiro University 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, 161-8539, Japan tokimoto at mejiro.ac.jp ************************************************ From tzvetan.popov at uni-konstanz.de Sun Jan 10 13:08:58 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 10 Jan 2016 13:08:58 +0100 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> Message-ID: Dear Shingo, You get this error because of a missing neighborhood structure with respect to your electrodes. Since you mention one electrode I suggest to specify cfg.neighbours = []. Thus you perform cluster based analysis over time and frequency within the electrode of your interest. Good luck Tzvetan > Am 10.01.2016 um 12:30 schrieb Shingo Tokimoto : > > Dear Fieldtrip users, > > I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. > > -------------- > EEGLAB error in function ft_checkconfig() at line 147: > > Error: ft_checkconfig (line 147) > The field cfg.neighbours is required > > This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. > ------------ > > I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. > > ************************************************ > Shingo Tokimoto, Ph.D. > in Linguistics and Psychology > Department of Foreign Languages > Mejiro University > 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, > 161-8539, Japan > tokimoto at mejiro.ac.jp > ************************************************ > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tokimoto at mejiro.ac.jp Sun Jan 10 16:27:30 2016 From: tokimoto at mejiro.ac.jp (Shingo Tokimoto) Date: Mon, 11 Jan 2016 00:27:30 +0900 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> Message-ID: <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> Dear Dr. Tzvetan Popov, Thank you very much for the quick reply. I edited "cfg.neighbours = neighbors;" in ft_prepare_neighbours.m to be "cfg.neighbours = [];." However, the same error message appears. I am sorry, but I am new to Fieldtrip. I am not sticking to one electrode. I want to specify the electrodes where their power are significantly different from those of the control condition in some specific time-windows and frequencies. The cluster-based analysis works well for ERP. Should I edit other m files? Thank you in advance again. ************************************************ Shingo Tokimoto, Ph.D. in Linguistics and Psychology Department of Foreign Languages Mejiro University 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, 161-8539, Japan tokimoto at mejiro.ac.jp ************************************************ On 2016/01/10, at 21:08, Tzvetan Popov wrote: > Dear Shingo, > You get this error because of a missing neighborhood structure with respect to your electrodes. Since you mention one electrode I suggest to specify cfg.neighbours = []. Thus you perform cluster based analysis over time and frequency within the electrode of your interest. > Good luck > Tzvetan > >> Am 10.01.2016 um 12:30 schrieb Shingo Tokimoto : >> >> Dear Fieldtrip users, >> >> I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. >> >> -------------- >> EEGLAB error in function ft_checkconfig() at line 147: >> >> Error: ft_checkconfig (line 147) >> The field cfg.neighbours is required >> >> This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. >> ------------ >> >> I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. >> >> ************************************************ >> Shingo Tokimoto, Ph.D. >> in Linguistics and Psychology >> Department of Foreign Languages >> Mejiro University >> 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, >> 161-8539, Japan >> tokimoto at mejiro.ac.jp >> ************************************************ >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From tzvetan.popov at uni-konstanz.de Sun Jan 10 17:08:19 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 10 Jan 2016 17:08:19 +0100 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> Message-ID: Dear Shingo, lets keep it by Tzvetan ;-). I’m not familiar with the way EEGLAB deals with FieldTrip functions at all. So I may not be of any further help. However as a rule of thumb you should almost never change settings in the FieldTrip functions but provide the appropriate configurations always as cfg.xxx. When you mention your analysis works for ERP I don’t see any reason why it fails with time-freq data. Obviously you have your electrode positions and you were able to generate neighborhood structure. If so the same should work for t-f too. Maybe if you provide the syntax of your analysis me or others can help you in getting it done. I will advise to undone any changes you made to the FieldTrip code and try again. Probably a fresh version of EEGLAB, clean math lab path etc. and then do it again. best tzvetan > Dear Dr. Tzvetan Popov, > > Thank you very much for the quick reply. I edited "cfg.neighbours = neighbors;" in ft_prepare_neighbours.m to be "cfg.neighbours = [];." However, the same error message appears. I am sorry, but I am new to Fieldtrip. I am not sticking to one electrode. I want to specify the electrodes where their power are significantly different from those of the control condition in some specific time-windows and frequencies. The cluster-based analysis works well for ERP. Should I edit other m files? Thank you in advance again. > > ************************************************ > Shingo Tokimoto, Ph.D. > in Linguistics and Psychology > Department of Foreign Languages > Mejiro University > 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, > 161-8539, Japan > tokimoto at mejiro.ac.jp > ************************************************ > > > On 2016/01/10, at 21:08, Tzvetan Popov wrote: > >> Dear Shingo, >> You get this error because of a missing neighborhood structure with respect to your electrodes. Since you mention one electrode I suggest to specify cfg.neighbours = []. Thus you perform cluster based analysis over time and frequency within the electrode of your interest. >> Good luck >> Tzvetan >> >>> Am 10.01.2016 um 12:30 schrieb Shingo Tokimoto : >>> >>> Dear Fieldtrip users, >>> >>> I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. >>> >>> -------------- >>> EEGLAB error in function ft_checkconfig() at line 147: >>> >>> Error: ft_checkconfig (line 147) >>> The field cfg.neighbours is required >>> >>> This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. >>> ------------ >>> >>> I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. >>> >>> ************************************************ >>> Shingo Tokimoto, Ph.D. >>> in Linguistics and Psychology >>> Department of Foreign Languages >>> Mejiro University >>> 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, >>> 161-8539, Japan >>> tokimoto at mejiro.ac.jp >>> ************************************************ >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From changa5 at mcmaster.ca Sun Jan 10 21:17:40 2016 From: changa5 at mcmaster.ca (Andrew Chang) Date: Sun, 10 Jan 2016 15:17:40 -0500 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Message-ID: Dear Fieldtrip users, I am wondering whether anyone has compared the performances of the ICA methods among M/EEG toolboxes. Especially, how is the performance of ICA in BESA Research 6.0, compared to Fieldtrip? I have an EEG data set which has been processed in BESA, including removing artifact using ICA. I am wondering whether I can trust it, or I should reprocess it in Fieldtrip. Any comments will be appreciated! Happy new year! Best, Andrew -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From leilayou_54 at yahoo.com Mon Jan 11 11:50:01 2016 From: leilayou_54 at yahoo.com (Leila Ayoubian) Date: Mon, 11 Jan 2016 10:50:01 +0000 (UTC) Subject: [FieldTrip] loading data in GUI References: <253366430.2575220.1452509401650.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <253366430.2575220.1452509401650.JavaMail.yahoo@mail.yahoo.com> Good morning everyone: I am new to fieldtrip am having trouble loading EEG data in a GUI . While there is no trouble loading the same file in a script , when the same file is being loaded inside a simple GUI , Matlab hangs, and I have to press ctrl C to exit! I am really puzzled! I understand it could be the GUI issue and not fieldtrip function issue.I thought if someone have come across this problem can save me time. I attached the two codes to compare. This is the script that works ************************************ clear all; clc; close all; [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename) cfg1 = []; cfg1.trl = [1 61440 0]; cfg1.dataset = filename%'K_S_Event_Marker_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1);  display('Finished') ***************************** Here is the GUI code, which does not work function varargout = loadDataGUI(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @loadDataGUI_OpeningFcn, ...                    'gui_OutputFcn',  @loadDataGUI_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before loadDataGUI is made visible. function loadDataGUI_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to loadDataGUI (see VARARGIN) % Choose default command line output for loadDataGUI handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes loadDataGUI wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = loadDataGUI_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in loadData. function loadData_Callback(hObject, eventdata, handles) % hObject    handle to loadData (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %Load the EEG file if isempty(handles)     disp('ERROR:::Please select a valid Montage'); end [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename) cfg1 = []; % beginSample=1; %The indice of sample to begin % endSample=61440; %The indice of sample to end (1 min data to load, 60*1024=61440) % cfg1.trl = [1 61440 0]; cfg1.dataset = filename%'K_S_Event_Marker_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1); %set(handles.filePath,'string',file ); function filePath_Callback(hObject, eventdata, handles) % hObject    handle to filePath (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of filePath as text %        str2double(get(hObject,'String')) returns contents of filePath as a double % global handles; % display(handles.file)  set(handles.filePath,'string',handles.file ); ************************************************************* __________________________________________________ Leila Ayoubian, PhD. Institute of Psychiatry, Psychology and Neuroscience King's College London -------------- next part -------------- An HTML attachment was scrubbed... URL: From leilayou_54 at yahoo.com Mon Jan 11 16:19:25 2016 From: leilayou_54 at yahoo.com (Leila Ayoubian) Date: Mon, 11 Jan 2016 15:19:25 +0000 (UTC) Subject: [FieldTrip] GUi issue with ft_preprocessing References: <1162479313.2666505.1452525565497.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <1162479313.2666505.1452525565497.JavaMail.yahoo@mail.yahoo.com> Why Data do not load in GUI, but it loads in a script using fieldtrip ft-preprocessing function?  Look a the two code below. One which is a script work perfectly fine.The other one is inside a simple gui and Matlab crashes.....Can anyone enlighten me?! Thanks in advance function varargout = trial5(varargin) % TRIAL5 MATLAB code for trial5.fig %      TRIAL5, by itself, creates a new TRIAL5 or raises the existing %      singleton*. % %      H = TRIAL5 returns the handle to a new TRIAL5 or the handle to %      the existing singleton*. % %      TRIAL5('CALLBACK',hObject,eventData,handles,...) calls the local %      function named CALLBACK in TRIAL5.M with the given input arguments. % %      TRIAL5('Property','Value',...) creates a new TRIAL5 or raises the %      existing singleton*.  Starting from the left, property value pairs are %      applied to the GUI before trial5_OpeningFcn gets called.  An %      unrecognized property name or invalid value makes property application %      stop.  All inputs are passed to trial5_OpeningFcn via varargin. % %      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one %      instance to run (singleton)". % % See also: GUIDE, GUIDATA, GUIHANDLES % Edit the above text to modify the response to help trial5 % Last Modified by GUIDE v2.5 11-Jan-2016 13:20:07 % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @trial5_OpeningFcn, ...                    'gui_OutputFcn',  @trial5_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before trial5 is made visible. function trial5_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to trial5 (see VARARGIN) % Choose default command line output for trial5 handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes trial5 wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = trial5_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in pushbutton1. function pushbutton1_Callback(hObject, eventdata, handles) % hObject    handle to pushbutton1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %file = fullfile(pathname, filename) cfg1 = []; cfg1.trl = [1 61440 0]; cfg1.dataset = 'Event06_Interictal_Background_Sleep_Segment_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1); function edit1_Callback(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit1 as text %        str2double(get(hObject,'String')) returns contents of edit1 as a double % --- Executes during object creation, after setting all properties. function edit1_CreateFcn(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. %       See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))     set(hObject,'BackgroundColor','white'); end *************************************************************************** function varargout = trial5(varargin) % TRIAL5 MATLAB code for trial5.fig %      TRIAL5, by itself, creates a new TRIAL5 or raises the existing %      singleton*. % %      H = TRIAL5 returns the handle to a new TRIAL5 or the handle to %      the existing singleton*. % %      TRIAL5('CALLBACK',hObject,eventData,handles,...) calls the local %      function named CALLBACK in TRIAL5.M with the given input arguments. % %      TRIAL5('Property','Value',...) creates a new TRIAL5 or raises the %      existing singleton*.  Starting from the left, property value pairs are %      applied to the GUI before trial5_OpeningFcn gets called.  An %      unrecognized property name or invalid value makes property application %      stop.  All inputs are passed to trial5_OpeningFcn via varargin. % %      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one %      instance to run (singleton)". % % See also: GUIDE, GUIDATA, GUIHANDLES % Edit the above text to modify the response to help trial5 % Last Modified by GUIDE v2.5 11-Jan-2016 13:20:07 % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @trial5_OpeningFcn, ...                    'gui_OutputFcn',  @trial5_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before trial5 is made visible. function trial5_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to trial5 (see VARARGIN) % Choose default command line output for trial5 handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes trial5 wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = trial5_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in pushbutton1. function pushbutton1_Callback(hObject, eventdata, handles) % hObject    handle to pushbutton1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %file = fullfile(pathname, filename) cfg1 = []; cfg1.trl = [1 61440 0]; cfg1.dataset = 'Event06_Interictal_Background_Sleep_Segment_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1); function edit1_Callback(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit1 as text %        str2double(get(hObject,'String')) returns contents of edit1 as a double % --- Executes during object creation, after setting all properties. function edit1_CreateFcn(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. %       See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))     set(hObject,'BackgroundColor','white'); 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URL: From widmann at uni-leipzig.de Mon Jan 11 17:42:07 2016 From: widmann at uni-leipzig.de (Andreas Widmann) Date: Mon, 11 Jan 2016 17:42:07 +0100 Subject: [FieldTrip] Question about least-square FIR filter In-Reply-To: <247430E1-5A73-4DAD-8A8A-8FE5A8C430F3@bu.edu> References: <247430E1-5A73-4DAD-8A8A-8FE5A8C430F3@bu.edu> Message-ID: <9BABEA1A-A464-41E0-BBA2-5ABE35D540DB@uni-leipzig.de> Hi, > I am trying to process my data through Hilbert transform. I am used to the EEGLAB package, so I tried to use the same filter recommended by EEGLAB, which is least-square FIR filter in fieldtrip. However, I got a warning, when running the function ft_specest_hilbert, that least-square FIR 'is not recommended for neural signals, only proceed if you know what you are doing’. I am curious why least-square FIR is not appropriate for neural signals? Short version: See http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2453 Point (3) and first attachment (png). Long version: firls filters are also NOT recommended in EEGLAB. Where did you get this information? The EEGLAB firls filter are marked legacy/deprecated since 2012. See http://journal.frontiersin.org/article/10.3389/fpsyg.2012.00233/full for a more detailed description of the problem, in particular footnote 1. Filter roll-off/transition width is a function of the filter order. However, with MATLAB firls filters roll-off/transition width is defined independently from filter order. This might work if the selected parameters for both are appropriate, however, commonly it does not work resulting in various artifacts in the filter’s frequency and/or time domain responses, bad attenuation, non-unity DC gain etc. In Fieldtrip the problem was/is particularly problematic as a zero transition width (rectangular frequency response) filter is requested combined with an incorrect estimation of required filter order (actually infinite). Hope this helps! Best, Andreas From leilayou_54 at yahoo.com Tue Jan 12 11:42:27 2016 From: leilayou_54 at yahoo.com (Leila Ayoubian) Date: Tue, 12 Jan 2016 10:42:27 +0000 (UTC) Subject: [FieldTrip] importing large edf data In-Reply-To: References: Message-ID: <2128658446.3021319.1452595347079.JavaMail.yahoo@mail.yahoo.com>  Hi Steve:Happy new year. Following the code you sent me to import large  EDF data sets, I designed a simple GUI to select data and display the path.I simplified the GUI for convenience so you can have a look at it. When I run this GUI Matlab crashes, meaning it will be busy until I quite the execution by pressing ctrl C. The same code on a script is absolutely fine! I am really puzzled and not underestanding why this is happening. Could it be a bug of ft_preprocessing function? I have copied both files beow. Can you please have a look. I have been hanging around for couple days wondering and not getting to any conclusion. I appreciate if you can enlighten me.Thanks ******** THE GUI CODE***************** function varargout = loadDataGUI(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @loadDataGUI_OpeningFcn, ...                    'gui_OutputFcn',  @loadDataGUI_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before loadDataGUI is made visible. function loadDataGUI_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to loadDataGUI (see VARARGIN) % Choose default command line output for loadDataGUI handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes loadDataGUI wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = loadDataGUI_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in loadData. function loadData_Callback(hObject, eventdata, handles) % hObject    handle to loadData (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %Load the EEG file if isempty(handles)     disp('ERROR:::Please select a valid Montage'); end [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename)  cfg = [];  cfg.trl = [1 61440 0];  cfg.dataset = filename%'K_S_Event_Marker_1.edf';  cfg= ft_definetrial( cfg );  cfg.continuous = 'yes'; data = ft_preprocessing(cfg); % [hdr, record] = edfread(file); set(handles.filePath,'string',file ); function filePath_Callback(hObject, eventdata, handles) % hObject    handle to filePath (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of filePath as text %        str2double(get(hObject,'String')) returns contents of filePath as a double % global handles; % display(handles.file)  set(handles.filePath,'string',handles.file ); *************** THE SCRIPT************ clear all; clc; close all; %% [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename) %% cfg1 = []; cfg1.trl = [1 61440 0]; %cfg1.dataset = filename%'K_S_Event_Marker_1.edf'; cfg1.dataset = 'Event06_Interictal_Background_Sleep_Segment_1.edf' cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes'; data1 = ft_preprocessing(cfg1); %% %[hdr, record] = edfread(file); %%  display('Finished') __________________________________________________ Leila Ayoubian, PhD. Institute of Psychiatry, Psychology and Neuroscience King's College London From: Stephen Politzer-Ahles To: fieldtrip at science.ru.nl Sent: Saturday, December 19, 2015 2:06 PM Subject: Re: [FieldTrip] importing large edf data Hi Leila, I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me: cfg = []; cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf'; cfg.trl = [1 500 0]; cfg.continuous = 'yes'; data_500samples = ft_preprocessing(cfg); cfg = []; cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf'; cfg.trl = [1 1000 0]; cfg.continuous = 'yes'; data_1000samples = ft_preprocessing(cfg); Here's the output: >> data_500samples data_500samples =            hdr: [1x1 struct]          label: {37x1 cell}           time: {[1x500 double]}          trial: {[37x500 double]}        fsample: 200     sampleinfo: [1 500]            cfg: [1x1 struct] >> data_1000samples data_1000samples =            hdr: [1x1 struct]          label: {37x1 cell}           time: {[1x1000 double]}          trial: {[37x1000 double]}        fsample: 200     sampleinfo: [1 1000]            cfg: [1x1 struct] Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/  ------------------------------ Message: 5 Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC) From: Leila Ayoubian To: FieldTrip discussion list Subject: Re: [FieldTrip] importing large edf data Message-ID:         <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com> Content-Type: text/plain; charset="utf-8" ?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same! So this is what I get: ?? hdr: [1x1 struct] ???????? label: {51x1 cell} ????????? time: {1x50710 cell} ???????? trial: {1x50710 cell} ?????? fsample: 1024 ??? sampleinfo: [50710x2 double] ?????????? cfg: [1x1 struct] so the actual data which is in data.trial? is this in both cases! size(data.trial) ans = ?????????? 1?????? 50710 How could that happen if you are segmenting it in two different chunks? Best regards ___________________________________________________ Leila Ayoubian       From: Stephen Politzer-Ahles  To: fieldtrip at science.ru.nl  Sent: Friday, December 18, 2015 12:37 PM  Subject: Re: [FieldTrip] importing large edf data Hello Leila, I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size. If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add: cfg.trl = [1 1000 0]; and then use ft_preprocessing. By way of example, here is code that reads in raw data as a series of 1-second "trials": cfg = []; cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr'; cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters cfg.trialdef.ntrials = Inf; cfg = ft_definetrial( cfg ); cfg.continuous = 'yes'; data = ft_preprocessing(cfg); After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details). Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/ On Fri, Dec 18, 2015 at 11:00 AM, wrote: Send fieldtrip mailing list submissions to ? ? ? ? fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit ? ? ? ? http://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to ? ? ? ? fieldtrip-request at science.ru.nl You can reach the person managing the list at ? ? ? ? fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: ? ?1. importing large edf data (Leila Ayoubian) ---------------------------------------------------------------------- Message: 1 Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC) From: Leila Ayoubian To: "fieldtrip at science.ru.nl" Subject: [FieldTrip] importing large edf data Message-ID: ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com> Content-Type: text/plain; charset="utf-8" Hi:Thanks for providing us with this amazing toolbox. I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.? So trying to load the data like this: cfg.dataset= ('mydata.edf'); rawdata=ft_preprocessing(cfg); This is the error message I get : %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Error using zeros Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information. Error in read_edf (line 403) ? dat = zeros(length(chanindx),nepochs*epochlength); Error in ft_read_data (line 622) ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx); Error in ft_preprocessing (line 566) ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat); Error in ReadFedfiles (line 8) rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf' ?hdr?? = ft_read_header(filename); ?sample.start=1 ?sample.end=100 dat = ft_read_data(filename,'sample.start','1','sample.end','100') and here is again the error message: Error using zeros Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information. Error in read_edf (line 403) ? dat = zeros(length(chanindx),nepochs*epochlength); Error in ft_read_data (line 622) ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx); Error in ReadFedfiles (line 31) dat = ft_read_data(filename,'sample.start','1','sample.end','100') ? >> Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful. Thanks again for your support and assistance. We appreciate your effort. Kind regards ___________________________________________________ Dr. Leila Ayoubian -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lorenzomagazzini at gmail.com Tue Jan 12 15:46:44 2016 From: lorenzomagazzini at gmail.com (Lorenzo Magazzini) Date: Tue, 12 Jan 2016 14:46:44 +0000 Subject: [FieldTrip] Help understanding the lcmv beamformer output Message-ID: Hi, I hope someone can help me to understand the use of the lcmv beamformer, because either I am using it incorrectly, or I misunderstood the meaning of its output. I am trying to get source-level power estimates of 'baseline' and 'active' time-windows. I first compute a common filter, and then apply it separately to the two conditions. I thought the power estimates would be stored, voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. However, the values I get in the '.pow' field for the analysis of 'baseline' and 'active' windows are identical. Furthermore, the '.pow' values are identical to the '.noise' values when using cfg.projectnoise = 'yes';. I have checked if the sensor-level data that passed on to ft_sourceanalysis is different between baseline and active - it is. Also, if I do the following... 1. reconstruct virtual sensors by applying the common filter separately to baseline and active, 2. average the single-trial (virtual sensor) power estimates, 3. replace the '.pow' value for each voxel, ...then the contrast between baseline and active is correct. Can anyone please help me figure out what I'm doing wrong here? Below I copied part of the code. Many thanks in advance! Lorenzo %compute the leadfield cfg = []; cfg.channel = {'MEG'}; cfg.grid = sourcemodel; cfg.vol = hdm; cfg.grad = grad; cfg.normalize = 'yes'; leadfield = ft_prepare_leadfield(cfg); %compute covariance matrix cfg = []; cfg.channel = {'MEG'}; cfg.removemean = 'no'; cfg.covariance = 'yes'; cfg.covariancewindow = [-1.5 1.5]; tlck = ft_timelockanalysis(cfg, data); %get the common spatial filter cfg = []; cfg.method = 'lcmv'; cfg.grid = leadfield; cfg.vol = hdm; cfg.grad = grad; cfg.lcmv.fixedori = 'yes'; cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.projectnoise = 'yes'; cfg.lcmv.lambda = '5%'; src = ft_sourceanalysis(cfg, tlck); %store the filter wts = src.avg.filter; %separate baseline and active windows of bandpass-filtered data cfg = []; cfg.toilim = [-1.5 -0.3]; data_bsln = ft_redefinetrial(cfg, data); cfg = []; cfg.toilim = [0.3 1.5]; data_actv = ft_redefinetrial(cfg, data); %timelock analysis of baseline and active cfg = []; cfg.channel = {'MEG'}; cfg.keeptrials = 'yes'; tlck_bsln = ft_timelockanalysis(cfg, data_bsln); tlck_actv = ft_timelockanalysis(cfg, data_actv); %get source-power estimates of bsln and actv separately using the pre-computed common filter (wts) cfg = []; cfg.method = 'lcmv'; cfg.vol = hdm; cfg.grid = leadfield; cfg.grid.filter = wts; % cfg.keepfilter = 'no'; cfg.lcmv.fixedori = 'yes'; cfg.projectnoise = 'yes'; cfg.lambda = '5%'; cfg.keeptrials = 'yes'; src_bsln = ft_sourceanalysis(cfg, tlck_bsln); src_actv = ft_sourceanalysis(cfg, tlck_actv); -------------- next part -------------- An HTML attachment was scrubbed... URL: From ervin.poljac at donders.ru.nl Tue Jan 12 16:32:52 2016 From: ervin.poljac at donders.ru.nl (Poljac, E. (Ervin)) Date: Tue, 12 Jan 2016 15:32:52 +0000 Subject: [FieldTrip] Help understanding the lcmv beamformer output In-Reply-To: References: Message-ID: Hi Marjolein, Even een snelle vraag, wat is de risingedge(mask)? Groetjes, Ervin -- Ervin Poljac, PhD Donders Institute for Brain, Cognition and Behaviour Centre for Cognition (DCC) Radboud University Nijmegen Room B.00.78A Montessorilaan 3 6500 HE Nijmegen T. 024 36 15457 ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Lorenzo Magazzini [lorenzomagazzini at gmail.com] Sent: Tuesday, January 12, 2016 3:46 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Help understanding the lcmv beamformer output Hi, I hope someone can help me to understand the use of the lcmv beamformer, because either I am using it incorrectly, or I misunderstood the meaning of its output. I am trying to get source-level power estimates of 'baseline' and 'active' time-windows. I first compute a common filter, and then apply it separately to the two conditions. I thought the power estimates would be stored, voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. However, the values I get in the '.pow' field for the analysis of 'baseline' and 'active' windows are identical. Furthermore, the '.pow' values are identical to the '.noise' values when using cfg.projectnoise = 'yes';. I have checked if the sensor-level data that passed on to ft_sourceanalysis is different between baseline and active - it is. Also, if I do the following... 1. reconstruct virtual sensors by applying the common filter separately to baseline and active, 2. average the single-trial (virtual sensor) power estimates, 3. replace the '.pow' value for each voxel, ...then the contrast between baseline and active is correct. Can anyone please help me figure out what I'm doing wrong here? Below I copied part of the code. Many thanks in advance! Lorenzo %compute the leadfield cfg = []; cfg.channel = {'MEG'}; cfg.grid = sourcemodel; cfg.vol = hdm; cfg.grad = grad; cfg.normalize = 'yes'; leadfield = ft_prepare_leadfield(cfg); %compute covariance matrix cfg = []; cfg.channel = {'MEG'}; cfg.removemean = 'no'; cfg.covariance = 'yes'; cfg.covariancewindow = [-1.5 1.5]; tlck = ft_timelockanalysis(cfg, data); %get the common spatial filter cfg = []; cfg.method = 'lcmv'; cfg.grid = leadfield; cfg.vol = hdm; cfg.grad = grad; cfg.lcmv.fixedori = 'yes'; cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.projectnoise = 'yes'; cfg.lcmv.lambda = '5%'; src = ft_sourceanalysis(cfg, tlck); %store the filter wts = src.avg.filter; %separate baseline and active windows of bandpass-filtered data cfg = []; cfg.toilim = [-1.5 -0.3]; data_bsln = ft_redefinetrial(cfg, data); cfg = []; cfg.toilim = [0.3 1.5]; data_actv = ft_redefinetrial(cfg, data); %timelock analysis of baseline and active cfg = []; cfg.channel = {'MEG'}; cfg.keeptrials = 'yes'; tlck_bsln = ft_timelockanalysis(cfg, data_bsln); tlck_actv = ft_timelockanalysis(cfg, data_actv); %get source-power estimates of bsln and actv separately using the pre-computed common filter (wts) cfg = []; cfg.method = 'lcmv'; cfg.vol = hdm; cfg.grid = leadfield; cfg.grid.filter = wts; % cfg.keepfilter = 'no'; cfg.lcmv.fixedori = 'yes'; cfg.projectnoise = 'yes'; cfg.lambda = '5%'; cfg.keeptrials = 'yes'; src_bsln = ft_sourceanalysis(cfg, tlck_bsln); src_actv = ft_sourceanalysis(cfg, tlck_actv); -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Wed Jan 13 16:23:22 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Wed, 13 Jan 2016 17:23:22 +0200 Subject: [FieldTrip] Fieldtrip compatibility In-Reply-To: References: Message-ID: Dear Robert, Thank you to put in our problem from the first question, yes we want to localize the contractions of the uterus, and thank you to provide me with the careful consideration of the inverse model assumptions for this case. I have looked at http://www.fieldtriptoolbox.org/dataformat, but the data what I have is: 1- a real signal generated from 16 electrodes saved as ".mat", 2- the meshes as ".off"( I seperated the points and faces and I saved each one on ".mat") it is already segmented, and 3- the simulated potential (99084x201) given from our team who works on the model and I want to convert it to in the form of signal collected from the 16 electrode (16x201). The algorithm of my colleague was as below, but I didn't convinced in the computation of the inverse problem using the gain matrix not the lead field, it is possible to use the gain matrix as done below in the bold inverse problem part or in another word what does gain represent? % Set the radius and conductivities of each of the compartments addpath(cd) % 3 Layers r = [0 0.936 2.068 2.268]; c = [0.2 0.3 0.04 0.5]; %% Description of the spherical mesh pnt=point_square(:,2:4); tri=faces_square(:,3:5); %% Create a set of electrodes on the outer surface % sensor = [pnt(10201,:);pnt(17376,:);pnt(24756,:);pnt(31931,:);pnt(10166,:);pnt(17341,:);pnt(24721,:);pnt(31896,:);pnt(10130,:);pnt(17305,:);pnt(24685,:);pnt(31860,:);pnt(10095,:);pnt(17270,:);pnt(24650,:);pnt(31825,:)]; sensor = [pnt(664,:);pnt(1080,:);pnt(1600,:);pnt(2016,:);pnt(656,:);pnt(1072,:);pnt(1592,:);pnt(2008,:);pnt(646,:);pnt(1062,:);pnt(1582,:);pnt(1998,:);pnt(638,:);pnt(1054,:);pnt(1574,:);pnt(1990,:)]; sensor(:,3)=sensor(:,3)+max(r)+0.1; sens.elecpos = sensor; sens.label = {}; nsens = size(sens.elecpos,1); for ii=1:nsens sens.label{ii} = sprintf('vertex%03d', ii); end %% Set the position of the probe dipole %%Un source pos = pnt(1326,:);%[5 5 0] maillage complet pos(:,3) = pos(:,3)+0.1; %%Deux source % S1 = pnt(10609,:);%[2.5 2.5 0] maillage complet % S1(:,3) = S1(:,3)+0.1; % S2 = pnt(31417,:);%[7.5 7.5 0] maillage complet % S2(:,3) = S2(:,3)+0.1; % pos=[S1;S2]; %%All the uterine muscle mesh %S=pnt(:,:,:); %S(:,3) = S(:,3)+0.1; %pos=S; %% Create a BEM volume conduction model vol = []; for ii=1:length(r) uterus=pnt; uterus(:,3)=uterus(:,3)+r(ii)+0.1; vol.bnd(ii).pnt = uterus; vol.bnd(ii).tri = fliplr(tri); % pointing inwards!!! end vol.cond = c; %% Compute the BEM cfg=[]; cfg.method = 'bemcp'; vol = ft_prepare_headmodel(cfg, vol); cfg.vol = vol; cfg.grid.pos = pos; cfg.elec = sens; [grid,gain] = ft_prepare_leadfield(cfg); lf_openmeeg = grid.leadfield{1}; %% Inverse problem %load data data_simulated = hdf5read('Sources_EHG_1.hdf5','/surface/EHG'); %real=load('W4_P_27_07_10_CTMono3_deb.mat'); %data_real=real.XXF2D1; %MNE lambda = 1e-1; % MNE_1 = inverse_operator_MNE(gain,lambda); % A: Gain matrix S_MNE_1 = bayesian_inverse_solution(data_simulated',MNE_1); % X: Signal mean_S_MNE_1=mean(S_MNE_1,2); % % MNE_2 = inverse_operator_MNE(gain,lambda); % A: Gain matrix % S_MNE_2 = bayesian_inverse_solution(data_real',MNE_2); % X: Signal % mean_S_MNE_2=mean(S_MNE_2,2); bnd = struct('pnt', pnt, 'tri', tri); figure;ft_plot_mesh(bnd, 'vertexcolor', mean_S_MNE_1(1:size(pnt,1))); % figure;ft_plot_mesh(bnd, 'vertexcolor', mean_S_MNE_2(1:size(pnt,1))); To be more accurate I want to use your algorithm in: http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate?s[]=mne but my obstacle was cfg.dataset = 'Subject01.ds'; I didn't know in our cases what is the "Subject01.ds", and also the same in: http://www.fieldtriptoolbox.org/tutorial/beamformer,... Thank you very much for any suggestions Best regards Saeed -------------- next part -------------- An HTML attachment was scrubbed... URL: From mail at philipp-ruhnau.de Wed Jan 13 16:46:09 2016 From: mail at philipp-ruhnau.de (Philipp Ruhnau) Date: Wed, 13 Jan 2016 16:46:09 +0100 Subject: [FieldTrip] Help understanding the lcmv beamformer output In-Reply-To: References: Message-ID: <9EDB2B94-3D95-4084-82F2-71968FF04217@philipp-ruhnau.de> Dear Lorenzo and others, I’ve just looked into this, can reproduce the issue (same result with two different conditions/activity-baseline) The issue arises because power is calculated based on the filter and the covariance of the input data (following VanVeen or a slight change for precomputed filters), yet in the example below no covariance is precomputed for activity/baseline timelock structures (only for the common dataset) and in that case fieldtrip creates an identity matrix for both activity and baseline (around line 713 in ft_sourceanalysis). there is actually a warning about this, yet just from this warning (No covariance matrix found - will assume identity covariance matrix (mininum-norm solution)) it might to hard to get that this explains the results: in essence from what I understand, the input data is ignored in the formula (for those interested this is line 278 in beamformer_lcmv) to compute the time series power, because the covariance is an identity matrix, and only the filter determines what ends up in the .pow field. and as the filter is the same for activity and baseline, the difference between the .pow output is zero. now, computing covariances for the to-be-beamed segments (add a cfg.covariance = ‘yes’ to the timelock step for baseline and activity in the example) produces different power values (just tested with a simple auditory ERF dataset). I suppose this is desired behavior (the identity matrix covariance), otherwise I would suggest to produce an error. how well the ERF/timeseries is reconstructed of course depends on the data (time window) you use to create the filters. still it seems to me using the .mom field or creating virtual sensors yields better (in a sense of more focused) results. I still wonder why virtual sensors/.mom averages and .pow results are quite different, maybe one of the more knowledgeable ft developers could comment on at some point, but this might exceed the limit of this list… cheers philipp > On 12 Jan 2016, at 15:46, Lorenzo Magazzini wrote: > > Hi, > > I hope someone can help me to understand the use of the lcmv beamformer, because either I am using it incorrectly, or I misunderstood the meaning of its output. > > I am trying to get source-level power estimates of 'baseline' and 'active' time-windows. I first compute a common filter, and then apply it separately to the two conditions. I thought the power estimates would be stored, voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. However, the values I get in the '.pow' field for the analysis of 'baseline' and 'active' windows are identical. Furthermore, the '.pow' values are identical to the '.noise' values when using cfg.projectnoise = 'yes';. > > I have checked if the sensor-level data that passed on to ft_sourceanalysis is different between baseline and active - it is. > > Also, if I do the following... > 1. reconstruct virtual sensors by applying the common filter separately to baseline and active, > 2. average the single-trial (virtual sensor) power estimates, > 3. replace the '.pow' value for each voxel, > ...then the contrast between baseline and active is correct. > > Can anyone please help me figure out what I'm doing wrong here? Below I copied part of the code. > > Many thanks in advance! > > Lorenzo > > > %compute the leadfield > cfg = []; > cfg.channel = {'MEG'}; > cfg.grid = sourcemodel; > cfg.vol = hdm; > cfg.grad = grad; > cfg.normalize = 'yes'; > leadfield = ft_prepare_leadfield(cfg); > > %compute covariance matrix > cfg = []; > cfg.channel = {'MEG'}; > cfg.removemean = 'no'; > cfg.covariance = 'yes'; > cfg.covariancewindow = [-1.5 1.5]; > tlck = ft_timelockanalysis(cfg, data); > > %get the common spatial filter > cfg = []; > cfg.method = 'lcmv'; > cfg.grid = leadfield; > cfg.vol = hdm; > cfg.grad = grad; > cfg.lcmv.fixedori = 'yes'; > cfg.lcmv.keepfilter = 'yes'; > cfg.lcmv.projectnoise = 'yes'; > cfg.lcmv.lambda = '5%'; > src = ft_sourceanalysis(cfg, tlck); > > %store the filter > wts = src.avg.filter; > > %separate baseline and active windows of bandpass-filtered data > cfg = []; > cfg.toilim = [-1.5 -0.3]; > data_bsln = ft_redefinetrial(cfg, data); > cfg = []; > cfg.toilim = [0.3 1.5]; > data_actv = ft_redefinetrial(cfg, data); > > %timelock analysis of baseline and active > cfg = []; > cfg.channel = {'MEG'}; > cfg.keeptrials = 'yes'; > tlck_bsln = ft_timelockanalysis(cfg, data_bsln); > tlck_actv = ft_timelockanalysis(cfg, data_actv); > > %get source-power estimates of bsln and actv separately using the pre-computed common filter (wts) > cfg = []; > cfg.method = 'lcmv'; > cfg.vol = hdm; > cfg.grid = leadfield; > cfg.grid.filter = wts; > % cfg.keepfilter = 'no'; > cfg.lcmv.fixedori = 'yes'; > cfg.projectnoise = 'yes'; > cfg.lambda = '5%'; > cfg.keeptrials = 'yes'; > src_bsln = ft_sourceanalysis(cfg, tlck_bsln); > src_actv = ft_sourceanalysis(cfg, tlck_actv); > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lorenzomagazzini at gmail.com Wed Jan 13 19:44:26 2016 From: lorenzomagazzini at gmail.com (Lorenzo Magazzini) Date: Wed, 13 Jan 2016 18:44:26 +0000 Subject: [FieldTrip] Help understanding the lcmv beamformer output Message-ID: Hi Philipp, Thanks so much for your answer, it does indeed solve the problem! I thought the covariance matrix was no longer necessary after computation of the (common) filter, but, as you showed by pointing to the code, this is clearly not the case. Now, I compared the results of a) calculating power from the virtual sensors time-series (data multiplied by the filter, estimated using the 'common' covariance), and b) power taken from the output of ft_sourceanalysis, using two different 'condition-specific' covariance matrices. Results are pretty identical in my case, apart from minor differences in the power values. I wonder if anyone could help me figure out if there is a mathematical difference between these two approaches? Anyway, many thanks again for your help! Best wishes, Lorenzo > *From: *Philipp Ruhnau > *Subject: **Re: [FieldTrip] Help understanding the lcmv beamformer output* > *Date: *13 January 2016 at 16:46:09 GMT+1 > *To: *FieldTrip discussion list > > Dear Lorenzo and others, > I’ve just looked into this, can reproduce the issue (same result with two > different conditions/activity-baseline) > > The issue arises because power is calculated based on the filter and the > covariance of the input data (following VanVeen or a slight change for > precomputed filters), yet in the example below no covariance is precomputed > for activity/baseline timelock structures (only for the common dataset) and > in that case fieldtrip creates an identity matrix for both activity and > baseline (around line 713 in ft_sourceanalysis). > there is actually a warning about this, yet just from this warning (No > covariance matrix found - will assume identity covariance matrix > (mininum-norm solution)) it might to hard to get that this explains the > results: > > in essence from what I understand, the input data is ignored in the > formula (for those interested this is line 278 in beamformer_lcmv) to > compute the time series power, because the covariance is an identity > matrix, and only the filter determines what ends up in the .pow field. and > as the filter is the same for activity and baseline, the difference between > the .pow output is zero. > > now, computing covariances for the to-be-beamed segments (add a > cfg.covariance = ‘yes’ to the timelock step for baseline and activity in > the example) produces different power values (just tested with a simple > auditory ERF dataset). > > I suppose this is desired behavior (the identity matrix covariance), > otherwise I would suggest to produce an error. > > how well the ERF/timeseries is reconstructed of course depends on the data > (time window) you use to create the filters. still it seems to me using the > .mom field or creating virtual sensors yields better (in a sense of more > focused) results. I still wonder why virtual sensors/.mom averages and .pow > results are quite different, maybe one of the more knowledgeable ft > developers could comment on at some point, but this might exceed the limit > of this list… > > cheers > philipp > > On 12 Jan 2016, at 15:46, Lorenzo Magazzini > wrote: > > Hi, > > I hope someone can help me to understand the use of the lcmv beamformer, > because either I am using it incorrectly, or I misunderstood the meaning of > its output. > > I am trying to get source-level power estimates of 'baseline' and 'active' > time-windows. I first compute a common filter, and then apply it separately > to the two conditions. I thought the power estimates would be stored, > voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. > However, the values I get in the '.pow' field for the analysis of > 'baseline' and 'active' windows are identical. Furthermore, the '.pow' > values are identical to the '.noise' values when using cfg.projectnoise = > 'yes';. > > I have checked if the sensor-level data that passed on to > ft_sourceanalysis is different between baseline and active - it is. > > Also, if I do the following... > 1. reconstruct virtual sensors by applying the common filter separately to > baseline and active, > 2. average the single-trial (virtual sensor) power estimates, > 3. replace the '.pow' value for each voxel, > ...then the contrast between baseline and active is correct. > > Can anyone please help me figure out what I'm doing wrong here? Below I > copied part of the code. > > Many thanks in advance! > > Lorenzo > > > %compute the leadfield > cfg = []; > cfg.channel = {'MEG'}; > cfg.grid = sourcemodel; > cfg.vol = hdm; > cfg.grad = grad; > cfg.normalize = 'yes'; > leadfield = ft_prepare_leadfield(cfg); > > %compute covariance matrix > cfg = []; > cfg.channel = {'MEG'}; > cfg.removemean = 'no'; > cfg.covariance = 'yes'; > cfg.covariancewindow = [-1.5 1.5]; > tlck = ft_timelockanalysis(cfg, data); > > %get the common spatial filter > cfg = []; > cfg.method = 'lcmv'; > cfg.grid = leadfield; > cfg.vol = hdm; > cfg.grad = grad; > cfg.lcmv.fixedori = 'yes'; > cfg.lcmv.keepfilter = 'yes'; > cfg.lcmv.projectnoise = 'yes'; > cfg.lcmv.lambda = '5%'; > src = ft_sourceanalysis(cfg, tlck); > > %store the filter > wts = src.avg.filter; > > %separate baseline and active windows of bandpass-filtered data > cfg = []; > cfg.toilim = [-1.5 -0.3]; > data_bsln = ft_redefinetrial(cfg, data); > cfg = []; > cfg.toilim = [0.3 1.5]; > data_actv = ft_redefinetrial(cfg, data); > > %timelock analysis of baseline and active > cfg = []; > cfg.channel = {'MEG'}; > cfg.keeptrials = 'yes'; > tlck_bsln = ft_timelockanalysis(cfg, data_bsln); > tlck_actv = ft_timelockanalysis(cfg, data_actv); > > %get source-power estimates of bsln and actv separately using the > pre-computed common filter (wts) > cfg = []; > cfg.method = 'lcmv'; > cfg.vol = hdm; > cfg.grid = leadfield; > cfg.grid.filter = wts; > % cfg.keepfilter = 'no'; > cfg.lcmv.fixedori = 'yes'; > cfg.projectnoise = 'yes'; > cfg.lambda = '5%'; > cfg.keeptrials = 'yes'; > src_bsln = ft_sourceanalysis(cfg, tlck_bsln); > src_actv = ft_sourceanalysis(cfg, tlck_actv); > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dlozanosoldevilla at gmail.com Thu Jan 14 11:41:09 2016 From: dlozanosoldevilla at gmail.com (dlozanosoldevilla .) Date: Thu, 14 Jan 2016 11:41:09 +0100 Subject: [FieldTrip] Fieldtrip tutor WANTED: Coimbra workshop Message-ID: Dear Fieldtrippers, I am organizing a Fieldtrip workshop at Coimbra (Portugal) with talented alumni from Coimbra University, Champalimaud Center for the Unknown and Imperial College of London. I am looking for a highly motivated researcher that would like to be a tutor that available on any of the following dates: - May 9th - 11th - June 6th - 9th The workshop is two and a half days long and a draft of the program can be found here: http://www.fieldtriptoolbox.org/workshop/coimbra There will be around 12-13 people, most of them with EEG and/or MEG experience. The audience has a special interest in connectivity and source space analysis so a tutor with experience on these topics is mandatory. - Tutor activities: 1. Teach one or two lecture sessions. The tutor need to teach two lecture sessions; see program above. Besides the teaching material (slides + video ) is available and will be provided. In addition, the preparation of the lectures includes that the tutor will have a videoconferencing session with the main developers in Nijmegen to ensure that all aspects that are not clear in the slides are resolved. 2. Support hands-on sessions. After each theory session there is a hands-on session using tested tutorial data and code. The last day, the alumni bring their on data and the mission is to help the users with their analysis goals as much as time allows. All costs associated to travel and accommodation are covered (Only restricted to researchers working within Europe). If you are interested and/or you want to know more about it, please do not hesitate to contact me (dlozanosoldevilla at gmail.com). Preparing and teaching in such a workshop is a great opportunity to increase your own skills and to boost your CV! Looking forward to hear from you, Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Jan 15 09:16:20 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 15 Jan 2016 09:16:20 +0100 Subject: [FieldTrip] MEG/EEG FieldTrip toolkit course in Nijmegen: pre-registration now open Message-ID: Dear All, — Please disseminate to PhD students and postdoctoral researchers working with MEG, EEG and ECoG data analysis. --- On April 18-21, 2016 we will host the "Toolkit of Cognitive Neuroscience: advanced data analysis and source modelling of EEG and MEG data" at the Donders Institute in Nijmegen. This intense 4-day toolkit course will teach you advanced MEG and EEG data analysis skills. Preprocessing, frequency analysis, source reconstruction, connectivity and various statistical methods will be covered. The toolkit will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG data set using the FieldTrip toolbox. The lectures and tutoring will be provided by the core FieldTrip development team, and there will also be plenty of opportunity to interact and ask questions to us about your research and data. On the final day you will have the opportunity to work on your own dataset under supervision of the tutors. We can host a limited number of participants. From past experience we expect the course to be oversubscribed, hence we will start with pre-registration. The final selection of the participants will be based on the motivation, background experience and research interests that are provided in the registration form. The deadline for pre-registration is March 1, 2016. More information, including a preliminary program, can be found at http://www.ru.nl/donders/agenda-news/tool-kits-cognitive/toolkit-meg/ Looking forward to welcoming you in Nijmegen, Robert Oostenveld and Jan-Mathijs Schoffelen. ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Radboud University, Nijmegen, The Netherlands Visiting Professor NatMEG - the Swedish National MEG facility Karolinska Institute, Stockholm, Sweden tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/donders skype: r.oostenveld ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Jan 15 11:18:31 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 15 Jan 2016 11:18:31 +0100 Subject: [FieldTrip] fixed bug in MEG localspheres forward model Message-ID: <8543B5C2-731C-4AEA-9CFE-894B5E35D40D@donders.ru.nl> Dear FieldTrip users, We found (and fixed) a bug in the MEG localspheres forward model, which may have affected your recent analyses. The consequence is that MEG source reconstructions would have been of very poor quaility. This was pointed out to me by Fraincois Tadel (thanks!) who noticed that dipole fits of clean topographies ended up in completely unexpected locations. Also MNE and beamformer results will have been wrong, although there it was less obvious to detect the flaw. I have included the fix in SVN revision 11061, which you can also find on https://github.com/fieldtrip/fieldtrip. If you use the download version from our FTP server: the version that is released this evening will include the fix. Further details can be found on http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3037 Sorry for the inconvenience, Robert PS If you use singlesphere, BEM or singleshell models, you have not been affected by this. From vic.schroeder2 at gmail.com Fri Jan 15 11:26:14 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Fri, 15 Jan 2016 10:26:14 +0000 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: Thank you Tzvetan. 2016-01-03 20:18 GMT+00:00 Tzvetan Popov : > > Dear Victoria, > the system you are working with is already equipped with two orthogonal > planar gradiometer sensors. Thus you should not try to create planar > gradients on the basis of the planar gradients. Yet you might want to use > the magnetometers only. There you can represent the activity as if it was > picked up by planar gradients. Could you please skip the planar > transformation bit and redo your analysis? > FieldTrip provides three types of layouts for the Neuromag system: *NM306all.lay > NM306mag.lay NM306grad.lay*. For example if you want to plot > magnetometers only you’d specify *cfg.layout = 'neuromag306mag.lay’; > cfg.channel = 'MEG*1’*; Here MEG*1 refers to magnetometers and MEG*2 and > MEG*3 would be the two orthogonal planar gradients respectively. Also the > neighbours are provided as* neuromag306cmb_neighb.mat; > neuromag306mag_neighb.mat; neuromag306planar_neighb.ma > *t;. You might consider loading the > structure of your choice directly. > Here is an example tutorial that might help: > http://www.fieldtriptoolbox.org/tutorial/natmeg/timefrequency > Good luck, > tzvetan > > Dear Fieldtrip team, > > I am currently working on data acquired from an elektra system (neuromag). > I have done all the preprocessing and the ft_freqanalysis with the > gradiometers only. I combined the gradiometers to create planar > gradients.However , later when doing the statistics problems occur when i > want to specify the channels. The error tells me that no degrees of freedom > are found for the analysis. However, when i remove the cfg.channel form the > script it runs through without an error. (please see code below). > My question is whether the output of the stastistic is correct without > specifying the channels? If not, does anybody have suggestions how to fix > the problem? > > I have run into similar problems when wanting to plot the time frequency > data from the planar gradients after having used ft_combineplanar. Here i > cannot find a layout file that suits the output of ft_combineplanar. Thus, > i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, > however, the layouts provided by fieldtrip does not fit that number. > Has anybody run into similar problems? Or does anybody know a possible > solution? > > Thank you very much for any suggestions > Victoria > > %combine planar > cfg = []; > cfg.method ='sum'; > %ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > cfg = []; > %cfg.channel = {'MEG'}; > cfg.latency = 'all'; > cfg.frequency = [14.5 16]; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); > > design = zeros(1,size(ComGrad_con.powspctrm,1) + > size(ComGrad_incon.powspctrm,1)); > design(1,1:size(ComGrad_con.powspctrm,1)) = 1; > > design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... > size(ComGrad_incon.powspctrm,1))) = 2; > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Fri Jan 15 12:09:07 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Fri, 15 Jan 2016 11:09:07 +0000 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: Dear Tzvetan, I did not do any planar transformation with the gradiometers. I only did the ft_combineplanar. Should i also omit that? Cheers Victoria 2016-01-15 10:26 GMT+00:00 victoria schroeder : > Thank you Tzvetan. > > 2016-01-03 20:18 GMT+00:00 Tzvetan Popov : > >> >> Dear Victoria, >> the system you are working with is already equipped with two orthogonal >> planar gradiometer sensors. Thus you should not try to create planar >> gradients on the basis of the planar gradients. Yet you might want to use >> the magnetometers only. There you can represent the activity as if it was >> picked up by planar gradients. Could you please skip the planar >> transformation bit and redo your analysis? >> FieldTrip provides three types of layouts for the Neuromag system: *NM306all.lay >> NM306mag.lay NM306grad.lay*. For example if you want to plot >> magnetometers only you’d specify *cfg.layout = 'neuromag306mag.lay’; >> cfg.channel = 'MEG*1’*; Here MEG*1 refers to magnetometers and MEG*2 and >> MEG*3 would be the two orthogonal planar gradients respectively. Also the >> neighbours are provided as* neuromag306cmb_neighb.mat; >> neuromag306mag_neighb.mat; neuromag306planar_neighb.ma >> *t;. You might consider loading the >> structure of your choice directly. >> Here is an example tutorial that might help: >> http://www.fieldtriptoolbox.org/tutorial/natmeg/timefrequency >> Good luck, >> tzvetan >> >> Dear Fieldtrip team, >> >> I am currently working on data acquired from an elektra system >> (neuromag). I have done all the preprocessing and the ft_freqanalysis with >> the gradiometers only. I combined the gradiometers to create planar >> gradients.However , later when doing the statistics problems occur when i >> want to specify the channels. The error tells me that no degrees of freedom >> are found for the analysis. However, when i remove the cfg.channel form the >> script it runs through without an error. (please see code below). >> My question is whether the output of the stastistic is correct without >> specifying the channels? If not, does anybody have suggestions how to fix >> the problem? >> >> I have run into similar problems when wanting to plot the time frequency >> data from the planar gradients after having used ft_combineplanar. Here i >> cannot find a layout file that suits the output of ft_combineplanar. Thus, >> i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, >> however, the layouts provided by fieldtrip does not fit that number. >> Has anybody run into similar problems? Or does anybody know a possible >> solution? >> >> Thank you very much for any suggestions >> Victoria >> >> %combine planar >> cfg = []; >> cfg.method ='sum'; >> %ComCon = ft_combineplanar(cfg,FreqCon); >> ComIncon = ft_combineplanar(cfg, FreqIncon); >> >> cfg = []; >> %cfg.channel = {'MEG'}; >> cfg.latency = 'all'; >> cfg.frequency = [14.5 16]; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'ft_statfun_indepsamplesT'; >> cfg.correctm = 'cluster'; >> cfg.clusteralpha = 0.05; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan = 2; >> cfg.tail = 0; >> cfg.clustertail = 0; >> cfg.alpha = 0.025; >> cfg.numrandomization = 500; >> cfg_neighb.method = 'distance'; >> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); >> >> design = zeros(1,size(ComGrad_con.powspctrm,1) + >> size(ComGrad_incon.powspctrm,1)); >> design(1,1:size(ComGrad_con.powspctrm,1)) = 1; >> >> design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... >> size(ComGrad_incon.powspctrm,1))) = 2; >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Harald.Bornfleth at besa.de Fri Jan 15 14:35:11 2016 From: Harald.Bornfleth at besa.de (Harald Bornfleth) Date: Fri, 15 Jan 2016 14:35:11 +0100 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Message-ID: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Dear Andrew, Thanks for bringing this up. I can try to shed some light on the ICA method used in BESA Research; however, I can not comment on the implementation in FieldTrip. The method behind ICA analysis in BESA Research is the extended infomax ICA algorithm (Lee TW et al.: Independent component analysis using an extended infomax algorithm for mixed sub-Gaussian and super-Gaussian sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very well suited to remove cardiac and powerline artifacts. Depending on the data, it may also be used to remove ocular (blink) and electrode artifacts. To assess whether your artifact removal is trustworthy more information about your processing steps are needed. What types of artifacts are you trying to correct? What segments are you using to determine the artifact topographies and what segments are you finally correcting? Best regards, Harald Dr. Harald Bornfleth Product Manager BESA Research BESA GmbH Freihamer Strasse 18 82166 Graefelfing/Germany http://www.besa.de E: Harald.Bornfleth at besa.de T: +49 89 8980 9968 HRB Munich 109956 CEO: Dr. Tobias Scherg, CFO: Theodor Scherg Director of Research: Dr. Michael Scherg From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Andrew Chang Sent: Sonntag, 10. Januar 2016 21:18 To: fieldtrip at science.ru.nl Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Dear Fieldtrip users, I am wondering whether anyone has compared the performances of the ICA methods among M/EEG toolboxes. Especially, how is the performance of ICA in BESA Research 6.0, compared to Fieldtrip? I have an EEG data set which has been processed in BESA, including removing artifact using ICA. I am wondering whether I can trust it, or I should reprocess it in Fieldtrip. Any comments will be appreciated! Happy new year! Best, Andrew -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ATT00004.txt URL: From michele.scaltritti at gmail.com Fri Jan 15 16:03:18 2016 From: michele.scaltritti at gmail.com (Michele Scaltritti) Date: Fri, 15 Jan 2016 16:03:18 +0100 Subject: [FieldTrip] unexpected boundary effects using Morlet wavelets Message-ID: Dears, I am Michele Scaltritti, and this is my first post on this mailing list. I work on ERPs in the context of psycholinguistics, and I just recently started working with Fieldtrip to perform time-frequency analyses. I am encountering a problem with respect to boundary effects, as these affects time windows that I didn't expect. More precisely, I' running my analysis on epochs going from -1.1s before stimulus onset (0 s), to 4 s afterwards (for a total length of 5.1s). In order to do that, I am using Morlet wavelets of 7 cycles, with 50 milliseconds time-steps. I am estimating frequencies ranging from 10 to 35 Hz. At 10Hz frequency, the length of my wavelet should be 7/10/pi, so around 222 ms. As such, I would expect to be able to estimate frequency power at -800 ms in my epoch (which corresponds to the starting time of what I would like to be my baseline): in fact, I would expect to be able to estimate 10Hz frequency power as soon as the third time-step (150 ms), corresponding to -950 in my epochs. However, I don't get any value for 10Hz frequency at -800 ms. Clearly, my reasoning is wrong, but I can't figure out what I am missing. In the following lines, I'll post the code of the configuration I used to run the frequency decomposition cfg = [] cfg.channel = 'all'; cfg.method = 'wavelet'; cfg.width = 7; cfg.output = 'pow'; cfg.foi = 10:1:35; cfg.toi = -1.1:0.05:4 TF_data = ft_freqanalysis(cfg,data) Thank you very much for the attention, and please excuse eventual gross mistakes in my arguments. michele -------------- next part -------------- An HTML attachment was scrubbed... URL: From fosco.bernasconi at gmail.com Sat Jan 16 15:42:50 2016 From: fosco.bernasconi at gmail.com (fosco bernasconi) Date: Sat, 16 Jan 2016 15:42:50 +0100 Subject: [FieldTrip] Fwd: ft_statfun_actvsblT & ft_timelockstatistics error In-Reply-To: References: Message-ID: Hi all, I would like to identify ECoG electrodes that are active during my task, by comparing the post-stimulus activity vs. the baseline. I would like to do this on LFP (and not on time-frequency data). Unfortunately, I keep having the error "Inappropriate dimord for the statistics function STATFUN_ACTVSBLT.". My cfg.dimord = 'rpt_chan_time'; I am missing something, any suggestion? Thanks a lot in advance! fosco Here my code: datafldtrp= eeglab2fieldtrip(EEG,'preprocessing'); % define intervals: cfg = []; cfg.channel = {'GA1'}; cfg.toilim = [-.2 0]; dataFIC_baseline = ft_redefinetrial(cfg,datafldtrp); cfg = []; cfg.channel = {'GA1'}; cfg.toilim = [0.05 0.25]; dataFIC_activation = ft_redefinetrial(cfg,datafldtrp); cfg = []; cfg.keeptrials = 'yes'; cfg.removemean = 'no'; [timelock_baseline] = ft_timelockanalysis(cfg,dataFIC_baseline); [timelock_activation] = ft_timelockanalysis(cfg,dataFIC_activation); timelock_activation.time = timelock_baseline.time; cfg = []; ntrials = size(timelock_activation.trial,1); design = zeros(2,2*ntrials); design(1,1:ntrials) = 1; design(1,ntrials+1:2*ntrials) = 2; design(2,1:ntrials) = [1:ntrials]; design(2,ntrials+1:2*ntrials) = [1:ntrials]; cfg.design = design; cfg.statistic = 'ft_statfun_actvsblT'; cfg.method = 'montecarlo'; cfg.numrandomization = 500; cfg.parameter = 'trial'; cfg.ivar = 1; cfg.tail = 0; [stat] = ft_timelockstatistics(cfg,timelock_activation,timelock_baseline); -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Sat Jan 16 18:26:53 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Sat, 16 Jan 2016 17:26:53 +0000 Subject: [FieldTrip] plotting neighbours Message-ID: Hi ! I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243* *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243* however what i see is: *Selected channel MEG0741, which has 0 neighbours: * *Selected channel MEG0731, which has 0 neighbours: * *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243* *Selected channel MEG0711, which has 0 neighbours: * *Selected channel MEG0741, which has 0 neighbours: * It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243* or *Selected channel MEG1031, which has 0 neighbours: * Do you have any suggestions why this happen? Are the channels not grouped correctly? Below is the code starting from the time-frequency analysis of the data. Thank you very much Victoria cfg = []; cfg.output = 'pow'; cfg.channel = 'MEGGRAD'; cfg.method = 'mtmconvol'; cfg.taper = 'hanning'; cfg.foi = [2:2:30]; %cfg.keeptrials = 'yes'; for stats keep trials cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec cfg.toi = [-1.3:0.05:1]; cfg.keeptrials = 'yes'; FreqCon = ft_freqanalysis(cfg, Con_clean); FreqIncon = ft_freqanalysis(cfg, Incon_clean); %combine planar cfg = []; cfg.method ='sum'; ComCon = ft_combineplanar(cfg,FreqCon); ComIncon = ft_combineplanar(cfg, FreqIncon); % plot neighbours cfg=[]; cfg.method = 'triangulation'; cfg.layout = 'neuromag306cmb.lay'; ft_neighbourplot(cfg,ComCon) -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Sat Jan 16 19:00:48 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sat, 16 Jan 2016 19:00:48 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: Dear Victoria, you should remove the ft_combineplanar step from your analysis pipeline. This function takes input from ft_megplanar. The latter is applied only to magnetometers or axial gradiometers. best tzvetan > Hi ! > > I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > > however what i see is: > > Selected channel MEG0741, which has 0 neighbours: > Selected channel MEG0731, which has 0 neighbours: > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > Selected channel MEG0711, which has 0 neighbours: > Selected channel MEG0741, which has 0 neighbours: > > It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > > or > > Selected channel MEG1031, which has 0 neighbours: > > Do you have any suggestions why this happen? Are the channels not grouped correctly? > > Below is the code starting from the time-frequency analysis of the data. > > Thank you very much > Victoria > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEGGRAD'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = [2:2:30]; > %cfg.keeptrials = 'yes'; for stats keep trials > cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec > cfg.toi = [-1.3:0.05:1]; > cfg.keeptrials = 'yes'; > FreqCon = ft_freqanalysis(cfg, Con_clean); > FreqIncon = ft_freqanalysis(cfg, Incon_clean); > > %combine planar > cfg = []; > cfg.method ='sum'; > ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > % plot neighbours > cfg=[]; > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg,ComCon) > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tokimoto at mejiro.ac.jp Sun Jan 17 11:39:24 2016 From: tokimoto at mejiro.ac.jp (Shingo Tokimoto) Date: Sun, 17 Jan 2016 19:39:24 +0900 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> Message-ID: <73BB8BE6-8BC7-40AF-B785-E600CCA77ED6@mejiro.ac.jp> Dear Dr. Tzvetan Popov and FieldTrip users, Thank you for the comment again. I undone the changes, but the same error message appears. The cluster-based permutation test works well for ERP, but it doesn't work for ERSP. Attached is the window of EEGLAB for statistic parameters. I understand you are not familiar with EEGLAB. Could you give me any suggestions for the parameters of FieldTrip statistics? The messages in the command window of Matlab is as follows. Using pre-loaded data. To force rereading data from disk use the 'forceread' flag 1 x 2, paired data, computing T values the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 6 MB Thank you in advance again. ************************************************ Shingo Tokimoto, Ph.D. in Linguistics and Psychology Department of Foreign Languages Mejiro University 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, 161-8539, Japan tokimoto at mejiro.ac.jp ************************************************ On 2016/01/11, at 1:08, Tzvetan Popov wrote: > Dear Shingo, > lets keep it by Tzvetan ;-). I’m not familiar with the way EEGLAB deals with FieldTrip functions at all. So I may not be of any further help. > However as a rule of thumb you should almost never change settings in the FieldTrip functions but provide the appropriate configurations always as cfg.xxx. When you mention your analysis works for ERP I don’t see any reason why it fails with time-freq data. Obviously you have your electrode positions and you were able to generate neighborhood structure. If so the same should work for t-f too. > Maybe if you provide the syntax of your analysis me or others can help you in getting it done. > I will advise to undone any changes you made to the FieldTrip code and try again. Probably a fresh version of EEGLAB, clean math lab path etc. and then do it again. > best > tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Window_EEGLAB.png Type: image/png Size: 79275 bytes Desc: not available URL: From changa5 at mcmaster.ca Sun Jan 17 19:57:03 2016 From: changa5 at mcmaster.ca (Andrew Chang) Date: Sun, 17 Jan 2016 13:57:03 -0500 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) In-Reply-To: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> References: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Message-ID: Hi Dr. Bornfleth, Thanks for your reply very much. I would like to use ICA to remove eye blinks and eye movements, neck movements, as well as cardiac and powerline artifacts. The segment I have is a continuous EEG recording for 10 minutes, which is one block of my experiment including many trials. Before ICA, the segment have been high-pass (0.3 Hz) and low-pass (100 Hz). The components showing activities around the eyes, the back of the neck, and 60 Hz were removed. As for the cardiac artifact, I it is based on visual inspection on the waveform to see whether it looks like an EKG. Any further comments are appreciated! Best, Andrew On Fri, Jan 15, 2016 at 8:35 AM, Harald Bornfleth wrote: > Dear Andrew, > > > > Thanks for bringing this up. I can try to shed some light on the ICA > method used in BESA Research; however, I can not comment on the > implementation in FieldTrip. > > > > The method behind ICA analysis in BESA Research is the extended infomax > ICA algorithm (Lee TW et al.: Independent component analysis using an > extended infomax algorithm for mixed sub-Gaussian and super-Gaussian > sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very > well suited to remove cardiac and powerline artifacts. Depending on the > data, it may also be used to remove ocular (blink) and electrode artifacts. > To assess whether your artifact removal is trustworthy more information > about your processing steps are needed. What types of artifacts are you > trying to correct? What segments are you using to determine the artifact > topographies and what segments are you finally correcting? > > > > Best regards, > > Harald > > > > > > *Dr. Harald Bornfleth* > > Product Manager BESA Research > > > > *BESA GmbH* > > Freihamer Strasse 18 > > 82166 Graefelfing/Germany > > http://www.besa.de > > > > E: Harald.Bornfleth at besa.de > > T: +49 89 8980 9968 > > > > > > HRB Munich 109956 > > CEO: Dr. Tobias Scherg, CFO: Theodor Scherg > > Director of Research: Dr. Michael Scherg > > > > > > > > > > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > mailto:fieldtrip-bounces at science.ru.nl ] *On > Behalf Of *Andrew Chang > *Sent:* Sonntag, 10. Januar 2016 21:18 > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. > Fieldtrip) > > > > Dear Fieldtrip users, > > > > I am wondering whether anyone has compared the performances of the ICA > methods among M/EEG toolboxes. Especially, how is the performance of ICA in > BESA Research 6.0, compared to Fieldtrip? > > I have an EEG data set which has been processed in BESA, including > removing artifact using ICA. I am wondering whether I can trust it, or > I should reprocess it in Fieldtrip. Any comments will be appreciated! > > > > Happy new year! > > > > Best, > > Andrew > > > > -- > > Andrew Chang > Ph.D. Candidate > Auditory Development Lab > > Department of Psychology, Neuroscience & Behaviour > McMaster University > > http://changa5.wordpress.com/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Mon Jan 18 12:38:39 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Mon, 18 Jan 2016 11:38:39 +0000 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: Dear Tzvetan Are you sure about that in the tutorial http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing neuromag data is used and ft_combineplanar is used to combine the gradiometers. This is a paragraph from this tutorial: In fact, we are now plotting the two different gradiometers together. You can see the channel locations being in pairs, one above the other. They are in reality, however, at the same location but oriented differently - radially and axially *with respect to the surface of the helmet*. They can thereby pick up both radial orientations of the magnetic fields. To use them properly for the purpose of plotting, we should therefor combine them first, adding their fields. TFR_left_MEG_comb = ft_combineplanar([],TFR_left_MEG); TFR_right_MEG_comb = ft_combineplanar([],TFR_right_MEG); cfg = []; cfg.baseline = [-0.5 -0.1]; cfg.baselinetype = 'absolute'; cfg.xlim = [0.4 0.8]; cfg.ylim = [15 25]; cfg.zlim = [-4e-24 4e-24]; cfg.marker = 'on'; cfg.layout = 'neuromag306cmb.lay'; figure ; ft_topoplotTFR(cfg, TFR_left_MEG_comb);print -dpng natmeg_freq13.png Thus, it should be possible to use ft_combineplanar for neuromag data. What do you think? Cheers Victoria 2016-01-16 18:00 GMT+00:00 Tzvetan Popov : > Dear Victoria, > you should remove the ft_combineplanar step from your analysis pipeline. > This function takes input from ft_megplanar. The latter is applied only to > magnetometers or axial gradiometers. > > best > tzvetan > > > Hi ! > > I am working with a neuromag system and want to do cluster based > permutation tests with time frequency data. However, before running the > stats i would like to check the clusters which are formed by > ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the > plot and clicking on the channels i would expect to see something like : > > *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, > MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, > MEG1242+1243* > > *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, > MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, > MEG2242+2243* > > however what i see is: > > *Selected channel MEG0741, which has 0 neighbours: * > *Selected channel MEG0731, which has 0 neighbours: * > *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, > MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, > MEG2242+2243* > *Selected channel MEG0711, which has 0 neighbours: * > *Selected channel MEG0741, which has 0 neighbours: * > > It is absolutely random when the correct output occurs. When clicking on a > particular channel it would randomly show me the following results: > > *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, > MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, > MEG1242+1243* > > or > > *Selected channel MEG1031, which has 0 neighbours: * > > Do you have any suggestions why this happen? Are the channels not grouped > correctly? > > Below is the code starting from the time-frequency analysis of the data. > > Thank you very much > Victoria > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEGGRAD'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = [2:2:30]; > %cfg.keeptrials = 'yes'; for stats keep trials > cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window > = 0.5 sec > cfg.toi = [-1.3:0.05:1]; > cfg.keeptrials = 'yes'; > FreqCon = ft_freqanalysis(cfg, Con_clean); > FreqIncon = ft_freqanalysis(cfg, Incon_clean); > > %combine planar > cfg = []; > cfg.method ='sum'; > ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > % plot neighbours > cfg=[]; > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg,ComCon) > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Harald.Bornfleth at besa.de Mon Jan 18 13:49:32 2016 From: Harald.Bornfleth at besa.de (Harald Bornfleth) Date: Mon, 18 Jan 2016 13:49:32 +0100 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) In-Reply-To: References: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Message-ID: Dear Andrew, A couple of questions popped up. 1) The neck movement artifact, is this something with low frequency, or is it a muscle artifact? 2) Did you calculate the ICA on one data screen (e.g. 10 seconds or 20 seconds), or over the whole data set? If you could send us screen shots showing the ICA wave forms and the accompanying topographies, then we could comment on the classification. (In BESA, you right-click on the label of a component and select “Map topography” to show the topography map of that component.) I include my colleague and ICA expert Nicole Ille on CC. Best regards, Harald From: c.andrew123 at gmail.com [mailto:c.andrew123 at gmail.com] On Behalf Of Andrew Chang Sent: 17 January 2016 19:57 To: Harald.Bornfleth at besa.de; FieldTrip discussion list Subject: Re: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Hi Dr. Bornfleth, Thanks for your reply very much. I would like to use ICA to remove eye blinks and eye movements, neck movements, as well as cardiac and powerline artifacts. The segment I have is a continuous EEG recording for 10 minutes, which is one block of my experiment including many trials. Before ICA, the segment have been high-pass (0.3 Hz) and low-pass (100 Hz). The components showing activities around the eyes, the back of the neck, and 60 Hz were removed. As for the cardiac artifact, I it is based on visual inspection on the waveform to see whether it looks like an EKG. Any further comments are appreciated! Best, Andrew On Fri, Jan 15, 2016 at 8:35 AM, Harald Bornfleth > wrote: Dear Andrew, Thanks for bringing this up. I can try to shed some light on the ICA method used in BESA Research; however, I can not comment on the implementation in FieldTrip. The method behind ICA analysis in BESA Research is the extended infomax ICA algorithm (Lee TW et al.: Independent component analysis using an extended infomax algorithm for mixed sub-Gaussian and super-Gaussian sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very well suited to remove cardiac and powerline artifacts. Depending on the data, it may also be used to remove ocular (blink) and electrode artifacts. To assess whether your artifact removal is trustworthy more information about your processing steps are needed. What types of artifacts are you trying to correct? What segments are you using to determine the artifact topographies and what segments are you finally correcting? Best regards, Harald Dr. Harald Bornfleth Product Manager BESA Research BESA GmbH Freihamer Strasse 18 82166 Graefelfing/Germany http://www.besa.de E: Harald.Bornfleth at besa.de T: +49 89 8980 9968 HRB Munich 109956 CEO: Dr. Tobias Scherg, CFO: Theodor Scherg Director of Research: Dr. Michael Scherg From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Andrew Chang Sent: Sonntag, 10. Januar 2016 21:18 To: fieldtrip at science.ru.nl Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Dear Fieldtrip users, I am wondering whether anyone has compared the performances of the ICA methods among M/EEG toolboxes. Especially, how is the performance of ICA in BESA Research 6.0, compared to Fieldtrip? I have an EEG data set which has been processed in BESA, including removing artifact using ICA. I am wondering whether I can trust it, or I should reprocess it in Fieldtrip. Any comments will be appreciated! Happy new year! Best, Andrew -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon Jan 18 13:59:20 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 Jan 2016 13:59:20 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> Hi Victoria, well if you work with the magnetometers yes. Maybe I misunderstood your previous posts. Yet this configuration from your post below cfg.channel = 'MEGGRAD’; results in time-frequency representation of power on the planar gradiometers only. In that case neither ft_megplanar nor ft_combineplanar are appropriate since the data stems from planar gradiometers. The tutorial you mentioned deals only with the magnetometers thus ft_megplanar and ft_combineplanar are used. best tzvetan > Dear Tzvetan > > Are you sure about that in the tutorial http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing neuromag data is used and ft_combineplanar is used to combine the gradiometers. This is a paragraph from this tutorial: > > In fact, we are now plotting the two different gradiometers together. You can see the channel locations being in pairs, one above the other. They are in reality, however, at the same location but oriented differently - radially and axially with respect to the surface of the helmet. They can thereby pick up both radial orientations of the magnetic fields. To use them properly for the purpose of plotting, we should therefor combine them first, adding their fields. > > TFR_left_MEG_comb = ft_combineplanar([],TFR_left_MEG); > TFR_right_MEG_comb = ft_combineplanar([],TFR_right_MEG); > > cfg = []; > cfg.baseline = [-0.5 -0.1]; > cfg.baselinetype = 'absolute'; > cfg.xlim = [0.4 0.8]; > cfg.ylim = [15 25]; > cfg.zlim = [-4e-24 4e-24]; > cfg.marker = 'on'; > cfg.layout = 'neuromag306cmb.lay'; > > figure; > ft_topoplotTFR(cfg, TFR_left_MEG_comb); > print -dpng natmeg_freq13.png > Thus, it should be possible to use ft_combineplanar for neuromag data. > What do you think? > > Cheers > Victoria > > 2016-01-16 18:00 GMT+00:00 Tzvetan Popov : > Dear Victoria, > you should remove the ft_combineplanar step from your analysis pipeline. This function takes input from ft_megplanar. The latter is applied only to magnetometers or axial gradiometers. > > best > tzvetan > > >> Hi ! >> >> I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : >> >> Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 >> Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 >> >> however what i see is: >> >> Selected channel MEG0741, which has 0 neighbours: >> Selected channel MEG0731, which has 0 neighbours: >> Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 >> Selected channel MEG0711, which has 0 neighbours: >> Selected channel MEG0741, which has 0 neighbours: >> >> It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: >> >> Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 >> >> or >> >> Selected channel MEG1031, which has 0 neighbours: >> >> Do you have any suggestions why this happen? Are the channels not grouped correctly? >> >> Below is the code starting from the time-frequency analysis of the data. >> >> Thank you very much >> Victoria >> >> cfg = []; >> cfg.output = 'pow'; >> cfg.channel = 'MEGGRAD'; >> cfg.method = 'mtmconvol'; >> cfg.taper = 'hanning'; >> cfg.foi = [2:2:30]; >> %cfg.keeptrials = 'yes'; for stats keep trials >> cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec >> cfg.toi = [-1.3:0.05:1]; >> cfg.keeptrials = 'yes'; >> FreqCon = ft_freqanalysis(cfg, Con_clean); >> FreqIncon = ft_freqanalysis(cfg, Incon_clean); >> >> %combine planar >> cfg = []; >> cfg.method ='sum'; >> ComCon = ft_combineplanar(cfg,FreqCon); >> ComIncon = ft_combineplanar(cfg, FreqIncon); >> >> % plot neighbours >> cfg=[]; >> cfg.method = 'triangulation'; >> cfg.layout = 'neuromag306cmb.lay'; >> ft_neighbourplot(cfg,ComCon) >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Mon Jan 18 17:45:22 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Mon, 18 Jan 2016 16:45:22 +0000 Subject: [FieldTrip] plotting neighbours In-Reply-To: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> References: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> Message-ID: Dear Tzvetan I get your point. I am only using that gradiometers. However, in the text which i copied into the previous email it is stated that ft_combineplanar is used for 'plotting the two different gradiometers together'. They mention gradiometers specifically. Also when running the code it is clear that the gradiometers not the magnetometers are combined. This is the resulting matrix when running the tutorial : [image: Inline-Bild 1] With this in mind, can you clarify why the toturial only uses magnetometers? As i understand it , it uses gradiometers. Thank you a lot Victoria 2016-01-18 12:59 GMT+00:00 Tzvetan Popov : > Hi Victoria, > well if you work with the magnetometers yes. Maybe I misunderstood your > previous posts. Yet this configuration from your post below cfg.channel = > 'MEGGRAD’; results in time-frequency representation of power on the planar > gradiometers only. In that case neither ft_megplanar nor ft_combineplanar > are appropriate since the data stems from planar gradiometers. The tutorial > you mentioned deals only with the magnetometers thus ft_megplanar and > ft_combineplanar are used. > > best > tzvetan > > > Dear Tzvetan > > Are you sure about that in the tutorial > http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing neuromag > data is used and ft_combineplanar is used to combine the gradiometers. This > is a paragraph from this tutorial: > > In fact, we are now plotting the two different gradiometers together. You > can see the channel locations being in pairs, one above the other. They are > in reality, however, at the same location but oriented differently - > radially and axially *with respect to the surface of the helmet*. They > can thereby pick up both radial orientations of the magnetic fields. To use > them properly for the purpose of plotting, we should therefor combine them > first, adding their fields. > > TFR_left_MEG_comb = ft_combineplanar([],TFR_left_MEG); > TFR_right_MEG_comb = ft_combineplanar([],TFR_right_MEG); > > cfg = []; > cfg.baseline = [-0.5 -0.1]; > cfg.baselinetype = 'absolute'; > cfg.xlim = [0.4 0.8]; > cfg.ylim = [15 25]; > cfg.zlim = [-4e-24 4e-24]; > cfg.marker = 'on'; > cfg.layout = 'neuromag306cmb.lay'; > figure ; > ft_topoplotTFR(cfg, TFR_left_MEG_comb);print -dpng natmeg_freq13.png > > Thus, it should be possible to use ft_combineplanar for neuromag data. > What do you think? > > Cheers > Victoria > > 2016-01-16 18:00 GMT+00:00 Tzvetan Popov : > >> Dear Victoria, >> you should remove the ft_combineplanar step from your analysis pipeline. >> This function takes input from ft_megplanar. The latter is applied only to >> magnetometers or axial gradiometers. >> >> best >> tzvetan >> >> >> Hi ! >> >> I am working with a neuromag system and want to do cluster based >> permutation tests with time frequency data. However, before running the >> stats i would like to check the clusters which are formed by >> ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the >> plot and clicking on the channels i would expect to see something like : >> >> *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, >> MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, >> MEG1242+1243* >> >> *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, >> MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, >> MEG2242+2243* >> >> however what i see is: >> >> *Selected channel MEG0741, which has 0 neighbours: * >> *Selected channel MEG0731, which has 0 neighbours: * >> *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, >> MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, >> MEG2242+2243* >> *Selected channel MEG0711, which has 0 neighbours: * >> *Selected channel MEG0741, which has 0 neighbours: * >> >> It is absolutely random when the correct output occurs. When clicking on >> a particular channel it would randomly show me the following results: >> >> *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, >> MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, >> MEG1242+1243* >> >> or >> >> *Selected channel MEG1031, which has 0 neighbours: * >> >> Do you have any suggestions why this happen? Are the channels not grouped >> correctly? >> >> Below is the code starting from the time-frequency analysis of the data. >> >> Thank you very much >> Victoria >> >> cfg = []; >> cfg.output = 'pow'; >> cfg.channel = 'MEGGRAD'; >> cfg.method = 'mtmconvol'; >> cfg.taper = 'hanning'; >> cfg.foi = [2:2:30]; >> %cfg.keeptrials = 'yes'; for stats keep trials >> cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time >> window = 0.5 sec >> cfg.toi = [-1.3:0.05:1]; >> cfg.keeptrials = 'yes'; >> FreqCon = ft_freqanalysis(cfg, Con_clean); >> FreqIncon = ft_freqanalysis(cfg, Incon_clean); >> >> %combine planar >> cfg = []; >> cfg.method ='sum'; >> ComCon = ft_combineplanar(cfg,FreqCon); >> ComIncon = ft_combineplanar(cfg, FreqIncon); >> >> % plot neighbours >> cfg=[]; >> cfg.method = 'triangulation'; >> cfg.layout = 'neuromag306cmb.lay'; >> ft_neighbourplot(cfg,ComCon) >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Combineplanar.PNG Type: image/png Size: 38714 bytes Desc: not available URL: From mail at philipp-ruhnau.de Mon Jan 18 18:00:59 2016 From: mail at philipp-ruhnau.de (Philipp Ruhnau) Date: Mon, 18 Jan 2016 18:00:59 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: Dear Victoria, I think there might be something odd with the channel selection in your data (or maybe also something that happens in ft_neighborplot) as I see it you have two options 1) I would instead suggest to use ft_prepare neighbors with your data as input cfg = [] cfg.method = ‘triangulation’ cfg.feedback = ‘yes’ % with this you get the feedback plot neigh = ft_prepare_neighbours(cfg, your_data) I am not entirely sure which layout the function uses if you feed in the default layout (which should be fine though), but I think it still uses the data’s for me clicking in the function didn’t work properly, but I think that is a different (gui?) issue, more importantly however the graphical layout and the labels that are grouped make sense that’s also true for what you posted. the only thing odd there is that your neighbor-structure still has magnetometers (MEG***1) that should have been removed, thus my hunch that they are somehow still in the data you feed in to ft_neighbourplot [i just quickly try and I can to a certain extend replicate your problem, but not fully as clicking doesn’t work…but also all the magnetometers with 0 neighbours] and as Tzvetan said, one magnetometer and two gradiometers are in the same position, so I would expect an alternating output between, say, MEG1031 and MEG1032+1033 the easiest thing you can try is use ft_selectdata again before you create the neighbors cfg = []; cfg.channel = ‘MEGGRAD’; data = ft_selectdata(cfg, data) just as a check, if your problem vanishes, the mags were still in there somewhere. 2) just load the default/use the layout field with the function above without the data input. then for me the plotting works and the output is like you predicted cfg = [] cfg.method = ‘triangulation’ cfg.feedback = ‘yes’ % with this you get the feedback plot cfg.layout = ‘neuromag306cmb.lay' neigh = ft_prepare_neighbours(cfg) as for the whether you should use ft_combineplanar. as a neuromag user myself I always use it for plotting but also for statistics, similar to what the wiki says, so I’m a little confused there too. of course you can plot them each of course. I don’t think you need to specify the combination method there though, as ‘sum’ is default for power. cheers philipp > On 16 Jan 2016, at 18:26, victoria schroeder wrote: > > Hi ! > > I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > > however what i see is: > > Selected channel MEG0741, which has 0 neighbours: > Selected channel MEG0731, which has 0 neighbours: > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > Selected channel MEG0711, which has 0 neighbours: > Selected channel MEG0741, which has 0 neighbours: > > It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > > or > > Selected channel MEG1031, which has 0 neighbours: > > Do you have any suggestions why this happen? Are the channels not grouped correctly? > > Below is the code starting from the time-frequency analysis of the data. > > Thank you very much > Victoria > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEGGRAD'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = [2:2:30]; > %cfg.keeptrials = 'yes'; for stats keep trials > cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec > cfg.toi = [-1.3:0.05:1]; > cfg.keeptrials = 'yes'; > FreqCon = ft_freqanalysis(cfg, Con_clean); > FreqIncon = ft_freqanalysis(cfg, Incon_clean); > > %combine planar > cfg = []; > cfg.method ='sum'; > ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > % plot neighbours > cfg=[]; > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg,ComCon) > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon Jan 18 18:57:57 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 Jan 2016 18:57:57 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> Message-ID: <7B5CC5BE-033A-41D6-8112-331FE3B71580@uni-konstanz.de> Hi Victoria, oopsy, I think I confused you dramatically. I’m sorry for this. You are right I was only scrolling up to the part where the mags were analyzed. As for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can threat them separately, as I was naively thinking as non-neuormag user, but indeed combination of both is recommended as I have now learned :-)(thanks Phillip). I ran the following steps and I guess this should work for you. best tzvetan %% cfg = []; ComCon = ft_combineplanar(cfg,FreqCon); %% cfg = [] cfg.method = 'triangulation'; cfg.layout = 'neuromag306cmb.lay'; cfg.senstype = 'MEG'; neighbours = ft_prepare_neighbours(cfg, ComCon) %% % plot neighbours cfg=[]; cfg.neighbours = neighbours; cfg.layout = 'neuromag306cmb.lay'; ft_neighbourplot(cfg); -------------- next part -------------- An HTML attachment was scrubbed... URL: From jim.f.cav at gmail.com Mon Jan 18 20:47:45 2016 From: jim.f.cav at gmail.com (Jim Cavanagh) Date: Mon, 18 Jan 2016 12:47:45 -0700 Subject: [FieldTrip] Restrict source reconstruction to gray matter: Any updates? Message-ID: Has there been any followup on this thread? I'm finding it rather difficult to constrain the source projection to grey matter only - surely someone else has tried this using FT? http://mailman.science.ru.nl/pipermail/fieldtrip/2012-March/004984.html -- Jim Cavanagh Assistant Professor University of New Mexico https://sites.google.com/site/jcavanaghunm/home -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Tue Jan 19 15:35:00 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Tue, 19 Jan 2016 15:35:00 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de> Dear community, My name is Laith Hamid and I am working in the University Medical Complex of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and seizures. Currently I am analysing an EEG data set that was recorded using a 256-channel EGI system and I wanted to ask whether you have a standard BEM or FEM head model that extends enough downwards to accomodate all 256 electrodes. The current standard BEM model in the template folder of Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. Thank you very much in advance for your help! Best, Laith -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Jan 19 16:16:54 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 19 Jan 2016 16:16:54 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps In-Reply-To: <0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de> References: <0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de> Message-ID: Dear Laith, thanks for your question. You could refer to a factory schematic layout such as the one in figure 4 of this publication: http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract and subsequently use the function ft_prepare_layout to manually track the points of the custom design on your own (if you dont want to wait for somebody from the FT to do the same for you). cfg = []; cfg.image = 'figure4_layout_256_Frontiers.png'; lay = ft_prepare_layout(cfg); The following tutorial describes the procedure in more details: http://www.fieldtriptoolbox.org/tutorial/layout Please do not hesitate to get in touch with me for this and other matters. All the best Cris Micheli On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid wrote: > Dear community, > > My name is Laith Hamid and I am working in the University Medical Complex > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > seizures. Currently I am analysing an EEG data set that was recorded using > a 256-channel EGI system and I wanted to ask whether you have a standard > BEM or FEM head model that extends enough downwards to accomodate all 256 > electrodes. The current standard BEM model in the template folder of > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > Thank you very much in advance for your help! > > Best, > > Laith > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Tue Jan 19 17:41:48 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Tue, 19 Jan 2016 17:41:48 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de> Dear Cris, thank you very much for your answer. I am refering to an issue that was discussed in this thread from April 2013: [FieldTrip] source analysis EEG data without MRI The thread however does not offer a segmentation or head model for download. Some electrodes in the EGI 256-electrodes cap are placed on the cheeks or on the back of the neck and these areas are not modeled by the standard BEM skin compartment in the standard BEM model. My question was about a standard segmentation that extends the skin (and skull) compartment downwards to allow these electrodes to sit on the nodes of the skin mesh. Best, Laith -------------- next part -------------- An HTML attachment was scrubbed... URL: From aishwaryaselvaraj1708 at gmail.com Tue Jan 19 17:52:55 2016 From: aishwaryaselvaraj1708 at gmail.com (aishwarya selvaraj) Date: Tue, 19 Jan 2016 16:52:55 +0000 Subject: [FieldTrip] Source Localisation Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> Hi guys, I'm currently working on source localization of EEG signals . Im very new to it . Can Anyone provide any inputs ?? It would be of great help . -- Regards, Aishwarya -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Homolle at donders.ru.nl Tue Jan 19 18:06:13 2016 From: S.Homolle at donders.ru.nl (=?iso-8859-1?Q?Hom=F6lle=2C_S=2E_=28Simon=29?=) Date: Tue, 19 Jan 2016 17:06:13 +0000 Subject: [FieldTrip] Source Localisation In-Reply-To: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> References: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> Message-ID: <2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl> Dear Aishwarya, Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. My recommended start would be: http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate Hopefully this provides you good start working with EEG source reconstruction Best regards, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] Sent: Tuesday, January 19, 2016 5:52 PM To: fieldtrip, donders Subject: [FieldTrip] Source Localisation Hi guys, I'm currently working on source localization of EEG signals . Im very new to it . Can Anyone provide any inputs ?? It would be of great help . -- Regards, Aishwarya -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Tue Jan 19 18:49:21 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Tue, 19 Jan 2016 17:49:21 +0000 Subject: [FieldTrip] plotting neighbours In-Reply-To: <7B5CC5BE-033A-41D6-8112-331FE3B71580@uni-konstanz.de> References: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> <7B5CC5BE-033A-41D6-8112-331FE3B71580@uni-konstanz.de> Message-ID: Thank you very much Philipp and Tzvetan! Things have become much clearer now. I would like to follow up with a very related question. I am trying to replicate the analysis for the cluster based permutation test using the code and the data provided. However, i run into two problems here First, i get the following error if i use the original code: Attempted to access cfg.frequency(2); index out of bounds because numel(cfg.frequency)=1. Error in ft_freqstatistics (line 187) cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. However, then no significant clusters are found. Which becomes clear when trying to plot the cluster or by looking at the output of ft_freqstatistics. Does the change in the code , change the output? How can i avoid the error mentioned above and still get the same output from ft_freqstatistics as the one provided on the webpage? The relevant section of the toturial is provided below. Thank you! Victoria Permutation test Now, run *ft_freqstatistics * to compare freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, the following configuration is identical to the configuration that was used for comparing event-related averages in the cluster-based permutation tests on event related fields tutorial . Also see this tutorial for a detailed explanation of all the configuration settings. You can read more about the *ft_prepare_neighbours * function in the FAQ's . To load the planar gradient TFRs (also available on the FieldTrip FTP servers,freqFIC_planar_cmb.mat and freqFC_planar_cmb.mat ), use: load freqFIC_planar_cmb load freqFC_planar_cmb cfg = []; cfg.channel = {'MEG', '-MLP31', '-MLO12'}; cfg.latency = 'all'; cfg.frequency = 20; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; % prepare_neighbours determines what sensors may form clusters cfg_neighb.method = 'distance'; cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + size(freqFC_planar_cmb.powspctrm,1)); design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... size(freqFC_planar_cmb.powspctrm,1))) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > Hi Victoria, > > oopsy, I think I confused you dramatically. I’m sorry for this. You are > right I was only scrolling up to the part where the mags were analyzed. As > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > threat them separately, as I was naively thinking as non-neuormag user, but > indeed combination of both is recommended as I have now learned :-)(thanks > Phillip). I ran the following steps and I guess this should work for you. > best > tzvetan > > %% > cfg = []; > ComCon = ft_combineplanar(cfg,FreqCon); > %% > cfg = [] > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > cfg.senstype = 'MEG'; > neighbours = ft_prepare_neighbours(cfg, ComCon) > %% > % plot neighbours > cfg=[]; > cfg.neighbours = neighbours; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg); > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Jan 19 20:50:24 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 19 Jan 2016 20:50:24 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps In-Reply-To: <61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de> References: <61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de> Message-ID: Dear Laith, this might be possible if you have the subject-specific MRI by following the tutorial here: http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem and using the function ft_prepare_mesh and the tutorial command: cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); which uses the segmented MRI (see tutorial). The bnd(3) variable should contain your triangulated surface with 1000 vertices. Let me know if that works. Of course you should see the skin and the neck in the original MRI. If you do not have an anatomical MRI that extends down to the chin you could try with a template, such as this: ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri and the corresponding segmented version ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat This goes down to the chin. Then you take care of rearranging the position of the EEG electrodes according to this: http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel I hope this helped Cris On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid wrote: > Dear Cris, > > thank you very much for your answer. I am refering to an issue that was > discussed in this thread from April 2013: > > > [FieldTrip] source analysis EEG data without MRI > > > The thread however does not offer a segmentation or head model for > download. Some electrodes in the EGI 256-electrodes cap are placed on the > cheeks or on the back of the neck and these areas are not modeled by the > standard BEM skin compartment in the standard BEM model. My question was > about a standard segmentation that extends the skin (and skull) compartment > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > Best, > Laith > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From munsif.jatoi at gmail.com Wed Jan 20 05:17:12 2016 From: munsif.jatoi at gmail.com (Munsif Jatoi) Date: Wed, 20 Jan 2016 12:17:12 +0800 Subject: [FieldTrip] Source Localisation In-Reply-To: <2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl> References: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> <2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl> Message-ID: Dear Aishwarya, Please refer to main help tutorials. Also, you can find out the survey papers written in this area. For more, SPM website can provide good help. Best, Munsif. On Wed, Jan 20, 2016 at 1:06 AM, Homölle, S. (Simon) < S.Homolle at donders.ru.nl> wrote: > Dear Aishwarya, > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > My recommended start would be: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > Hopefully this provides you good start working with EEG source > reconstruction > > Best regards, > > Simon Homölle > PhD Candidate > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Phone: +31-(0)24-36-65059 > ------------------------------ > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > *Sent:* Tuesday, January 19, 2016 5:52 PM > *To:* fieldtrip, donders > *Subject:* [FieldTrip] Source Localisation > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Munsif Ali H.Jatoi, Ph D Scholar, Centre for Intelligent Signals and Imaging Research, Universiti Teknologi PETRONAS, Malaysia. http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: From olga.v.sysoeva at gmail.com Wed Jan 20 11:36:16 2016 From: olga.v.sysoeva at gmail.com (Olga Sysoeva) Date: Wed, 20 Jan 2016 13:36:16 +0300 Subject: [FieldTrip] problems with mri interpolation Message-ID: Dear Fieldtrippers, I'm encounter the problem with MRI interpolation and reslicing using FT_VOLUMERESLICE. I have read my MRI from fif.file and this mri variable contains mri_K0012.unit, 'm' mri_K0012.dim, [432, 512, 180] mri_K0012.anatomy, <432, 512, 180 int16> mri_K0012.hdr, (1*1 structure) mri_K0012.transform, (4*4 double) mri_K0012.coordsys 'neuromag'. Than I used mri = ft_volumereslice([], mri); the output is “the input is volume data with dimensions [432 512 180] reslicing from [432 512 180] to [256 256 256] the input is volume data with dimensions [256 256 256] the input is volume data with dimensions [432 512 180] selecting subvolume of 0.0% reslicing and interpolating anatomy interpolating ??? Attempted to access sel(1); index out of bounds because numel(sel)=0. Error in ==> ft_sourceinterpolate>my_interpn at 663 ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ==> ft_sourceinterpolate at 583 av( sel) = my_interpn(fv, ax(sel), ay(sel), az(sel), cfg.interpmethod, cfg.feedback); Error in ==> ft_volumereslice at 176 resliced = ft_sourceinterpolate(tmpcfg, mri, resliced);” I'm using matlab 7.6.0 (R2008a) and recently downloaded fieltrip (also in my previous version of 2013 the error was the same). I'd be thankful for the comments. Best Regards, Olga. P.S.Actually, I can project my sources meaningfully into not interpolated MRI, altoough the images are plotted upside down. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Wed Jan 20 13:39:30 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Wed, 20 Jan 2016 13:39:30 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1@mail.uni-kiel.de> Dear Cris, thank you very much for your answers yesterday. The segmentedmri contained 'white', 'grey' and 'csf' so I needed to repeat the segmentation using 'brain', 'skull' and 'scalp' as described in the tutorial "Creating a BEM volume conduction model of the head for source-reconstruction of EEG data" and everything worked smoothly afterwards. The problem is solved now. Best, Laith -------------- next part -------------- An HTML attachment was scrubbed... URL: From RICHARDS at mailbox.sc.edu Wed Jan 20 15:39:13 2016 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Wed, 20 Jan 2016 14:39:13 +0000 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps (Laith Hamid) Message-ID: Laith: I have a “neurodevelopmental MRI database” (Richards, Sanchez et al., 2015; see my www site) that has average MRI templates that could be used. Each average has the whole head down to about the top of the neck. I did these purposely since I use EEG recording and the MNI template did not even go down far enough for the EGI 128 channel net. The database has average MRI templates for head (T1, T2) and brain. I also have FEM segmented heads for the entire head that could be used for this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, scalp), but ironically, I cut these off about 10% below the EGI 128 channel electrodes. However, you could use the three inner compartments for this and just add the rest of the head below the compartment—or use the whole-head FEM as is for a FEM-model, or use the segmented area below the skull for a whole-head BEM model. I also have average 128-channel EGI electrodes for each template. Additionally, the “developmental” part of the “neurodevelopmental MRI database” is that I have these for a wide range of ages (all ages?). I have a average for young adults (20-24 yrs), and average templates and FEM/BEM models for groups from 3 months through adulthood, and into late adulthood. So if you have specific neuro-pediatric applications you might be interested in using an age appropriate MRI average template rather than an adult template. See my www site for journal article references re this, and http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ Finally… I have been using these head models for FT-based FEM and BEM models. Possibly some of the actually field trip models I have would be useful to you. Some of the parts of the model do not use the electrodes (e.g., grid-dipoles, head-model) whereas the final models (leadfield) requires the electrode locations. The database also includes “virtual” electrodes for the 10-10 system, which might be used to generate the 256 channel locations by knowing the relation between the 10-10 system and the EGI system based on EGI ELP files for the 256 channels. John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: richards-john at sc.edu HTTP: jerlab.psych.sc.edu *********************************************** >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 19 Jan 2016 15:35:00 +0100 >From: Laith Hamid >To: fieldtrip at science.ru.nl >Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> >Content-Type: text/plain; charset="us-ascii" > > > >Dear community, > >My name is Laith Hamid and I am working in the University Medical >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic >spikes and seizures. Currently I am analysing an EEG data set that was >recorded using a 256-channel EGI system and I wanted to ask whether you >have a standard BEM or FEM head model that extends enough downwards to >accomodate all 256 electrodes. The current standard BEM model in the >template folder of Fieldtrip isn't appropriate for source analysis of >256-channel EGI data. > >Thank you very much in advance for your help! > >Best, > >Laith From saeedzahran at hotmail.com Wed Jan 20 18:37:32 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Wed, 20 Jan 2016 19:37:32 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 In-Reply-To: References: Message-ID: Dear Fieldtrip community, I define the volume conductor as: vol = []; vol.bnd(1).pnt=skinpnt vol.bnd(1).tri=skinf vol.bnd(2).pnt=uteruspnt vol.bnd(2).tri=uterusf vol.bnd(3).pnt=uterinecontentpnt vol.bnd(3).tri=uterinecontentf vol.cond = c; But it result with the below error: Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); Thank you very much in advance for your help! Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 18 > To: fieldtrip at science.ru.nl > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 3. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 4. Source Localisation (aishwarya selvaraj) > 5. Re: Source Localisation (Hom?lle) > 6. Re: plotting neighbours (victoria schroeder) > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 8. Re: Source Localisation (Munsif Jatoi) > 9. problems with mri interpolation (Olga Sysoeva) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 19 Jan 2016 15:35:00 +0100 > From: Laith Hamid > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear community, > > My name is Laith Hamid and I am working in the University Medical > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and seizures. Currently I am analysing an EEG data set that was > recorded using a 256-channel EGI system and I wanted to ask whether you > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); model that extends enough downwards to > accomodate all 256 electrodes. The current standard BEM model in the > template folder of Fieldtrip isn't appropriate for source analysis of > 256-channel EGI data. > > Thank you very much in advance for your help! > > Best, > > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Tue, 19 Jan 2016 16:16:54 +0100 > From: Cristiano Micheli > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > thanks for your question. You could refer to a factory schematic layout > such as the one in figure 4 of this publication: > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > and subsequently use the function ft_prepare_layout to manually track the > points of the custom design on your own (if you dont want to wait for > somebody from the FT to do the same for you). > > cfg = []; > cfg.image = 'figure4_layout_256_Frontiers.png'; > lay = ft_prepare_layout(cfg); > > The following tutorial describes the procedure in more details: > http://www.fieldtriptoolbox.org/tutorial/layout > > Please do not hesitate to get in touch with me for this and other matters. > > All the best > Cris Micheli > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > wrote: > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical Complex > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > seizures. Currently I am analysing an EEG data set that was recorded using > > a 256-channel EGI system and I wanted to ask whether you have a standard > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > electrodes. The current standard BEM model in the template folder of > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Tue, 19 Jan 2016 17:41:48 +0100 > From: Laith Hamid > To: Fieldtrip > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear Cris, > > thank you very much for your answer. I am refering to an issue that was > discussed in this thread from April 2013: > > [FieldTrip] source analysis EEG data without MRI > > The thread however does not offer a segmentation or head model for > download. Some electrodes in the EGI 256-electrodes cap are placed on > the cheeks or on the back of the neck and these areas are not modeled by > the standard BEM skin compartment in the standard BEM model. My question > was about a standard segmentation that extends the skin (and skull) > compartment downwards to allow these electrodes to sit on the nodes of > the skin mesh. > > Best, > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Tue, 19 Jan 2016 16:52:55 +0000 > From: aishwarya selvaraj > To: "fieldtrip, donders" > Subject: [FieldTrip] Source Localisation > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 5 > Date: Tue, 19 Jan 2016 17:06:13 +0000 > From: Hom?lle, S. (Simon) > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Aishwarya, > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > My recommended start would be: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > Hopefully this provides you good start working with EEG source reconstruction > > Best regards, > > Simon Hom?lle > PhD Candidate > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Phone: +31-(0)24-36-65059 > ________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > Sent: Tuesday, January 19, 2016 5:52 PM > To: fieldtrip, donders > Subject: [FieldTrip] Source Localisation > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 6 > Date: Tue, 19 Jan 2016 17:49:21 +0000 > From: victoria schroeder > To: FieldTrip discussion list > Subject: Re: [FieldTrip] plotting neighbours > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Thank you very much Philipp and Tzvetan! > > Things have become much clearer now. > > I would like to follow up with a very related question. I am trying to > replicate the analysis for the cluster based permutation test using the > code and the data provided. However, i run into two problems here > > First, i get the following error if i use the original code: > Attempted to access cfg.frequency(2); index out of bounds because > numel(cfg.frequency)=1. > > Error in ft_freqstatistics (line 187) > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > However, then no significant clusters are found. Which becomes clear when > trying to plot the cluster or by looking at the output of > ft_freqstatistics. > > Does the change in the code , change the output? How can i avoid the error > mentioned above and still get the same output from ft_freqstatistics as the > one provided on the webpage? > > > The relevant section of the toturial is provided below. > Thank you! > > Victoria > > Permutation test > > Now, run *ft_freqstatistics > * to compare > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > the following configuration is identical to the configuration that was used > for comparing event-related averages in the cluster-based permutation tests > on event related fields tutorial > . > Also see this tutorial > for > a detailed explanation of all the configuration settings. You can read more > about the *ft_prepare_neighbours > * function > in the FAQ's > . > > To load the planar gradient TFRs (also available on the FieldTrip FTP > servers,freqFIC_planar_cmb.mat > > and freqFC_planar_cmb.mat > ), > use: > > load freqFIC_planar_cmb > load freqFC_planar_cmb > > cfg = []; > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > cfg.latency = 'all'; > cfg.frequency = 20; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > % prepare_neighbours determines what sensors may form clusters > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > size(freqFC_planar_cmb.powspctrm,1)); > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > cfg.design = design; > cfg.ivar = 1; > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > > > > Hi Victoria, > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > right I was only scrolling up to the part where the mags were analyzed. As > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > threat them separately, as I was naively thinking as non-neuormag user, but > > indeed combination of both is recommended as I have now learned :-)(thanks > > Phillip). I ran the following steps and I guess this should work for you. > > best > > tzvetan > > > > %% > > cfg = []; > > ComCon = ft_combineplanar(cfg,FreqCon); > > %% > > cfg = [] > > cfg.method = 'triangulation'; > > cfg.layout = 'neuromag306cmb.lay'; > > cfg.senstype = 'MEG'; > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > %% > > % plot neighbours > > cfg=[]; > > cfg.neighbours = neighbours; > > cfg.layout = 'neuromag306cmb.lay'; > > ft_neighbourplot(cfg); > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 7 > Date: Tue, 19 Jan 2016 20:50:24 +0100 > From: Cristiano Micheli > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > this might be possible if you have the subject-specific MRI by following > the tutorial here: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > and using the function ft_prepare_mesh and the tutorial command: > > cfg=[]; > cfg.tissue={'brain','skull','scalp'}; > cfg.numvertices = [3000 2000 1000]; > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > contain your triangulated surface with 1000 vertices. Let me know if that > works. Of course you should see the skin and the neck in the original MRI. > > If you do not have an anatomical MRI that extends down to the chin you > could try with a template, such as this: > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > and the corresponding segmented version > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > This goes down to the chin. Then you take care of rearranging the position > of the EEG electrodes according to this: > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > I hope this helped > Cris > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > wrote: > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > cheeks or on the back of the neck and these areas are not modeled by the > > standard BEM skin compartment in the standard BEM model. My question was > > about a standard segmentation that extends the skin (and skull) compartment > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > Best, > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 8 > Date: Wed, 20 Jan 2016 12:17:12 +0800 > From: Munsif Jatoi > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Aishwarya, > > Please refer to main help tutorials. > > Also, you can find out the survey papers written in this area. For more, > SPM website can provide good help. > > Best, > Munsif. > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > S.Homolle at donders.ru.nl> wrote: > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source > > reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ------------------------------ > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > *To:* fieldtrip, donders > > *Subject:* [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > Munsif Ali H.Jatoi, > > Ph D Scholar, > Centre for Intelligent Signals and Imaging Research, > Universiti Teknologi PETRONAS, > Malaysia. > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 9 > Date: Wed, 20 Jan 2016 13:36:16 +0300 > From: Olga Sysoeva > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] problems with mri interpolation > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > > I'm encounter the problem with MRI interpolation and reslicing using > > FT_VOLUMERESLICE. > > I have read my MRI from fif.file and this mri variable contains > > mri_K0012.unit, 'm' > > mri_K0012.dim, [432, 512, 180] > > mri_K0012.anatomy, <432, 512, 180 int16> > > mri_K0012.hdr, (1*1 structure) > > mri_K0012.transform, (4*4 double) > > mri_K0012.coordsys 'neuromag'. > > > Than I used > > > mri = ft_volumereslice([], mri); > > > the output is > > > ?the input is volume data with dimensions [432 > 512 180] > > reslicing from [432 512 180] to [256 256 256] > > the input is volume data with dimensions [256 > 256 256] > > the input is volume data with dimensions [432 > 512 180] > > selecting subvolume of 0.0% > > reslicing and interpolating anatomy > > interpolating > > ??? Attempted to access sel(1); index out of > bounds because numel(sel)=0. > > > Error in ==> ft_sourceinterpolate>my_interpn > at 663 > > ft_progress(sel(1)/num, 'interpolating > %.1f%%\n', 100*sel(1)/num); > > > Error in ==> ft_sourceinterpolate at 583 > > av( sel) = my_interpn(fv, ax(sel), > ay(sel), az(sel), cfg.interpmethod, > > cfg.feedback); > > > Error in ==> ft_volumereslice at 176 > > resliced = ft_sourceinterpolate(tmpcfg, mri, > resliced);? > > > I'm using matlab 7.6.0 (R2008a) and recently > downloaded fieltrip (also in my previous version of 2013 the error > was the same). > > > I'd be thankful for the comments. > > > Best Regards, > > Olga. > > P.S.Actually, I can project my sources > meaningfully into not interpolated MRI, altoough the images are > plotted upside down. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 18 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jan 21 09:16:55 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 21 Jan 2016 08:16:55 +0000 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 In-Reply-To: References: Message-ID: Saeed, are you using 0 or 1 indexing for your triangles? You probably want to use 1 indexing. Best, Jan-Mathijs On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: Dear Fieldtrip community, I define the volume conductor as: vol = []; vol.bnd(1).pnt=skinpnt vol.bnd(1).tri=skinf vol.bnd(2).pnt=uteruspnt vol.bnd(2).tri=uterusf vol.bnd(3).pnt=uterinecontentpnt vol.bnd(3).tri=uterinecontentf vol.cond = c; But it result with the below error: Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); Thank you very much in advance for your help! Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 18 > To: fieldtrip at science.ru.nl > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 3. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 4. Source Localisation (aishwarya selvaraj) > 5. Re: Source Localisation (Hom?lle) > 6. Re: plotting neighbours (victoria schroeder) > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 8. Re: Source Localisation (Munsif Jatoi) > 9. problems with mri interpolation (Olga Sysoeva) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 19 Jan 2016 15:35:00 +0100 > From: Laith Hamid > > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear community, > > My name is Laith Hamid and I am working in the University Medical > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and seizures. Currently I am analysing an EEG data set that was > recorded using a 256-channel EGI system and I wanted to ask whether you > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); model that extends enough downwards to > accomodate all 256 electrodes. The current standard BEM model in the > template folder of Fieldtrip isn't appropriate for source analysis of > 256-channel EGI data. > > Thank you very much in advance for your help! > > Best, > > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Tue, 19 Jan 2016 16:16:54 +0100 > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > thanks for your question. You could refer to a factory schematic layout > such as the one in figure 4 of this publication: > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > and subsequently use the function ft_prepare_layout to manually track the > points of the custom design on your own (if you dont want to wait for > somebody from the FT to do the same for you). > > cfg = []; > cfg.image = 'figure4_layout_256_Frontiers.png'; > lay = ft_prepare_layout(cfg); > > The following tutorial describes the procedure in more details: > http://www.fieldtriptoolbox.org/tutorial/layout > > Please do not hesitate to get in touch with me for this and other matters. > > All the best > Cris Micheli > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > wrote: > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical Complex > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > seizures. Currently I am analysing an EEG data set that was recorded using > > a 256-channel EGI system and I wanted to ask whether you have a standard > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > electrodes. The current standard BEM model in the template folder of > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Tue, 19 Jan 2016 17:41:48 +0100 > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear Cris, > > thank you very much for your answer. I am refering to an issue that was > discussed in this thread from April 2013: > > [FieldTrip] source analysis EEG data without MRI > > The thread however does not offer a segmentation or head model for > download. Some electrodes in the EGI 256-electrodes cap are placed on > the cheeks or on the back of the neck and these areas are not modeled by > the standard BEM skin compartment in the standard BEM model. My question > was about a standard segmentation that extends the skin (and skull) > compartment downwards to allow these electrodes to sit on the nodes of > the skin mesh. > > Best, > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Tue, 19 Jan 2016 16:52:55 +0000 > From: aishwarya selvaraj > > To: "fieldtrip, donders" > > Subject: [FieldTrip] Source Localisation > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 5 > Date: Tue, 19 Jan 2016 17:06:13 +0000 > From: Hom?lle, S. (Simon) > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Aishwarya, > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > My recommended start would be: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > Hopefully this provides you good start working with EEG source reconstruction > > Best regards, > > Simon Hom?lle > PhD Candidate > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Phone: +31-(0)24-36-65059 > ________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > Sent: Tuesday, January 19, 2016 5:52 PM > To: fieldtrip, donders > Subject: [FieldTrip] Source Localisation > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 6 > Date: Tue, 19 Jan 2016 17:49:21 +0000 > From: victoria schroeder > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] plotting neighbours > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Thank you very much Philipp and Tzvetan! > > Things have become much clearer now. > > I would like to follow up with a very related question. I am trying to > replicate the analysis for the cluster based permutation test using the > code and the data provided. However, i run into two problems here > > First, i get the following error if i use the original code: > Attempted to access cfg.frequency(2); index out of bounds because > numel(cfg.frequency)=1. > > Error in ft_freqstatistics (line 187) > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > However, then no significant clusters are found. Which becomes clear when > trying to plot the cluster or by looking at the output of > ft_freqstatistics. > > Does the change in the code , change the output? How can i avoid the error > mentioned above and still get the same output from ft_freqstatistics as the > one provided on the webpage? > > > The relevant section of the toturial is provided below. > Thank you! > > Victoria > > Permutation test > > Now, run *ft_freqstatistics > * to compare > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > the following configuration is identical to the configuration that was used > for comparing event-related averages in the cluster-based permutation tests > on event related fields tutorial > . > Also see this tutorial > for > a detailed explanation of all the configuration settings. You can read more > about the *ft_prepare_neighbours > * function > in the FAQ's > . > > To load the planar gradient TFRs (also available on the FieldTrip FTP > servers,freqFIC_planar_cmb.mat > > and freqFC_planar_cmb.mat > ), > use: > > load freqFIC_planar_cmb > load freqFC_planar_cmb > > cfg = []; > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > cfg.latency = 'all'; > cfg.frequency = 20; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > % prepare_neighbours determines what sensors may form clusters > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > size(freqFC_planar_cmb.powspctrm,1)); > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > cfg.design = design; > cfg.ivar = 1; > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > Hi Victoria, > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > right I was only scrolling up to the part where the mags were analyzed. As > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > threat them separately, as I was naively thinking as non-neuormag user, but > > indeed combination of both is recommended as I have now learned :-)(thanks > > Phillip). I ran the following steps and I guess this should work for you. > > best > > tzvetan > > > > %% > > cfg = []; > > ComCon = ft_combineplanar(cfg,FreqCon); > > %% > > cfg = [] > > cfg.method = 'triangulation'; > > cfg.layout = 'neuromag306cmb.lay'; > > cfg.senstype = 'MEG'; > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > %% > > % plot neighbours > > cfg=[]; > > cfg.neighbours = neighbours; > > cfg.layout = 'neuromag306cmb.lay'; > > ft_neighbourplot(cfg); > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 7 > Date: Tue, 19 Jan 2016 20:50:24 +0100 > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > this might be possible if you have the subject-specific MRI by following > the tutorial here: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > and using the function ft_prepare_mesh and the tutorial command: > > cfg=[]; > cfg.tissue={'brain','skull','scalp'}; > cfg.numvertices = [3000 2000 1000]; > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > contain your triangulated surface with 1000 vertices. Let me know if that > works. Of course you should see the skin and the neck in the original MRI. > > If you do not have an anatomical MRI that extends down to the chin you > could try with a template, such as this: > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > and the corresponding segmented version > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > This goes down to the chin. Then you take care of rearranging the position > of the EEG electrodes according to this: > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > I hope this helped > Cris > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > wrote: > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > cheeks or on the back of the neck and these areas are not modeled by the > > standard BEM skin compartment in the standard BEM model. My question was > > about a standard segmentation that extends the skin (and skull) compartment > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > Best, > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 8 > Date: Wed, 20 Jan 2016 12:17:12 +0800 > From: Munsif Jatoi > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Aishwarya, > > Please refer to main help tutorials. > > Also, you can find out the survey papers written in this area. For more, > SPM website can provide good help. > > Best, > Munsif. > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > S.Homolle at donders.ru.nl> wrote: > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source > > reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ------------------------------ > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > *To:* fieldtrip, donders > > *Subject:* [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > Munsif Ali H.Jatoi, > > Ph D Scholar, > Centre for Intelligent Signals and Imaging Research, > Universiti Teknologi PETRONAS, > Malaysia. > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 9 > Date: Wed, 20 Jan 2016 13:36:16 +0300 > From: Olga Sysoeva > > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] problems with mri interpolation > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > > I'm encounter the problem with MRI interpolation and reslicing using > > FT_VOLUMERESLICE. > > I have read my MRI from fif.file and this mri variable contains > > mri_K0012.unit, 'm' > > mri_K0012.dim, [432, 512, 180] > > mri_K0012.anatomy, <432, 512, 180 int16> > > mri_K0012.hdr, (1*1 structure) > > mri_K0012.transform, (4*4 double) > > mri_K0012.coordsys 'neuromag'. > > > Than I used > > > mri = ft_volumereslice([], mri); > > > the output is > > > ?the input is volume data with dimensions [432 > 512 180] > > reslicing from [432 512 180] to [256 256 256] > > the input is volume data with dimensions [256 > 256 256] > > the input is volume data with dimensions [432 > 512 180] > > selecting subvolume of 0.0% > > reslicing and interpolating anatomy > > interpolating > > ??? Attempted to access sel(1); index out of > bounds because numel(sel)=0. > > > Error in ==> ft_sourceinterpolate>my_interpn > at 663 > > ft_progress(sel(1)/num, 'interpolating > %.1f%%\n', 100*sel(1)/num); > > > Error in ==> ft_sourceinterpolate at 583 > > av( sel) = my_interpn(fv, ax(sel), > ay(sel), az(sel), cfg.interpmethod, > > cfg.feedback); > > > Error in ==> ft_volumereslice at 176 > > resliced = ft_sourceinterpolate(tmpcfg, mri, > resliced);? > > > I'm using matlab 7.6.0 (R2008a) and recently > downloaded fieltrip (also in my previous version of 2013 the error > was the same). > > > I'd be thankful for the comments. > > > Best Regards, > > Olga. > > P.S.Actually, I can project my sources > meaningfully into not interpolated MRI, altoough the images are > plotted upside down. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 18 > ***************************************** _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Thu Jan 21 12:06:13 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Thu, 21 Jan 2016 12:06:13 +0100 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 In-Reply-To: References: Message-ID: Hi Saeed, if the content of your triangulation connectivity matrices *skinf, uterusf, **uterinecontentf* is not made of integers you probably get the error you mentioned. Could this be the case? Out of curiosity, are you doing fetal recordings? Cris On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran wrote: > Dear Fieldtrip community, > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > > > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > To: fieldtrip at science.ru.nl > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 4. Source Localisation (aishwarya selvaraj) > > 5. Re: Source Localisation (Hom?lle) > > 6. Re: plotting neighbours (victoria schroeder) > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 8. Re: Source Localisation (Munsif Jatoi) > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > From: Laith Hamid > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > spikes and seizures. Currently I am analysing an EEG data set that was > > recorded using a 256-channel EGI system and I wanted to ask whether you > > have a standard BEM or FEM head Subscript indices must either be real > positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > model that extends enough downwards to > > accomodate all 256 electrodes. The current standard BEM model in the > > template folder of Fieldtrip isn't appropriate for source analysis of > > 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > thanks for your question. You could refer to a factory schematic layout > > such as the one in figure 4 of this publication: > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > and subsequently use the function ft_prepare_layout to manually track the > > points of the custom design on your own (if you dont want to wait for > > somebody from the FT to do the same for you). > > > > cfg = []; > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > lay = ft_prepare_layout(cfg); > > > > The following tutorial describes the procedure in more details: > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > Please do not hesitate to get in touch with me for this and other > matters. > > > > All the best > > Cris Micheli > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > wrote: > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > Complex > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes > and > > > seizures. Currently I am analysing an EEG data set that was recorded > using > > > a 256-channel EGI system and I wanted to ask whether you have a > standard > > > BEM or FEM head model that extends enough downwards to accomodate all > 256 > > > electrodes. The current standard BEM model in the template folder of > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > [FieldTrip] source analysis EEG data without MRI > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the cheeks or on the back of the neck and these areas are not modeled by > > the standard BEM skin compartment in the standard BEM model. My question > > was about a standard segmentation that extends the skin (and skull) > > compartment downwards to allow these electrodes to sit on the nodes of > > the skin mesh. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 4 > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > From: aishwarya selvaraj > > To: "fieldtrip, donders" > > Subject: [FieldTrip] Source Localisation > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > From: Hom?lle, S. (Simon) > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source > reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ________________________________ > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > Sent: Tuesday, January 19, 2016 5:52 PM > > To: fieldtrip, donders > > Subject: [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 6 > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > From: victoria schroeder > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] plotting neighbours > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Thank you very much Philipp and Tzvetan! > > > > Things have become much clearer now. > > > > I would like to follow up with a very related question. I am trying to > > replicate the analysis for the cluster based permutation test using the > > code and the data provided. However, i run into two problems here > > > > First, i get the following error if i use the original code: > > Attempted to access cfg.frequency(2); index out of bounds because > > numel(cfg.frequency)=1. > > > > Error in ft_freqstatistics (line 187) > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > fmax)]; > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > However, then no significant clusters are found. Which becomes clear when > > trying to plot the cluster or by looking at the output of > > ft_freqstatistics. > > > > Does the change in the code , change the output? How can i avoid the > error > > mentioned above and still get the same output from ft_freqstatistics as > the > > one provided on the webpage? > > > > > > The relevant section of the toturial is provided below. > > Thank you! > > > > Victoria > > > > Permutation test > > > > Now, run *ft_freqstatistics > > * to > compare > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > cfg.latency, > > the following configuration is identical to the configuration that was > used > > for comparing event-related averages in the cluster-based permutation > tests > > on event related fields tutorial > > . > > Also see this tutorial > > > for > > a detailed explanation of all the configuration settings. You can read > more > > about the *ft_prepare_neighbours > > * > function > > in the FAQ's > > >. > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > servers,freqFIC_planar_cmb.mat > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > and freqFC_planar_cmb.mat > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > >), > > use: > > > > load freqFIC_planar_cmb > > load freqFC_planar_cmb > > > > cfg = []; > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > cfg.latency = 'all'; > > cfg.frequency = 20; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > cfg.correctm = 'cluster'; > > cfg.clusteralpha = 0.05; > > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.tail = 0; > > cfg.clustertail = 0; > > cfg.alpha = 0.025; > > cfg.numrandomization = 500; > > % prepare_neighbours determines what sensors may form clusters > > cfg_neighb.method = 'distance'; > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > size(freqFC_planar_cmb.powspctrm,1)); > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > cfg.design = design; > > cfg.ivar = 1; > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > > > > Hi Victoria, > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > right I was only scrolling up to the part where the mags were > analyzed. As > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you > can > > > threat them separately, as I was naively thinking as non-neuormag > user, but > > > indeed combination of both is recommended as I have now learned > :-)(thanks > > > Phillip). I ran the following steps and I guess this should work for > you. > > > best > > > tzvetan > > > > > > %% > > > cfg = []; > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > %% > > > cfg = [] > > > cfg.method = 'triangulation'; > > > cfg.layout = 'neuromag306cmb.lay'; > > > cfg.senstype = 'MEG'; > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > %% > > > % plot neighbours > > > cfg=[]; > > > cfg.neighbours = neighbours; > > > cfg.layout = 'neuromag306cmb.lay'; > > > ft_neighbourplot(cfg); > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 7 > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > this might be possible if you have the subject-specific MRI by following > > the tutorial here: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > cfg=[]; > > cfg.tissue={'brain','skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > contain your triangulated surface with 1000 vertices. Let me know if that > > works. Of course you should see the skin and the neck in the original > MRI. > > > > If you do not have an anatomical MRI that extends down to the chin you > > could try with a template, such as this: > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > and the corresponding segmented version > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > This goes down to the chin. Then you take care of rearranging the > position > > of the EEG electrodes according to this: > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > I hope this helped > > Cris > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > wrote: > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > the > > > cheeks or on the back of the neck and these areas are not modeled by > the > > > standard BEM skin compartment in the standard BEM model. My question > was > > > about a standard segmentation that extends the skin (and skull) > compartment > > > downwards to allow these electrodes to sit on the nodes of the skin > mesh. > > > > > > Best, > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 8 > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > From: Munsif Jatoi > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Aishwarya, > > > > Please refer to main help tutorials. > > > > Also, you can find out the survey papers written in this area. For more, > > SPM website can provide good help. > > > > Best, > > Munsif. > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > S.Homolle at donders.ru.nl> wrote: > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ------------------------------ > > > *From:* fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > *To:* fieldtrip, donders > > > *Subject:* [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > -- > > Munsif Ali H.Jatoi, > > > > Ph D Scholar, > > Centre for Intelligent Signals and Imaging Research, > > Universiti Teknologi PETRONAS, > > Malaysia. > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 9 > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > From: Olga Sysoeva > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] problems with mri interpolation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Fieldtrippers, > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > FT_VOLUMERESLICE. > > > > I have read my MRI from fif.file and this mri variable contains > > > > mri_K0012.unit, 'm' > > > > mri_K0012.dim, [432, 512, 180] > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > mri_K0012.hdr, (1*1 structure) > > > > mri_K0012.transform, (4*4 double) > > > > mri_K0012.coordsys 'neuromag'. > > > > > > Than I used > > > > > > mri = ft_volumereslice([], mri); > > > > > > the output is > > > > > > ?the input is volume data with dimensions [432 > > 512 180] > > > > reslicing from [432 512 180] to [256 256 256] > > > > the input is volume data with dimensions [256 > > 256 256] > > > > the input is volume data with dimensions [432 > > 512 180] > > > > selecting subvolume of 0.0% > > > > reslicing and interpolating anatomy > > > > interpolating > > > > ??? Attempted to access sel(1); index out of > > bounds because numel(sel)=0. > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > at 663 > > > > ft_progress(sel(1)/num, 'interpolating > > %.1f%%\n', 100*sel(1)/num); > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > av( sel) = my_interpn(fv, ax(sel), > > ay(sel), az(sel), cfg.interpmethod, > > > > cfg.feedback); > > > > > > Error in ==> ft_volumereslice at 176 > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > resliced);? > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > downloaded fieltrip (also in my previous version of 2013 the error > > was the same). > > > > > > I'd be thankful for the comments. > > > > > > Best Regards, > > > > Olga. > > > > P.S.Actually, I can project my sources > > meaningfully into not interpolated MRI, altoough the images are > > plotted upside down. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mniqureshi at gist.ac.kr Thu Jan 21 13:59:06 2016 From: mniqureshi at gist.ac.kr (Muhammad Naveed Iqbal Qureshi) Date: Thu, 21 Jan 2016 21:59:06 +0900 Subject: [FieldTrip] difficulty in loading BCI-IV-2a dataset into fieldtrip for preprocessing Message-ID: <000b01d1544b$8323d8e0$896b8aa0$@gist.ac.kr> Hi, I am using BCI competition IV dataset 2a for my experiment. I want to preprocess it with field trip. I have written the following code for this task. addpath(genpath('E:\bbci_data\fieldtrip-20160118\fieldtrip-20160118')); cd 'E:\bbci_data\BCICIV_2a_gdf\'; %% Field Trip preprocessing code for i=1:9 file=num2str(i); file=strcat('A0',file,'T.gdf'); cfg = []; cfg.dataset = file ; cfg.trialdef.eventtype = 'Stimulus'; cfg.trialdef.eventvalue = {'left', 'right', 'both feet', 'tongue'}; cfg.trialdef.triallength = 8; % duration in seconds cfg.trialdef.ntrials = inf; % number of trials, inf results in as many as possible cfg.trialdef.prestim = 3; cfg.trialdef.poststim = 6; cfg = ft_definetrial(cfg); cfg.bpfilter = 'yes'; cfg.bpfreq = [0.5 100]; cfg.bpfilttype = 'but'; cfg.bpfiltord = 5; cfg.demean = 'yes'; cfg.detrend = 'yes'; trialdata_EO{i} = ft_preprocessing(cfg); end However, this code does not import the event and trigger information from the header file of the data. I will be highly obliged if anyone can help me in this regard. Thank in advance. Best Regards, Muhammad Naveed Iqbal Qureshi -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Thu Jan 21 19:14:01 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Thu, 21 Jan 2016 20:14:01 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 19 In-Reply-To: References: Message-ID: Thank you Jan and Cristiano; I downloaded another version of Fieldtrip thus the below error disappear: Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); But now I have another error: Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example (line 100) vol = ft_prepare_headmodel(cfg, vol); Thank you for any suggestion Cristiano, I record the contraction of the uterus; Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 19 > To: fieldtrip at science.ru.nl > Date: Thu, 21 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) (RICHARDS, JOHN) > 3. Re: fieldtrip Digest, Vol 62, Issue 18 (saeed zahran) > 4. Re: fieldtrip Digest, Vol 62, Issue 18 > (Schoffelen, J.M. (Jan Mathijs)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Jan 2016 13:39:30 +0100 > From: Laith Hamid > To: Fieldtrip > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1 at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear Cris, > > thank you very much for your answers yesterday. The segmentedmri > contained 'white', 'grey' and 'csf' so I needed to repeat the > segmentation using 'brain', 'skull' and 'scalp' as described in the > tutorial "Creating a BEM volume conduction model of the head for > source-reconstruction of EEG data" and everything worked smoothly > afterwards. The problem is solved now. > > Best, > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Wed, 20 Jan 2016 14:39:13 +0000 > From: "RICHARDS, JOHN" > To: "fieldtrip at science.ru.nl" , > "lah at pedneuro.uni-kiel.de" > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps (Laith Hamid) > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Laith: > > I have a ?neurodevelopmental MRI database? (Richards, Sanchez et al., 2015; see my www site) that has average MRI templates that could be used. Each average has the whole head down to about the top of the neck. I did these purposely since I use EEG recording and the MNI template did not even go down far enough for the EGI 128 channel net. > > The database has average MRI templates for head (T1, T2) and brain. I also have FEM segmented heads for the entire head that could be used for this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, scalp), but ironically, I cut these off about 10% below the EGI 128 channel electrodes. However, you could use the three inner compartments for this and just add the rest of the head below the compartment?or use the whole-head FEM as is for a FEM-model, or use the segmented area below the skull for a whole-head BEM model. I also have average 128-channel EGI electrodes for each template. > > Additionally, the ?developmental? part of the ?neurodevelopmental MRI database? is that I have these for a wide range of ages (all ages?). I have a average for young adults (20-24 yrs), and average templates and FEM/BEM models for groups from 3 months through adulthood, and into late adulthood. So if you have specific neuro-pediatric applications you might be interested in using an age appropriate MRI average template rather than an adult template. > > See my www site for journal article references re this, and http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > Finally? I have been using these head models for FT-based FEM and BEM models. Possibly some of the actually field trip models I have would be useful to you. Some of the parts of the model do not use the electrodes (e.g., grid-dipoles, head-model) whereas the final models (leadfield) requires the electrode locations. The database also includes ?virtual? electrodes for the 10-10 system, which might be used to generate the 256 channel locations by knowing the relation between the 10-10 system and the EGI system based on EGI ELP files for the 256 channels. > > John > > *********************************************** > John E. Richards Carolina Distinguished Professor > Department of Psychology > University of South Carolina > Columbia, SC 29208 > Dept Phone: 803 777 2079 > Fax: 803 777 9558 > Email: richards-john at sc.edu > HTTP: jerlab.psych.sc.edu > *********************************************** > > > > > >---------------------------------------------------------------------- > > > >Message: 1 > >Date: Tue, 19 Jan 2016 15:35:00 +0100 > >From: Laith Hamid > >To: fieldtrip at science.ru.nl > >Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > >Content-Type: text/plain; charset="us-ascii" > > > > > > > >Dear community, > > > >My name is Laith Hamid and I am working in the University Medical > >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > >spikes and seizures. Currently I am analysing an EEG data set that was > >recorded using a 256-channel EGI system and I wanted to ask whether you > >have a standard BEM or FEM head model that extends enough downwards to > >accomodate all 256 electrodes. The current standard BEM model in the > >template folder of Fieldtrip isn't appropriate for source analysis of > >256-channel EGI data. > > > >Thank you very much in advance for your help! > > > >Best, > > > >Laith > > > > ------------------------------ > > Message: 3 > Date: Wed, 20 Jan 2016 19:37:32 +0200 > From: saeed zahran > To: "fieldtrip at science.ru.nl" > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Dear Fieldtrip community, > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > > > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > To: fieldtrip at science.ru.nl > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 4. Source Localisation (aishwarya selvaraj) > > 5. Re: Source Localisation (Hom?lle) > > 6. Re: plotting neighbours (victoria schroeder) > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 8. Re: Source Localisation (Munsif Jatoi) > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > From: Laith Hamid > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > spikes and seizures. Currently I am analysing an EEG data set that was > > recorded using a 256-channel EGI system and I wanted to ask whether you > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > model that extends enough downwards to > > accomodate all 256 electrodes. The current standard BEM model in the > > template folder of Fieldtrip isn't appropriate for source analysis of > > 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > thanks for your question. You could refer to a factory schematic layout > > such as the one in figure 4 of this publication: > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > and subsequently use the function ft_prepare_layout to manually track the > > points of the custom design on your own (if you dont want to wait for > > somebody from the FT to do the same for you). > > > > cfg = []; > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > lay = ft_prepare_layout(cfg); > > > > The following tutorial describes the procedure in more details: > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > All the best > > Cris Micheli > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > wrote: > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > electrodes. The current standard BEM model in the template folder of > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > [FieldTrip] source analysis EEG data without MRI > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the cheeks or on the back of the neck and these areas are not modeled by > > the standard BEM skin compartment in the standard BEM model. My question > > was about a standard segmentation that extends the skin (and skull) > > compartment downwards to allow these electrodes to sit on the nodes of > > the skin mesh. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 4 > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > From: aishwarya selvaraj > > To: "fieldtrip, donders" > > Subject: [FieldTrip] Source Localisation > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > From: Hom?lle, S. (Simon) > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ________________________________ > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > Sent: Tuesday, January 19, 2016 5:52 PM > > To: fieldtrip, donders > > Subject: [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 6 > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > From: victoria schroeder > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] plotting neighbours > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Thank you very much Philipp and Tzvetan! > > > > Things have become much clearer now. > > > > I would like to follow up with a very related question. I am trying to > > replicate the analysis for the cluster based permutation test using the > > code and the data provided. However, i run into two problems here > > > > First, i get the following error if i use the original code: > > Attempted to access cfg.frequency(2); index out of bounds because > > numel(cfg.frequency)=1. > > > > Error in ft_freqstatistics (line 187) > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > However, then no significant clusters are found. Which becomes clear when > > trying to plot the cluster or by looking at the output of > > ft_freqstatistics. > > > > Does the change in the code , change the output? How can i avoid the error > > mentioned above and still get the same output from ft_freqstatistics as the > > one provided on the webpage? > > > > > > The relevant section of the toturial is provided below. > > Thank you! > > > > Victoria > > > > Permutation test > > > > Now, run *ft_freqstatistics > > * to compare > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > the following configuration is identical to the configuration that was used > > for comparing event-related averages in the cluster-based permutation tests > > on event related fields tutorial > > . > > Also see this tutorial > > for > > a detailed explanation of all the configuration settings. You can read more > > about the *ft_prepare_neighbours > > * function > > in the FAQ's > > . > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > servers,freqFIC_planar_cmb.mat > > > > and freqFC_planar_cmb.mat > > ), > > use: > > > > load freqFIC_planar_cmb > > load freqFC_planar_cmb > > > > cfg = []; > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > cfg.latency = 'all'; > > cfg.frequency = 20; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > cfg.correctm = 'cluster'; > > cfg.clusteralpha = 0.05; > > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.tail = 0; > > cfg.clustertail = 0; > > cfg.alpha = 0.025; > > cfg.numrandomization = 500; > > % prepare_neighbours determines what sensors may form clusters > > cfg_neighb.method = 'distance'; > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > size(freqFC_planar_cmb.powspctrm,1)); > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > cfg.design = design; > > cfg.ivar = 1; > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > > > > > > > Hi Victoria, > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > right I was only scrolling up to the part where the mags were analyzed. As > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > Phillip). I ran the following steps and I guess this should work for you. > > > best > > > tzvetan > > > > > > %% > > > cfg = []; > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > %% > > > cfg = [] > > > cfg.method = 'triangulation'; > > > cfg.layout = 'neuromag306cmb.lay'; > > > cfg.senstype = 'MEG'; > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > %% > > > % plot neighbours > > > cfg=[]; > > > cfg.neighbours = neighbours; > > > cfg.layout = 'neuromag306cmb.lay'; > > > ft_neighbourplot(cfg); > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 7 > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > this might be possible if you have the subject-specific MRI by following > > the tutorial here: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > cfg=[]; > > cfg.tissue={'brain','skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > contain your triangulated surface with 1000 vertices. Let me know if that > > works. Of course you should see the skin and the neck in the original MRI. > > > > If you do not have an anatomical MRI that extends down to the chin you > > could try with a template, such as this: > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > and the corresponding segmented version > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > This goes down to the chin. Then you take care of rearranging the position > > of the EEG electrodes according to this: > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > I hope this helped > > Cris > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > wrote: > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > cheeks or on the back of the neck and these areas are not modeled by the > > > standard BEM skin compartment in the standard BEM model. My question was > > > about a standard segmentation that extends the skin (and skull) compartment > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 8 > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > From: Munsif Jatoi > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Aishwarya, > > > > Please refer to main help tutorials. > > > > Also, you can find out the survey papers written in this area. For more, > > SPM website can provide good help. > > > > Best, > > Munsif. > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > S.Homolle at donders.ru.nl> wrote: > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ------------------------------ > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > *To:* fieldtrip, donders > > > *Subject:* [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > -- > > Munsif Ali H.Jatoi, > > > > Ph D Scholar, > > Centre for Intelligent Signals and Imaging Research, > > Universiti Teknologi PETRONAS, > > Malaysia. > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 9 > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > From: Olga Sysoeva > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] problems with mri interpolation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Fieldtrippers, > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > FT_VOLUMERESLICE. > > > > I have read my MRI from fif.file and this mri variable contains > > > > mri_K0012.unit, 'm' > > > > mri_K0012.dim, [432, 512, 180] > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > mri_K0012.hdr, (1*1 structure) > > > > mri_K0012.transform, (4*4 double) > > > > mri_K0012.coordsys 'neuromag'. > > > > > > Than I used > > > > > > mri = ft_volumereslice([], mri); > > > > > > the output is > > > > > > ?the input is volume data with dimensions [432 > > 512 180] > > > > reslicing from [432 512 180] to [256 256 256] > > > > the input is volume data with dimensions [256 > > 256 256] > > > > the input is volume data with dimensions [432 > > 512 180] > > > > selecting subvolume of 0.0% > > > > reslicing and interpolating anatomy > > > > interpolating > > > > ??? Attempted to access sel(1); index out of > > bounds because numel(sel)=0. > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > at 663 > > > > ft_progress(sel(1)/num, 'interpolating > > %.1f%%\n', 100*sel(1)/num); > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > av( sel) = my_interpn(fv, ax(sel), > > ay(sel), az(sel), cfg.interpmethod, > > > > cfg.feedback); > > > > > > Error in ==> ft_volumereslice at 176 > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > resliced);? > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > downloaded fieltrip (also in my previous version of 2013 the error > > was the same). > > > > > > I'd be thankful for the comments. > > > > > > Best Regards, > > > > Olga. > > > > P.S.Actually, I can project my sources > > meaningfully into not interpolated MRI, altoough the images are > > plotted upside down. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > ***************************************** > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Thu, 21 Jan 2016 08:16:55 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Saeed, > > are you using 0 or 1 indexing for your triangles? You probably want to use 1 indexing. > > Best, > Jan-Mathijs > > > On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: > > Dear Fieldtrip community, > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > > > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > To: fieldtrip at science.ru.nl > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 4. Source Localisation (aishwarya selvaraj) > > 5. Re: Source Localisation (Hom?lle) > > 6. Re: plotting neighbours (victoria schroeder) > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 8. Re: Source Localisation (Munsif Jatoi) > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > From: Laith Hamid > > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > spikes and seizures. Currently I am analysing an EEG data set that was > > recorded using a 256-channel EGI system and I wanted to ask whether you > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > model that extends enough downwards to > > accomodate all 256 electrodes. The current standard BEM model in the > > template folder of Fieldtrip isn't appropriate for source analysis of > > 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > thanks for your question. You could refer to a factory schematic layout > > such as the one in figure 4 of this publication: > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > and subsequently use the function ft_prepare_layout to manually track the > > points of the custom design on your own (if you dont want to wait for > > somebody from the FT to do the same for you). > > > > cfg = []; > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > lay = ft_prepare_layout(cfg); > > > > The following tutorial describes the procedure in more details: > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > All the best > > Cris Micheli > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > wrote: > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > electrodes. The current standard BEM model in the template folder of > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > [FieldTrip] source analysis EEG data without MRI > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the cheeks or on the back of the neck and these areas are not modeled by > > the standard BEM skin compartment in the standard BEM model. My question > > was about a standard segmentation that extends the skin (and skull) > > compartment downwards to allow these electrodes to sit on the nodes of > > the skin mesh. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 4 > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > From: aishwarya selvaraj > > > To: "fieldtrip, donders" > > > Subject: [FieldTrip] Source Localisation > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > From: Hom?lle, S. (Simon) > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ________________________________ > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > Sent: Tuesday, January 19, 2016 5:52 PM > > To: fieldtrip, donders > > Subject: [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 6 > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > From: victoria schroeder > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] plotting neighbours > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Thank you very much Philipp and Tzvetan! > > > > Things have become much clearer now. > > > > I would like to follow up with a very related question. I am trying to > > replicate the analysis for the cluster based permutation test using the > > code and the data provided. However, i run into two problems here > > > > First, i get the following error if i use the original code: > > Attempted to access cfg.frequency(2); index out of bounds because > > numel(cfg.frequency)=1. > > > > Error in ft_freqstatistics (line 187) > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > However, then no significant clusters are found. Which becomes clear when > > trying to plot the cluster or by looking at the output of > > ft_freqstatistics. > > > > Does the change in the code , change the output? How can i avoid the error > > mentioned above and still get the same output from ft_freqstatistics as the > > one provided on the webpage? > > > > > > The relevant section of the toturial is provided below. > > Thank you! > > > > Victoria > > > > Permutation test > > > > Now, run *ft_freqstatistics > > * to compare > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > the following configuration is identical to the configuration that was used > > for comparing event-related averages in the cluster-based permutation tests > > on event related fields tutorial > > . > > Also see this tutorial > > for > > a detailed explanation of all the configuration settings. You can read more > > about the *ft_prepare_neighbours > > * function > > in the FAQ's > > . > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > servers,freqFIC_planar_cmb.mat > > > > and freqFC_planar_cmb.mat > > ), > > use: > > > > load freqFIC_planar_cmb > > load freqFC_planar_cmb > > > > cfg = []; > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > cfg.latency = 'all'; > > cfg.frequency = 20; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > cfg.correctm = 'cluster'; > > cfg.clusteralpha = 0.05; > > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.tail = 0; > > cfg.clustertail = 0; > > cfg.alpha = 0.025; > > cfg.numrandomization = 500; > > % prepare_neighbours determines what sensors may form clusters > > cfg_neighb.method = 'distance'; > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > size(freqFC_planar_cmb.powspctrm,1)); > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > cfg.design = design; > > cfg.ivar = 1; > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > > > > Hi Victoria, > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > right I was only scrolling up to the part where the mags were analyzed. As > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > Phillip). I ran the following steps and I guess this should work for you. > > > best > > > tzvetan > > > > > > %% > > > cfg = []; > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > %% > > > cfg = [] > > > cfg.method = 'triangulation'; > > > cfg.layout = 'neuromag306cmb.lay'; > > > cfg.senstype = 'MEG'; > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > %% > > > % plot neighbours > > > cfg=[]; > > > cfg.neighbours = neighbours; > > > cfg.layout = 'neuromag306cmb.lay'; > > > ft_neighbourplot(cfg); > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 7 > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > this might be possible if you have the subject-specific MRI by following > > the tutorial here: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > cfg=[]; > > cfg.tissue={'brain','skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > contain your triangulated surface with 1000 vertices. Let me know if that > > works. Of course you should see the skin and the neck in the original MRI. > > > > If you do not have an anatomical MRI that extends down to the chin you > > could try with a template, such as this: > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > and the corresponding segmented version > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > This goes down to the chin. Then you take care of rearranging the position > > of the EEG electrodes according to this: > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > I hope this helped > > Cris > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > wrote: > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > cheeks or on the back of the neck and these areas are not modeled by the > > > standard BEM skin compartment in the standard BEM model. My question was > > > about a standard segmentation that extends the skin (and skull) compartment > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 8 > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > From: Munsif Jatoi > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Aishwarya, > > > > Please refer to main help tutorials. > > > > Also, you can find out the survey papers written in this area. For more, > > SPM website can provide good help. > > > > Best, > > Munsif. > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > S.Homolle at donders.ru.nl> wrote: > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ------------------------------ > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > *To:* fieldtrip, donders > > > *Subject:* [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > -- > > Munsif Ali H.Jatoi, > > > > Ph D Scholar, > > Centre for Intelligent Signals and Imaging Research, > > Universiti Teknologi PETRONAS, > > Malaysia. > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 9 > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > From: Olga Sysoeva > > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] problems with mri interpolation > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Fieldtrippers, > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > FT_VOLUMERESLICE. > > > > I have read my MRI from fif.file and this mri variable contains > > > > mri_K0012.unit, 'm' > > > > mri_K0012.dim, [432, 512, 180] > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > mri_K0012.hdr, (1*1 structure) > > > > mri_K0012.transform, (4*4 double) > > > > mri_K0012.coordsys 'neuromag'. > > > > > > Than I used > > > > > > mri = ft_volumereslice([], mri); > > > > > > the output is > > > > > > ?the input is volume data with dimensions [432 > > 512 180] > > > > reslicing from [432 512 180] to [256 256 256] > > > > the input is volume data with dimensions [256 > > 256 256] > > > > the input is volume data with dimensions [432 > > 512 180] > > > > selecting subvolume of 0.0% > > > > reslicing and interpolating anatomy > > > > interpolating > > > > ??? Attempted to access sel(1); index out of > > bounds because numel(sel)=0. > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > at 663 > > > > ft_progress(sel(1)/num, 'interpolating > > %.1f%%\n', 100*sel(1)/num); > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > av( sel) = my_interpn(fv, ax(sel), > > ay(sel), az(sel), cfg.interpmethod, > > > > cfg.feedback); > > > > > > Error in ==> ft_volumereslice at 176 > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > resliced);? > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > downloaded fieltrip (also in my previous version of 2013 the error > > was the same). > > > > > > I'd be thankful for the comments. > > > > > > Best Regards, > > > > Olga. > > > > P.S.Actually, I can project my sources > > meaningfully into not interpolated MRI, altoough the images are > > plotted upside down. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > ***************************************** > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 19 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Thu Jan 21 19:22:42 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Thu, 21 Jan 2016 20:22:42 +0200 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Dear Fieldtrip Community, Dear Fieldtrip community, What does the error of the surface nesting means; I define the volume conductor as: vol = []; vol.bnd(1).pnt=skinpnt vol.bnd(1).tri=skinf vol.bnd(2).pnt=uteruspnt vol.bnd(2).tri=uterusf vol.bnd(3).pnt=uterinecontentpnt vol.bnd(3).tri=uterinecontentf vol.cond = c; But it result with the below error: Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example (line 100) vol = ft_prepare_headmodel(cfg, vol); Thank you very much in advance for your help! Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 20 > To: fieldtrip at science.ru.nl > Date: Thu, 21 Jan 2016 19:14:24 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: fieldtrip Digest, Vol 62, Issue 18 (Cristiano Micheli) > 2. difficulty in loading BCI-IV-2a dataset into fieldtrip for > preprocessing (Muhammad Naveed Iqbal Qureshi) > 3. Re: fieldtrip Digest, Vol 62, Issue 19 (saeed zahran) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Jan 2016 12:06:13 +0100 > From: Cristiano Micheli > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Saeed, > if the content of your triangulation connectivity matrices *skinf, > uterusf, **uterinecontentf* is not made of integers you probably get the > error you mentioned. Could this be the case? > Out of curiosity, are you doing fetal recordings? > > Cris > > > On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran > wrote: > > > Dear Fieldtrip community, > > > > I define the volume conductor as: > > > > vol = []; > > vol.bnd(1).pnt=skinpnt > > vol.bnd(1).tri=skinf > > > > vol.bnd(2).pnt=uteruspnt > > vol.bnd(2).tri=uterusf > > > > vol.bnd(3).pnt=uterinecontentpnt > > vol.bnd(3).tri=uterinecontentf > > > > vol.cond = c; > > > > > > But it result with the below error: > > > > Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > Thank you very much in advance for your help! > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > To: fieldtrip at science.ru.nl > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 4. Source Localisation (aishwarya selvaraj) > > > 5. Re: Source Localisation (Hom?lle) > > > 6. Re: plotting neighbours (victoria schroeder) > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 8. Re: Source Localisation (Munsif Jatoi) > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > From: Laith Hamid > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > spikes and seizures. Currently I am analysing an EEG data set that was > > > recorded using a 256-channel EGI system and I wanted to ask whether you > > > have a standard BEM or FEM head Subscript indices must either be real > > positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > model that extends enough downwards to > > > accomodate all 256 electrodes. The current standard BEM model in the > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > thanks for your question. You could refer to a factory schematic layout > > > such as the one in figure 4 of this publication: > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > and subsequently use the function ft_prepare_layout to manually track the > > > points of the custom design on your own (if you dont want to wait for > > > somebody from the FT to do the same for you). > > > > > > cfg = []; > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > lay = ft_prepare_layout(cfg); > > > > > > The following tutorial describes the procedure in more details: > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > Please do not hesitate to get in touch with me for this and other > > matters. > > > > > > All the best > > > Cris Micheli > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > wrote: > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > Complex > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes > > and > > > > seizures. Currently I am analysing an EEG data set that was recorded > > using > > > > a 256-channel EGI system and I wanted to ask whether you have a > > standard > > > > BEM or FEM head model that extends enough downwards to accomodate all > > 256 > > > > electrodes. The current standard BEM model in the template folder of > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > > data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > the cheeks or on the back of the neck and these areas are not modeled by > > > the standard BEM skin compartment in the standard BEM model. My question > > > was about a standard segmentation that extends the skin (and skull) > > > compartment downwards to allow these electrodes to sit on the nodes of > > > the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > From: aishwarya selvaraj > > > To: "fieldtrip, donders" > > > Subject: [FieldTrip] Source Localisation > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > From: Hom?lle, S. (Simon) > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ________________________________ > > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > To: fieldtrip, donders > > > Subject: [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 6 > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > From: victoria schroeder > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] plotting neighbours > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > Things have become much clearer now. > > > > > > I would like to follow up with a very related question. I am trying to > > > replicate the analysis for the cluster based permutation test using the > > > code and the data provided. However, i run into two problems here > > > > > > First, i get the following error if i use the original code: > > > Attempted to access cfg.frequency(2); index out of bounds because > > > numel(cfg.frequency)=1. > > > > > > Error in ft_freqstatistics (line 187) > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > > fmax)]; > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > > However, then no significant clusters are found. Which becomes clear when > > > trying to plot the cluster or by looking at the output of > > > ft_freqstatistics. > > > > > > Does the change in the code , change the output? How can i avoid the > > error > > > mentioned above and still get the same output from ft_freqstatistics as > > the > > > one provided on the webpage? > > > > > > > > > The relevant section of the toturial is provided below. > > > Thank you! > > > > > > Victoria > > > > > > Permutation test > > > > > > Now, run *ft_freqstatistics > > > * to > > compare > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > > cfg.latency, > > > the following configuration is identical to the configuration that was > > used > > > for comparing event-related averages in the cluster-based permutation > > tests > > > on event related fields tutorial > > > . > > > Also see this tutorial > > > > > for > > > a detailed explanation of all the configuration settings. You can read > > more > > > about the *ft_prepare_neighbours > > > * > > function > > > in the FAQ's > > > > >. > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > servers,freqFIC_planar_cmb.mat > > > < > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > < > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > > >), > > > use: > > > > > > load freqFIC_planar_cmb > > > load freqFC_planar_cmb > > > > > > cfg = []; > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > cfg.latency = 'all'; > > > cfg.frequency = 20; > > > cfg.method = 'montecarlo'; > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > cfg.correctm = 'cluster'; > > > cfg.clusteralpha = 0.05; > > > cfg.clusterstatistic = 'maxsum'; > > > cfg.minnbchan = 2; > > > cfg.tail = 0; > > > cfg.clustertail = 0; > > > cfg.alpha = 0.025; > > > cfg.numrandomization = 500; > > > % prepare_neighbours determines what sensors may form clusters > > > cfg_neighb.method = 'distance'; > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > size(freqFC_planar_cmb.powspctrm,1)); > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > cfg.design = design; > > > cfg.ivar = 1; > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov > >: > > > > > > > > > > > Hi Victoria, > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > > right I was only scrolling up to the part where the mags were > > analyzed. As > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you > > can > > > > threat them separately, as I was naively thinking as non-neuormag > > user, but > > > > indeed combination of both is recommended as I have now learned > > :-)(thanks > > > > Phillip). I ran the following steps and I guess this should work for > > you. > > > > best > > > > tzvetan > > > > > > > > %% > > > > cfg = []; > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > %% > > > > cfg = [] > > > > cfg.method = 'triangulation'; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > cfg.senstype = 'MEG'; > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > %% > > > > % plot neighbours > > > > cfg=[]; > > > > cfg.neighbours = neighbours; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 7 > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > this might be possible if you have the subject-specific MRI by following > > > the tutorial here: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > cfg=[]; > > > cfg.tissue={'brain','skull','scalp'}; > > > cfg.numvertices = [3000 2000 1000]; > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > > contain your triangulated surface with 1000 vertices. Let me know if that > > > works. Of course you should see the skin and the neck in the original > > MRI. > > > > > > If you do not have an anatomical MRI that extends down to the chin you > > > could try with a template, such as this: > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > and the corresponding segmented version > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > This goes down to the chin. Then you take care of rearranging the > > position > > > of the EEG electrodes according to this: > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > I hope this helped > > > Cris > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > wrote: > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that was > > > > discussed in this thread from April 2013: > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the > > > > cheeks or on the back of the neck and these areas are not modeled by > > the > > > > standard BEM skin compartment in the standard BEM model. My question > > was > > > > about a standard segmentation that extends the skin (and skull) > > compartment > > > > downwards to allow these electrodes to sit on the nodes of the skin > > mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 8 > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > From: Munsif Jatoi > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Aishwarya, > > > > > > Please refer to main help tutorials. > > > > > > Also, you can find out the survey papers written in this area. For more, > > > SPM website can provide good help. > > > > > > Best, > > > Munsif. > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ------------------------------ > > > > *From:* fieldtrip-bounces at science.ru.nl [ > > fieldtrip-bounces at science.ru.nl] > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > *To:* fieldtrip, donders > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > -- > > > Munsif Ali H.Jatoi, > > > > > > Ph D Scholar, > > > Centre for Intelligent Signals and Imaging Research, > > > Universiti Teknologi PETRONAS, > > > Malaysia. > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 9 > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > From: Olga Sysoeva > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] problems with mri interpolation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Fieldtrippers, > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > FT_VOLUMERESLICE. > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > mri_K0012.unit, 'm' > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > mri_K0012.transform, (4*4 double) > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > Than I used > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > the output is > > > > > > > > > ?the input is volume data with dimensions [432 > > > 512 180] > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > the input is volume data with dimensions [256 > > > 256 256] > > > > > > the input is volume data with dimensions [432 > > > 512 180] > > > > > > selecting subvolume of 0.0% > > > > > > reslicing and interpolating anatomy > > > > > > interpolating > > > > > > ??? Attempted to access sel(1); index out of > > > bounds because numel(sel)=0. > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > at 663 > > > > > > ft_progress(sel(1)/num, 'interpolating > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > cfg.feedback); > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > resliced);? > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > downloaded fieltrip (also in my previous version of 2013 the error > > > was the same). > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > Best Regards, > > > > > > Olga. > > > > > > P.S.Actually, I can project my sources > > > meaningfully into not interpolated MRI, altoough the images are > > > plotted upside down. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > ***************************************** > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Thu, 21 Jan 2016 21:59:06 +0900 > From: "Muhammad Naveed Iqbal Qureshi" > To: > Subject: [FieldTrip] difficulty in loading BCI-IV-2a dataset into > fieldtrip for preprocessing > Message-ID: <000b01d1544b$8323d8e0$896b8aa0$@gist.ac.kr> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > > > I am using BCI competition IV dataset 2a for my experiment. > > I want to preprocess it with field trip. > > > > I have written the following code for this task. > > > > addpath(genpath('E:\bbci_data\fieldtrip-20160118\fieldtrip-20160118')); > > cd 'E:\bbci_data\BCICIV_2a_gdf\'; > > > > %% Field Trip preprocessing code > > for i=1:9 > > file=num2str(i); > > file=strcat('A0',file,'T.gdf'); > > cfg = []; > > cfg.dataset = file ; > > cfg.trialdef.eventtype = 'Stimulus'; > > cfg.trialdef.eventvalue = {'left', 'right', 'both feet', 'tongue'}; > > cfg.trialdef.triallength = 8; % duration in seconds > > cfg.trialdef.ntrials = inf; % number of trials, inf > results in as many as possible > > cfg.trialdef.prestim = 3; > > cfg.trialdef.poststim = 6; > > cfg = ft_definetrial(cfg); > > > > cfg.bpfilter = 'yes'; > > cfg.bpfreq = [0.5 100]; > > cfg.bpfilttype = 'but'; > > cfg.bpfiltord = 5; > > cfg.demean = 'yes'; > > cfg.detrend = 'yes'; > > trialdata_EO{i} = ft_preprocessing(cfg); > > end > > > > However, this code does not import the event and trigger information from > the header file of the data. > > I will be highly obliged if anyone can help me in this regard. > > > > Thank in advance. > > > > Best Regards, > Muhammad Naveed Iqbal Qureshi > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Thu, 21 Jan 2016 20:14:01 +0200 > From: saeed zahran > To: "fieldtrip at science.ru.nl" > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 19 > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Thank you Jan and Cristiano; > > I downloaded another version of Fieldtrip thus the below error disappear: > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > But now I have another error: > > Error using surface_nesting (line 26) > the compartment nesting cannot be determined > > Error in ft_headmodel_bemcp (line 66) > order = surface_nesting(vol.bnd, 'insidefirst'); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example (line 100) > vol = ft_prepare_headmodel(cfg, vol); > Thank you for any suggestion > > Cristiano, I record the contraction of the uterus; > > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 19 > > To: fieldtrip at science.ru.nl > > Date: Thu, 21 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) (RICHARDS, JOHN) > > 3. Re: fieldtrip Digest, Vol 62, Issue 18 (saeed zahran) > > 4. Re: fieldtrip Digest, Vol 62, Issue 18 > > (Schoffelen, J.M. (Jan Mathijs)) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 20 Jan 2016 13:39:30 +0100 > > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1 at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answers yesterday. The segmentedmri > > contained 'white', 'grey' and 'csf' so I needed to repeat the > > segmentation using 'brain', 'skull' and 'scalp' as described in the > > tutorial "Creating a BEM volume conduction model of the head for > > source-reconstruction of EEG data" and everything worked smoothly > > afterwards. The problem is solved now. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 2 > > Date: Wed, 20 Jan 2016 14:39:13 +0000 > > From: "RICHARDS, JOHN" > > To: "fieldtrip at science.ru.nl" , > > "lah at pedneuro.uni-kiel.de" > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps (Laith Hamid) > > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > > > Laith: > > > > I have a ?neurodevelopmental MRI database? (Richards, Sanchez et al., 2015; see my www site) that has average MRI templates that could be used. Each average has the whole head down to about the top of the neck. I did these purposely since I use EEG recording and the MNI template did not even go down far enough for the EGI 128 channel net. > > > > The database has average MRI templates for head (T1, T2) and brain. I also have FEM segmented heads for the entire head that could be used for this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, scalp), but ironically, I cut these off about 10% below the EGI 128 channel electrodes. However, you could use the three inner compartments for this and just add the rest of the head below the compartment?or use the whole-head FEM as is for a FEM-model, or use the segmented area below the skull for a whole-head BEM model. I also have average 128-channel EGI electrodes for each template. > > > > Additionally, the ?developmental? part of the ?neurodevelopmental MRI database? is that I have these for a wide range of ages (all ages?). I have a average for young adults (20-24 yrs), and average templates and FEM/BEM models for groups from 3 months through adulthood, and into late adulthood. So if you have specific neuro-pediatric applications you might be interested in using an age appropriate MRI average template rather than an adult template. > > > > See my www site for journal article references re this, and http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > > > Finally? I have been using these head models for FT-based FEM and BEM models. Possibly some of the actually field trip models I have would be useful to you. Some of the parts of the model do not use the electrodes (e.g., grid-dipoles, head-model) whereas the final models (leadfield) requires the electrode locations. The database also includes ?virtual? electrodes for the 10-10 system, which might be used to generate the 256 channel locations by knowing the relation between the 10-10 system and the EGI system based on EGI ELP files for the 256 channels. > > > > John > > > > *********************************************** > > John E. Richards Carolina Distinguished Professor > > Department of Psychology > > University of South Carolina > > Columbia, SC 29208 > > Dept Phone: 803 777 2079 > > Fax: 803 777 9558 > > Email: richards-john at sc.edu > > HTTP: jerlab.psych.sc.edu > > *********************************************** > > > > > > > > > > >---------------------------------------------------------------------- > > > > > >Message: 1 > > >Date: Tue, 19 Jan 2016 15:35:00 +0100 > > >From: Laith Hamid > > >To: fieldtrip at science.ru.nl > > >Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > >Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > >Dear community, > > > > > >My name is Laith Hamid and I am working in the University Medical > > >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > >spikes and seizures. Currently I am analysing an EEG data set that was > > >recorded using a 256-channel EGI system and I wanted to ask whether you > > >have a standard BEM or FEM head model that extends enough downwards to > > >accomodate all 256 electrodes. The current standard BEM model in the > > >template folder of Fieldtrip isn't appropriate for source analysis of > > >256-channel EGI data. > > > > > >Thank you very much in advance for your help! > > > > > >Best, > > > > > >Laith > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Wed, 20 Jan 2016 19:37:32 +0200 > > From: saeed zahran > > To: "fieldtrip at science.ru.nl" > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Fieldtrip community, > > > > I define the volume conductor as: > > > > vol = []; > > vol.bnd(1).pnt=skinpnt > > vol.bnd(1).tri=skinf > > > > vol.bnd(2).pnt=uteruspnt > > vol.bnd(2).tri=uterusf > > > > vol.bnd(3).pnt=uterinecontentpnt > > vol.bnd(3).tri=uterinecontentf > > > > vol.cond = c; > > > > > > But it result with the below error: > > > > Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > Thank you very much in advance for your help! > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > To: fieldtrip at science.ru.nl > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 4. Source Localisation (aishwarya selvaraj) > > > 5. Re: Source Localisation (Hom?lle) > > > 6. Re: plotting neighbours (victoria schroeder) > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 8. Re: Source Localisation (Munsif Jatoi) > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > From: Laith Hamid > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > spikes and seizures. Currently I am analysing an EEG data set that was > > > recorded using a 256-channel EGI system and I wanted to ask whether you > > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > model that extends enough downwards to > > > accomodate all 256 electrodes. The current standard BEM model in the > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > thanks for your question. You could refer to a factory schematic layout > > > such as the one in figure 4 of this publication: > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > and subsequently use the function ft_prepare_layout to manually track the > > > points of the custom design on your own (if you dont want to wait for > > > somebody from the FT to do the same for you). > > > > > > cfg = []; > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > lay = ft_prepare_layout(cfg); > > > > > > The following tutorial describes the procedure in more details: > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > > > All the best > > > Cris Micheli > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > wrote: > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > > electrodes. The current standard BEM model in the template folder of > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > the cheeks or on the back of the neck and these areas are not modeled by > > > the standard BEM skin compartment in the standard BEM model. My question > > > was about a standard segmentation that extends the skin (and skull) > > > compartment downwards to allow these electrodes to sit on the nodes of > > > the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > From: aishwarya selvaraj > > > To: "fieldtrip, donders" > > > Subject: [FieldTrip] Source Localisation > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > From: Hom?lle, S. (Simon) > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ________________________________ > > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > To: fieldtrip, donders > > > Subject: [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 6 > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > From: victoria schroeder > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] plotting neighbours > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > Things have become much clearer now. > > > > > > I would like to follow up with a very related question. I am trying to > > > replicate the analysis for the cluster based permutation test using the > > > code and the data provided. However, i run into two problems here > > > > > > First, i get the following error if i use the original code: > > > Attempted to access cfg.frequency(2); index out of bounds because > > > numel(cfg.frequency)=1. > > > > > > Error in ft_freqstatistics (line 187) > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > > However, then no significant clusters are found. Which becomes clear when > > > trying to plot the cluster or by looking at the output of > > > ft_freqstatistics. > > > > > > Does the change in the code , change the output? How can i avoid the error > > > mentioned above and still get the same output from ft_freqstatistics as the > > > one provided on the webpage? > > > > > > > > > The relevant section of the toturial is provided below. > > > Thank you! > > > > > > Victoria > > > > > > Permutation test > > > > > > Now, run *ft_freqstatistics > > > * to compare > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > > the following configuration is identical to the configuration that was used > > > for comparing event-related averages in the cluster-based permutation tests > > > on event related fields tutorial > > > . > > > Also see this tutorial > > > for > > > a detailed explanation of all the configuration settings. You can read more > > > about the *ft_prepare_neighbours > > > * function > > > in the FAQ's > > > . > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > servers,freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > ), > > > use: > > > > > > load freqFIC_planar_cmb > > > load freqFC_planar_cmb > > > > > > cfg = []; > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > cfg.latency = 'all'; > > > cfg.frequency = 20; > > > cfg.method = 'montecarlo'; > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > cfg.correctm = 'cluster'; > > > cfg.clusteralpha = 0.05; > > > cfg.clusterstatistic = 'maxsum'; > > > cfg.minnbchan = 2; > > > cfg.tail = 0; > > > cfg.clustertail = 0; > > > cfg.alpha = 0.025; > > > cfg.numrandomization = 500; > > > % prepare_neighbours determines what sensors may form clusters > > > cfg_neighb.method = 'distance'; > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > size(freqFC_planar_cmb.powspctrm,1)); > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > cfg.design = design; > > > cfg.ivar = 1; > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > > > > > > > > > > Hi Victoria, > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > > right I was only scrolling up to the part where the mags were analyzed. As > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > > Phillip). I ran the following steps and I guess this should work for you. > > > > best > > > > tzvetan > > > > > > > > %% > > > > cfg = []; > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > %% > > > > cfg = [] > > > > cfg.method = 'triangulation'; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > cfg.senstype = 'MEG'; > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > %% > > > > % plot neighbours > > > > cfg=[]; > > > > cfg.neighbours = neighbours; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 7 > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > this might be possible if you have the subject-specific MRI by following > > > the tutorial here: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > cfg=[]; > > > cfg.tissue={'brain','skull','scalp'}; > > > cfg.numvertices = [3000 2000 1000]; > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > > contain your triangulated surface with 1000 vertices. Let me know if that > > > works. Of course you should see the skin and the neck in the original MRI. > > > > > > If you do not have an anatomical MRI that extends down to the chin you > > > could try with a template, such as this: > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > and the corresponding segmented version > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > This goes down to the chin. Then you take care of rearranging the position > > > of the EEG electrodes according to this: > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > I hope this helped > > > Cris > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > wrote: > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that was > > > > discussed in this thread from April 2013: > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > > cheeks or on the back of the neck and these areas are not modeled by the > > > > standard BEM skin compartment in the standard BEM model. My question was > > > > about a standard segmentation that extends the skin (and skull) compartment > > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 8 > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > From: Munsif Jatoi > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Aishwarya, > > > > > > Please refer to main help tutorials. > > > > > > Also, you can find out the survey papers written in this area. For more, > > > SPM website can provide good help. > > > > > > Best, > > > Munsif. > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ------------------------------ > > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > *To:* fieldtrip, donders > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > -- > > > Munsif Ali H.Jatoi, > > > > > > Ph D Scholar, > > > Centre for Intelligent Signals and Imaging Research, > > > Universiti Teknologi PETRONAS, > > > Malaysia. > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 9 > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > From: Olga Sysoeva > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] problems with mri interpolation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Fieldtrippers, > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > FT_VOLUMERESLICE. > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > mri_K0012.unit, 'm' > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > mri_K0012.transform, (4*4 double) > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > Than I used > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > the output is > > > > > > > > > ?the input is volume data with dimensions [432 > > > 512 180] > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > the input is volume data with dimensions [256 > > > 256 256] > > > > > > the input is volume data with dimensions [432 > > > 512 180] > > > > > > selecting subvolume of 0.0% > > > > > > reslicing and interpolating anatomy > > > > > > interpolating > > > > > > ??? Attempted to access sel(1); index out of > > > bounds because numel(sel)=0. > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > at 663 > > > > > > ft_progress(sel(1)/num, 'interpolating > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > cfg.feedback); > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > resliced);? > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > downloaded fieltrip (also in my previous version of 2013 the error > > > was the same). > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > Best Regards, > > > > > > Olga. > > > > > > P.S.Actually, I can project my sources > > > meaningfully into not interpolated MRI, altoough the images are > > > plotted upside down. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > ***************************************** > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 4 > > Date: Thu, 21 Jan 2016 08:16:55 +0000 > > From: "Schoffelen, J.M. (Jan Mathijs)" > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Saeed, > > > > are you using 0 or 1 indexing for your triangles? You probably want to use 1 indexing. > > > > Best, > > Jan-Mathijs > > > > > > On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: > > > > Dear Fieldtrip community, > > > > I define the volume conductor as: > > > > vol = []; > > vol.bnd(1).pnt=skinpnt > > vol.bnd(1).tri=skinf > > > > vol.bnd(2).pnt=uteruspnt > > vol.bnd(2).tri=uterusf > > > > vol.bnd(3).pnt=uterinecontentpnt > > vol.bnd(3).tri=uterinecontentf > > > > vol.cond = c; > > > > > > But it result with the below error: > > > > Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > Thank you very much in advance for your help! > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > To: fieldtrip at science.ru.nl > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 4. Source Localisation (aishwarya selvaraj) > > > 5. Re: Source Localisation (Hom?lle) > > > 6. Re: plotting neighbours (victoria schroeder) > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 8. Re: Source Localisation (Munsif Jatoi) > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > From: Laith Hamid > > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > spikes and seizures. Currently I am analysing an EEG data set that was > > > recorded using a 256-channel EGI system and I wanted to ask whether you > > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > model that extends enough downwards to > > > accomodate all 256 electrodes. The current standard BEM model in the > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > thanks for your question. You could refer to a factory schematic layout > > > such as the one in figure 4 of this publication: > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > and subsequently use the function ft_prepare_layout to manually track the > > > points of the custom design on your own (if you dont want to wait for > > > somebody from the FT to do the same for you). > > > > > > cfg = []; > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > lay = ft_prepare_layout(cfg); > > > > > > The following tutorial describes the procedure in more details: > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > > > All the best > > > Cris Micheli > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > > wrote: > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > > electrodes. The current standard BEM model in the template folder of > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > From: Laith Hamid > > > > To: Fieldtrip > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > the cheeks or on the back of the neck and these areas are not modeled by > > > the standard BEM skin compartment in the standard BEM model. My question > > > was about a standard segmentation that extends the skin (and skull) > > > compartment downwards to allow these electrodes to sit on the nodes of > > > the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > From: aishwarya selvaraj > > > > To: "fieldtrip, donders" > > > > Subject: [FieldTrip] Source Localisation > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > From: Hom?lle, S. (Simon) > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ________________________________ > > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > To: fieldtrip, donders > > > Subject: [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 6 > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > From: victoria schroeder > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] plotting neighbours > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > Things have become much clearer now. > > > > > > I would like to follow up with a very related question. I am trying to > > > replicate the analysis for the cluster based permutation test using the > > > code and the data provided. However, i run into two problems here > > > > > > First, i get the following error if i use the original code: > > > Attempted to access cfg.frequency(2); index out of bounds because > > > numel(cfg.frequency)=1. > > > > > > Error in ft_freqstatistics (line 187) > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > > However, then no significant clusters are found. Which becomes clear when > > > trying to plot the cluster or by looking at the output of > > > ft_freqstatistics. > > > > > > Does the change in the code , change the output? How can i avoid the error > > > mentioned above and still get the same output from ft_freqstatistics as the > > > one provided on the webpage? > > > > > > > > > The relevant section of the toturial is provided below. > > > Thank you! > > > > > > Victoria > > > > > > Permutation test > > > > > > Now, run *ft_freqstatistics > > > * to compare > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > > the following configuration is identical to the configuration that was used > > > for comparing event-related averages in the cluster-based permutation tests > > > on event related fields tutorial > > > . > > > Also see this tutorial > > > for > > > a detailed explanation of all the configuration settings. You can read more > > > about the *ft_prepare_neighbours > > > * function > > > in the FAQ's > > > . > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > servers,freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > ), > > > use: > > > > > > load freqFIC_planar_cmb > > > load freqFC_planar_cmb > > > > > > cfg = []; > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > cfg.latency = 'all'; > > > cfg.frequency = 20; > > > cfg.method = 'montecarlo'; > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > cfg.correctm = 'cluster'; > > > cfg.clusteralpha = 0.05; > > > cfg.clusterstatistic = 'maxsum'; > > > cfg.minnbchan = 2; > > > cfg.tail = 0; > > > cfg.clustertail = 0; > > > cfg.alpha = 0.025; > > > cfg.numrandomization = 500; > > > % prepare_neighbours determines what sensors may form clusters > > > cfg_neighb.method = 'distance'; > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > size(freqFC_planar_cmb.powspctrm,1)); > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > cfg.design = design; > > > cfg.ivar = 1; > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > > > > > > > Hi Victoria, > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > > right I was only scrolling up to the part where the mags were analyzed. As > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > > Phillip). I ran the following steps and I guess this should work for you. > > > > best > > > > tzvetan > > > > > > > > %% > > > > cfg = []; > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > %% > > > > cfg = [] > > > > cfg.method = 'triangulation'; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > cfg.senstype = 'MEG'; > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > %% > > > > % plot neighbours > > > > cfg=[]; > > > > cfg.neighbours = neighbours; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 7 > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > this might be possible if you have the subject-specific MRI by following > > > the tutorial here: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > cfg=[]; > > > cfg.tissue={'brain','skull','scalp'}; > > > cfg.numvertices = [3000 2000 1000]; > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > > contain your triangulated surface with 1000 vertices. Let me know if that > > > works. Of course you should see the skin and the neck in the original MRI. > > > > > > If you do not have an anatomical MRI that extends down to the chin you > > > could try with a template, such as this: > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > and the corresponding segmented version > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > This goes down to the chin. Then you take care of rearranging the position > > > of the EEG electrodes according to this: > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > I hope this helped > > > Cris > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > > wrote: > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that was > > > > discussed in this thread from April 2013: > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > > cheeks or on the back of the neck and these areas are not modeled by the > > > > standard BEM skin compartment in the standard BEM model. My question was > > > > about a standard segmentation that extends the skin (and skull) compartment > > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 8 > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > From: Munsif Jatoi > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Aishwarya, > > > > > > Please refer to main help tutorials. > > > > > > Also, you can find out the survey papers written in this area. For more, > > > SPM website can provide good help. > > > > > > Best, > > > Munsif. > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ------------------------------ > > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > *To:* fieldtrip, donders > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > -- > > > Munsif Ali H.Jatoi, > > > > > > Ph D Scholar, > > > Centre for Intelligent Signals and Imaging Research, > > > Universiti Teknologi PETRONAS, > > > Malaysia. > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 9 > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > From: Olga Sysoeva > > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] problems with mri interpolation > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Fieldtrippers, > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > FT_VOLUMERESLICE. > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > mri_K0012.unit, 'm' > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > mri_K0012.transform, (4*4 double) > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > Than I used > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > the output is > > > > > > > > > ?the input is volume data with dimensions [432 > > > 512 180] > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > the input is volume data with dimensions [256 > > > 256 256] > > > > > > the input is volume data with dimensions [432 > > > 512 180] > > > > > > selecting subvolume of 0.0% > > > > > > reslicing and interpolating anatomy > > > > > > interpolating > > > > > > ??? Attempted to access sel(1); index out of > > > bounds because numel(sel)=0. > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > at 663 > > > > > > ft_progress(sel(1)/num, 'interpolating > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > cfg.feedback); > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > resliced);? > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > downloaded fieltrip (also in my previous version of 2013 the error > > > was the same). > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > Best Regards, > > > > > > Olga. > > > > > > P.S.Actually, I can project my sources > > > meaningfully into not interpolated MRI, altoough the images are > > > plotted upside down. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > ***************************************** > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 19 > > ***************************************** > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 20 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.thomas at nin.knaw.nl Fri Jan 22 12:16:59 2016 From: r.thomas at nin.knaw.nl (Rajat Thomas) Date: Fri, 22 Jan 2016 11:16:59 +0000 Subject: [FieldTrip] ROI based analysis Message-ID: <1453461419134.82627@nin.knaw.nl> ?Dear Fieldtrippers, Has anyone fixed with problem with ROI based analysis in Fieldtrip. I see that it says ROI analysis needs to be fixed for new implementation. Are there newer functions that do this? Any help would be highly appreciated. Thanks Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam -------------- next part -------------- An HTML attachment was scrubbed... URL: From mortaheb.sepehr at yahoo.com Sat Jan 23 13:39:07 2016 From: mortaheb.sepehr at yahoo.com (Sepehr Mortaheb) Date: Sat, 23 Jan 2016 12:39:07 +0000 (UTC) Subject: [FieldTrip] Synthetic EEG References: <814709100.138411.1453552747072.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <814709100.138411.1453552747072.JavaMail.yahoo@mail.yahoo.com> Hi, How can I generate a synthetic EEG signal using forward models of FieldTrip?  -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Sat Jan 23 17:14:06 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Sat, 23 Jan 2016 17:14:06 +0100 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Dear Saeed, it might depend on the boundaries. If they are not nested (one is inside another, which is inside another, etc... like chinese boxes) then you have a fundamental problem. This is a constraint of the BEM algorithm in order for it to work properly. Have you tried plotting the triangulated meshes? Do they look nested? I hope this helps for now, Cris On Thu, Jan 21, 2016 at 7:22 PM, saeed zahran wrote: > Dear Fieldtrip Community, > > Dear Fieldtrip community, > > > What does the error of the surface nesting means; > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Error using surface_nesting (line 26) > the compartment nesting cannot be determined > > Error in ft_headmodel_bemcp (line 66) > order = surface_nesting(vol.bnd, 'insidefirst'); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example (line 100) > vol = ft_prepare_headmodel(cfg, vol); > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 20 > > To: fieldtrip at science.ru.nl > > Date: Thu, 21 Jan 2016 19:14:24 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Re: fieldtrip Digest, Vol 62, Issue 18 (Cristiano Micheli) > > 2. difficulty in loading BCI-IV-2a dataset into fieldtrip for > > preprocessing (Muhammad Naveed Iqbal Qureshi) > > 3. Re: fieldtrip Digest, Vol 62, Issue 19 (saeed zahran) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 21 Jan 2016 12:06:13 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Hi Saeed, > > if the content of your triangulation connectivity matrices *skinf, > > uterusf, **uterinecontentf* is not made of integers you probably get the > > error you mentioned. Could this be the case? > > Out of curiosity, are you doing fetal recordings? > > > > Cris > > > > > > On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran > > wrote: > > > > > Dear Fieldtrip community, > > > > > > I define the volume conductor as: > > > > > > vol = []; > > > vol.bnd(1).pnt=skinpnt > > > vol.bnd(1).tri=skinf > > > > > > vol.bnd(2).pnt=uteruspnt > > > vol.bnd(2).tri=uterusf > > > > > > vol.bnd(3).pnt=uterinecontentpnt > > > vol.bnd(3).tri=uterinecontentf > > > > > > vol.cond = c; > > > > > > > > > But it result with the below error: > > > > > > Subscript indices must either be real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > > > > Thank you very much in advance for your help! > > > > > > Best regards > > > Saeed Zahran > > > > > > > From: fieldtrip-request at science.ru.nl > > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > > To: fieldtrip at science.ru.nl > > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > > > Send fieldtrip mailing list submissions to > > > > fieldtrip at science.ru.nl > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > or, via email, send a message with subject or body 'help' to > > > > fieldtrip-request at science.ru.nl > > > > > > > > You can reach the person managing the list at > > > > fieldtrip-owner at science.ru.nl > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 4. Source Localisation (aishwarya selvaraj) > > > > 5. Re: Source Localisation (Hom?lle) > > > > 6. Re: plotting neighbours (victoria schroeder) > > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 8. Re: Source Localisation (Munsif Jatoi) > > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > > From: Laith Hamid > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > > spikes and seizures. Currently I am analysing an EEG data set that > was > > > > recorded using a 256-channel EGI system and I wanted to ask whether > you > > > > have a standard BEM or FEM head Subscript indices must either be real > > > positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > model that extends enough downwards to > > > > accomodate all 256 electrodes. The current standard BEM model in the > > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > > 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > thanks for your question. You could refer to a factory schematic > layout > > > > such as the one in figure 4 of this publication: > > > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > > > and subsequently use the function ft_prepare_layout to manually > track the > > > > points of the custom design on your own (if you dont want to wait for > > > > somebody from the FT to do the same for you). > > > > > > > > cfg = []; > > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > > lay = ft_prepare_layout(cfg); > > > > > > > > The following tutorial describes the procedure in more details: > > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > > > Please do not hesitate to get in touch with me for this and other > > > matters. > > > > > > > > All the best > > > > Cris Micheli > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear community, > > > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex > > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes > > > and > > > > > seizures. Currently I am analysing an EEG data set that was > recorded > > > using > > > > > a 256-channel EGI system and I wanted to ask whether you have a > > > standard > > > > > BEM or FEM head model that extends enough downwards to accomodate > all > > > 256 > > > > > electrodes. The current standard BEM model in the template folder > of > > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > > > data. > > > > > > > > > > Thank you very much in advance for your help! > > > > > > > > > > Best, > > > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > > From: Laith Hamid > > > > To: Fieldtrip > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that > was > > > > discussed in this thread from April 2013: > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > > the cheeks or on the back of the neck and these areas are not > modeled by > > > > the standard BEM skin compartment in the standard BEM model. My > question > > > > was about a standard segmentation that extends the skin (and skull) > > > > compartment downwards to allow these electrodes to sit on the nodes > of > > > > the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 4 > > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > > From: aishwarya selvaraj > > > > To: "fieldtrip, donders" > > > > Subject: [FieldTrip] Source Localisation > > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 5 > > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > > From: Hom?lle, S. (Simon) > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ________________________________ > > > > From: fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > > To: fieldtrip, donders > > > > Subject: [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 6 > > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > > From: victoria schroeder > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] plotting neighbours > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > > > Things have become much clearer now. > > > > > > > > I would like to follow up with a very related question. I am trying > to > > > > replicate the analysis for the cluster based permutation test using > the > > > > code and the data provided. However, i run into two problems here > > > > > > > > First, i get the following error if i use the original code: > > > > Attempted to access cfg.frequency(2); index out of bounds because > > > > numel(cfg.frequency)=1. > > > > > > > > Error in ft_freqstatistics (line 187) > > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > > > fmax)]; > > > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 > 20]. > > > > However, then no significant clusters are found. Which becomes clear > when > > > > trying to plot the cluster or by looking at the output of > > > > ft_freqstatistics. > > > > > > > > Does the change in the code , change the output? How can i avoid the > > > error > > > > mentioned above and still get the same output from ft_freqstatistics > as > > > the > > > > one provided on the webpage? > > > > > > > > > > > > The relevant section of the toturial is provided below. > > > > Thank you! > > > > > > > > Victoria > > > > > > > > Permutation test > > > > > > > > Now, run *ft_freqstatistics > > > > * to > > > compare > > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > > > cfg.latency, > > > > the following configuration is identical to the configuration that > was > > > used > > > > for comparing event-related averages in the cluster-based permutation > > > tests > > > > on event related fields tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>. > > > > Also see this tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> > > > for > > > > a detailed explanation of all the configuration settings. You can > read > > > more > > > > about the *ft_prepare_neighbours > > > > * > > > function > > > > in the FAQ's > > > > < > http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work > > > >. > > > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > > servers,freqFIC_planar_cmb.mat > > > > < > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > > > and freqFC_planar_cmb.mat > > > > < > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > > > >), > > > > use: > > > > > > > > load freqFIC_planar_cmb > > > > load freqFC_planar_cmb > > > > > > > > cfg = []; > > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > > cfg.latency = 'all'; > > > > cfg.frequency = 20; > > > > cfg.method = 'montecarlo'; > > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > > cfg.correctm = 'cluster'; > > > > cfg.clusteralpha = 0.05; > > > > cfg.clusterstatistic = 'maxsum'; > > > > cfg.minnbchan = 2; > > > > cfg.tail = 0; > > > > cfg.clustertail = 0; > > > > cfg.alpha = 0.025; > > > > cfg.numrandomization = 500; > > > > % prepare_neighbours determines what sensors may form clusters > > > > cfg_neighb.method = 'distance'; > > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > > size(freqFC_planar_cmb.powspctrm,1)); > > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > > > cfg.design = design; > > > > cfg.ivar = 1; > > > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, > freqFC_planar_cmb); > > > > > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov < > tzvetan.popov at uni-konstanz.de > > > >: > > > > > > > > > > > > > > Hi Victoria, > > > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. > You are > > > > > right I was only scrolling up to the part where the mags were > > > analyzed. As > > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course > you > > > can > > > > > threat them separately, as I was naively thinking as non-neuormag > > > user, but > > > > > indeed combination of both is recommended as I have now learned > > > :-)(thanks > > > > > Phillip). I ran the following steps and I guess this should work > for > > > you. > > > > > best > > > > > tzvetan > > > > > > > > > > %% > > > > > cfg = []; > > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > > %% > > > > > cfg = [] > > > > > cfg.method = 'triangulation'; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > cfg.senstype = 'MEG'; > > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > > %% > > > > > % plot neighbours > > > > > cfg=[]; > > > > > cfg.neighbours = neighbours; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 7 > > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > this might be possible if you have the subject-specific MRI by > following > > > > the tutorial here: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > > > cfg=[]; > > > > cfg.tissue={'brain','skull','scalp'}; > > > > cfg.numvertices = [3000 2000 1000]; > > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable > should > > > > contain your triangulated surface with 1000 vertices. Let me know if > that > > > > works. Of course you should see the skin and the neck in the original > > > MRI. > > > > > > > > If you do not have an anatomical MRI that extends down to the chin > you > > > > could try with a template, such as this: > > > > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > > and the corresponding segmented version > > > > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > > > This goes down to the chin. Then you take care of rearranging the > > > position > > > > of the EEG electrodes according to this: > > > > > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > > > I hope this helped > > > > Cris > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear Cris, > > > > > > > > > > thank you very much for your answer. I am refering to an issue > that was > > > > > discussed in this thread from April 2013: > > > > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > > download. Some electrodes in the EGI 256-electrodes cap are placed > on > > > the > > > > > cheeks or on the back of the neck and these areas are not modeled > by > > > the > > > > > standard BEM skin compartment in the standard BEM model. My > question > > > was > > > > > about a standard segmentation that extends the skin (and skull) > > > compartment > > > > > downwards to allow these electrodes to sit on the nodes of the skin > > > mesh. > > > > > > > > > > Best, > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 8 > > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > > From: Munsif Jatoi > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Aishwarya, > > > > > > > > Please refer to main help tutorials. > > > > > > > > Also, you can find out the survey papers written in this area. For > more, > > > > SPM website can provide good help. > > > > > > > > Best, > > > > Munsif. > > > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > > > Dear Aishwarya, > > > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > > tutorials about source reconstruction. > > > > > > > > > > My recommended start would be: > > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > > reconstruction > > > > > > > > > > Best regards, > > > > > > > > > > Simon Hom?lle > > > > > PhD Candidate > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > Centre for Cognitive Neuroimaging > > > > > Radboud University Nijmegen > > > > > Phone: +31-(0)24-36-65059 > > > > > ------------------------------ > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > > > fieldtrip-bounces at science.ru.nl] > > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > > *To:* fieldtrip, donders > > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > > > Hi guys, > > > > > I'm currently working on source localization of EEG signals . > > > > > Im very new to it . > > > > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > > It would be of great help . > > > > > > > > > > -- > > > > > Regards, > > > > > Aishwarya > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > > > > > > -- > > > > Munsif Ali H.Jatoi, > > > > > > > > Ph D Scholar, > > > > Centre for Intelligent Signals and Imaging Research, > > > > Universiti Teknologi PETRONAS, > > > > Malaysia. > > > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 9 > > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > > From: Olga Sysoeva > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] problems with mri interpolation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Fieldtrippers, > > > > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > > > FT_VOLUMERESLICE. > > > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > > > mri_K0012.unit, 'm' > > > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > > > mri_K0012.transform, (4*4 double) > > > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > > > > Than I used > > > > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > > > > the output is > > > > > > > > > > > > ?the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > > > the input is volume data with dimensions [256 > > > > 256 256] > > > > > > > > the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > selecting subvolume of 0.0% > > > > > > > > reslicing and interpolating anatomy > > > > > > > > interpolating > > > > > > > > ??? Attempted to access sel(1); index out of > > > > bounds because numel(sel)=0. > > > > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > > at 663 > > > > > > > > ft_progress(sel(1)/num, 'interpolating > > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > > > cfg.feedback); > > > > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > > resliced);? > > > > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > > downloaded fieltrip (also in my previous version of 2013 the error > > > > was the same). > > > > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > > > > Best Regards, > > > > > > > > Olga. > > > > > > > > P.S.Actually, I can project my sources > > > > meaningfully into not interpolated MRI, altoough the images are > > > > plotted upside down. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > > ***************************************** > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/5f4a716a/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 2 > > Date: Thu, 21 Jan 2016 21:59:06 +0900 > > From: "Muhammad Naveed Iqbal Qureshi" > > To: > > Subject: [FieldTrip] difficulty in loading BCI-IV-2a dataset into > > fieldtrip for preprocessing > > Message-ID: <000b01d1544b$8323d8e0$896b8aa0$@gist.ac.kr> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi, > > > > > > > > I am using BCI competition IV dataset 2a for my experiment. > > > > I want to preprocess it with field trip. > > > > > > > > I have written the following code for this task. > > > > > > > > addpath(genpath('E:\bbci_data\fieldtrip-20160118\fieldtrip-20160118')); > > > > cd 'E:\bbci_data\BCICIV_2a_gdf\'; > > > > > > > > %% Field Trip preprocessing code > > > > for i=1:9 > > > > file=num2str(i); > > > > file=strcat('A0',file,'T.gdf'); > > > > cfg = []; > > > > cfg.dataset = file ; > > > > cfg.trialdef.eventtype = 'Stimulus'; > > > > cfg.trialdef.eventvalue = {'left', 'right', 'both feet', 'tongue'}; > > > > cfg.trialdef.triallength = 8; % duration in seconds > > > > cfg.trialdef.ntrials = inf; % number of trials, inf > > results in as many as possible > > > > cfg.trialdef.prestim = 3; > > > > cfg.trialdef.poststim = 6; > > > > cfg = ft_definetrial(cfg); > > > > > > > > cfg.bpfilter = 'yes'; > > > > cfg.bpfreq = [0.5 100]; > > > > cfg.bpfilttype = 'but'; > > > > cfg.bpfiltord = 5; > > > > cfg.demean = 'yes'; > > > > cfg.detrend = 'yes'; > > > > trialdata_EO{i} = ft_preprocessing(cfg); > > > > end > > > > > > > > However, this code does not import the event and trigger information from > > the header file of the data. > > > > I will be highly obliged if anyone can help me in this regard. > > > > > > > > Thank in advance. > > > > > > > > Best Regards, > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/1dbb2d2d/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 21 Jan 2016 20:14:01 +0200 > > From: saeed zahran > > To: "fieldtrip at science.ru.nl" > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 19 > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Thank you Jan and Cristiano; > > > > I downloaded another version of Fieldtrip thus the below error disappear: > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > But now I have another error: > > > > Error using surface_nesting (line 26) > > the compartment nesting cannot be determined > > > > Error in ft_headmodel_bemcp (line 66) > > order = surface_nesting(vol.bnd, 'insidefirst'); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example (line 100) > > vol = ft_prepare_headmodel(cfg, vol); > > Thank you for any suggestion > > > > Cristiano, I record the contraction of the uterus; > > > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 19 > > > To: fieldtrip at science.ru.nl > > > Date: Thu, 21 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) (RICHARDS, JOHN) > > > 3. Re: fieldtrip Digest, Vol 62, Issue 18 (saeed zahran) > > > 4. Re: fieldtrip Digest, Vol 62, Issue 18 > > > (Schoffelen, J.M. (Jan Mathijs)) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Wed, 20 Jan 2016 13:39:30 +0100 > > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1 at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answers yesterday. The segmentedmri > > > contained 'white', 'grey' and 'csf' so I needed to repeat the > > > segmentation using 'brain', 'skull' and 'scalp' as described in the > > > tutorial "Creating a BEM volume conduction model of the head for > > > source-reconstruction of EEG data" and everything worked smoothly > > > afterwards. The problem is solved now. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/e700c8d6/attachment-0001.html > > > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Wed, 20 Jan 2016 14:39:13 +0000 > > > From: "RICHARDS, JOHN" > > > To: "fieldtrip at science.ru.nl" , > > > "lah at pedneuro.uni-kiel.de" > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps (Laith Hamid) > > > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > > > > > Laith: > > > > > > I have a ?neurodevelopmental MRI database? (Richards, Sanchez et al., > 2015; see my www site) that has average MRI templates that could be used. > Each average has the whole head down to about the top of the neck. I did > these purposely since I use EEG recording and the MNI template did not even > go down far enough for the EGI 128 channel net. > > > > > > The database has average MRI templates for head (T1, T2) and brain. I > also have FEM segmented heads for the entire head that could be used for > this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, > scalp), but ironically, I cut these off about 10% below the EGI 128 channel > electrodes. However, you could use the three inner compartments for this > and just add the rest of the head below the compartment?or use the > whole-head FEM as is for a FEM-model, or use the segmented area below the > skull for a whole-head BEM model. I also have average 128-channel EGI > electrodes for each template. > > > > > > Additionally, the ?developmental? part of the ?neurodevelopmental MRI > database? is that I have these for a wide range of ages (all ages?). I have > a average for young adults (20-24 yrs), and average templates and FEM/BEM > models for groups from 3 months through adulthood, and into late adulthood. > So if you have specific neuro-pediatric applications you might be > interested in using an age appropriate MRI average template rather than an > adult template. > > > > > > See my www site for journal article references re this, and > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > > > > > Finally? I have been using these head models for FT-based FEM and BEM > models. Possibly some of the actually field trip models I have would be > useful to you. Some of the parts of the model do not use the electrodes > (e.g., grid-dipoles, head-model) whereas the final models (leadfield) > requires the electrode locations. The database also includes ?virtual? > electrodes for the 10-10 system, which might be used to generate the 256 > channel locations by knowing the relation between the 10-10 system and the > EGI system based on EGI ELP files for the 256 channels. > > > > > > John > > > > > > *********************************************** > > > John E. Richards Carolina Distinguished Professor > > > Department of Psychology > > > University of South Carolina > > > Columbia, SC 29208 > > > Dept Phone: 803 777 2079 > > > Fax: 803 777 9558 > > > Email: richards-john at sc.edu > > > HTTP: jerlab.psych.sc.edu > > > *********************************************** > > > > > > > > > > > > > > > >---------------------------------------------------------------------- > > > > > > > >Message: 1 > > > >Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > >From: Laith Hamid > > > >To: fieldtrip at science.ru.nl > > > >Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > >Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > >Dear community, > > > > > > > >My name is Laith Hamid and I am working in the University Medical > > > >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > >spikes and seizures. Currently I am analysing an EEG data set that was > > > >recorded using a 256-channel EGI system and I wanted to ask whether > you > > > >have a standard BEM or FEM head model that extends enough downwards to > > > >accomodate all 256 electrodes. The current standard BEM model in the > > > >template folder of Fieldtrip isn't appropriate for source analysis of > > > >256-channel EGI data. > > > > > > > >Thank you very much in advance for your help! > > > > > > > >Best, > > > > > > > >Laith > > > > > > > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Wed, 20 Jan 2016 19:37:32 +0200 > > > From: saeed zahran > > > To: "fieldtrip at science.ru.nl" > > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Fieldtrip community, > > > > > > I define the volume conductor as: > > > > > > vol = []; > > > vol.bnd(1).pnt=skinpnt > > > vol.bnd(1).tri=skinf > > > > > > vol.bnd(2).pnt=uteruspnt > > > vol.bnd(2).tri=uterusf > > > > > > vol.bnd(3).pnt=uterinecontentpnt > > > vol.bnd(3).tri=uterinecontentf > > > > > > vol.cond = c; > > > > > > > > > But it result with the below error: > > > > > > Subscript indices must either be real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > > > > Thank you very much in advance for your help! > > > > > > Best regards > > > Saeed Zahran > > > > > > > From: fieldtrip-request at science.ru.nl > > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > > To: fieldtrip at science.ru.nl > > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > > > Send fieldtrip mailing list submissions to > > > > fieldtrip at science.ru.nl > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > or, via email, send a message with subject or body 'help' to > > > > fieldtrip-request at science.ru.nl > > > > > > > > You can reach the person managing the list at > > > > fieldtrip-owner at science.ru.nl > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 4. Source Localisation (aishwarya selvaraj) > > > > 5. Re: Source Localisation (Hom?lle) > > > > 6. Re: plotting neighbours (victoria schroeder) > > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 8. Re: Source Localisation (Munsif Jatoi) > > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > > From: Laith Hamid > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > > spikes and seizures. Currently I am analysing an EEG data set that > was > > > > recorded using a 256-channel EGI system and I wanted to ask whether > you > > > > have a standard BEM or FEM head Subscript indices must either be > real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > model that extends enough downwards to > > > > accomodate all 256 electrodes. The current standard BEM model in the > > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > > 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > thanks for your question. You could refer to a factory schematic > layout > > > > such as the one in figure 4 of this publication: > > > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > > > and subsequently use the function ft_prepare_layout to manually > track the > > > > points of the custom design on your own (if you dont want to wait for > > > > somebody from the FT to do the same for you). > > > > > > > > cfg = []; > > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > > lay = ft_prepare_layout(cfg); > > > > > > > > The following tutorial describes the procedure in more details: > > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > > > Please do not hesitate to get in touch with me for this and other > matters. > > > > > > > > All the best > > > > Cris Micheli > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear community, > > > > > > > > > > My name is Laith Hamid and I am working in the University Medical > Complex > > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and > > > > > seizures. Currently I am analysing an EEG data set that was > recorded using > > > > > a 256-channel EGI system and I wanted to ask whether you have a > standard > > > > > BEM or FEM head model that extends enough downwards to accomodate > all 256 > > > > > electrodes. The current standard BEM model in the template folder > of > > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > data. > > > > > > > > > > Thank you very much in advance for your help! > > > > > > > > > > Best, > > > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > > From: Laith Hamid > > > > To: Fieldtrip > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that > was > > > > discussed in this thread from April 2013: > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > > the cheeks or on the back of the neck and these areas are not > modeled by > > > > the standard BEM skin compartment in the standard BEM model. My > question > > > > was about a standard segmentation that extends the skin (and skull) > > > > compartment downwards to allow these electrodes to sit on the nodes > of > > > > the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 4 > > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > > From: aishwarya selvaraj > > > > To: "fieldtrip, donders" > > > > Subject: [FieldTrip] Source Localisation > > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 5 > > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > > From: Hom?lle, S. (Simon) > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ________________________________ > > > > From: fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [ > aishwaryaselvaraj1708 at gmail.com] > > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > > To: fieldtrip, donders > > > > Subject: [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 6 > > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > > From: victoria schroeder > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] plotting neighbours > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > > > Things have become much clearer now. > > > > > > > > I would like to follow up with a very related question. I am trying > to > > > > replicate the analysis for the cluster based permutation test using > the > > > > code and the data provided. However, i run into two problems here > > > > > > > > First, i get the following error if i use the original code: > > > > Attempted to access cfg.frequency(2); index out of bounds because > > > > numel(cfg.frequency)=1. > > > > > > > > Error in ft_freqstatistics (line 187) > > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > fmax)]; > > > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 > 20]. > > > > However, then no significant clusters are found. Which becomes clear > when > > > > trying to plot the cluster or by looking at the output of > > > > ft_freqstatistics. > > > > > > > > Does the change in the code , change the output? How can i avoid the > error > > > > mentioned above and still get the same output from ft_freqstatistics > as the > > > > one provided on the webpage? > > > > > > > > > > > > The relevant section of the toturial is provided below. > > > > Thank you! > > > > > > > > Victoria > > > > > > > > Permutation test > > > > > > > > Now, run *ft_freqstatistics > > > > * to > compare > > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > cfg.latency, > > > > the following configuration is identical to the configuration that > was used > > > > for comparing event-related averages in the cluster-based > permutation tests > > > > on event related fields tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>. > > > > Also see this tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> for > > > > a detailed explanation of all the configuration settings. You can > read more > > > > about the *ft_prepare_neighbours > > > > * > function > > > > in the FAQ's > > > > < > http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work>. > > > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > > servers,freqFIC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > >), > > > > use: > > > > > > > > load freqFIC_planar_cmb > > > > load freqFC_planar_cmb > > > > > > > > cfg = []; > > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > > cfg.latency = 'all'; > > > > cfg.frequency = 20; > > > > cfg.method = 'montecarlo'; > > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > > cfg.correctm = 'cluster'; > > > > cfg.clusteralpha = 0.05; > > > > cfg.clusterstatistic = 'maxsum'; > > > > cfg.minnbchan = 2; > > > > cfg.tail = 0; > > > > cfg.clustertail = 0; > > > > cfg.alpha = 0.025; > > > > cfg.numrandomization = 500; > > > > % prepare_neighbours determines what sensors may form clusters > > > > cfg_neighb.method = 'distance'; > > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > > size(freqFC_planar_cmb.powspctrm,1)); > > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > > > cfg.design = design; > > > > cfg.ivar = 1; > > > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, > freqFC_planar_cmb); > > > > > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov < > tzvetan.popov at uni-konstanz.de>: > > > > > > > > > > > > > > Hi Victoria, > > > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. > You are > > > > > right I was only scrolling up to the part where the mags were > analyzed. As > > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course > you can > > > > > threat them separately, as I was naively thinking as non-neuormag > user, but > > > > > indeed combination of both is recommended as I have now learned > :-)(thanks > > > > > Phillip). I ran the following steps and I guess this should work > for you. > > > > > best > > > > > tzvetan > > > > > > > > > > %% > > > > > cfg = []; > > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > > %% > > > > > cfg = [] > > > > > cfg.method = 'triangulation'; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > cfg.senstype = 'MEG'; > > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > > %% > > > > > % plot neighbours > > > > > cfg=[]; > > > > > cfg.neighbours = neighbours; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 7 > > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > this might be possible if you have the subject-specific MRI by > following > > > > the tutorial here: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > > > cfg=[]; > > > > cfg.tissue={'brain','skull','scalp'}; > > > > cfg.numvertices = [3000 2000 1000]; > > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable > should > > > > contain your triangulated surface with 1000 vertices. Let me know if > that > > > > works. Of course you should see the skin and the neck in the > original MRI. > > > > > > > > If you do not have an anatomical MRI that extends down to the chin > you > > > > could try with a template, such as this: > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > > and the corresponding segmented version > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > > > This goes down to the chin. Then you take care of rearranging the > position > > > > of the EEG electrodes according to this: > > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > > > I hope this helped > > > > Cris > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear Cris, > > > > > > > > > > thank you very much for your answer. I am refering to an issue > that was > > > > > discussed in this thread from April 2013: > > > > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > > download. Some electrodes in the EGI 256-electrodes cap are placed > on the > > > > > cheeks or on the back of the neck and these areas are not modeled > by the > > > > > standard BEM skin compartment in the standard BEM model. My > question was > > > > > about a standard segmentation that extends the skin (and skull) > compartment > > > > > downwards to allow these electrodes to sit on the nodes of the > skin mesh. > > > > > > > > > > Best, > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 8 > > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > > From: Munsif Jatoi > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Aishwarya, > > > > > > > > Please refer to main help tutorials. > > > > > > > > Also, you can find out the survey papers written in this area. For > more, > > > > SPM website can provide good help. > > > > > > > > Best, > > > > Munsif. > > > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > > > Dear Aishwarya, > > > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > > tutorials about source reconstruction. > > > > > > > > > > My recommended start would be: > > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > > reconstruction > > > > > > > > > > Best regards, > > > > > > > > > > Simon Hom?lle > > > > > PhD Candidate > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > Centre for Cognitive Neuroimaging > > > > > Radboud University Nijmegen > > > > > Phone: +31-(0)24-36-65059 > > > > > ------------------------------ > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] > > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > > *To:* fieldtrip, donders > > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > > > Hi guys, > > > > > I'm currently working on source localization of EEG signals . > > > > > Im very new to it . > > > > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > > It would be of great help . > > > > > > > > > > -- > > > > > Regards, > > > > > Aishwarya > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > > > > > > -- > > > > Munsif Ali H.Jatoi, > > > > > > > > Ph D Scholar, > > > > Centre for Intelligent Signals and Imaging Research, > > > > Universiti Teknologi PETRONAS, > > > > Malaysia. > > > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 9 > > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > > From: Olga Sysoeva > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] problems with mri interpolation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Fieldtrippers, > > > > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > > > FT_VOLUMERESLICE. > > > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > > > mri_K0012.unit, 'm' > > > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > > > mri_K0012.transform, (4*4 double) > > > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > > > > Than I used > > > > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > > > > the output is > > > > > > > > > > > > ?the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > > > the input is volume data with dimensions [256 > > > > 256 256] > > > > > > > > the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > selecting subvolume of 0.0% > > > > > > > > reslicing and interpolating anatomy > > > > > > > > interpolating > > > > > > > > ??? Attempted to access sel(1); index out of > > > > bounds because numel(sel)=0. > > > > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > > at 663 > > > > > > > > ft_progress(sel(1)/num, 'interpolating > > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > > > cfg.feedback); > > > > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > > resliced);? > > > > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > > downloaded fieltrip (also in my previous version of 2013 the error > > > > was the same). > > > > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > > > > Best Regards, > > > > > > > > Olga. > > > > > > > > P.S.Actually, I can project my sources > > > > meaningfully into not interpolated MRI, altoough the images are > > > > plotted upside down. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > > ***************************************** > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/0d8cf652/attachment-0001.html > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Thu, 21 Jan 2016 08:16:55 +0000 > > > From: "Schoffelen, J.M. (Jan Mathijs)" > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Saeed, > > > > > > are you using 0 or 1 indexing for your triangles? You probably want to > use 1 indexing. > > > > > > Best, > > > Jan-Mathijs > > > > > > > > > On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: > > > > > > Dear Fieldtrip community, > > > > > > I define the volume conductor as: > > > > > > vol = []; > > > vol.bnd(1).pnt=skinpnt > > > vol.bnd(1).tri=skinf > > > > > > vol.bnd(2).pnt=uteruspnt > > > vol.bnd(2).tri=uterusf > > > > > > vol.bnd(3).pnt=uterinecontentpnt > > > vol.bnd(3).tri=uterinecontentf > > > > > > vol.cond = c; > > > > > > > > > But it result with the below error: > > > > > > Subscript indices must either be real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > > > > Thank you very much in advance for your help! > > > > > > Best regards > > > Saeed Zahran > > > > > > > From: fieldtrip-request at science.ru.nl fieldtrip-request at science.ru.nl> > > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > > To: fieldtrip at science.ru.nl > > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > > > Send fieldtrip mailing list submissions to > > > > fieldtrip at science.ru.nl > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > or, via email, send a message with subject or body 'help' to > > > > fieldtrip-request at science.ru.nl fieldtrip-request at science.ru.nl> > > > > > > > > You can reach the person managing the list at > > > > fieldtrip-owner at science.ru.nl > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 4. Source Localisation (aishwarya selvaraj) > > > > 5. Re: Source Localisation (Hom?lle) > > > > 6. Re: plotting neighbours (victoria schroeder) > > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 8. Re: Source Localisation (Munsif Jatoi) > > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > > From: Laith Hamid lah at pedneuro.uni-kiel.de>> > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > > spikes and seizures. Currently I am analysing an EEG data set that > was > > > > recorded using a 256-channel EGI system and I wanted to ask whether > you > > > > have a standard BEM or FEM head Subscript indices must either be > real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > model that extends enough downwards to > > > > accomodate all 256 electrodes. The current standard BEM model in the > > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > > 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > > From: Cristiano Micheli michelic72 at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > thanks for your question. You could refer to a factory schematic > layout > > > > such as the one in figure 4 of this publication: > > > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > > > and subsequently use the function ft_prepare_layout to manually > track the > > > > points of the custom design on your own (if you dont want to wait for > > > > somebody from the FT to do the same for you). > > > > > > > > cfg = []; > > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > > lay = ft_prepare_layout(cfg); > > > > > > > > The following tutorial describes the procedure in more details: > > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > > > Please do not hesitate to get in touch with me for this and other > matters. > > > > > > > > All the best > > > > Cris Micheli > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear community, > > > > > > > > > > My name is Laith Hamid and I am working in the University Medical > Complex > > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and > > > > > seizures. Currently I am analysing an EEG data set that was > recorded using > > > > > a 256-channel EGI system and I wanted to ask whether you have a > standard > > > > > BEM or FEM head model that extends enough downwards to accomodate > all 256 > > > > > electrodes. The current standard BEM model in the template folder > of > > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > data. > > > > > > > > > > Thank you very much in advance for your help! > > > > > > > > > > Best, > > > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > > From: Laith Hamid lah at pedneuro.uni-kiel.de>> > > > > To: Fieldtrip fieldtrip at science.ru.nl>> > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that > was > > > > discussed in this thread from April 2013: > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > > the cheeks or on the back of the neck and these areas are not > modeled by > > > > the standard BEM skin compartment in the standard BEM model. My > question > > > > was about a standard segmentation that extends the skin (and skull) > > > > compartment downwards to allow these electrodes to sit on the nodes > of > > > > the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 4 > > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > > From: aishwarya selvaraj aishwaryaselvaraj1708 at gmail.com>> > > > > To: "fieldtrip, donders" fieldtrip at donders.ru.nl>> > > > > Subject: [FieldTrip] Source Localisation > > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 5 > > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > > From: Hom?lle, S. (Simon) S.Homolle at donders.ru.nl>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ________________________________ > > > > From: fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl>] on behalf of aishwarya selvaraj [ > aishwaryaselvaraj1708 at gmail.com] > > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > > To: fieldtrip, donders > > > > Subject: [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 6 > > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > > From: victoria schroeder vic.schroeder2 at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] plotting neighbours > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > > > Things have become much clearer now. > > > > > > > > I would like to follow up with a very related question. I am trying > to > > > > replicate the analysis for the cluster based permutation test using > the > > > > code and the data provided. However, i run into two problems here > > > > > > > > First, i get the following error if i use the original code: > > > > Attempted to access cfg.frequency(2); index out of bounds because > > > > numel(cfg.frequency)=1. > > > > > > > > Error in ft_freqstatistics (line 187) > > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > fmax)]; > > > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 > 20]. > > > > However, then no significant clusters are found. Which becomes clear > when > > > > trying to plot the cluster or by looking at the output of > > > > ft_freqstatistics. > > > > > > > > Does the change in the code , change the output? How can i avoid the > error > > > > mentioned above and still get the same output from ft_freqstatistics > as the > > > > one provided on the webpage? > > > > > > > > > > > > The relevant section of the toturial is provided below. > > > > Thank you! > > > > > > > > Victoria > > > > > > > > Permutation test > > > > > > > > Now, run *ft_freqstatistics > > > > * to > compare > > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > cfg.latency, > > > > the following configuration is identical to the configuration that > was used > > > > for comparing event-related averages in the cluster-based > permutation tests > > > > on event related fields tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>. > > > > Also see this tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> for > > > > a detailed explanation of all the configuration settings. You can > read more > > > > about the *ft_prepare_neighbours > > > > * > function > > > > in the FAQ's > > > > < > http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work>. > > > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > > servers,freqFIC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > >), > > > > use: > > > > > > > > load freqFIC_planar_cmb > > > > load freqFC_planar_cmb > > > > > > > > cfg = []; > > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > > cfg.latency = 'all'; > > > > cfg.frequency = 20; > > > > cfg.method = 'montecarlo'; > > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > > cfg.correctm = 'cluster'; > > > > cfg.clusteralpha = 0.05; > > > > cfg.clusterstatistic = 'maxsum'; > > > > cfg.minnbchan = 2; > > > > cfg.tail = 0; > > > > cfg.clustertail = 0; > > > > cfg.alpha = 0.025; > > > > cfg.numrandomization = 500; > > > > % prepare_neighbours determines what sensors may form clusters > > > > cfg_neighb.method = 'distance'; > > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > > size(freqFC_planar_cmb.powspctrm,1)); > > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > > > cfg.design = design; > > > > cfg.ivar = 1; > > > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, > freqFC_planar_cmb); > > > > > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov < > tzvetan.popov at uni-konstanz.de>: > > > > > > > > > > > > > > Hi Victoria, > > > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. > You are > > > > > right I was only scrolling up to the part where the mags were > analyzed. As > > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course > you can > > > > > threat them separately, as I was naively thinking as non-neuormag > user, but > > > > > indeed combination of both is recommended as I have now learned > :-)(thanks > > > > > Phillip). I ran the following steps and I guess this should work > for you. > > > > > best > > > > > tzvetan > > > > > > > > > > %% > > > > > cfg = []; > > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > > %% > > > > > cfg = [] > > > > > cfg.method = 'triangulation'; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > cfg.senstype = 'MEG'; > > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > > %% > > > > > % plot neighbours > > > > > cfg=[]; > > > > > cfg.neighbours = neighbours; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 7 > > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > > From: Cristiano Micheli michelic72 at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > this might be possible if you have the subject-specific MRI by > following > > > > the tutorial here: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > > > cfg=[]; > > > > cfg.tissue={'brain','skull','scalp'}; > > > > cfg.numvertices = [3000 2000 1000]; > > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable > should > > > > contain your triangulated surface with 1000 vertices. Let me know if > that > > > > works. Of course you should see the skin and the neck in the > original MRI. > > > > > > > > If you do not have an anatomical MRI that extends down to the chin > you > > > > could try with a template, such as this: > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > > and the corresponding segmented version > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > > > This goes down to the chin. Then you take care of rearranging the > position > > > > of the EEG electrodes according to this: > > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > > > I hope this helped > > > > Cris > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear Cris, > > > > > > > > > > thank you very much for your answer. I am refering to an issue > that was > > > > > discussed in this thread from April 2013: > > > > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > > download. Some electrodes in the EGI 256-electrodes cap are placed > on the > > > > > cheeks or on the back of the neck and these areas are not modeled > by the > > > > > standard BEM skin compartment in the standard BEM model. My > question was > > > > > about a standard segmentation that extends the skin (and skull) > compartment > > > > > downwards to allow these electrodes to sit on the nodes of the > skin mesh. > > > > > > > > > > Best, > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 8 > > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > > From: Munsif Jatoi munsif.jatoi at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Aishwarya, > > > > > > > > Please refer to main help tutorials. > > > > > > > > Also, you can find out the survey papers written in this area. For > more, > > > > SPM website can provide good help. > > > > > > > > Best, > > > > Munsif. > > > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > > > Dear Aishwarya, > > > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > > tutorials about source reconstruction. > > > > > > > > > > My recommended start would be: > > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > > reconstruction > > > > > > > > > > Best regards, > > > > > > > > > > Simon Hom?lle > > > > > PhD Candidate > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > Centre for Cognitive Neuroimaging > > > > > Radboud University Nijmegen > > > > > Phone: +31-(0)24-36-65059 > > > > > ------------------------------ > > > > > *From:* fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl>] > > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com > ] > > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > > *To:* fieldtrip, donders > > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > > > Hi guys, > > > > > I'm currently working on source localization of EEG signals . > > > > > Im very new to it . > > > > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > > It would be of great help . > > > > > > > > > > -- > > > > > Regards, > > > > > Aishwarya > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > > > > > > -- > > > > Munsif Ali H.Jatoi, > > > > > > > > Ph D Scholar, > > > > Centre for Intelligent Signals and Imaging Research, > > > > Universiti Teknologi PETRONAS, > > > > Malaysia. > > > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 9 > > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > > From: Olga Sysoeva olga.v.sysoeva at gmail.com>> > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] problems with mri interpolation > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Fieldtrippers, > > > > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > > > FT_VOLUMERESLICE. > > > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > > > mri_K0012.unit, 'm' > > > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > > > mri_K0012.transform, (4*4 double) > > > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > > > > Than I used > > > > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > > > > the output is > > > > > > > > > > > > ?the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > > > the input is volume data with dimensions [256 > > > > 256 256] > > > > > > > > the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > selecting subvolume of 0.0% > > > > > > > > reslicing and interpolating anatomy > > > > > > > > interpolating > > > > > > > > ??? Attempted to access sel(1); index out of > > > > bounds because numel(sel)=0. > > > > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > > at 663 > > > > > > > > ft_progress(sel(1)/num, 'interpolating > > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > > > cfg.feedback); > > > > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > > resliced);? > > > > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > > downloaded fieltrip (also in my previous version of 2013 the error > > > > was the same). > > > > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > > > > Best Regards, > > > > > > > > Olga. > > > > > > > > P.S.Actually, I can project my sources > > > > meaningfully into not interpolated MRI, altoough the images are > > > > plotted upside down. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > > ***************************************** > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/d9124654/attachment-0001.html > > > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 19 > > > ***************************************** > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/043a7628/attachment.html > > > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 20 > > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.roux at bcbl.eu Mon Jan 25 11:55:27 2016 From: f.roux at bcbl.eu (=?utf-8?B?RnLDqWTDqXJpYw==?= Roux) Date: Mon, 25 Jan 2016 11:55:27 +0100 (CET) Subject: [FieldTrip] cross-frequency coupling between MEG planar channel twins? Message-ID: <1957967079.822957.1453719327381.JavaMail.zimbra@bcbl.eu> Dear all, in my MEG-data (Elekta Vectorview System) I am observing that the amplitude of higher frequencies over one planar gradient channel is coupled to the phase of lower frequencies on its corresponding twin-channel . I am attaching a figure to illustrate this. The upper row shows a low-frequency oscillation for one planar-channel and the bottom row shows the amplitude of a higher-frequency oscillation on its corresponding twin channel. Note that this separation is fairly consistent across other channels as well. My question relates to what could explain such a coupling of low and high freq activity over channel-pairs with different gradient orientations (ie vertical vs. horizontal)? Could this be an indicator of two separate sources which are being picked up by the different spatial sensitivity of the planar gradients and where the phase of one source modulates the amplitude of the other source? Any comments or suggestions on this would be highly appreciated. Fred -- Frédéric Roux Postdoctoral Scientist, Marie-Curie fellow BCBL. Basque Center on Cognition, Brain & Language. f.roux at bcbl.eu Tel: +34 943 309 300 Ext 211 Fax: +34 943 309 052 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer --------------------------------------------------------------------------- “The probability of success is difficult to estimate; but if we never search the chance of success is zero.” -------------- next part -------------- A non-text attachment was scrubbed... Name: low_high_coupling_planar_grads_TFR.png Type: image/png Size: 26838 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: low_high_coupling_planar_grads.png Type: image/png Size: 11179 bytes Desc: not available URL: From saeedzahran at hotmail.com Mon Jan 25 18:08:07 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Mon, 25 Jan 2016 19:08:07 +0200 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Thank you Cris, but I am sure that the meshes is nested, does it require to calculate the normal for each vertices? Best regards Saeed. > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 24 > To: fieldtrip at science.ru.nl > Date: Mon, 25 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. cross-frequency coupling between MEG planar channel twins? > (Fr?d?ric Roux) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 25 Jan 2016 11:55:27 +0100 (CET) > From: Fr?d?ric Roux > To: FieldTrip discussion list > Subject: [FieldTrip] cross-frequency coupling between MEG planar > channel twins? > Message-ID: <1957967079.822957.1453719327381.JavaMail.zimbra at bcbl.eu> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > in my MEG-data (Elekta Vectorview System) I am observing that the amplitude of higher frequencies over one planar gradient channel is coupled to the > phase of lower frequencies on its corresponding twin-channel . I am attaching a figure to illustrate this. The upper row shows a low-frequency oscillation for one planar-channel and the bottom row shows the amplitude of a higher-frequency oscillation on its corresponding twin channel. Note that this separation is fairly consistent across other channels as well. > > My question relates to what could explain such a coupling of low and high freq activity over channel-pairs with different gradient orientations (ie vertical vs. horizontal)? > > Could this be an indicator of two separate sources which are being picked up by the different spatial sensitivity of the planar gradients and where the phase of one source modulates the amplitude of the other source? > > Any comments or suggestions on this would be highly appreciated. > > Fred > > > > > > > > -- > Fr?d?ric Roux > Postdoctoral Scientist, Marie-Curie fellow > BCBL. Basque Center on Cognition, Brain & Language. > > f.roux at bcbl.eu > Tel: +34 943 309 300 Ext 211 > Fax: +34 943 309 052 > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > --------------------------------------------------------------------------- > > ?The probability of success is difficult to estimate; but if we never search the chance of success is zero.? > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: low_high_coupling_planar_grads_TFR.png > Type: image/png > Size: 26838 bytes > Desc: not available > URL: > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: low_high_coupling_planar_grads.png > Type: image/png > Size: 11179 bytes > Desc: not available > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 24 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From toni.rbaena at gmail.com Mon Jan 25 18:15:55 2016 From: toni.rbaena at gmail.com (Antonio Rodriguez) Date: Mon, 25 Jan 2016 18:15:55 +0100 Subject: [FieldTrip] =?utf-8?q?Can=C2=B4t_read_CFS_files=2E?= Message-ID: Dear Fieldtrippers, My name is Antonio Rodriguez, i´m very new with fieldtrip., We´re trying to open a file with CFS extension (Cambridge Electronic Design), which is the format that Signal Software returns, but i can´t read the file. I´m trying to load the file "dataset.cfs"; no error is prompted but nothing is loaded in the Workspace, I found in the tutorial that fieldtrip is able to open this kind of files. Am i doing anything wrong? Thank you. Antonio Rodriguez, University of Seville. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Mon Jan 25 18:57:04 2016 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Mon, 25 Jan 2016 09:57:04 -0800 Subject: [FieldTrip] =?utf-8?q?Can=C2=B4t_read_CFS_files=2E?= In-Reply-To: References: Message-ID: Hi Antonio, How are you trying to load the file? To see whether your format is supported, try: hdr = ft_read_header('dataset.cfs') Hope that gets you started, Arjen 2016-01-25 9:15 GMT-08:00 Antonio Rodriguez : > Dear Fieldtrippers, > > My name is Antonio Rodriguez, i´m very new with fieldtrip., We´re trying > to open a file with CFS extension (Cambridge Electronic Design), which is > the format that Signal Software returns, but i can´t read the file. > > I´m trying to load the file "dataset.cfs"; no error is prompted but > nothing is loaded in the Workspace, I found in the tutorial that fieldtrip > is able to open this kind of files. > > Am i doing anything wrong? > > Thank you. > > > Antonio Rodriguez, University of Seville. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Mon Jan 25 19:41:53 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Mon, 25 Jan 2016 19:41:53 +0100 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Hi Saeed, could you be more specific by attaching the nesting matrix? You find it by typing: dbstop if error in the matlab workspace. and then by running your script again. The script will stop at the line where it fails and at that point you will be able to look inside the local variables of the subfunction that is returning the error (in your case it is the private function surface_nesting.m). Please copy the content of the variables *nesting* and * numboundaries* in the next email. At that point I will have enough information to help you. I don't think the normals are a problem here. Best regards, Cris On Mon, Jan 25, 2016 at 6:08 PM, saeed zahran wrote: > Thank you Cris, but I am sure that the meshes is nested, > does it require to calculate the normal for each vertices? > > Best regards > Saeed. > > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 24 > > To: fieldtrip at science.ru.nl > > Date: Mon, 25 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. cross-frequency coupling between MEG planar channel twins? > > (Fr?d?ric Roux) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 25 Jan 2016 11:55:27 +0100 (CET) > > From: Fr?d?ric Roux > > To: FieldTrip discussion list > > Subject: [FieldTrip] cross-frequency coupling between MEG planar > > channel twins? > > Message-ID: <1957967079.822957.1453719327381.JavaMail.zimbra at bcbl.eu> > > Content-Type: text/plain; charset="utf-8" > > > > Dear all, > > > > in my MEG-data (Elekta Vectorview System) I am observing that the > amplitude of higher frequencies over one planar gradient channel is coupled > to the > > phase of lower frequencies on its corresponding twin-channel . I am > attaching a figure to illustrate this. The upper row shows a low-frequency > oscillation for one planar-channel and the bottom row shows the amplitude > of a higher-frequency oscillation on its corresponding twin channel. Note > that this separation is fairly consistent across other channels as well. > > > > My question relates to what could explain such a coupling of low and > high freq activity over channel-pairs with different gradient orientations > (ie vertical vs. horizontal)? > > > > Could this be an indicator of two separate sources which are being > picked up by the different spatial sensitivity of the planar gradients and > where the phase of one source modulates the amplitude of the other source? > > > > Any comments or suggestions on this would be highly appreciated. > > > > Fred > > > > > > > > > > > > > > > > -- > > Fr?d?ric Roux > > Postdoctoral Scientist, Marie-Curie fellow > > BCBL. Basque Center on Cognition, Brain & Language. > > > > f.roux at bcbl.eu > > Tel: +34 943 309 300 Ext 211 > > Fax: +34 943 309 052 > > > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > --------------------------------------------------------------------------- > > > > ?The probability of success is difficult to estimate; but if we never > search the chance of success is zero.? > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: low_high_coupling_planar_grads_TFR.png > > Type: image/png > > Size: 26838 bytes > > Desc: not available > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160125/c41f609c/attachment-0002.png > > > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: low_high_coupling_planar_grads.png > > Type: image/png > > Size: 11179 bytes > > Desc: not available > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160125/c41f609c/attachment-0003.png > > > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 24 > > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Tue Jan 26 00:25:13 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Tue, 26 Jan 2016 00:25:13 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: Message-ID: Dear FieldTrip users, I'm looking for the best method to analyse the relationship between ERP and behavioural data but all I've been able to find so far are methods to compare ERPs (or more generally time-series). Consider the following example: 20 participants performed a memory-related task in which they had to respond based on the difference between the target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 samples at 200 Hz) and responses were recorded; ERPs were then created based on epochs in which the responses were correct. Similarly, response accuracy was averaged over all successful epochs per each subject. The resulting data are therefore: 20 participants x 50 channels x 1000 samples (ERP) and 20 averages of accuracy (one value per participant). My objective is to identify which portion of the ERP data best explains (or predicts) the changes in accuracy. In other words, in which time interval is the most significant difference between people who do well in the task and those who don't. So far I've been doing correlations between ERP at each time point and overall accuracy, which is unreliable due to multiple comparisons (correction methods are reportedly too conservative). Nevertheless, certain channels show quite strong correlations in multiple time intervals. How would you approach this problem, please? Many thanks! Best regards, Harold -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue Jan 26 06:35:58 2016 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 26 Jan 2016 06:35:58 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: Message-ID: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Dear Harold, have you checked out ft_statfun_correlationT? This sounds like the function you're looking for. Use cfg.statistic = 'ft_statfun_correlationT' in your call to ft_timelockstatistics. Plus you can use all the correction methods available in FT. See the FAQ for more info: http://www.fieldtriptoolbox.org/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables Good luck, Julian ******************** Dr. Julian Keil AG Multisensorische Integration Psychiatrische Universitätsklinik der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11, Raum A007 10115 Berlin Telefon: +49-30-2311-1879 Fax: +49-30-2311-2209 http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration Am 26.01.2016 um 00:25 schrieb Harold Cavendish: > Dear FieldTrip users, > > I'm looking for the best method to analyse the relationship between ERP and behavioural data but all I've been able to find so far are methods to compare ERPs (or more generally time-series). > > Consider the following example: 20 participants performed a memory-related task in which they had to respond based on the difference between the target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 samples at 200 Hz) and responses were recorded; ERPs were then created based on epochs in which the responses were correct. Similarly, response accuracy was averaged over all successful epochs per each subject. > > The resulting data are therefore: 20 participants x 50 channels x 1000 samples (ERP) and 20 averages of accuracy (one value per participant). > > My objective is to identify which portion of the ERP data best explains (or predicts) the changes in accuracy. In other words, in which time interval is the most significant difference between people who do well in the task and those who don't. > > So far I've been doing correlations between ERP at each time point and overall accuracy, which is unreliable due to multiple comparisons (correction methods are reportedly too conservative). Nevertheless, certain channels show quite strong correlations in multiple time intervals. > > How would you approach this problem, please? > > Many thanks! > > Best regards, > Harold > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From stephen.politzer-ahles at ling-phil.ox.ac.uk Tue Jan 26 12:08:32 2016 From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles) Date: Tue, 26 Jan 2016 11:08:32 +0000 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data Message-ID: Hi Harold, If you're only interested in identifying which timepoints have the best correlation, multiple comparisons aren't really an issue; if you're not worried about testing for significance, then the place where you see the highest estimate is the highest. See e.g., Hauk et al. 2006 in NeuroImage, and Smith & Kutas 2015 in Psychophysiology, for similar analyses. If you're interested in finding a part of the waveform where the correlation is significantly different from zero while also dealing with multiple comparisons, you could use [spatio]temporal clustering (Maris & Oostenveld 2007). Just make an event-related regression coefficient (as described in Hauk et al.; just do a regression at each timepoint, and then rather than plotting the ERP amplitude at each timepoint, plot the regression estimate (*b*) at each timepoint, to derive a similar waveform) and then test that waveform against 0 using temporal clustering. Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/ > Message: 5 > Date: Tue, 26 Jan 2016 00:25:13 +0100 > From: Harold Cavendish > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Fwd: Identify a window of best correlation > between ERP and behavioural data > Message-ID: > < > CALOTjvZXPNWHLefXrG6uss7uF3kkXie7qjiWqEcesOUqWay6qA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear FieldTrip users, > > I'm looking for the best method to analyse the relationship between ERP and > behavioural data but all I've been able to find so far are methods to > compare ERPs (or more generally time-series). > > Consider the following example: 20 participants performed a memory-related > task in which they had to respond based on the difference between the > target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 > samples at 200 Hz) and responses were recorded; ERPs were then created > based on epochs in which the responses were correct. Similarly, response > accuracy was averaged over all successful epochs per each subject. > > The resulting data are therefore: 20 participants x 50 channels x 1000 > samples (ERP) and 20 averages of accuracy (one value per participant). > > My objective is to identify which portion of the ERP data best explains (or > predicts) the changes in accuracy. In other words, in which time interval > is the most significant difference between people who do well in the task > and those who don't. > > So far I've been doing correlations between ERP at each time point and > overall accuracy, which is unreliable due to multiple comparisons > (correction methods are reportedly too conservative). Nevertheless, certain > channels show quite strong correlations in multiple time intervals. > > How would you approach this problem, please? > > Many thanks! > > Best regards, > Harold > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160126/b5769634/attachment-0001.html > > > > ------------------------------ > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Wed Jan 27 10:51:13 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Wed, 27 Jan 2016 10:51:13 +0100 Subject: [FieldTrip] Two questions regarding source analysis in Fieldtrip Message-ID: <4fcc207813cc3640c68f3d637e011a79@mail.uni-kiel.de> Dear Community, I have two questions regarding source analysis in Fieldtrip. 1- Is it possible to estimate the regularization parameter (lambda) in ft_timelockanalysis or ft_sourceanalysis? How is it automatically determined if it is not specified by the user? 2- The source analysis results of ft_sourceanalysis contain information aobut time series of the sources. How can I show a specific point in time (e.g. the epileptic spike's peak) in ft_sourceplot? or is this information lost in ft_sourceinterpolate? Thank you very much for your help. Best, Laith Hamid -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Wed Jan 27 14:04:21 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Wed, 27 Jan 2016 14:04:21 +0100 Subject: [FieldTrip] Two questions regarding source analysis in Fieldtrip In-Reply-To: <4fcc207813cc3640c68f3d637e011a79@mail.uni-kiel.de> References: <4fcc207813cc3640c68f3d637e011a79@mail.uni-kiel.de> Message-ID: Hi Laith On Wed, Jan 27, 2016 at 10:51 AM, Laith Hamid wrote: > > Dear Community, > > I have two questions regarding source analysis in Fieldtrip. > > 1- Is it possible to estimate the regularization parameter (lambda) in > ft_timelockanalysis or ft_sourceanalysis? How is it automatically > determined if it is not specified by the user? > > I am reporting a mail by M Wibral (2-3-2009) from the FieldTrip mailing list here below: *Hi Marco,in a nutshell the effect of the lambda parameter is to smoothe your solution in space, it also makes it more stable in the presence of noise. You might know that the estimation of the covariance matrix for beamforming requires quite a lot of data. CTF/VSM (a MEG manufacturer) used to suggest to have your data satisfy the following relationship:3000 < BW[Hz] * #trials *EffectLength[s]Where BW[Hz] is the bandwidth of your effect of interest in Hz, #trials is the number of trials that contain that effect, and EffectLength[s] is the length of your effect in seconds (NOT ms!).Here's an example: You have an effect between 30 and 60Hz, so the bandwidth of that effect is 30Hz. The effect is visible (say at the electrode level) for 400ms=0.4s in each trial. Now you calculate the number of trials to be:#trials > 3000 / ( BW[Hz] * EffectLength[s]) = 3000/(0.4*30)= 250. This means that you would need 250 artifact free, valid trials. Choosing a larger lambda can help to reduce the amount of data necessary, but you get a more smeared out solution.A good introduction and simulation results for various values of lambda can be found in:Neuroimage. 2008 Feb 15;39(4):1788-802. Epub 2007 Oct 10Optimising experimental design for MEG beamformer imaging.Brookes MJ, Vrba J, Robinson SE, Stevenson CM, Peters AM, Barnes GR, Hillebrand A, Morris PG.Hope this helps,* *Michael* In short, if you have enough trials you do not need to smoothe your solution. If not, then apply the rule of thumb described above. I believe you have an option to declare lambda in percentages as well (e.g. lambda = '5%'; ) You can refer to this tutorial too: http://www.fieldtriptoolbox.org/tutorial/beamformer 2- The source analysis results of ft_sourceanalysis contain information > aobut time series of the sources. How can I show a specific point in time > (e.g. the epileptic spike's peak) in ft_sourceplot? or is this information > lost in ft_sourceinterpolate? > Can you add your scripts/code? This will add context to the conversation and allow users to help you further. If I understand your question, you can try to use the ft_sourcemovie function, for example like in this tutorial: http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate Here it is applied to minimum norm solutions, but the same concept holds for LCMV beamformer (which you are using right?) I hope this helps Cris > Thank you very much for your help. > > Best, > > Laith Hamid > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From adamaron at ucsd.edu Wed Jan 27 22:22:39 2016 From: adamaron at ucsd.edu (Adam Aron) Date: Wed, 27 Jan 2016 13:22:39 -0800 Subject: [FieldTrip] Postdoc position in simultaneous electrophysiology of frontal cortex and basal ganglia during action control in humans Message-ID: A funded postdoctoral position is available in the lab of Adam Aron (PhD) at University of California San Diego (www.aronlab.org ) to work collaboratively with Nader Pouratian (MD, PhD) at University of California Los Angeles (http://tinyurl.com/gwuvbja ). The studies will be done in the operating room in patients with Parkinson’s disease who are having electrodes implanted in global pallidus or subthalamic nucleus. The project is to design behavioral tasks, acquire simultaneous local field potential data from basal ganglia and frontal cortex (ECoG) while patients perform the tasks, and to analyze the data using time frequency methods and measures of connectivity and causal flow. The candidate will be based in San Diego with occasional travel to Los Angeles for data collection. This is a substantial postdoctoral training opportunity either for candidates with signal processing expertise (engineering/computer science/neuroscience) who want to branch out into cognition (especially as it pertains to action control); or for cognitive neuroscience candidates who already have cognitive (and frontal-basal-ganglia) expertise and want to learn human electrophysiological analysis methods. Candidates must have a PhD, or be about to be awarded one. Applications (and enquiries) should be sent to adamaron at ucsd.edu and should consist in: - a subject line “electrophysiology of frontal cortex and basal ganglia” - a cover letter describing research interests and how those are a match for the lab - a CV - contact info for references Salary is commensurate with NIH-rates. Non US Citizens are welcome. Full University of California benefits are provided. Applications for the position are open until March 15th 2016. The position is available immediately and for ~3 years. A delayed start time is also possible. --------------------------------------- Adam R. Aron Professor, Department of Psychology Neuroscience Graduate Program University of California, San Diego www.aronlab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From hayes.brenner at gmail.com Thu Jan 28 03:57:20 2016 From: hayes.brenner at gmail.com (Hayes Brenner) Date: Wed, 27 Jan 2016 20:57:20 -0600 Subject: [FieldTrip] How to select trials based on their timing Message-ID: Hello everyone! I'm fairly new to Fieldtrip, so I apologize if this question seems trivial, but I've been stuck for a while and I would greatly appreciate everyone's help. I have a set of data that I'm working on to get a better sense of how to process EEG data. I'm having trouble with this part when given these instructions: "let's only grab trials in which a '30' also appeared along side the '20'. [These labels are a part of cfg.trialdef.eventtype]. This '30' event code denotes a certain kind of trial in the experiment in which only the colored square was presented. The '30' event code should onset at the same time or within just a few milliseconds of the onset of the '20'. Third, let's also only grab trials in which subjects correctly responded with a button press to the stimulus (i.e., the colored square). To do this, you'll need to make sure there is a '90' following the '20'. The button press (or event code '90') should appear within 1000 ms of the onset of the '20'. My question is: how can I designate my code so that I can have a data set that meets the following conditions? I know I should use an 'if' or 'for' but I'm not sure how to write it exactly. Any advice? I've included my code as is without including the file upload. As of now, I created 3 data sets, each one with the required markers (20, 30, and 90). ft_defaults; cfg = []; cfg.trialdef.eventtype = '?'; ft_definetrial(cfg); cfg.trialdef.eventtype = 'Stim'; cfg.trialdef.prestim = 0.2; cfg.trialdef.poststim = .8; cfg.trialdef.eventvalue = '20'; cfg1=ft_definetrial(cfg); cfg.trialdef.eventvalue = '30'; cfg2=ft_definetrial(cfg); cfg.trialdef.eventvalue = '90'; cfg3=ft_definetrial(cfg); cfg.lpfilter='yes'; cfg.lpfreq = 30; cfg.reref = 'yes'; cfg.implicitref = 'REF'; cfg.refchannel = {'LM' 'REF'}; trialdata1 = ft_preprocessing(cfg1); trialdata2 = ft_preprocessing(cfg2); trialdata3 = ft_preprocessing(cfg3); Thank you all so much! Hayes Brenner -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Thu Jan 28 12:06:34 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Thu, 28 Jan 2016 13:06:34 +0200 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: , Message-ID: Dear Cris, Thank you for your time and consideration. I have solved the problem, after I add 1 to all the faces, since there was zeros in the faces, Faces=load('Faces.mat'); Faces=Faces.Faces; Points=load('Points.mat'); Points=Points.Points; Rfaces=load('Rfaces.mat'); Rfaces=Rfaces.Rfaces; Rpoints=load('Rpoints.mat'); Rpoints=Rpoints.Rpoints; RRfaces=load('RRfaces.mat'); RRfaces=RRfaces.RRfaces; RRpoints=load('RRpoints.mat'); RRpoints=RRpoints.RRpoints; Faces=Faces+1; Rfaces=Rfaces+1; RRfaces=RRfaces+1; vol = []; vol.bnd(1).pnt=Points; vol.bnd(1).tri=Faces; vol.bnd(2).pnt=Rpoints; vol.bnd(2).tri=Rfaces; vol.bnd(3).pnt=RRpoints; vol.bnd(3).tri=RRfaces; vol.cond = c; but I have the below error:Attempted to access vol.cond(4); index out of bounds because numel(vol.cond)=3. Error in ft_headmodel_bemcp (line 154) weight = (vol.cond(2)-vol.cond(3))/((vol.cond(3)+vol.cond(4)));%*2*pi); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 167) vol = ft_prepare_headmodel(cfg, vol); With two boundaries I have the below error: Attempted to access vol.cond(3); index out of bounds because numel(vol.cond)=2. Error in ft_headmodel_bemcp (line 129) weight = (vol.cond(1)-vol.cond(2))/((vol.cond(2)+vol.cond(3)));%*2*pi); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 167) vol = ft_prepare_headmodel(cfg, vol); Best regards Saeed. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.politzer-ahles at ling-phil.ox.ac.uk Thu Jan 28 12:10:16 2016 From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles) Date: Thu, 28 Jan 2016 11:10:16 +0000 Subject: [FieldTrip] How to select trials based on their timing Message-ID: Hi Hayes, This isn't really about Fieldtrip specifically, but is a MATLAB programming issue; that is to say, the solution isn't a special Fieldtrip function or anything like that, just basic MATLAB coding. (There might be a Fieldtrip-internal solution, like there is in ERPLAB for relatively complex trial selection, but I'm not aware of it.) All you really need to do is rewrite the trigger numbers so they distinguish the kinds of triggers you actually need. For example, rather than all trials of a given condition being coded as 30, you might want correct trials in that condition to be 31 and incorrect trials 32; the same logic also goes for recoding the trials based on whether or not there was a 20 nearby. All this information about trial timing is available in the 'cfg.trl' matrix that is created after you run ft_definetrial (see http://www.fieldtriptoolbox.org/reference/definetrial for details about how this matrix is organized). So all you need to do is write a FOR loop that iterates through each row of the trl matrix, and for each row checks (using an IF statement) whether that row meets the various conditions you outlined, and rewrites that row's trigger code if it meets those conditions. Then you can pull out a list of which trials you want (this is doable with basic MATLAB code, e.g., find(cfg.trl(:,3)==31) gives you a list of the row numbers of every trial with a code of 31) and use that list with ft_preprocessing to process just the trials you want. Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/ > Message: 3 > Date: Wed, 27 Jan 2016 20:57:20 -0600 > From: Hayes Brenner > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] How to select trials based on their timing > Message-ID: > < > CAB--YMYoCGP7KKCW-a7DwP2iZgyCVO-D_SJh1dmjUP79NtcLow at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello everyone! I'm fairly new to Fieldtrip, so I apologize if this > question seems trivial, but I've been stuck for a while and I would greatly > appreciate everyone's help. > > I have a set of data that I'm working on to get a better sense of how to > process EEG data. I'm having trouble with this part when given these > instructions: > > "let's only grab trials in which a '30' also appeared along side the '20'. > [These labels are a part of cfg.trialdef.eventtype]. This '30' event code > denotes a certain kind of trial in the experiment in which only the colored > square was presented. The '30' event code should onset at the same time or > within just a few milliseconds of the onset of the '20'. Third, let's also > only grab trials in which subjects correctly responded with a button press > to the stimulus (i.e., the colored square). To do this, you'll need to make > sure there is a '90' following the '20'. The button press (or event code > '90') should appear within 1000 ms of the onset of the '20'. > > My question is: how can I designate my code so that I can have a data set > that meets the following conditions? I know I should use an 'if' or 'for' > but I'm not sure how to write it exactly. Any advice? I've included my code > as is without including the file upload. As of now, I created 3 data sets, > each one with the required markers (20, 30, and 90). > > ft_defaults; > cfg = []; > cfg.trialdef.eventtype = '?'; > ft_definetrial(cfg); > cfg.trialdef.eventtype = 'Stim'; > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = .8; > cfg.trialdef.eventvalue = '20'; > cfg1=ft_definetrial(cfg); > cfg.trialdef.eventvalue = '30'; > cfg2=ft_definetrial(cfg); > cfg.trialdef.eventvalue = '90'; > cfg3=ft_definetrial(cfg); > cfg.lpfilter='yes'; > cfg.lpfreq = 30; > cfg.reref = 'yes'; > cfg.implicitref = 'REF'; > cfg.refchannel = {'LM' 'REF'}; > trialdata1 = ft_preprocessing(cfg1); > trialdata2 = ft_preprocessing(cfg2); > trialdata3 = ft_preprocessing(cfg3); > > Thank you all so much! > > Hayes Brenner > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160127/b0726da2/attachment-0001.html > > > > ------------------------------ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Thu Jan 28 13:31:37 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Thu, 28 Jan 2016 13:31:37 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> References: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Message-ID: Dear Julian, thank you for your help, I believe I read the same page but I didn't realise it could be used with ft_timelockstatistics – the way certain ft_ functions fit others is still a bit unclear to me (it's practically my first contact with FT). Now, it appears to be exactly what I'm looking for. I took me some time to figure out how to import my already processed data (ERPs averaged per subject) into FieldTrip and run the test but it seems I've succeeded. However, ft_timelockstatistics(cfg, data) gave me the following warnings: *1. Warning: the data does not contain a trial definition* *2. Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous* *recording* *3. Warning: doing a two-sided test without correcting p-values or alpha-level, p-values and alpha-level* *will reflect one-sided tests per tail* Should I be worried about these? (Here's the full output: https://gist.github.com/anonymous/1866a2b1a424dd9f0ac9) Finally, the resulting *stat* structure contains 10 fields but I'm not sure what *mask*, *stat* and *ref* represent. Is there any guidance on how to report the results like in the case of comparisons between conditions ( http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test )? Many thanks! Harold 2016-01-26 6:35 GMT+01:00 Julian Keil : > Dear Harold, > > have you checked out ft_statfun_correlationT? > This sounds like the function you're looking for. Use cfg.statistic = > 'ft_statfun_correlationT' in your call to ft_timelockstatistics. > Plus you can use all the correction methods available in FT. > See the FAQ for more info: > http://www.fieldtriptoolbox.org/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables > > Good luck, > > Julian > > ******************** > *Dr. Julian Keil* > > AG Multisensorische Integration > Psychiatrische Universitätsklinik > der Charité im St. Hedwig-Krankenhaus > Große Hamburger Straße 5-11, Raum A007 > 10115 Berlin > > Telefon: +49-30-2311-1879 > Fax: +49-30-2311-2209 > > http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration > > Am 26.01.2016 um 00:25 schrieb Harold Cavendish: > > Dear FieldTrip users, > > I'm looking for the best method to analyse the relationship between ERP > and behavioural data but all I've been able to find so far are methods to > compare ERPs (or more generally time-series). > > Consider the following example: 20 participants performed a memory-related > task in which they had to respond based on the difference between the > target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 > samples at 200 Hz) and responses were recorded; ERPs were then created > based on epochs in which the responses were correct. Similarly, response > accuracy was averaged over all successful epochs per each subject. > > The resulting data are therefore: 20 participants x 50 channels x 1000 > samples (ERP) and 20 averages of accuracy (one value per participant). > > My objective is to identify which portion of the ERP data best explains > (or predicts) the changes in accuracy. In other words, in which time > interval is the most significant difference between people who do well in > the task and those who don't. > > So far I've been doing correlations between ERP at each time point and > overall accuracy, which is unreliable due to multiple comparisons > (correction methods are reportedly too conservative). Nevertheless, certain > channels show quite strong correlations in multiple time intervals. > > How would you approach this problem, please? > > Many thanks! > > Best regards, > Harold > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Thu Jan 28 13:37:38 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Thu, 28 Jan 2016 13:37:38 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: Message-ID: Dear Steve, thank you for your help, the references are greatly appreciated! Indeed, I'd like to extend the analysis to identifying parts where the correlation is significantly different; I am going to try this approach. Best regards, Harold 2016-01-26 12:08 GMT+01:00 Stephen Politzer-Ahles < stephen.politzer-ahles at ling-phil.ox.ac.uk>: > Hi Harold, > > If you're only interested in identifying which timepoints have the best > correlation, multiple comparisons aren't really an issue; if you're not > worried about testing for significance, then the place where you see the > highest estimate is the highest. See e.g., Hauk et al. 2006 in NeuroImage, > and Smith & Kutas 2015 in Psychophysiology, for similar analyses. > > If you're interested in finding a part of the waveform where the > correlation is significantly different from zero while also dealing with > multiple comparisons, you could use [spatio]temporal clustering (Maris & > Oostenveld 2007). Just make an event-related regression coefficient (as > described in Hauk et al.; just do a regression at each timepoint, and then > rather than plotting the ERP amplitude at each timepoint, plot the > regression estimate (*b*) at each timepoint, to derive a similar > waveform) and then test that waveform against 0 using temporal clustering. > > Best, > Steve > > > > > --- > Stephen Politzer-Ahles > University of Oxford > Language and Brain Lab > Faculty of Linguistics, Phonetics & Philology > http://users.ox.ac.uk/~cpgl0080/ > > > >> Message: 5 >> Date: Tue, 26 Jan 2016 00:25:13 +0100 >> From: Harold Cavendish >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] Fwd: Identify a window of best correlation >> between ERP and behavioural data >> Message-ID: >> < >> CALOTjvZXPNWHLefXrG6uss7uF3kkXie7qjiWqEcesOUqWay6qA at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Dear FieldTrip users, >> >> I'm looking for the best method to analyse the relationship between ERP >> and >> behavioural data but all I've been able to find so far are methods to >> compare ERPs (or more generally time-series). >> >> Consider the following example: 20 participants performed a memory-related >> task in which they had to respond based on the difference between the >> target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 >> samples at 200 Hz) and responses were recorded; ERPs were then created >> based on epochs in which the responses were correct. Similarly, response >> accuracy was averaged over all successful epochs per each subject. >> >> The resulting data are therefore: 20 participants x 50 channels x 1000 >> samples (ERP) and 20 averages of accuracy (one value per participant). >> >> My objective is to identify which portion of the ERP data best explains >> (or >> predicts) the changes in accuracy. In other words, in which time interval >> is the most significant difference between people who do well in the task >> and those who don't. >> >> So far I've been doing correlations between ERP at each time point and >> overall accuracy, which is unreliable due to multiple comparisons >> (correction methods are reportedly too conservative). Nevertheless, >> certain >> channels show quite strong correlations in multiple time intervals. >> >> How would you approach this problem, please? >> >> Many thanks! >> >> Best regards, >> Harold >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160126/b5769634/attachment-0001.html >> > >> >> ------------------------------ >> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Thu Jan 28 14:25:42 2016 From: julian.keil at gmail.com (Julian Keil) Date: Thu, 28 Jan 2016 14:25:42 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Message-ID: Dear Harold, as far as the warnings go, maybe someone closer to the development team can chime in here. I think you can safely ignore warnings 1 and 2. With respect to warning 3, you actually need to set cfg.correcttail = 'alpha'; to set the alpha from e.g. .05 to 0.025 for a two sided test. As for your output, mask is a binary mask corrected for multiple comparisons, i.e. values of 1 designate the significant elements. stat contains the actual t-values. Depending on the method you used, the output will vary. If you also paste your code and the output, it's a bit easier to explain. I suggest to look at some papers in which fieldtrip-stats have been reported to get an idea what is appropriate. I'll blatantly advertise my own work here: Keil, J., Müller, N., Hartmann, T., & Weisz, N. (2014). Prestimulus beta power and phase synchrony influence the sound-induced flash illusion. Cerebral Cortex, 24(5), 1278–1288. http://doi.org/10.1093/cercor/bhs409 Keil, J., Müller, N., Ihssen, N., & Weisz, N. (2012). On the variability of the McGurk effect: audiovisual integration depends on prestimulus brain states. Cerebral Cortex, 22(1), 221–231. http://doi.org/10.1093/cercor/bhr125 And an excellent tutorial by Joachim Gross et al.: Gross, J., Baillet, S., Barnes, G. R., Henson, R. N., Hillebrand, A., Jensen, O., et al. (2012). Good practice for conducting and reporting MEG research. NeuroImage, 1–15. http://doi.org/10.1016/j.neuroimage.2012.10.001 Good luck, Julian Am 28.01.2016 um 13:31 schrieb Harold Cavendish: > Dear Julian, > > thank you for your help, I believe I read the same page but I didn't realise it could be used with ft_timelockstatistics – the way certain ft_ functions fit others is still a bit unclear to me (it's practically my first contact with FT). Now, it appears to be exactly what I'm looking for. > > I took me some time to figure out how to import my already processed data (ERPs averaged per subject) into FieldTrip and run the test but it seems I've succeeded. However, ft_timelockstatistics(cfg, data) gave me the following warnings: > > 1. Warning: the data does not contain a trial definition > 2. Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous > recording > 3. Warning: doing a two-sided test without correcting p-values or alpha-level, p-values and alpha-level > will reflect one-sided tests per tail > > Should I be worried about these? (Here's the full output: https://gist.github.com/anonymous/1866a2b1a424dd9f0ac9) > > Finally, the resulting stat structure contains 10 fields but I'm not sure what mask, stat and ref represent. Is there any guidance on how to report the results like in the case of comparisons between conditions (http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test)? > > Many thanks! > Harold > > > 2016-01-26 6:35 GMT+01:00 Julian Keil : > Dear Harold, > > have you checked out ft_statfun_correlationT? > This sounds like the function you're looking for. Use cfg.statistic = 'ft_statfun_correlationT' in your call to ft_timelockstatistics. > Plus you can use all the correction methods available in FT. > See the FAQ for more info: http://www.fieldtriptoolbox.org/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables > > Good luck, > > Julian > > ******************** > Dr. Julian Keil > > AG Multisensorische Integration > Psychiatrische Universitätsklinik > der Charité im St. Hedwig-Krankenhaus > Große Hamburger Straße 5-11, Raum A007 > 10115 Berlin > > Telefon: +49-30-2311-1879 > Fax: +49-30-2311-2209 > http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration > > Am 26.01.2016 um 00:25 schrieb Harold Cavendish: > >> Dear FieldTrip users, >> >> I'm looking for the best method to analyse the relationship between ERP and behavioural data but all I've been able to find so far are methods to compare ERPs (or more generally time-series). >> >> Consider the following example: 20 participants performed a memory-related task in which they had to respond based on the difference between the target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 samples at 200 Hz) and responses were recorded; ERPs were then created based on epochs in which the responses were correct. Similarly, response accuracy was averaged over all successful epochs per each subject. >> >> The resulting data are therefore: 20 participants x 50 channels x 1000 samples (ERP) and 20 averages of accuracy (one value per participant). >> >> My objective is to identify which portion of the ERP data best explains (or predicts) the changes in accuracy. In other words, in which time interval is the most significant difference between people who do well in the task and those who don't. >> >> So far I've been doing correlations between ERP at each time point and overall accuracy, which is unreliable due to multiple comparisons (correction methods are reportedly too conservative). Nevertheless, certain channels show quite strong correlations in multiple time intervals. >> >> How would you approach this problem, please? >> >> Many thanks! >> >> Best regards, >> Harold >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From changa5 at mcmaster.ca Fri Jan 29 04:25:47 2016 From: changa5 at mcmaster.ca (Andrew Chang) Date: Thu, 28 Jan 2016 22:25:47 -0500 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) In-Reply-To: References: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Message-ID: Hi Harald, I did the ICA based on the continuos recorded block (~7 minutes), including 100 trials, with PCA option on. The attached file is the ICA topography and waveform (ICA 22). The spectrum showed that the peak power was at ~11Hz. I suspected it is a neck movement artifact, because the generator seems to be in the front of the neck. Also, I got another similar ICA component from another subject, and the topography seems to be centered at the back of the neck, would it be considered as neck movement too. Thank you very much once again! Best, Andrew On Mon, Jan 18, 2016 at 7:49 AM, Harald Bornfleth wrote: > Dear Andrew, > > > > A couple of questions popped up. > > 1) The neck movement artifact, is this something with low frequency, > or is it a muscle artifact? > > 2) Did you calculate the ICA on one data screen (e.g. 10 seconds or > 20 seconds), or over the whole data set? > > > > If you could send us screen shots showing the ICA wave forms and the > accompanying topographies, then we could comment on the classification. (In > BESA, you right-click on the label of a component and select “Map > topography” to show the topography map of that component.) > > I include my colleague and ICA expert Nicole Ille on CC. > > > > Best regards, > > Harald > > > > > > *From:* c.andrew123 at gmail.com [mailto:c.andrew123 at gmail.com] *On Behalf > Of *Andrew Chang > *Sent:* 17 January 2016 19:57 > *To:* Harald.Bornfleth at besa.de; FieldTrip discussion list < > fieldtrip at science.ru.nl> > *Subject:* Re: [FieldTrip] Comparing ICA methods between toolboxes (BESA > vs. Fieldtrip) > > > > Hi Dr. Bornfleth, > > > > Thanks for your reply very much. > > I would like to use ICA to remove eye blinks and eye movements, neck > movements, as well as cardiac and powerline artifacts. The segment I have > is a continuous EEG recording for 10 minutes, which is one block of my > experiment including many trials. > > Before ICA, the segment have been high-pass (0.3 Hz) and low-pass (100 > Hz). The components showing activities around the eyes, the back of the > neck, and 60 Hz were removed. As for the cardiac artifact, I it is based on > visual inspection on the waveform to see whether it looks like an EKG. > > Any further comments are appreciated! > > > > Best, > > Andrew > > > > On Fri, Jan 15, 2016 at 8:35 AM, Harald Bornfleth < > Harald.Bornfleth at besa.de> wrote: > > Dear Andrew, > > > > Thanks for bringing this up. I can try to shed some light on the ICA > method used in BESA Research; however, I can not comment on the > implementation in FieldTrip. > > > > The method behind ICA analysis in BESA Research is the extended infomax > ICA algorithm (Lee TW et al.: Independent component analysis using an > extended infomax algorithm for mixed sub-Gaussian and super-Gaussian > sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very > well suited to remove cardiac and powerline artifacts. Depending on the > data, it may also be used to remove ocular (blink) and electrode artifacts. > To assess whether your artifact removal is trustworthy more information > about your processing steps are needed. What types of artifacts are you > trying to correct? What segments are you using to determine the artifact > topographies and what segments are you finally correcting? > > > > Best regards, > > Harald > > > > > > *Dr. Harald Bornfleth* > > Product Manager BESA Research > > > > *BESA GmbH* > > Freihamer Strasse 18 > > 82166 Graefelfing/Germany > > http://www.besa.de > > > > E: Harald.Bornfleth at besa.de > > T: +49 89 8980 9968 > > > > > > HRB Munich 109956 > > CEO: Dr. Tobias Scherg, CFO: Theodor Scherg > > Director of Research: Dr. Michael Scherg > > > > > > > > > > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > mailto:fieldtrip-bounces at science.ru.nl ] *On > Behalf Of *Andrew Chang > *Sent:* Sonntag, 10. Januar 2016 21:18 > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. > Fieldtrip) > > > > Dear Fieldtrip users, > > > > I am wondering whether anyone has compared the performances of the ICA > methods among M/EEG toolboxes. Especially, how is the performance of ICA in > BESA Research 6.0, compared to Fieldtrip? > > I have an EEG data set which has been processed in BESA, including > removing artifact using ICA. I am wondering whether I can trust it, or > I should reprocess it in Fieldtrip. Any comments will be appreciated! > > > > Happy new year! > > > > Best, > > Andrew > > > > -- > > Andrew Chang > Ph.D. Candidate > Auditory Development Lab > > Department of Psychology, Neuroscience & Behaviour > McMaster University > > http://changa5.wordpress.com/ > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > > Andrew Chang > Ph.D. Candidate > Auditory Development Lab > > Department of Psychology, Neuroscience & Behaviour > McMaster University > > http://changa5.wordpress.com/ > -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 螢幕快照 2016-01-28 下午10.14.20.png Type: image/png Size: 694915 bytes Desc: not available URL: From labdipsco at unitn.it Fri Jan 29 12:28:02 2016 From: labdipsco at unitn.it (Laboratori_Didattici Rovereto) Date: Fri, 29 Jan 2016 12:28:02 +0100 Subject: [FieldTrip] Problem importing cfg structure from eeg lab Message-ID: Dear FieldTripers, we are new in the field of Frequency Analysis. We have some problem in importing data from eeglab into ft (we are using the eeglab2fieldtrip function). data=eeglab2fieldtrip(EEG,'preprocessing','none'); data.label=data.label'; data.trialinfo=repmat(condition,1,length(data.trial))'; After the import, we checked the data with ft_databroswer([],data) and we see all the trials and the channels. However our cfg contains only "version" and then when we run ft_freqanalysis the function works but is applied only to 1 trial. Do we make a mistake in the importing phase or in applying ft_freqanalysis?? Thanks a lot, Paolo and Simone -------------- next part -------------- An HTML attachment was scrubbed... URL: From Darren.Kadis at cchmc.org Fri Jan 29 18:46:34 2016 From: Darren.Kadis at cchmc.org (Kadis, Darren) Date: Fri, 29 Jan 2016 17:46:34 +0000 Subject: [FieldTrip] Post-doctoral research position in language MEG (Cincinnati OH) Message-ID: <927408BECA23304AA310FCEDD94A02651110E1C8@MCEXMB1.chmccorp.cchmc.org> Post Doc, Cincinnati, USA Post-doctoral research position in language MEG We invite applications for a post-doctoral research position in Neurology at Cincinnati Children's Hospital Medical Center (CCHMC). The successful applicant will contribute to ongoing MEG studies of pediatric language and epilepsy. This is a two-year position focused in one or more of the following areas: * Methods for multimodal neuroimaging, with a focus on integration of fMRI and MEG data * Source-space connectivity techniques, designed to overcome challenges related to leakage, impact of inverse solution, etc. * Validation of integrated imaging and analysis protocols for mapping language in children undergoing epilepsy surgery (MEG, fMRI, EEG, ECoG, stimulation mapping, pathology, and outcome data available) The post-doctoral fellow will regularly interact with clinical and research faculty, other post-docs, graduate students, and research staff in the Divisions of Neurology and Radiology, the Pediatric Neuroimaging Research Consortium (PNRC) and the Imaging Research Center (IRC). He/she is expected to contribute to our regular research discussions, and to present at research meetings within CCHMC and at major conferences (e.g., BIOMAG, OHBM). The successful candidate will have completed their PhD in biomedical or electrical engineering, physics, computer science, psychology, neuroscience, or a related discipline. He/she will have experience in collection and analysis of electrophysiological data, expertise in signal processing, with strong programming skills (MATLAB or a similar environment). The ideal candidate would also have prior experience in neuroimaging and a solid background in neuroanatomy, and familiarity with M/EEG analysis software (e.g., FieldTrip/SPM, Brainstorm, Brainwave, BESA, MNE). All qualified recent graduates, or those nearing completion of their PhD, are encouraged to apply. CCHMC is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, age, genetic information, physical or mental disability, military or veteran status, sexual orientation, or other protected status in accordance with applicable federal, state, and local laws and regulations. Applicants should submit a cover letter and current CV (including a list of scholarly publications), along with the names and contact information for three referees to: Darren S. Kadis, PhD Assistant Professor, Division of Neurology Pediatric Neuroimaging Research Consortium Cincinnati Children's Hospital Medical Center c/o Kimra Smith Kimra.Smith at cchmc.org Review of applications will begin immediately. We anticipate a start date in the spring, 2016. -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Sat Jan 30 22:24:22 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Sat, 30 Jan 2016 22:24:22 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Message-ID: Dear Julian, thank you for your help so far! I've read the papers and I'm starting to piece it all together. I've ran into some issues with FieldTrip (hence my delay) which are still persistent but I don't want to come here with every problem I encounter so I'm going to give it a couple more days on my own. My original question has been fully answered and the rest is another matter. Best wishes, Harold -------------- next part -------------- An HTML attachment was scrubbed... URL: From moessing at uni-muenster.de Fri Jan 1 16:20:53 2016 From: moessing at uni-muenster.de (=?utf-8?Q?Wanja_M=C3=B6ssing?=) Date: Fri, 1 Jan 2016 16:20:53 +0100 Subject: [FieldTrip] =?utf-8?q?Vacant_Postdoc_Position_in_Visual_Cognition?= =?utf-8?q?/Cognitive_Neuroscience_at_the_University_of_M=C3=BCnster=2C_Ge?= =?utf-8?q?rmany?= Message-ID: <20160101152051.CE178BF402@SECMAIL.UNI-MUENSTER.DE> Our lab at the Institute of Psychology/University of Muenster, Germany, is currently looking for a postdoctoral researcher (TVL13 Mitarbeiterstelle). The initial appointment is for 3 years (extension possible). In brief, the successful applicant will contribute to the group's research projects and teaching in the Bachelor in Psychology program. Research in the lab focuses on visual cognition and cognitive neuroscience. Our research topics include visual masking, scene perception, and the role of brain oscillations in perception, attention and visual memory. Our arsenal of research methods includes psychophysics, EEG, and eye tracking (fMRI, MEG, and brain stimulation are available at other institutions in Muenster). Applicants should have strong interest in our research topics and solid experience with any of these research methods. Most of the teaching at our institute is in German; thus, good command of German is also a requirement. Application deadline is January 31 2016; we would like to fill this position until April 1. The detailed job ad is available (only in German; see requirement above) here: http://www.uni-muenster.de/Rektorat/Stellen/ausschreibungen/st_20150412_sk19.html If you are potentially interested in this position, I would be glad to answer any informal questions about the position, research, or application requirements (niko.busch at uni-muenster.de). Furthermore, I would be grateful if you could pass this information on to potentially interested colleagues. -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Sun Jan 3 00:49:25 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Sun, 3 Jan 2016 01:49:25 +0200 Subject: [FieldTrip] Fieldtrip compatibility Message-ID: Dear Fieldtrip team, Hope you are well and in good health, I am a PhD student in Compiegne University, working on "source localization and connectivity study of the sources of uterine activity for the prediction of the preterm labor''. The uterine electrical activity, measured noninvasively on the woman's abdomen by means of surface electrodes is referred to as the electrohysterogram (EHG= uterine electromyogram). We have the meshes of the uterus layers segmented from MRI, and we have a database for real pregnancy and labor signal. My question is does Fieldtrip toolbox able to deal with my data? Best regards, Saeed Zahran -------------- next part -------------- An HTML attachment was scrubbed... URL: From senakahks at gmail.com Sun Jan 3 04:38:49 2016 From: senakahks at gmail.com (Senaka Amarakeerthi) Date: Sun, 3 Jan 2016 09:08:49 +0530 Subject: [FieldTrip] Ft_databrowser layout error Message-ID: I am trying to visualise data from databrowser. But I end up with following error message. reading layout from file horizontal.lay Attempted to access laysels(14); index out of bounds because numel(laysels)=13. Error in ft_databrowser>redraw_cb (line 1821) laysel = laysels(i); Error in ft_databrowser (line 725) redraw_cb(h); Error in main (line 29) fg = ft_databrowser(cfg,data); script: cfg = []; cfg.dataset = 'Thilina.edf'; cfg.trl = [4 10 0; 12 20 0; 18 20 0; 22 110 0]; cfg.continuous = 'yes'; cfg.channel = {'all', '-COUNTER', '-INTERPOLATED', '-RAW_CQ', '-GYROX', '-GYROY', '-MARKER', '-SYNC', '-TIME_STAMP_s', '-TIME_STAMP_ms', '-CQ_AF3', '-CQ_F7', '-CQ_F3', '-CQ_FC5', '-CQ_T7', '-CQ_P7', '-CQ_O1', '-CQ_O2', '-CQ_P8', '-CQ_T8', '-CQ_FC6', '-CQ_F4', '-CQ_F8', '-CQ_AF4', '-CQ_CMS', '-CQ_DRL'}; data = ft_preprocessing(cfg); cfg.viewmode = 'horizontal'; fg = ft_databrowser(cfg,data); horizontal.lay file: 1 -0.545830 1.170536 0.290000 0.230000 AF3 2 -0.659023 0.813825 0.290000 0.230000 F3 3 -1.299041 0.943808 0.290000 0.230000 F7 4 -1.173172 0.450338 0.290000 0.230000 FC5 5 -1.299041 -0.943808 0.290000 0.230000 P7 6 -1.605703 -0.000000 0.290000 0.230000 T7 7 -0.496189 -1.527114 0.290000 0.230000 O1 8 0.545830 1.170536 0.290000 0.230000 AF4 9 0.659023 0.813825 0.290000 0.230000 F4 10 1.299041 0.943808 0.290000 0.230000 F8 11 1.173172 0.450338 0.290000 0.230000 FC6 12 1.299041 -0.943808 0.290000 0.230000 P8 13 1.527114 -0.496189 0.290000 0.230000 TP8 14 0.496189 -1.527114 0.290000 0.230000 O2 Your support to get this error fixed is highly appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Sun Jan 3 20:20:12 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Sun, 3 Jan 2016 19:20:12 +0000 Subject: [FieldTrip] (no subject) Message-ID: Dear Fieldtrip team, I am currently working on data acquired from an elektra system (neuromag). I have done all the preprocessing and the ft_freqanalysis with the gradiometers only. I combined the gradiometers to create planar gradients.However , later when doing the statistics problems occur when i want to specify the channels. The error tells me that no degrees of freedom are found for the analysis. However, when i remove the cfg.channel form the script it runs through without an error. (please see code below). My question is whether the output of the stastistic is correct without specifying the channels? If not, does anybody have suggestions how to fix the problem? I have run into similar problems when wanting to plot the time frequency data from the planar gradients after having used ft_combineplanar. Here i cannot find a layout file that suits the output of ft_combineplanar. Thus, i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, however, the layouts provided by fieldtrip does not fit that number. Has anybody run into similar problems? Or does anybody know a possible solution? Thank you very much for any suggestions Victoria %combine planar cfg = []; cfg.method ='sum'; %ComCon = ft_combineplanar(cfg,FreqCon); ComIncon = ft_combineplanar(cfg, FreqIncon); cfg = []; %cfg.channel = {'MEG'}; cfg.latency = 'all'; cfg.frequency = [14.5 16]; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; cfg_neighb.method = 'distance'; cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); design = zeros(1,size(ComGrad_con.powspctrm,1) + size(ComGrad_incon.powspctrm,1)); design(1,1:size(ComGrad_con.powspctrm,1)) = 1; design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... size(ComGrad_incon.powspctrm,1))) = 2; -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Sun Jan 3 21:18:22 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 3 Jan 2016 21:18:22 +0100 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: Dear Victoria, the system you are working with is already equipped with two orthogonal planar gradiometer sensors. Thus you should not try to create planar gradients on the basis of the planar gradients. Yet you might want to use the magnetometers only. There you can represent the activity as if it was picked up by planar gradients. Could you please skip the planar transformation bit and redo your analysis? FieldTrip provides three types of layouts for the Neuromag system: NM306all.lay NM306mag.lay NM306grad.lay. For example if you want to plot magnetometers only you’d specify cfg.layout = 'neuromag306mag.lay’; cfg.channel = 'MEG*1’; Here MEG*1 refers to magnetometers and MEG*2 and MEG*3 would be the two orthogonal planar gradients respectively. Also the neighbours are provided as neuromag306cmb_neighb.mat; neuromag306mag_neighb.mat; neuromag306planar_neighb.mat;. You might consider loading the structure of your choice directly. Here is an example tutorial that might help: http://www.fieldtriptoolbox.org/tutorial/natmeg/timefrequency Good luck, tzvetan > Dear Fieldtrip team, > > I am currently working on data acquired from an elektra system (neuromag). I have done all the preprocessing and the ft_freqanalysis with the gradiometers only. I combined the gradiometers to create planar gradients.However , later when doing the statistics problems occur when i want to specify the channels. The error tells me that no degrees of freedom are found for the analysis. However, when i remove the cfg.channel form the script it runs through without an error. (please see code below). > My question is whether the output of the stastistic is correct without specifying the channels? If not, does anybody have suggestions how to fix the problem? > > I have run into similar problems when wanting to plot the time frequency data from the planar gradients after having used ft_combineplanar. Here i cannot find a layout file that suits the output of ft_combineplanar. Thus, i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, however, the layouts provided by fieldtrip does not fit that number. > Has anybody run into similar problems? Or does anybody know a possible solution? > > Thank you very much for any suggestions > Victoria > > %combine planar > cfg = []; > cfg.method ='sum'; > %ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > cfg = []; > %cfg.channel = {'MEG'}; > cfg.latency = 'all'; > cfg.frequency = [14.5 16]; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); > > design = zeros(1,size(ComGrad_con.powspctrm,1) + size(ComGrad_incon.powspctrm,1)); > design(1,1:size(ComGrad_con.powspctrm,1)) = 1; > design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... > size(ComGrad_incon.powspctrm,1))) = 2; > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From slama at berkeley.edu Mon Jan 4 02:22:43 2016 From: slama at berkeley.edu (Katarina Slama) Date: Sun, 3 Jan 2016 17:22:43 -0800 Subject: [FieldTrip] Inferential statistics on connectivity data? Message-ID: Dear Fieldtrip community, My name is Katarina Slama. I’m a graduate student in the Knight lab at UC Berkeley, and I use ECoG to study visual attention. I am currently examining connectivity in ECoG data using ft_connectivityanalysis (cfg and data structures below). I have computed partial coherence values for a network of electrodes. Now I would like to assess the statistical significance of each of the edges by computing a non-parametric equivalent of a one-sample t-test on the coherence values over trials. I have two questions: 1. Is there a way to obtain a separate partial coherence value for each trial? At present, the partial coherence structure that ft_connectivityanalysis creates has the dimord “chan_chan_freq”. 2. Is there a fieldtrip function that is designed for computing statistics on connectivity metrics? I have been advised to look into ft_freqstatistics, but this function does not seem to be designed for the output of ft_connectivityanalysis. — input structure (freq): label: {'34' '35' '36' '37' '38' '39' '44' '45' '47' '48' '49' '50' '51' '52' '53' '54' '55' '56' '57' '62' '63' '64' '76' '77' '80' '99' '100' '101'} dimord: 'rpttap_chan_freq' freq: [2.0000 3.0000 4.0000] fourierspctrm: [220x28x3 double] cumsumcnt: [220x1 double] cumtapcnt: [220x1 double] trialinfo: [220x1 double] cfg: [1x1 struct] configuration (cfg): cfg = []; cfg.method = 'coh'; cfg.partchannel = freq.label(1); cfg.keeptrials = 'yes'; partcoh = ft_connectivityanalysis(cfg,freq); output structure (partcoh) label: {27x1 cell} dimord: 'chan_chan_freq' cohspctrm: [27x27x3 double] freq: [2.0000 3.0000 4.0000] cfg: [1x1 struct] — Thank you and best wishes, Kata -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Jan 4 09:16:28 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 4 Jan 2016 09:16:28 +0100 Subject: [FieldTrip] Fieldtrip compatibility In-Reply-To: References: Message-ID: <5E6A3CD3-4736-4AD6-B815-78713B323FC6@donders.ru.nl> Dear Saeed, Happy New Year. FieldTrip can be used for channel level time series analysis and forward and inverse volume conduction modelling of ExG. The typical application (besides MEG, i.e. magnetic measurements of brain activity) is EEG, but we also use if for intracranial EEG and for EMG. I see no reason why EHG would not work. The way you have your data represented in files on disk might be different than what is common for EEG, but see here http://www.fieldtriptoolbox.org/dataformat. This should not be too hard to deal with. The more important difference might be in the assumptions on the sources that are required for the inverse modelling. In EHG I presume you will be interested in localizing the contractions of the uterus. That is muscle activity which propagates (i.e. changes spatially over time), which may have different characteristics than the activity that we model in the brain. Also this is something that can be dealt with, but it is not merely a technical detail and it requires careful consideration of the inverse model assumptions. I know that Ahmad Diab (who I suppose is a colleague of yours) used FieldTrip for his thesis https://tel.archives-ouvertes.fr/tel-01237525/document. I suggest you look at details there and consult Ahmad. best regards, Robert On 03 Jan 2016, at 00:49, saeed zahran wrote: > Dear Fieldtrip team, > > Hope you are well and in good health, > > I am a PhD student in Compiegne University, working on "source localization and connectivity study of the sources of uterine activity for the prediction of the preterm labor''. > > The uterine electrical activity, measured noninvasively on the woman's abdomen by means of surface electrodes is referred to as the electrohysterogram (EHG= uterine electromyogram). > > We have the meshes of the uterus layers segmented from MRI, and we have a database for real pregnancy and labor signal. My question is does Fieldtrip toolbox able to deal with my data? > > Best regards, > Saeed Zahran > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Mon Jan 4 10:27:31 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 4 Jan 2016 10:27:31 +0100 Subject: [FieldTrip] clarification on beam forming evoked fields in MEG In-Reply-To: <7E884835-8D6B-47E6-987E-7C174A828C07@gmail.com> References: <7E884835-8D6B-47E6-987E-7C174A828C07@gmail.com> Message-ID: Hi Russ, The units that are used by FieldTrip in data processing are not always consistent. The problem already starts at the level of reading (where we sometimes use our own FT code, and sometimes code from other projects). MEG data might be represented in T or fT, but for Eleka there are also gradiometers that have their data expressed as T/m or fT/cm or T/mm or … Then the anatomical MRi is read in, coregistered and used to construct a volume conduction model. In that volume conduction model there is again geometrical units (m, cm, mm) but also units of conductivity. You can imagine that combining data (in algorithms) that has different units will lead to unexpected results. Hence I usually play it safe and report on the results of computations as “arbitrary units”. Mostly in statistics and interpretation it does not matter anyway. If you use SI units throughout, then the low-level FieldTrip code will work as expected and also represent the output of all computations in SI units. For anatomical models you can use ft_convert_units to scale it to meters. For electrode and gradiometer arrays you should use the distance and amplitude option in ft_datatype_sens (see the code, it is not mentioned in the help) and for Elekta the scaling should be specified as ‘amplitude/distance’. The unit handling is a known issue and we have a number of ideas on http://bugzilla.fieldtriptoolbox.org to improve it, but to little resources to actually get it resolved. best regards, Robert PS Note that for spectral analysis it is again different, since spectral power or density can be differently normalized. Also in that aspect the FT code is not 100% consistent. But since you mention ERFs that does not apply. On 31 Dec 2015, at 22:51, russ port wrote: > Dear Robert and Jan-Mathijs > > I was hoping for someone to help me with a point of clarification concerning the fieldtrip wiki. I have followed Fieldtrip’s example of creating virtual sensor ERFs for MEG data using LMCV beamforming (e.g. http://www.fieldtriptoolbox.org/tutorial/aarhus/beamformingerf). I get great ERFs for auditory responses that I’m happy with. There is a point on contention left between my lab mates and I though. Following what was discuss previously (http://mailman.science.ru.nl/pipermail/fieldtrip/2015-September/009609.html), I think that the ERF are in a “unit-less” unit. They suggest however, that these (as mentioned in the wiki) are related to equivalent current dipoles for the chosen sources (and so the unit would be A/m [or since we used cm in the head model, A/cm]). Please can you help clear up this point of contention? > > Thanks > Russ -------------- next part -------------- An HTML attachment was scrubbed... URL: From marta.bortoletto at cognitiveneuroscience.it Mon Jan 4 14:33:44 2016 From: marta.bortoletto at cognitiveneuroscience.it (Marta Bortoletto) Date: Mon, 4 Jan 2016 13:33:44 +0000 (UTC) Subject: [FieldTrip] Applying wPLI to sLORETA-derived sources? References: <1782756321.10177641.1451914424709.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <1782756321.10177641.1451914424709.JavaMail.yahoo@mail.yahoo.com> Dear Community,I have resting-state data obtained by 70-channel EEGrecording. I have calculated EEG sources and obtained estimated signal in 88 Brodmannareas (BAs) by means of sLORETA. Now I would like to measure connectivitybetween these BAs. I have seen that many connectivity measures have beendeveloped in fieldtrip, including the weighted Phase Lag Index (wPLI). Giventhat wPLI estimates time-lagged interdependences, is it appropriate to apply wPLIto sLORETA estimated sources? Thank you for your help! Marta Marta Bortoletto, PhD Cognitive Neuroscience Section, IRCCS Centro San Giovanni di Dio Fatebenefratelli Via Pilastroni 4, 25125 Brescia, Italy Phone number: (+39) 0303501594 E-mail: marta.bortoletto at cognitiveneuroscience.it web: http://www.cognitiveneuroscience.it/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon Jan 4 17:02:49 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 4 Jan 2016 17:02:49 +0100 Subject: [FieldTrip] Applying wPLI to sLORETA-derived sources? In-Reply-To: <1782756321.10177641.1451914424709.JavaMail.yahoo@mail.yahoo.com> References: <1782756321.10177641.1451914424709.JavaMail.yahoo.ref@mail.yahoo.com> <1782756321.10177641.1451914424709.JavaMail.yahoo@mail.yahoo.com> Message-ID: <269EB91B-FE42-4B47-A470-8AD7A5C71EC0@uni-konstanz.de> Dear Marta, the applicability of connectivity metrics in FieldTrip (including wPLI) is independent of the inverse operator. So the answer is yes and no. It is appropriate if you have the single observations (i.e. epochs that you cut the data into) kept in the output of your source reconstruction analysis. I guess you have 88 source waveforms and not 88 x Ntrials time series. If this is correct wPLI or any phase metric is rather inappropriate. Good luck, tzvetan > Dear Community, > I have resting-state data obtained by 70-channel EEG recording. I have calculated EEG sources and obtained estimated signal in 88 Brodmann areas (BAs) by means of sLORETA. Now I would like to measure connectivity between these BAs. I have seen that many connectivity measures have been developed in fieldtrip, including the weighted Phase Lag Index (wPLI). Given that wPLI estimates time-lagged interdependences, is it appropriate to apply wPLI to sLORETA estimated sources? > > Thank you for your help! > > Marta > > Marta Bortoletto, PhD > Cognitive Neuroscience Section, > IRCCS Centro San Giovanni di Dio Fatebenefratelli > Via Pilastroni 4, 25125 Brescia, Italy > Phone number: (+39) 0303501594 > E-mail: marta.bortoletto at cognitiveneuroscience.it > web: http://www.cognitiveneuroscience.it/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tmadsen at emory.edu Mon Jan 4 21:29:55 2016 From: tmadsen at emory.edu (Teresa Madsen) Date: Mon, 4 Jan 2016 15:29:55 -0500 Subject: [FieldTrip] How are bugs triaged? Message-ID: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 -------------- next part -------------- An HTML attachment was scrubbed... URL: From slama at berkeley.edu Tue Jan 5 01:14:42 2016 From: slama at berkeley.edu (Katarina Slama) Date: Mon, 4 Jan 2016 16:14:42 -0800 Subject: [FieldTrip] How to interpret content of partial PLV-spectrum when dimensionality is inconsistent with dimord? Message-ID: Dear Fieldtrip community, Happy new year! I have a question about computing partial PLV-values using ft_connectivityanalysis: When I try to compute PLV-values, and request that one channel be partialized, the resulting PLV-spectrum has the dimensionality 27 x 27 x 28 x 3, while dimord reports it to be: chan_chan_freq. Why this inconsistency, and how should I interpret the contents of this PLV-spectrum? I provide information about my input and output structures below. — input structure (freq): label: {'34' '35' '36' '37' '38' '39' '44' '45' '47' '48' '49' '50' '51' '52' '53' '54' '55' '56' '57' '62' '63' '64' '76' '77' '80' '99' '100' '101'} dimord: 'rpttap_chan_freq' freq: [2.0000 3.0000 4.0000] fourierspctrm: [220x28x3 double] cumsumcnt: [220x1 double] cumtapcnt: [220x1 double] trialinfo: [220x1 double] cfg: [1x1 struct] configuration structure (cfg): method: 'plv' partchannel: {'34'} plv_struct = ft_connectivityanalysis(cfg,freq); output structure (plv_struct): label: {27x1 cell} dimord: 'chan_chan_freq' plvspctrm: [4-D double] freq: [2.0000 3.0000 4.0000] dof: 220 cfg: [1x1 struct] — Thank you very much for your help! Best, Kata -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jan 5 09:10:21 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 5 Jan 2016 08:10:21 +0000 Subject: [FieldTrip] How to interpret content of partial PLV-spectrum when dimensionality is inconsistent with dimord? In-Reply-To: References: Message-ID: <0AE94B5A-16C1-40C1-8FD3-4523B25FC6FF@fcdonders.ru.nl> Hi Katarina, Good question. Could be a bug. Could you file this on bugzilla.fieldtriptoolbox.org, and upload the necessary data so that we can try and reproduce it? Thanks and best, Jan-Mathijs On Jan 5, 2016, at 1:14 AM, Katarina Slama wrote: > Dear Fieldtrip community, > > Happy new year! > > I have a question about computing partial PLV-values using ft_connectivityanalysis: > > When I try to compute PLV-values, and request that one channel be partialized, the resulting PLV-spectrum has the dimensionality 27 x 27 x 28 x 3, while dimord reports it to be: chan_chan_freq. Why this inconsistency, and how should I interpret the contents of this PLV-spectrum? > > I provide information about my input and output structures below. > > — > input structure (freq): > label: {'34' '35' '36' '37' '38' '39' '44' '45' '47' '48' '49' '50' '51' '52' '53' '54' '55' '56' '57' '62' '63' '64' '76' '77' '80' '99' '100' '101'} > dimord: 'rpttap_chan_freq' > freq: [2.0000 3.0000 4.0000] > fourierspctrm: [220x28x3 double] > cumsumcnt: [220x1 double] > cumtapcnt: [220x1 double] > trialinfo: [220x1 double] > cfg: [1x1 struct] > > configuration structure (cfg): > method: 'plv' > partchannel: {'34'} > > plv_struct = ft_connectivityanalysis(cfg,freq); > > output structure (plv_struct): > label: {27x1 cell} > dimord: 'chan_chan_freq' > plvspctrm: [4-D double] > freq: [2.0000 3.0000 4.0000] > dof: 220 > cfg: [1x1 struct] > — > > Thank you very much for your help! > > Best, > Kata > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Tue Jan 5 09:27:18 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 5 Jan 2016 08:27:18 +0000 Subject: [FieldTrip] How are bugs triaged? In-Reply-To: References: Message-ID: Hi Teresa, Generally, we don’t have an ‘official’ triage system for the bugs that are filed. The speed with which a bug is considered/resolved depends on a combination of things: 1) the quality of the bug report. 2) the perceived urgency by the people who would be able to resolve it. 3) the estimated cost-benefit relationship for the people who would be able to resolve it. 4) the amount of other piled-up work for the people who would be able to resolve it. 5) the level of serotonin. 6) the prospect of compensation in kind (beer/chocolate/formal involvement in projects etc). Thus, in general, there may be things that the bug filer can do to increase the probability for consideration/resolution, including adding code snippets and data that allow for a reproduction of a genuine bug, or by including code snippets that implement a new feature. Note that in general feature requests that are not a priority for the daily scientific work of the development/fixing team will get a low priority. In addition it should be noted that anybody who is on the list is allowed to contribute fixes/patches/features, and that it is not the responsibility of the core development team (which nowadays extends far beyond the people at the Donders Centre). Also, it should be noted that nobody has a formal requirement to provide fieldtrip/bugzilla support, it’s all pro bono. This means that we have to squeeze it in besides our daily scientific work and additional chores. Anyway, the problem is that we are just short-handed, which indeed sometimes results in bugs already being ‘open’ for a long time. Our oldest one still open dates from 2010, so the 2013 you mention is not that bad :o). With regard to the NEX file reader error you mentioned, if you think your workaround might be of benefit of other users, don’t hesitate to contribute! Best wishes, Jan-Mathijs On Jan 4, 2016, at 9:29 PM, Teresa Madsen > wrote: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tmadsen at emory.edu Tue Jan 5 18:39:14 2016 From: tmadsen at emory.edu (Teresa Madsen) Date: Tue, 5 Jan 2016 12:39:14 -0500 Subject: [FieldTrip] How are bugs triaged? (Schoffelen, J.M. (Jan Mathijs)) Message-ID: Thanks for the insight, Jan-Mathijs. I'm not exactly sure how to contribute... I'm not familiar with SVN or GIT, and it would likely be small improvements that I would suggest, not whole new functions or anything. So could I just post the applicable snippets of code as a comment on the bug report? Will anyone see it there? When I update a previously posted bug, I see this message: Changes submitted for bug 2093 Email sent to:no oneExcluding:fieldtrip-bugs at donders.ru.nl, braingirl at gmail.com So I'm assuming no one knows. Is there a way to send it back to the bug listserv? Or should I really just learn how to use GIT (which seems more straightforward than SVN - is that true?)? ;-) Thanks again, Teresa ------------------------------ > > Message: 6 > Date: Tue, 5 Jan 2016 08:27:18 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] How are bugs triaged? > Message-ID: > Content-Type: text/plain; charset="windows-1252" > > Hi Teresa, > > Generally, we don?t have an ?official? triage system for the bugs that are > filed. The speed with which a bug is considered/resolved depends on a > combination of things: > > 1) the quality of the bug report. > 2) the perceived urgency by the people who would be able to resolve it. > 3) the estimated cost-benefit relationship for the people who would be > able to resolve it. > 4) the amount of other piled-up work for the people who would be able to > resolve it. > 5) the level of serotonin. > 6) the prospect of compensation in kind (beer/chocolate/formal involvement > in projects etc). > > Thus, in general, there may be things that the bug filer can do to > increase the probability for consideration/resolution, including adding > code snippets and data that allow for a reproduction of a genuine bug, or > by including code snippets that implement a new feature. Note that in > general feature requests that are not a priority for the daily scientific > work of the development/fixing team will get a low priority. > > In addition it should be noted that anybody who is on the list is allowed > to contribute fixes/patches/features, and that it is not the responsibility > of the core development team (which nowadays extends far beyond the people > at the Donders Centre). Also, it should be noted that nobody has a formal > requirement to provide fieldtrip/bugzilla support, it?s all pro bono. > This means that we have to squeeze it in besides our daily scientific work > and additional chores. > > Anyway, the problem is that we are just short-handed, which indeed > sometimes results in bugs already being ?open? for a long time. Our oldest > one still open dates from 2010, so the 2013 you mention is not that bad > :o). With regard to the NEX file reader error you mentioned, if you think > your workaround might be of benefit of other users, don?t hesitate to > contribute! > > Best wishes, > Jan-Mathijs > > > > > On Jan 4, 2016, at 9:29 PM, Teresa Madsen tmadsen at emory.edu>> wrote: > > I'm just curious because I've gotten such quick responses and fixes on > some bugs, while others sit around for long periods of time without any > feedback. Luckily, they're not anything stopping me from doing my work, > but I was just curious if they've been seen and determined to be of low > priority, or simply overlooked. > > Examples: > http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" > button on GUI for ft_rejectvisual (summary mode) plots average of all > trials instead of the single trial requested - first posted in October > http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file > reader errors - posted in 2013 - Obviously, I've worked around it, but it's > still there with a status of "new"! > > Hope I'm not being a pest. > Thanks, > Teresa > > -- > Teresa E. Madsen, PhD > Division of Behavioral Neuroscience and Psychiatric Disorders > Yerkes National Primate Research Center > Emory University > Rainnie Lab, NSB 5233 > 954 Gatewood Rd. NE > Atlanta, GA 30329 > (770) 296-9119 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160105/9b0ab1ac/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 4 > **************************************** > -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Jan 6 09:09:12 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 6 Jan 2016 08:09:12 +0000 Subject: [FieldTrip] How are bugs triaged? In-Reply-To: References: Message-ID: <9670C70F-D4E8-4445-865C-5B41FAF81D3E@fcdonders.ru.nl> Hi Teresa, Yes, one way of contributing would be to add snippets of code to the bug. In order to attract other people’s attention, you could add (judiciously) people to the CC-list of the bug. That way you ensure that these people receive an e-mail message once the bug is updated. Note, that people then can remove themselves again if they don’t like to be updated, which is a thing that needs to be respected. Note also, that adding a group e-mail address, such as fieldtrip-bugs at donders.ru.nl is likely less efficient than adding named persons, because members of the group may feel less inclined to be actively involved if addressed as a group, rather than as an individual. Best, Jan-Mathijs On Jan 5, 2016, at 6:39 PM, Teresa Madsen > wrote: Thanks for the insight, Jan-Mathijs. I'm not exactly sure how to contribute... I'm not familiar with SVN or GIT, and it would likely be small improvements that I would suggest, not whole new functions or anything. So could I just post the applicable snippets of code as a comment on the bug report? Will anyone see it there? When I update a previously posted bug, I see this message: Changes submitted for bug 2093 Email sent to: no one Excluding: fieldtrip-bugs at donders.ru.nl, braingirl at gmail.com So I'm assuming no one knows. Is there a way to send it back to the bug listserv? Or should I really just learn how to use GIT (which seems more straightforward than SVN - is that true?)? ;-) Thanks again, Teresa ------------------------------ Message: 6 Date: Tue, 5 Jan 2016 08:27:18 +0000 From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] How are bugs triaged? Message-ID: > Content-Type: text/plain; charset="windows-1252" Hi Teresa, Generally, we don?t have an ?official? triage system for the bugs that are filed. The speed with which a bug is considered/resolved depends on a combination of things: 1) the quality of the bug report. 2) the perceived urgency by the people who would be able to resolve it. 3) the estimated cost-benefit relationship for the people who would be able to resolve it. 4) the amount of other piled-up work for the people who would be able to resolve it. 5) the level of serotonin. 6) the prospect of compensation in kind (beer/chocolate/formal involvement in projects etc). Thus, in general, there may be things that the bug filer can do to increase the probability for consideration/resolution, including adding code snippets and data that allow for a reproduction of a genuine bug, or by including code snippets that implement a new feature. Note that in general feature requests that are not a priority for the daily scientific work of the development/fixing team will get a low priority. In addition it should be noted that anybody who is on the list is allowed to contribute fixes/patches/features, and that it is not the responsibility of the core development team (which nowadays extends far beyond the people at the Donders Centre). Also, it should be noted that nobody has a formal requirement to provide fieldtrip/bugzilla support, it?s all pro bono. This means that we have to squeeze it in besides our daily scientific work and additional chores. Anyway, the problem is that we are just short-handed, which indeed sometimes results in bugs already being ?open? for a long time. Our oldest one still open dates from 2010, so the 2013 you mention is not that bad :o). With regard to the NEX file reader error you mentioned, if you think your workaround might be of benefit of other users, don?t hesitate to contribute! Best wishes, Jan-Mathijs On Jan 4, 2016, at 9:29 PM, Teresa Madsen >> wrote: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 62, Issue 4 **************************************** -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jorn at artinis.com Wed Jan 6 09:28:16 2016 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 Jan 2016 09:28:16 +0100 Subject: [FieldTrip] How are bugs triaged? In-Reply-To: <9670C70F-D4E8-4445-865C-5B41FAF81D3E@fcdonders.ru.nl> References: <9670C70F-D4E8-4445-865C-5B41FAF81D3E@fcdonders.ru.nl> Message-ID: <001d01d1485c$3128bec0$937a3c40$@artinis.com> Hi Teresa, Adding to JM’s last mail, it might be important to note that every new bug is automatically sent out to fieldtrip-bugs at donders.ru.nl , so that the core dev team will get notified, so the dev team is aware of new bugs being posted. But as JM said, depending on subjective prioritization, it might get ignored anyhow. Best, Jörn -- Jörn M. Horschig, PhD, Software Engineer Artinis Medical Systems | +31 481 350 980 From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Schoffelen, J.M. (Jan Mathijs) Sent: Wednesday, January 6, 2016 9:09 To: FieldTrip discussion list Subject: Re: [FieldTrip] How are bugs triaged? Hi Teresa, Yes, one way of contributing would be to add snippets of code to the bug. In order to attract other people’s attention, you could add (judiciously) people to the CC-list of the bug. That way you ensure that these people receive an e-mail message once the bug is updated. Note, that people then can remove themselves again if they don’t like to be updated, which is a thing that needs to be respected. Note also, that adding a group e-mail address, such as fieldtrip-bugs at donders.ru.nl is likely less efficient than adding named persons, because members of the group may feel less inclined to be actively involved if addressed as a group, rather than as an individual. Best, Jan-Mathijs On Jan 5, 2016, at 6:39 PM, Teresa Madsen > wrote: Thanks for the insight, Jan-Mathijs. I'm not exactly sure how to contribute... I'm not familiar with SVN or GIT, and it would likely be small improvements that I would suggest, not whole new functions or anything. So could I just post the applicable snippets of code as a comment on the bug report? Will anyone see it there? When I update a previously posted bug, I see this message: Changes submitted for bug 2093 Email sent to: no one Excluding: fieldtrip-bugs at donders.ru.nl , braingirl at gmail.com So I'm assuming no one knows. Is there a way to send it back to the bug listserv? Or should I really just learn how to use GIT (which seems more straightforward than SVN - is that true?)? ;-) Thanks again, Teresa ------------------------------ Message: 6 Date: Tue, 5 Jan 2016 08:27:18 +0000 From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] How are bugs triaged? Message-ID: > Content-Type: text/plain; charset="windows-1252" Hi Teresa, Generally, we don?t have an ?official? triage system for the bugs that are filed. The speed with which a bug is considered/resolved depends on a combination of things: 1) the quality of the bug report. 2) the perceived urgency by the people who would be able to resolve it. 3) the estimated cost-benefit relationship for the people who would be able to resolve it. 4) the amount of other piled-up work for the people who would be able to resolve it. 5) the level of serotonin. 6) the prospect of compensation in kind (beer/chocolate/formal involvement in projects etc). Thus, in general, there may be things that the bug filer can do to increase the probability for consideration/resolution, including adding code snippets and data that allow for a reproduction of a genuine bug, or by including code snippets that implement a new feature. Note that in general feature requests that are not a priority for the daily scientific work of the development/fixing team will get a low priority. In addition it should be noted that anybody who is on the list is allowed to contribute fixes/patches/features, and that it is not the responsibility of the core development team (which nowadays extends far beyond the people at the Donders Centre). Also, it should be noted that nobody has a formal requirement to provide fieldtrip/bugzilla support, it?s all pro bono. This means that we have to squeeze it in besides our daily scientific work and additional chores. Anyway, the problem is that we are just short-handed, which indeed sometimes results in bugs already being ?open? for a long time. Our oldest one still open dates from 2010, so the 2013 you mention is not that bad :o). With regard to the NEX file reader error you mentioned, if you think your workaround might be of benefit of other users, don?t hesitate to contribute! Best wishes, Jan-Mathijs On Jan 4, 2016, at 9:29 PM, Teresa Madsen >> wrote: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 62, Issue 4 **************************************** -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Wed Jan 6 19:57:31 2016 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Wed, 6 Jan 2016 18:57:31 +0000 Subject: [FieldTrip] =?windows-1252?q?3rd_ESCAN_Porto_CONFERENCE_=96_EXTEN?= =?windows-1252?q?DED_SUBMISSION_DEADLINE_=96_22nd_January_2016?= Message-ID: <2BAB036A9BAEA44984A131DFCE446108010BFDAB11@SRVMBX01.fpceup.psi.up.pt> Dear colleagues, In order to allow for a full recovery from the holiday season the submission deadline for the 3rd International Conference of the European Society for Cognitive and Affective Neuroscience (ESCAN) in Porto has been extended to the 22nd of January, 2016. To submit your abstract for a symposium or oral/poster presentation and for all details on the conference please visit the website: www.escan2016.eu We would appreciate it if you could pass this information along to other colleagues and students. We are looking forward to seeing you in Porto in 2016! ESCAN 2016 Porto Local Organizing Committee -------------- next part -------------- An HTML attachment was scrubbed... URL: From mbj0310 at gmail.com Thu Jan 7 14:23:03 2016 From: mbj0310 at gmail.com (Beom Jun Min) Date: Thu, 7 Jan 2016 22:23:03 +0900 Subject: [FieldTrip] Using loreta2fieldtrip Message-ID: Dear community, I tried to load sLORETA data into the fieldtrip. My experiment is a kind of ERP experiment. And currently I have 5 subjects' data with 6 different conditions. With the related instructions ( http://www.fieldtriptoolbox.org/integrating_with/integrating_with_loreta), I made the volume structures of each condition (averaged over trials) for each subject (30 files). My converted volume structures have the following contents. dim [37,44,36] transform <44 double> inside <6239x1 double> outside <52369x1 double> {mom} <37x44x36 cell> cfg <1x1 struct> Is this structure is compatible with the up-to-date version of fieldtrip? It seems the ft_sourcegrandaverage function requires parameters such as pow, nai or coh. Best regards -- BeomJun Min, M.D. Department of Medical System Engineering (DMSE) Gwangju Institute of Science and Technology (GIST) 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 500-712, Republic of Korea (South) Phone: +82-62-715-3266 / Fax: +82-62-715-3244 E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Jan 7 17:58:09 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 7 Jan 2016 17:58:09 +0100 Subject: [FieldTrip] Job vacancies MRI/MEG physicists/engineers in Oldenburg References: <568E815B.7080205@uni-oldenburg.de> Message-ID: On 07 Jan 2016, at 16:16, Stefan Debener wrote: > The European Medical School is a cooperation project between the Universities of Oldenburg and Groningen and three local hospitals. > The newly founded Neuroimaging Center at the University of Oldenburg, Germany, offers the following two positions > > 1. MEG-Physicist/Engineer (E13/TV-L, initially 3 years) > > 2. MRI-Physicist/Engineer (E13/TV-L, initially 3 years) > > The positions are suitable for part-time work. > > The Neuroimaging Center hosts a state of the art magnetoencephalograph (ElektaTriux) and a magnetic resonance tomograph (Siemens Prisma 3T) and is embedded in an excellent interdisciplinary scientific environment with a strong research focus on neurosensory, neurocognitive, and medicalresearch. > > We seek for highly motivated post-doctoral candidates (with PhD) with an academic university degree in physics, engineering or related fields, with documented research experience in magnetoencephalography (position 1) or magnetic resonance imaging (position 2). For both positions, fluency in English is necessary. German and experience in the design of neurocognitive experiments are desirable. > > Successful candidates will be responsible for the operation and administration of the MEG system and MRI system respectively, their infrastructure, the development and improvement of measurement and analyses techniques and user consultancy. > > The University of Oldenburg is rapidly growing and offers a vibrant scientific environment with strong foci on cognitive and sensory neuroscience and a new medical school. Oldenburg is an attractive city in Germany's northwest with excellent quality of life. It is close to Bremen, Hamburg, Groningen, and approx. 1 h from the north sea. > > The University of Oldenburg is dedicated to increasing the percentage of women in science. Therefore, female candidates are particularly encouraged to apply and will be given preference in cases of equal qualification. Handicapped applicants will be given preference if equally qualified. > > Electronic applications (one pdf file) are preferred and can be send to: > Professor Dr. JochemRieger: Jochem.rieger at uni-oldenburg.de > Applications by mail should be sent to > Prof. Jochem Rieger > Universität Oldenburg > Kuepkersweg 74 (W30) > 26129 Oldenburg > Germany > > The application process is open until January 31st 2016. Applications should include your CV, a list of most recent publications, and a statement (max. 3 pages). > From RICHARDS at mailbox.sc.edu Fri Jan 8 18:15:01 2016 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Fri, 8 Jan 2016 17:15:01 +0000 Subject: [FieldTrip] Using loreta2fieldtrip (Beom Jun Min) Message-ID: <2215ED56-32F8-491B-9CD4-87B8D820A719@mailbox.sc.edu> Beom Jun Min: I am not sure of the exact answer, but…. Many of FT procedures require a pos (position) matrix, which is the s/c/a x/y/z positions of each dipole, and some other position information (e.g., mm; name of space; ft volume realign). This may not be necessary for a specific proc (ft_sourcegrandaverage) but is for other (ft_sourceinterpolate). pow can be calculated from mom, either with 3-dipole-moment or single-dipole-moment. Alternatively. I have been using the Nutmeg sLORETA procedure from the FT structures and data. If you have all your data in the FT format (head model, electrodes, lf), there is a routine that “almost” works to translate your FT LF to Nutmeg, and the sLORETA and dSPM routines from Nutmeg seem to work well. One advantage of FT/Nutmeg over LORETA or sLORETA packages is the FT is oriented to single participant head models. John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: richards-john at sc.edu HTTP: jerlab.psych.sc.edu *********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From zjyao at bu.edu Fri Jan 8 20:31:15 2016 From: zjyao at bu.edu (Zhaojie Yao) Date: Fri, 8 Jan 2016 14:31:15 -0500 Subject: [FieldTrip] Question about least-square FIR filter Message-ID: <247430E1-5A73-4DAD-8A8A-8FE5A8C430F3@bu.edu> Hi I am trying to process my data through Hilbert transform. I am used to the EEGLAB package, so I tried to use the same filter recommended by EEGLAB, which is least-square FIR filter in fieldtrip. However, I got a warning, when running the function ft_specest_hilbert, that least-square FIR 'is not recommended for neural signals, only proceed if you know what you are doing’. I am curious why least-square FIR is not appropriate for neural signals? Zhaojie Yao From tokimoto at mejiro.ac.jp Sun Jan 10 12:30:14 2016 From: tokimoto at mejiro.ac.jp (Shingo Tokimoto) Date: Sun, 10 Jan 2016 20:30:14 +0900 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB Message-ID: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> Dear Fieldtrip users, I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. -------------- EEGLAB error in function ft_checkconfig() at line 147: Error: ft_checkconfig (line 147) The field cfg.neighbours is required This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. ------------ I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. ************************************************ Shingo Tokimoto, Ph.D. in Linguistics and Psychology Department of Foreign Languages Mejiro University 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, 161-8539, Japan tokimoto at mejiro.ac.jp ************************************************ From tzvetan.popov at uni-konstanz.de Sun Jan 10 13:08:58 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 10 Jan 2016 13:08:58 +0100 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> Message-ID: Dear Shingo, You get this error because of a missing neighborhood structure with respect to your electrodes. Since you mention one electrode I suggest to specify cfg.neighbours = []. Thus you perform cluster based analysis over time and frequency within the electrode of your interest. Good luck Tzvetan > Am 10.01.2016 um 12:30 schrieb Shingo Tokimoto : > > Dear Fieldtrip users, > > I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. > > -------------- > EEGLAB error in function ft_checkconfig() at line 147: > > Error: ft_checkconfig (line 147) > The field cfg.neighbours is required > > This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. > ------------ > > I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. > > ************************************************ > Shingo Tokimoto, Ph.D. > in Linguistics and Psychology > Department of Foreign Languages > Mejiro University > 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, > 161-8539, Japan > tokimoto at mejiro.ac.jp > ************************************************ > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tokimoto at mejiro.ac.jp Sun Jan 10 16:27:30 2016 From: tokimoto at mejiro.ac.jp (Shingo Tokimoto) Date: Mon, 11 Jan 2016 00:27:30 +0900 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> Message-ID: <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> Dear Dr. Tzvetan Popov, Thank you very much for the quick reply. I edited "cfg.neighbours = neighbors;" in ft_prepare_neighbours.m to be "cfg.neighbours = [];." However, the same error message appears. I am sorry, but I am new to Fieldtrip. I am not sticking to one electrode. I want to specify the electrodes where their power are significantly different from those of the control condition in some specific time-windows and frequencies. The cluster-based analysis works well for ERP. Should I edit other m files? Thank you in advance again. ************************************************ Shingo Tokimoto, Ph.D. in Linguistics and Psychology Department of Foreign Languages Mejiro University 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, 161-8539, Japan tokimoto at mejiro.ac.jp ************************************************ On 2016/01/10, at 21:08, Tzvetan Popov wrote: > Dear Shingo, > You get this error because of a missing neighborhood structure with respect to your electrodes. Since you mention one electrode I suggest to specify cfg.neighbours = []. Thus you perform cluster based analysis over time and frequency within the electrode of your interest. > Good luck > Tzvetan > >> Am 10.01.2016 um 12:30 schrieb Shingo Tokimoto : >> >> Dear Fieldtrip users, >> >> I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. >> >> -------------- >> EEGLAB error in function ft_checkconfig() at line 147: >> >> Error: ft_checkconfig (line 147) >> The field cfg.neighbours is required >> >> This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. >> ------------ >> >> I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. >> >> ************************************************ >> Shingo Tokimoto, Ph.D. >> in Linguistics and Psychology >> Department of Foreign Languages >> Mejiro University >> 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, >> 161-8539, Japan >> tokimoto at mejiro.ac.jp >> ************************************************ >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From tzvetan.popov at uni-konstanz.de Sun Jan 10 17:08:19 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 10 Jan 2016 17:08:19 +0100 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> Message-ID: Dear Shingo, lets keep it by Tzvetan ;-). I’m not familiar with the way EEGLAB deals with FieldTrip functions at all. So I may not be of any further help. However as a rule of thumb you should almost never change settings in the FieldTrip functions but provide the appropriate configurations always as cfg.xxx. When you mention your analysis works for ERP I don’t see any reason why it fails with time-freq data. Obviously you have your electrode positions and you were able to generate neighborhood structure. If so the same should work for t-f too. Maybe if you provide the syntax of your analysis me or others can help you in getting it done. I will advise to undone any changes you made to the FieldTrip code and try again. Probably a fresh version of EEGLAB, clean math lab path etc. and then do it again. best tzvetan > Dear Dr. Tzvetan Popov, > > Thank you very much for the quick reply. I edited "cfg.neighbours = neighbors;" in ft_prepare_neighbours.m to be "cfg.neighbours = [];." However, the same error message appears. I am sorry, but I am new to Fieldtrip. I am not sticking to one electrode. I want to specify the electrodes where their power are significantly different from those of the control condition in some specific time-windows and frequencies. The cluster-based analysis works well for ERP. Should I edit other m files? Thank you in advance again. > > ************************************************ > Shingo Tokimoto, Ph.D. > in Linguistics and Psychology > Department of Foreign Languages > Mejiro University > 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, > 161-8539, Japan > tokimoto at mejiro.ac.jp > ************************************************ > > > On 2016/01/10, at 21:08, Tzvetan Popov wrote: > >> Dear Shingo, >> You get this error because of a missing neighborhood structure with respect to your electrodes. Since you mention one electrode I suggest to specify cfg.neighbours = []. Thus you perform cluster based analysis over time and frequency within the electrode of your interest. >> Good luck >> Tzvetan >> >>> Am 10.01.2016 um 12:30 schrieb Shingo Tokimoto : >>> >>> Dear Fieldtrip users, >>> >>> I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. >>> >>> -------------- >>> EEGLAB error in function ft_checkconfig() at line 147: >>> >>> Error: ft_checkconfig (line 147) >>> The field cfg.neighbours is required >>> >>> This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. >>> ------------ >>> >>> I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. >>> >>> ************************************************ >>> Shingo Tokimoto, Ph.D. >>> in Linguistics and Psychology >>> Department of Foreign Languages >>> Mejiro University >>> 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, >>> 161-8539, Japan >>> tokimoto at mejiro.ac.jp >>> ************************************************ >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From changa5 at mcmaster.ca Sun Jan 10 21:17:40 2016 From: changa5 at mcmaster.ca (Andrew Chang) Date: Sun, 10 Jan 2016 15:17:40 -0500 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Message-ID: Dear Fieldtrip users, I am wondering whether anyone has compared the performances of the ICA methods among M/EEG toolboxes. Especially, how is the performance of ICA in BESA Research 6.0, compared to Fieldtrip? I have an EEG data set which has been processed in BESA, including removing artifact using ICA. I am wondering whether I can trust it, or I should reprocess it in Fieldtrip. Any comments will be appreciated! Happy new year! Best, Andrew -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From leilayou_54 at yahoo.com Mon Jan 11 11:50:01 2016 From: leilayou_54 at yahoo.com (Leila Ayoubian) Date: Mon, 11 Jan 2016 10:50:01 +0000 (UTC) Subject: [FieldTrip] loading data in GUI References: <253366430.2575220.1452509401650.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <253366430.2575220.1452509401650.JavaMail.yahoo@mail.yahoo.com> Good morning everyone: I am new to fieldtrip am having trouble loading EEG data in a GUI . While there is no trouble loading the same file in a script , when the same file is being loaded inside a simple GUI , Matlab hangs, and I have to press ctrl C to exit! I am really puzzled! I understand it could be the GUI issue and not fieldtrip function issue.I thought if someone have come across this problem can save me time. I attached the two codes to compare. This is the script that works ************************************ clear all; clc; close all; [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename) cfg1 = []; cfg1.trl = [1 61440 0]; cfg1.dataset = filename%'K_S_Event_Marker_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1);  display('Finished') ***************************** Here is the GUI code, which does not work function varargout = loadDataGUI(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @loadDataGUI_OpeningFcn, ...                    'gui_OutputFcn',  @loadDataGUI_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before loadDataGUI is made visible. function loadDataGUI_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to loadDataGUI (see VARARGIN) % Choose default command line output for loadDataGUI handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes loadDataGUI wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = loadDataGUI_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in loadData. function loadData_Callback(hObject, eventdata, handles) % hObject    handle to loadData (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %Load the EEG file if isempty(handles)     disp('ERROR:::Please select a valid Montage'); end [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename) cfg1 = []; % beginSample=1; %The indice of sample to begin % endSample=61440; %The indice of sample to end (1 min data to load, 60*1024=61440) % cfg1.trl = [1 61440 0]; cfg1.dataset = filename%'K_S_Event_Marker_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1); %set(handles.filePath,'string',file ); function filePath_Callback(hObject, eventdata, handles) % hObject    handle to filePath (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of filePath as text %        str2double(get(hObject,'String')) returns contents of filePath as a double % global handles; % display(handles.file)  set(handles.filePath,'string',handles.file ); ************************************************************* __________________________________________________ Leila Ayoubian, PhD. Institute of Psychiatry, Psychology and Neuroscience King's College London -------------- next part -------------- An HTML attachment was scrubbed... URL: From leilayou_54 at yahoo.com Mon Jan 11 16:19:25 2016 From: leilayou_54 at yahoo.com (Leila Ayoubian) Date: Mon, 11 Jan 2016 15:19:25 +0000 (UTC) Subject: [FieldTrip] GUi issue with ft_preprocessing References: <1162479313.2666505.1452525565497.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <1162479313.2666505.1452525565497.JavaMail.yahoo@mail.yahoo.com> Why Data do not load in GUI, but it loads in a script using fieldtrip ft-preprocessing function?  Look a the two code below. One which is a script work perfectly fine.The other one is inside a simple gui and Matlab crashes.....Can anyone enlighten me?! Thanks in advance function varargout = trial5(varargin) % TRIAL5 MATLAB code for trial5.fig %      TRIAL5, by itself, creates a new TRIAL5 or raises the existing %      singleton*. % %      H = TRIAL5 returns the handle to a new TRIAL5 or the handle to %      the existing singleton*. % %      TRIAL5('CALLBACK',hObject,eventData,handles,...) calls the local %      function named CALLBACK in TRIAL5.M with the given input arguments. % %      TRIAL5('Property','Value',...) creates a new TRIAL5 or raises the %      existing singleton*.  Starting from the left, property value pairs are %      applied to the GUI before trial5_OpeningFcn gets called.  An %      unrecognized property name or invalid value makes property application %      stop.  All inputs are passed to trial5_OpeningFcn via varargin. % %      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one %      instance to run (singleton)". % % See also: GUIDE, GUIDATA, GUIHANDLES % Edit the above text to modify the response to help trial5 % Last Modified by GUIDE v2.5 11-Jan-2016 13:20:07 % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @trial5_OpeningFcn, ...                    'gui_OutputFcn',  @trial5_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before trial5 is made visible. function trial5_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to trial5 (see VARARGIN) % Choose default command line output for trial5 handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes trial5 wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = trial5_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in pushbutton1. function pushbutton1_Callback(hObject, eventdata, handles) % hObject    handle to pushbutton1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %file = fullfile(pathname, filename) cfg1 = []; cfg1.trl = [1 61440 0]; cfg1.dataset = 'Event06_Interictal_Background_Sleep_Segment_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1); function edit1_Callback(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit1 as text %        str2double(get(hObject,'String')) returns contents of edit1 as a double % --- Executes during object creation, after setting all properties. function edit1_CreateFcn(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. %       See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))     set(hObject,'BackgroundColor','white'); end *************************************************************************** function varargout = trial5(varargin) % TRIAL5 MATLAB code for trial5.fig %      TRIAL5, by itself, creates a new TRIAL5 or raises the existing %      singleton*. % %      H = TRIAL5 returns the handle to a new TRIAL5 or the handle to %      the existing singleton*. % %      TRIAL5('CALLBACK',hObject,eventData,handles,...) calls the local %      function named CALLBACK in TRIAL5.M with the given input arguments. % %      TRIAL5('Property','Value',...) creates a new TRIAL5 or raises the %      existing singleton*.  Starting from the left, property value pairs are %      applied to the GUI before trial5_OpeningFcn gets called.  An %      unrecognized property name or invalid value makes property application %      stop.  All inputs are passed to trial5_OpeningFcn via varargin. % %      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one %      instance to run (singleton)". % % See also: GUIDE, GUIDATA, GUIHANDLES % Edit the above text to modify the response to help trial5 % Last Modified by GUIDE v2.5 11-Jan-2016 13:20:07 % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @trial5_OpeningFcn, ...                    'gui_OutputFcn',  @trial5_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before trial5 is made visible. function trial5_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to trial5 (see VARARGIN) % Choose default command line output for trial5 handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes trial5 wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = trial5_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in pushbutton1. function pushbutton1_Callback(hObject, eventdata, handles) % hObject    handle to pushbutton1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %file = fullfile(pathname, filename) cfg1 = []; cfg1.trl = [1 61440 0]; cfg1.dataset = 'Event06_Interictal_Background_Sleep_Segment_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1); function edit1_Callback(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit1 as text %        str2double(get(hObject,'String')) returns contents of edit1 as a double % --- Executes during object creation, after setting all properties. function edit1_CreateFcn(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. %       See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))     set(hObject,'BackgroundColor','white'); end -------------- next part -------------- An HTML attachment was scrubbed... URL: From widmann at uni-leipzig.de Mon Jan 11 17:42:07 2016 From: widmann at uni-leipzig.de (Andreas Widmann) Date: Mon, 11 Jan 2016 17:42:07 +0100 Subject: [FieldTrip] Question about least-square FIR filter In-Reply-To: <247430E1-5A73-4DAD-8A8A-8FE5A8C430F3@bu.edu> References: <247430E1-5A73-4DAD-8A8A-8FE5A8C430F3@bu.edu> Message-ID: <9BABEA1A-A464-41E0-BBA2-5ABE35D540DB@uni-leipzig.de> Hi, > I am trying to process my data through Hilbert transform. I am used to the EEGLAB package, so I tried to use the same filter recommended by EEGLAB, which is least-square FIR filter in fieldtrip. However, I got a warning, when running the function ft_specest_hilbert, that least-square FIR 'is not recommended for neural signals, only proceed if you know what you are doing’. I am curious why least-square FIR is not appropriate for neural signals? Short version: See http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2453 Point (3) and first attachment (png). Long version: firls filters are also NOT recommended in EEGLAB. Where did you get this information? The EEGLAB firls filter are marked legacy/deprecated since 2012. See http://journal.frontiersin.org/article/10.3389/fpsyg.2012.00233/full for a more detailed description of the problem, in particular footnote 1. Filter roll-off/transition width is a function of the filter order. However, with MATLAB firls filters roll-off/transition width is defined independently from filter order. This might work if the selected parameters for both are appropriate, however, commonly it does not work resulting in various artifacts in the filter’s frequency and/or time domain responses, bad attenuation, non-unity DC gain etc. In Fieldtrip the problem was/is particularly problematic as a zero transition width (rectangular frequency response) filter is requested combined with an incorrect estimation of required filter order (actually infinite). Hope this helps! Best, Andreas From leilayou_54 at yahoo.com Tue Jan 12 11:42:27 2016 From: leilayou_54 at yahoo.com (Leila Ayoubian) Date: Tue, 12 Jan 2016 10:42:27 +0000 (UTC) Subject: [FieldTrip] importing large edf data In-Reply-To: References: Message-ID: <2128658446.3021319.1452595347079.JavaMail.yahoo@mail.yahoo.com>  Hi Steve:Happy new year. Following the code you sent me to import large  EDF data sets, I designed a simple GUI to select data and display the path.I simplified the GUI for convenience so you can have a look at it. When I run this GUI Matlab crashes, meaning it will be busy until I quite the execution by pressing ctrl C. The same code on a script is absolutely fine! I am really puzzled and not underestanding why this is happening. Could it be a bug of ft_preprocessing function? I have copied both files beow. Can you please have a look. I have been hanging around for couple days wondering and not getting to any conclusion. I appreciate if you can enlighten me.Thanks ******** THE GUI CODE***************** function varargout = loadDataGUI(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @loadDataGUI_OpeningFcn, ...                    'gui_OutputFcn',  @loadDataGUI_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before loadDataGUI is made visible. function loadDataGUI_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to loadDataGUI (see VARARGIN) % Choose default command line output for loadDataGUI handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes loadDataGUI wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = loadDataGUI_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in loadData. function loadData_Callback(hObject, eventdata, handles) % hObject    handle to loadData (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %Load the EEG file if isempty(handles)     disp('ERROR:::Please select a valid Montage'); end [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename)  cfg = [];  cfg.trl = [1 61440 0];  cfg.dataset = filename%'K_S_Event_Marker_1.edf';  cfg= ft_definetrial( cfg );  cfg.continuous = 'yes'; data = ft_preprocessing(cfg); % [hdr, record] = edfread(file); set(handles.filePath,'string',file ); function filePath_Callback(hObject, eventdata, handles) % hObject    handle to filePath (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of filePath as text %        str2double(get(hObject,'String')) returns contents of filePath as a double % global handles; % display(handles.file)  set(handles.filePath,'string',handles.file ); *************** THE SCRIPT************ clear all; clc; close all; %% [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename) %% cfg1 = []; cfg1.trl = [1 61440 0]; %cfg1.dataset = filename%'K_S_Event_Marker_1.edf'; cfg1.dataset = 'Event06_Interictal_Background_Sleep_Segment_1.edf' cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes'; data1 = ft_preprocessing(cfg1); %% %[hdr, record] = edfread(file); %%  display('Finished') __________________________________________________ Leila Ayoubian, PhD. Institute of Psychiatry, Psychology and Neuroscience King's College London From: Stephen Politzer-Ahles To: fieldtrip at science.ru.nl Sent: Saturday, December 19, 2015 2:06 PM Subject: Re: [FieldTrip] importing large edf data Hi Leila, I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me: cfg = []; cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf'; cfg.trl = [1 500 0]; cfg.continuous = 'yes'; data_500samples = ft_preprocessing(cfg); cfg = []; cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf'; cfg.trl = [1 1000 0]; cfg.continuous = 'yes'; data_1000samples = ft_preprocessing(cfg); Here's the output: >> data_500samples data_500samples =            hdr: [1x1 struct]          label: {37x1 cell}           time: {[1x500 double]}          trial: {[37x500 double]}        fsample: 200     sampleinfo: [1 500]            cfg: [1x1 struct] >> data_1000samples data_1000samples =            hdr: [1x1 struct]          label: {37x1 cell}           time: {[1x1000 double]}          trial: {[37x1000 double]}        fsample: 200     sampleinfo: [1 1000]            cfg: [1x1 struct] Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/  ------------------------------ Message: 5 Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC) From: Leila Ayoubian To: FieldTrip discussion list Subject: Re: [FieldTrip] importing large edf data Message-ID:         <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com> Content-Type: text/plain; charset="utf-8" ?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same! So this is what I get: ?? hdr: [1x1 struct] ???????? label: {51x1 cell} ????????? time: {1x50710 cell} ???????? trial: {1x50710 cell} ?????? fsample: 1024 ??? sampleinfo: [50710x2 double] ?????????? cfg: [1x1 struct] so the actual data which is in data.trial? is this in both cases! size(data.trial) ans = ?????????? 1?????? 50710 How could that happen if you are segmenting it in two different chunks? Best regards ___________________________________________________ Leila Ayoubian       From: Stephen Politzer-Ahles  To: fieldtrip at science.ru.nl  Sent: Friday, December 18, 2015 12:37 PM  Subject: Re: [FieldTrip] importing large edf data Hello Leila, I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size. If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add: cfg.trl = [1 1000 0]; and then use ft_preprocessing. By way of example, here is code that reads in raw data as a series of 1-second "trials": cfg = []; cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr'; cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters cfg.trialdef.ntrials = Inf; cfg = ft_definetrial( cfg ); cfg.continuous = 'yes'; data = ft_preprocessing(cfg); After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details). Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/ On Fri, Dec 18, 2015 at 11:00 AM, wrote: Send fieldtrip mailing list submissions to ? ? ? ? fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit ? ? ? ? http://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to ? ? ? ? fieldtrip-request at science.ru.nl You can reach the person managing the list at ? ? ? ? fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: ? ?1. importing large edf data (Leila Ayoubian) ---------------------------------------------------------------------- Message: 1 Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC) From: Leila Ayoubian To: "fieldtrip at science.ru.nl" Subject: [FieldTrip] importing large edf data Message-ID: ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com> Content-Type: text/plain; charset="utf-8" Hi:Thanks for providing us with this amazing toolbox. I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.? So trying to load the data like this: cfg.dataset= ('mydata.edf'); rawdata=ft_preprocessing(cfg); This is the error message I get : %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Error using zeros Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information. Error in read_edf (line 403) ? dat = zeros(length(chanindx),nepochs*epochlength); Error in ft_read_data (line 622) ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx); Error in ft_preprocessing (line 566) ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat); Error in ReadFedfiles (line 8) rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf' ?hdr?? = ft_read_header(filename); ?sample.start=1 ?sample.end=100 dat = ft_read_data(filename,'sample.start','1','sample.end','100') and here is again the error message: Error using zeros Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information. Error in read_edf (line 403) ? dat = zeros(length(chanindx),nepochs*epochlength); Error in ft_read_data (line 622) ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx); Error in ReadFedfiles (line 31) dat = ft_read_data(filename,'sample.start','1','sample.end','100') ? >> Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful. Thanks again for your support and assistance. We appreciate your effort. Kind regards ___________________________________________________ Dr. Leila Ayoubian -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lorenzomagazzini at gmail.com Tue Jan 12 15:46:44 2016 From: lorenzomagazzini at gmail.com (Lorenzo Magazzini) Date: Tue, 12 Jan 2016 14:46:44 +0000 Subject: [FieldTrip] Help understanding the lcmv beamformer output Message-ID: Hi, I hope someone can help me to understand the use of the lcmv beamformer, because either I am using it incorrectly, or I misunderstood the meaning of its output. I am trying to get source-level power estimates of 'baseline' and 'active' time-windows. I first compute a common filter, and then apply it separately to the two conditions. I thought the power estimates would be stored, voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. However, the values I get in the '.pow' field for the analysis of 'baseline' and 'active' windows are identical. Furthermore, the '.pow' values are identical to the '.noise' values when using cfg.projectnoise = 'yes';. I have checked if the sensor-level data that passed on to ft_sourceanalysis is different between baseline and active - it is. Also, if I do the following... 1. reconstruct virtual sensors by applying the common filter separately to baseline and active, 2. average the single-trial (virtual sensor) power estimates, 3. replace the '.pow' value for each voxel, ...then the contrast between baseline and active is correct. Can anyone please help me figure out what I'm doing wrong here? Below I copied part of the code. Many thanks in advance! Lorenzo %compute the leadfield cfg = []; cfg.channel = {'MEG'}; cfg.grid = sourcemodel; cfg.vol = hdm; cfg.grad = grad; cfg.normalize = 'yes'; leadfield = ft_prepare_leadfield(cfg); %compute covariance matrix cfg = []; cfg.channel = {'MEG'}; cfg.removemean = 'no'; cfg.covariance = 'yes'; cfg.covariancewindow = [-1.5 1.5]; tlck = ft_timelockanalysis(cfg, data); %get the common spatial filter cfg = []; cfg.method = 'lcmv'; cfg.grid = leadfield; cfg.vol = hdm; cfg.grad = grad; cfg.lcmv.fixedori = 'yes'; cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.projectnoise = 'yes'; cfg.lcmv.lambda = '5%'; src = ft_sourceanalysis(cfg, tlck); %store the filter wts = src.avg.filter; %separate baseline and active windows of bandpass-filtered data cfg = []; cfg.toilim = [-1.5 -0.3]; data_bsln = ft_redefinetrial(cfg, data); cfg = []; cfg.toilim = [0.3 1.5]; data_actv = ft_redefinetrial(cfg, data); %timelock analysis of baseline and active cfg = []; cfg.channel = {'MEG'}; cfg.keeptrials = 'yes'; tlck_bsln = ft_timelockanalysis(cfg, data_bsln); tlck_actv = ft_timelockanalysis(cfg, data_actv); %get source-power estimates of bsln and actv separately using the pre-computed common filter (wts) cfg = []; cfg.method = 'lcmv'; cfg.vol = hdm; cfg.grid = leadfield; cfg.grid.filter = wts; % cfg.keepfilter = 'no'; cfg.lcmv.fixedori = 'yes'; cfg.projectnoise = 'yes'; cfg.lambda = '5%'; cfg.keeptrials = 'yes'; src_bsln = ft_sourceanalysis(cfg, tlck_bsln); src_actv = ft_sourceanalysis(cfg, tlck_actv); -------------- next part -------------- An HTML attachment was scrubbed... URL: From ervin.poljac at donders.ru.nl Tue Jan 12 16:32:52 2016 From: ervin.poljac at donders.ru.nl (Poljac, E. (Ervin)) Date: Tue, 12 Jan 2016 15:32:52 +0000 Subject: [FieldTrip] Help understanding the lcmv beamformer output In-Reply-To: References: Message-ID: Hi Marjolein, Even een snelle vraag, wat is de risingedge(mask)? Groetjes, Ervin -- Ervin Poljac, PhD Donders Institute for Brain, Cognition and Behaviour Centre for Cognition (DCC) Radboud University Nijmegen Room B.00.78A Montessorilaan 3 6500 HE Nijmegen T. 024 36 15457 ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Lorenzo Magazzini [lorenzomagazzini at gmail.com] Sent: Tuesday, January 12, 2016 3:46 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Help understanding the lcmv beamformer output Hi, I hope someone can help me to understand the use of the lcmv beamformer, because either I am using it incorrectly, or I misunderstood the meaning of its output. I am trying to get source-level power estimates of 'baseline' and 'active' time-windows. I first compute a common filter, and then apply it separately to the two conditions. I thought the power estimates would be stored, voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. However, the values I get in the '.pow' field for the analysis of 'baseline' and 'active' windows are identical. Furthermore, the '.pow' values are identical to the '.noise' values when using cfg.projectnoise = 'yes';. I have checked if the sensor-level data that passed on to ft_sourceanalysis is different between baseline and active - it is. Also, if I do the following... 1. reconstruct virtual sensors by applying the common filter separately to baseline and active, 2. average the single-trial (virtual sensor) power estimates, 3. replace the '.pow' value for each voxel, ...then the contrast between baseline and active is correct. Can anyone please help me figure out what I'm doing wrong here? Below I copied part of the code. Many thanks in advance! Lorenzo %compute the leadfield cfg = []; cfg.channel = {'MEG'}; cfg.grid = sourcemodel; cfg.vol = hdm; cfg.grad = grad; cfg.normalize = 'yes'; leadfield = ft_prepare_leadfield(cfg); %compute covariance matrix cfg = []; cfg.channel = {'MEG'}; cfg.removemean = 'no'; cfg.covariance = 'yes'; cfg.covariancewindow = [-1.5 1.5]; tlck = ft_timelockanalysis(cfg, data); %get the common spatial filter cfg = []; cfg.method = 'lcmv'; cfg.grid = leadfield; cfg.vol = hdm; cfg.grad = grad; cfg.lcmv.fixedori = 'yes'; cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.projectnoise = 'yes'; cfg.lcmv.lambda = '5%'; src = ft_sourceanalysis(cfg, tlck); %store the filter wts = src.avg.filter; %separate baseline and active windows of bandpass-filtered data cfg = []; cfg.toilim = [-1.5 -0.3]; data_bsln = ft_redefinetrial(cfg, data); cfg = []; cfg.toilim = [0.3 1.5]; data_actv = ft_redefinetrial(cfg, data); %timelock analysis of baseline and active cfg = []; cfg.channel = {'MEG'}; cfg.keeptrials = 'yes'; tlck_bsln = ft_timelockanalysis(cfg, data_bsln); tlck_actv = ft_timelockanalysis(cfg, data_actv); %get source-power estimates of bsln and actv separately using the pre-computed common filter (wts) cfg = []; cfg.method = 'lcmv'; cfg.vol = hdm; cfg.grid = leadfield; cfg.grid.filter = wts; % cfg.keepfilter = 'no'; cfg.lcmv.fixedori = 'yes'; cfg.projectnoise = 'yes'; cfg.lambda = '5%'; cfg.keeptrials = 'yes'; src_bsln = ft_sourceanalysis(cfg, tlck_bsln); src_actv = ft_sourceanalysis(cfg, tlck_actv); -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Wed Jan 13 16:23:22 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Wed, 13 Jan 2016 17:23:22 +0200 Subject: [FieldTrip] Fieldtrip compatibility In-Reply-To: References: Message-ID: Dear Robert, Thank you to put in our problem from the first question, yes we want to localize the contractions of the uterus, and thank you to provide me with the careful consideration of the inverse model assumptions for this case. I have looked at http://www.fieldtriptoolbox.org/dataformat, but the data what I have is: 1- a real signal generated from 16 electrodes saved as ".mat", 2- the meshes as ".off"( I seperated the points and faces and I saved each one on ".mat") it is already segmented, and 3- the simulated potential (99084x201) given from our team who works on the model and I want to convert it to in the form of signal collected from the 16 electrode (16x201). The algorithm of my colleague was as below, but I didn't convinced in the computation of the inverse problem using the gain matrix not the lead field, it is possible to use the gain matrix as done below in the bold inverse problem part or in another word what does gain represent? % Set the radius and conductivities of each of the compartments addpath(cd) % 3 Layers r = [0 0.936 2.068 2.268]; c = [0.2 0.3 0.04 0.5]; %% Description of the spherical mesh pnt=point_square(:,2:4); tri=faces_square(:,3:5); %% Create a set of electrodes on the outer surface % sensor = [pnt(10201,:);pnt(17376,:);pnt(24756,:);pnt(31931,:);pnt(10166,:);pnt(17341,:);pnt(24721,:);pnt(31896,:);pnt(10130,:);pnt(17305,:);pnt(24685,:);pnt(31860,:);pnt(10095,:);pnt(17270,:);pnt(24650,:);pnt(31825,:)]; sensor = [pnt(664,:);pnt(1080,:);pnt(1600,:);pnt(2016,:);pnt(656,:);pnt(1072,:);pnt(1592,:);pnt(2008,:);pnt(646,:);pnt(1062,:);pnt(1582,:);pnt(1998,:);pnt(638,:);pnt(1054,:);pnt(1574,:);pnt(1990,:)]; sensor(:,3)=sensor(:,3)+max(r)+0.1; sens.elecpos = sensor; sens.label = {}; nsens = size(sens.elecpos,1); for ii=1:nsens sens.label{ii} = sprintf('vertex%03d', ii); end %% Set the position of the probe dipole %%Un source pos = pnt(1326,:);%[5 5 0] maillage complet pos(:,3) = pos(:,3)+0.1; %%Deux source % S1 = pnt(10609,:);%[2.5 2.5 0] maillage complet % S1(:,3) = S1(:,3)+0.1; % S2 = pnt(31417,:);%[7.5 7.5 0] maillage complet % S2(:,3) = S2(:,3)+0.1; % pos=[S1;S2]; %%All the uterine muscle mesh %S=pnt(:,:,:); %S(:,3) = S(:,3)+0.1; %pos=S; %% Create a BEM volume conduction model vol = []; for ii=1:length(r) uterus=pnt; uterus(:,3)=uterus(:,3)+r(ii)+0.1; vol.bnd(ii).pnt = uterus; vol.bnd(ii).tri = fliplr(tri); % pointing inwards!!! end vol.cond = c; %% Compute the BEM cfg=[]; cfg.method = 'bemcp'; vol = ft_prepare_headmodel(cfg, vol); cfg.vol = vol; cfg.grid.pos = pos; cfg.elec = sens; [grid,gain] = ft_prepare_leadfield(cfg); lf_openmeeg = grid.leadfield{1}; %% Inverse problem %load data data_simulated = hdf5read('Sources_EHG_1.hdf5','/surface/EHG'); %real=load('W4_P_27_07_10_CTMono3_deb.mat'); %data_real=real.XXF2D1; %MNE lambda = 1e-1; % MNE_1 = inverse_operator_MNE(gain,lambda); % A: Gain matrix S_MNE_1 = bayesian_inverse_solution(data_simulated',MNE_1); % X: Signal mean_S_MNE_1=mean(S_MNE_1,2); % % MNE_2 = inverse_operator_MNE(gain,lambda); % A: Gain matrix % S_MNE_2 = bayesian_inverse_solution(data_real',MNE_2); % X: Signal % mean_S_MNE_2=mean(S_MNE_2,2); bnd = struct('pnt', pnt, 'tri', tri); figure;ft_plot_mesh(bnd, 'vertexcolor', mean_S_MNE_1(1:size(pnt,1))); % figure;ft_plot_mesh(bnd, 'vertexcolor', mean_S_MNE_2(1:size(pnt,1))); To be more accurate I want to use your algorithm in: http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate?s[]=mne but my obstacle was cfg.dataset = 'Subject01.ds'; I didn't know in our cases what is the "Subject01.ds", and also the same in: http://www.fieldtriptoolbox.org/tutorial/beamformer,... Thank you very much for any suggestions Best regards Saeed -------------- next part -------------- An HTML attachment was scrubbed... URL: From mail at philipp-ruhnau.de Wed Jan 13 16:46:09 2016 From: mail at philipp-ruhnau.de (Philipp Ruhnau) Date: Wed, 13 Jan 2016 16:46:09 +0100 Subject: [FieldTrip] Help understanding the lcmv beamformer output In-Reply-To: References: Message-ID: <9EDB2B94-3D95-4084-82F2-71968FF04217@philipp-ruhnau.de> Dear Lorenzo and others, I’ve just looked into this, can reproduce the issue (same result with two different conditions/activity-baseline) The issue arises because power is calculated based on the filter and the covariance of the input data (following VanVeen or a slight change for precomputed filters), yet in the example below no covariance is precomputed for activity/baseline timelock structures (only for the common dataset) and in that case fieldtrip creates an identity matrix for both activity and baseline (around line 713 in ft_sourceanalysis). there is actually a warning about this, yet just from this warning (No covariance matrix found - will assume identity covariance matrix (mininum-norm solution)) it might to hard to get that this explains the results: in essence from what I understand, the input data is ignored in the formula (for those interested this is line 278 in beamformer_lcmv) to compute the time series power, because the covariance is an identity matrix, and only the filter determines what ends up in the .pow field. and as the filter is the same for activity and baseline, the difference between the .pow output is zero. now, computing covariances for the to-be-beamed segments (add a cfg.covariance = ‘yes’ to the timelock step for baseline and activity in the example) produces different power values (just tested with a simple auditory ERF dataset). I suppose this is desired behavior (the identity matrix covariance), otherwise I would suggest to produce an error. how well the ERF/timeseries is reconstructed of course depends on the data (time window) you use to create the filters. still it seems to me using the .mom field or creating virtual sensors yields better (in a sense of more focused) results. I still wonder why virtual sensors/.mom averages and .pow results are quite different, maybe one of the more knowledgeable ft developers could comment on at some point, but this might exceed the limit of this list… cheers philipp > On 12 Jan 2016, at 15:46, Lorenzo Magazzini wrote: > > Hi, > > I hope someone can help me to understand the use of the lcmv beamformer, because either I am using it incorrectly, or I misunderstood the meaning of its output. > > I am trying to get source-level power estimates of 'baseline' and 'active' time-windows. I first compute a common filter, and then apply it separately to the two conditions. I thought the power estimates would be stored, voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. However, the values I get in the '.pow' field for the analysis of 'baseline' and 'active' windows are identical. Furthermore, the '.pow' values are identical to the '.noise' values when using cfg.projectnoise = 'yes';. > > I have checked if the sensor-level data that passed on to ft_sourceanalysis is different between baseline and active - it is. > > Also, if I do the following... > 1. reconstruct virtual sensors by applying the common filter separately to baseline and active, > 2. average the single-trial (virtual sensor) power estimates, > 3. replace the '.pow' value for each voxel, > ...then the contrast between baseline and active is correct. > > Can anyone please help me figure out what I'm doing wrong here? Below I copied part of the code. > > Many thanks in advance! > > Lorenzo > > > %compute the leadfield > cfg = []; > cfg.channel = {'MEG'}; > cfg.grid = sourcemodel; > cfg.vol = hdm; > cfg.grad = grad; > cfg.normalize = 'yes'; > leadfield = ft_prepare_leadfield(cfg); > > %compute covariance matrix > cfg = []; > cfg.channel = {'MEG'}; > cfg.removemean = 'no'; > cfg.covariance = 'yes'; > cfg.covariancewindow = [-1.5 1.5]; > tlck = ft_timelockanalysis(cfg, data); > > %get the common spatial filter > cfg = []; > cfg.method = 'lcmv'; > cfg.grid = leadfield; > cfg.vol = hdm; > cfg.grad = grad; > cfg.lcmv.fixedori = 'yes'; > cfg.lcmv.keepfilter = 'yes'; > cfg.lcmv.projectnoise = 'yes'; > cfg.lcmv.lambda = '5%'; > src = ft_sourceanalysis(cfg, tlck); > > %store the filter > wts = src.avg.filter; > > %separate baseline and active windows of bandpass-filtered data > cfg = []; > cfg.toilim = [-1.5 -0.3]; > data_bsln = ft_redefinetrial(cfg, data); > cfg = []; > cfg.toilim = [0.3 1.5]; > data_actv = ft_redefinetrial(cfg, data); > > %timelock analysis of baseline and active > cfg = []; > cfg.channel = {'MEG'}; > cfg.keeptrials = 'yes'; > tlck_bsln = ft_timelockanalysis(cfg, data_bsln); > tlck_actv = ft_timelockanalysis(cfg, data_actv); > > %get source-power estimates of bsln and actv separately using the pre-computed common filter (wts) > cfg = []; > cfg.method = 'lcmv'; > cfg.vol = hdm; > cfg.grid = leadfield; > cfg.grid.filter = wts; > % cfg.keepfilter = 'no'; > cfg.lcmv.fixedori = 'yes'; > cfg.projectnoise = 'yes'; > cfg.lambda = '5%'; > cfg.keeptrials = 'yes'; > src_bsln = ft_sourceanalysis(cfg, tlck_bsln); > src_actv = ft_sourceanalysis(cfg, tlck_actv); > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lorenzomagazzini at gmail.com Wed Jan 13 19:44:26 2016 From: lorenzomagazzini at gmail.com (Lorenzo Magazzini) Date: Wed, 13 Jan 2016 18:44:26 +0000 Subject: [FieldTrip] Help understanding the lcmv beamformer output Message-ID: Hi Philipp, Thanks so much for your answer, it does indeed solve the problem! I thought the covariance matrix was no longer necessary after computation of the (common) filter, but, as you showed by pointing to the code, this is clearly not the case. Now, I compared the results of a) calculating power from the virtual sensors time-series (data multiplied by the filter, estimated using the 'common' covariance), and b) power taken from the output of ft_sourceanalysis, using two different 'condition-specific' covariance matrices. Results are pretty identical in my case, apart from minor differences in the power values. I wonder if anyone could help me figure out if there is a mathematical difference between these two approaches? Anyway, many thanks again for your help! Best wishes, Lorenzo > *From: *Philipp Ruhnau > *Subject: **Re: [FieldTrip] Help understanding the lcmv beamformer output* > *Date: *13 January 2016 at 16:46:09 GMT+1 > *To: *FieldTrip discussion list > > Dear Lorenzo and others, > I’ve just looked into this, can reproduce the issue (same result with two > different conditions/activity-baseline) > > The issue arises because power is calculated based on the filter and the > covariance of the input data (following VanVeen or a slight change for > precomputed filters), yet in the example below no covariance is precomputed > for activity/baseline timelock structures (only for the common dataset) and > in that case fieldtrip creates an identity matrix for both activity and > baseline (around line 713 in ft_sourceanalysis). > there is actually a warning about this, yet just from this warning (No > covariance matrix found - will assume identity covariance matrix > (mininum-norm solution)) it might to hard to get that this explains the > results: > > in essence from what I understand, the input data is ignored in the > formula (for those interested this is line 278 in beamformer_lcmv) to > compute the time series power, because the covariance is an identity > matrix, and only the filter determines what ends up in the .pow field. and > as the filter is the same for activity and baseline, the difference between > the .pow output is zero. > > now, computing covariances for the to-be-beamed segments (add a > cfg.covariance = ‘yes’ to the timelock step for baseline and activity in > the example) produces different power values (just tested with a simple > auditory ERF dataset). > > I suppose this is desired behavior (the identity matrix covariance), > otherwise I would suggest to produce an error. > > how well the ERF/timeseries is reconstructed of course depends on the data > (time window) you use to create the filters. still it seems to me using the > .mom field or creating virtual sensors yields better (in a sense of more > focused) results. I still wonder why virtual sensors/.mom averages and .pow > results are quite different, maybe one of the more knowledgeable ft > developers could comment on at some point, but this might exceed the limit > of this list… > > cheers > philipp > > On 12 Jan 2016, at 15:46, Lorenzo Magazzini > wrote: > > Hi, > > I hope someone can help me to understand the use of the lcmv beamformer, > because either I am using it incorrectly, or I misunderstood the meaning of > its output. > > I am trying to get source-level power estimates of 'baseline' and 'active' > time-windows. I first compute a common filter, and then apply it separately > to the two conditions. I thought the power estimates would be stored, > voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. > However, the values I get in the '.pow' field for the analysis of > 'baseline' and 'active' windows are identical. Furthermore, the '.pow' > values are identical to the '.noise' values when using cfg.projectnoise = > 'yes';. > > I have checked if the sensor-level data that passed on to > ft_sourceanalysis is different between baseline and active - it is. > > Also, if I do the following... > 1. reconstruct virtual sensors by applying the common filter separately to > baseline and active, > 2. average the single-trial (virtual sensor) power estimates, > 3. replace the '.pow' value for each voxel, > ...then the contrast between baseline and active is correct. > > Can anyone please help me figure out what I'm doing wrong here? Below I > copied part of the code. > > Many thanks in advance! > > Lorenzo > > > %compute the leadfield > cfg = []; > cfg.channel = {'MEG'}; > cfg.grid = sourcemodel; > cfg.vol = hdm; > cfg.grad = grad; > cfg.normalize = 'yes'; > leadfield = ft_prepare_leadfield(cfg); > > %compute covariance matrix > cfg = []; > cfg.channel = {'MEG'}; > cfg.removemean = 'no'; > cfg.covariance = 'yes'; > cfg.covariancewindow = [-1.5 1.5]; > tlck = ft_timelockanalysis(cfg, data); > > %get the common spatial filter > cfg = []; > cfg.method = 'lcmv'; > cfg.grid = leadfield; > cfg.vol = hdm; > cfg.grad = grad; > cfg.lcmv.fixedori = 'yes'; > cfg.lcmv.keepfilter = 'yes'; > cfg.lcmv.projectnoise = 'yes'; > cfg.lcmv.lambda = '5%'; > src = ft_sourceanalysis(cfg, tlck); > > %store the filter > wts = src.avg.filter; > > %separate baseline and active windows of bandpass-filtered data > cfg = []; > cfg.toilim = [-1.5 -0.3]; > data_bsln = ft_redefinetrial(cfg, data); > cfg = []; > cfg.toilim = [0.3 1.5]; > data_actv = ft_redefinetrial(cfg, data); > > %timelock analysis of baseline and active > cfg = []; > cfg.channel = {'MEG'}; > cfg.keeptrials = 'yes'; > tlck_bsln = ft_timelockanalysis(cfg, data_bsln); > tlck_actv = ft_timelockanalysis(cfg, data_actv); > > %get source-power estimates of bsln and actv separately using the > pre-computed common filter (wts) > cfg = []; > cfg.method = 'lcmv'; > cfg.vol = hdm; > cfg.grid = leadfield; > cfg.grid.filter = wts; > % cfg.keepfilter = 'no'; > cfg.lcmv.fixedori = 'yes'; > cfg.projectnoise = 'yes'; > cfg.lambda = '5%'; > cfg.keeptrials = 'yes'; > src_bsln = ft_sourceanalysis(cfg, tlck_bsln); > src_actv = ft_sourceanalysis(cfg, tlck_actv); > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dlozanosoldevilla at gmail.com Thu Jan 14 11:41:09 2016 From: dlozanosoldevilla at gmail.com (dlozanosoldevilla .) Date: Thu, 14 Jan 2016 11:41:09 +0100 Subject: [FieldTrip] Fieldtrip tutor WANTED: Coimbra workshop Message-ID: Dear Fieldtrippers, I am organizing a Fieldtrip workshop at Coimbra (Portugal) with talented alumni from Coimbra University, Champalimaud Center for the Unknown and Imperial College of London. I am looking for a highly motivated researcher that would like to be a tutor that available on any of the following dates: - May 9th - 11th - June 6th - 9th The workshop is two and a half days long and a draft of the program can be found here: http://www.fieldtriptoolbox.org/workshop/coimbra There will be around 12-13 people, most of them with EEG and/or MEG experience. The audience has a special interest in connectivity and source space analysis so a tutor with experience on these topics is mandatory. - Tutor activities: 1. Teach one or two lecture sessions. The tutor need to teach two lecture sessions; see program above. Besides the teaching material (slides + video ) is available and will be provided. In addition, the preparation of the lectures includes that the tutor will have a videoconferencing session with the main developers in Nijmegen to ensure that all aspects that are not clear in the slides are resolved. 2. Support hands-on sessions. After each theory session there is a hands-on session using tested tutorial data and code. The last day, the alumni bring their on data and the mission is to help the users with their analysis goals as much as time allows. All costs associated to travel and accommodation are covered (Only restricted to researchers working within Europe). If you are interested and/or you want to know more about it, please do not hesitate to contact me (dlozanosoldevilla at gmail.com). Preparing and teaching in such a workshop is a great opportunity to increase your own skills and to boost your CV! Looking forward to hear from you, Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Jan 15 09:16:20 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 15 Jan 2016 09:16:20 +0100 Subject: [FieldTrip] MEG/EEG FieldTrip toolkit course in Nijmegen: pre-registration now open Message-ID: Dear All, — Please disseminate to PhD students and postdoctoral researchers working with MEG, EEG and ECoG data analysis. --- On April 18-21, 2016 we will host the "Toolkit of Cognitive Neuroscience: advanced data analysis and source modelling of EEG and MEG data" at the Donders Institute in Nijmegen. This intense 4-day toolkit course will teach you advanced MEG and EEG data analysis skills. Preprocessing, frequency analysis, source reconstruction, connectivity and various statistical methods will be covered. The toolkit will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG data set using the FieldTrip toolbox. The lectures and tutoring will be provided by the core FieldTrip development team, and there will also be plenty of opportunity to interact and ask questions to us about your research and data. On the final day you will have the opportunity to work on your own dataset under supervision of the tutors. We can host a limited number of participants. From past experience we expect the course to be oversubscribed, hence we will start with pre-registration. The final selection of the participants will be based on the motivation, background experience and research interests that are provided in the registration form. The deadline for pre-registration is March 1, 2016. More information, including a preliminary program, can be found at http://www.ru.nl/donders/agenda-news/tool-kits-cognitive/toolkit-meg/ Looking forward to welcoming you in Nijmegen, Robert Oostenveld and Jan-Mathijs Schoffelen. ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Radboud University, Nijmegen, The Netherlands Visiting Professor NatMEG - the Swedish National MEG facility Karolinska Institute, Stockholm, Sweden tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/donders skype: r.oostenveld ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Jan 15 11:18:31 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 15 Jan 2016 11:18:31 +0100 Subject: [FieldTrip] fixed bug in MEG localspheres forward model Message-ID: <8543B5C2-731C-4AEA-9CFE-894B5E35D40D@donders.ru.nl> Dear FieldTrip users, We found (and fixed) a bug in the MEG localspheres forward model, which may have affected your recent analyses. The consequence is that MEG source reconstructions would have been of very poor quaility. This was pointed out to me by Fraincois Tadel (thanks!) who noticed that dipole fits of clean topographies ended up in completely unexpected locations. Also MNE and beamformer results will have been wrong, although there it was less obvious to detect the flaw. I have included the fix in SVN revision 11061, which you can also find on https://github.com/fieldtrip/fieldtrip. If you use the download version from our FTP server: the version that is released this evening will include the fix. Further details can be found on http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3037 Sorry for the inconvenience, Robert PS If you use singlesphere, BEM or singleshell models, you have not been affected by this. From vic.schroeder2 at gmail.com Fri Jan 15 11:26:14 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Fri, 15 Jan 2016 10:26:14 +0000 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: Thank you Tzvetan. 2016-01-03 20:18 GMT+00:00 Tzvetan Popov : > > Dear Victoria, > the system you are working with is already equipped with two orthogonal > planar gradiometer sensors. Thus you should not try to create planar > gradients on the basis of the planar gradients. Yet you might want to use > the magnetometers only. There you can represent the activity as if it was > picked up by planar gradients. Could you please skip the planar > transformation bit and redo your analysis? > FieldTrip provides three types of layouts for the Neuromag system: *NM306all.lay > NM306mag.lay NM306grad.lay*. For example if you want to plot > magnetometers only you’d specify *cfg.layout = 'neuromag306mag.lay’; > cfg.channel = 'MEG*1’*; Here MEG*1 refers to magnetometers and MEG*2 and > MEG*3 would be the two orthogonal planar gradients respectively. Also the > neighbours are provided as* neuromag306cmb_neighb.mat; > neuromag306mag_neighb.mat; neuromag306planar_neighb.ma > *t;. You might consider loading the > structure of your choice directly. > Here is an example tutorial that might help: > http://www.fieldtriptoolbox.org/tutorial/natmeg/timefrequency > Good luck, > tzvetan > > Dear Fieldtrip team, > > I am currently working on data acquired from an elektra system (neuromag). > I have done all the preprocessing and the ft_freqanalysis with the > gradiometers only. I combined the gradiometers to create planar > gradients.However , later when doing the statistics problems occur when i > want to specify the channels. The error tells me that no degrees of freedom > are found for the analysis. However, when i remove the cfg.channel form the > script it runs through without an error. (please see code below). > My question is whether the output of the stastistic is correct without > specifying the channels? If not, does anybody have suggestions how to fix > the problem? > > I have run into similar problems when wanting to plot the time frequency > data from the planar gradients after having used ft_combineplanar. Here i > cannot find a layout file that suits the output of ft_combineplanar. Thus, > i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, > however, the layouts provided by fieldtrip does not fit that number. > Has anybody run into similar problems? Or does anybody know a possible > solution? > > Thank you very much for any suggestions > Victoria > > %combine planar > cfg = []; > cfg.method ='sum'; > %ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > cfg = []; > %cfg.channel = {'MEG'}; > cfg.latency = 'all'; > cfg.frequency = [14.5 16]; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); > > design = zeros(1,size(ComGrad_con.powspctrm,1) + > size(ComGrad_incon.powspctrm,1)); > design(1,1:size(ComGrad_con.powspctrm,1)) = 1; > > design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... > size(ComGrad_incon.powspctrm,1))) = 2; > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Fri Jan 15 12:09:07 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Fri, 15 Jan 2016 11:09:07 +0000 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: Dear Tzvetan, I did not do any planar transformation with the gradiometers. I only did the ft_combineplanar. Should i also omit that? Cheers Victoria 2016-01-15 10:26 GMT+00:00 victoria schroeder : > Thank you Tzvetan. > > 2016-01-03 20:18 GMT+00:00 Tzvetan Popov : > >> >> Dear Victoria, >> the system you are working with is already equipped with two orthogonal >> planar gradiometer sensors. Thus you should not try to create planar >> gradients on the basis of the planar gradients. Yet you might want to use >> the magnetometers only. There you can represent the activity as if it was >> picked up by planar gradients. Could you please skip the planar >> transformation bit and redo your analysis? >> FieldTrip provides three types of layouts for the Neuromag system: *NM306all.lay >> NM306mag.lay NM306grad.lay*. For example if you want to plot >> magnetometers only you’d specify *cfg.layout = 'neuromag306mag.lay’; >> cfg.channel = 'MEG*1’*; Here MEG*1 refers to magnetometers and MEG*2 and >> MEG*3 would be the two orthogonal planar gradients respectively. Also the >> neighbours are provided as* neuromag306cmb_neighb.mat; >> neuromag306mag_neighb.mat; neuromag306planar_neighb.ma >> *t;. You might consider loading the >> structure of your choice directly. >> Here is an example tutorial that might help: >> http://www.fieldtriptoolbox.org/tutorial/natmeg/timefrequency >> Good luck, >> tzvetan >> >> Dear Fieldtrip team, >> >> I am currently working on data acquired from an elektra system >> (neuromag). I have done all the preprocessing and the ft_freqanalysis with >> the gradiometers only. I combined the gradiometers to create planar >> gradients.However , later when doing the statistics problems occur when i >> want to specify the channels. The error tells me that no degrees of freedom >> are found for the analysis. However, when i remove the cfg.channel form the >> script it runs through without an error. (please see code below). >> My question is whether the output of the stastistic is correct without >> specifying the channels? If not, does anybody have suggestions how to fix >> the problem? >> >> I have run into similar problems when wanting to plot the time frequency >> data from the planar gradients after having used ft_combineplanar. Here i >> cannot find a layout file that suits the output of ft_combineplanar. Thus, >> i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, >> however, the layouts provided by fieldtrip does not fit that number. >> Has anybody run into similar problems? Or does anybody know a possible >> solution? >> >> Thank you very much for any suggestions >> Victoria >> >> %combine planar >> cfg = []; >> cfg.method ='sum'; >> %ComCon = ft_combineplanar(cfg,FreqCon); >> ComIncon = ft_combineplanar(cfg, FreqIncon); >> >> cfg = []; >> %cfg.channel = {'MEG'}; >> cfg.latency = 'all'; >> cfg.frequency = [14.5 16]; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'ft_statfun_indepsamplesT'; >> cfg.correctm = 'cluster'; >> cfg.clusteralpha = 0.05; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan = 2; >> cfg.tail = 0; >> cfg.clustertail = 0; >> cfg.alpha = 0.025; >> cfg.numrandomization = 500; >> cfg_neighb.method = 'distance'; >> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); >> >> design = zeros(1,size(ComGrad_con.powspctrm,1) + >> size(ComGrad_incon.powspctrm,1)); >> design(1,1:size(ComGrad_con.powspctrm,1)) = 1; >> >> design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... >> size(ComGrad_incon.powspctrm,1))) = 2; >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Harald.Bornfleth at besa.de Fri Jan 15 14:35:11 2016 From: Harald.Bornfleth at besa.de (Harald Bornfleth) Date: Fri, 15 Jan 2016 14:35:11 +0100 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Message-ID: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Dear Andrew, Thanks for bringing this up. I can try to shed some light on the ICA method used in BESA Research; however, I can not comment on the implementation in FieldTrip. The method behind ICA analysis in BESA Research is the extended infomax ICA algorithm (Lee TW et al.: Independent component analysis using an extended infomax algorithm for mixed sub-Gaussian and super-Gaussian sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very well suited to remove cardiac and powerline artifacts. Depending on the data, it may also be used to remove ocular (blink) and electrode artifacts. To assess whether your artifact removal is trustworthy more information about your processing steps are needed. What types of artifacts are you trying to correct? What segments are you using to determine the artifact topographies and what segments are you finally correcting? Best regards, Harald Dr. Harald Bornfleth Product Manager BESA Research BESA GmbH Freihamer Strasse 18 82166 Graefelfing/Germany http://www.besa.de E: Harald.Bornfleth at besa.de T: +49 89 8980 9968 HRB Munich 109956 CEO: Dr. Tobias Scherg, CFO: Theodor Scherg Director of Research: Dr. Michael Scherg From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Andrew Chang Sent: Sonntag, 10. Januar 2016 21:18 To: fieldtrip at science.ru.nl Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Dear Fieldtrip users, I am wondering whether anyone has compared the performances of the ICA methods among M/EEG toolboxes. Especially, how is the performance of ICA in BESA Research 6.0, compared to Fieldtrip? I have an EEG data set which has been processed in BESA, including removing artifact using ICA. I am wondering whether I can trust it, or I should reprocess it in Fieldtrip. Any comments will be appreciated! Happy new year! Best, Andrew -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ATT00004.txt URL: From michele.scaltritti at gmail.com Fri Jan 15 16:03:18 2016 From: michele.scaltritti at gmail.com (Michele Scaltritti) Date: Fri, 15 Jan 2016 16:03:18 +0100 Subject: [FieldTrip] unexpected boundary effects using Morlet wavelets Message-ID: Dears, I am Michele Scaltritti, and this is my first post on this mailing list. I work on ERPs in the context of psycholinguistics, and I just recently started working with Fieldtrip to perform time-frequency analyses. I am encountering a problem with respect to boundary effects, as these affects time windows that I didn't expect. More precisely, I' running my analysis on epochs going from -1.1s before stimulus onset (0 s), to 4 s afterwards (for a total length of 5.1s). In order to do that, I am using Morlet wavelets of 7 cycles, with 50 milliseconds time-steps. I am estimating frequencies ranging from 10 to 35 Hz. At 10Hz frequency, the length of my wavelet should be 7/10/pi, so around 222 ms. As such, I would expect to be able to estimate frequency power at -800 ms in my epoch (which corresponds to the starting time of what I would like to be my baseline): in fact, I would expect to be able to estimate 10Hz frequency power as soon as the third time-step (150 ms), corresponding to -950 in my epochs. However, I don't get any value for 10Hz frequency at -800 ms. Clearly, my reasoning is wrong, but I can't figure out what I am missing. In the following lines, I'll post the code of the configuration I used to run the frequency decomposition cfg = [] cfg.channel = 'all'; cfg.method = 'wavelet'; cfg.width = 7; cfg.output = 'pow'; cfg.foi = 10:1:35; cfg.toi = -1.1:0.05:4 TF_data = ft_freqanalysis(cfg,data) Thank you very much for the attention, and please excuse eventual gross mistakes in my arguments. michele -------------- next part -------------- An HTML attachment was scrubbed... URL: From fosco.bernasconi at gmail.com Sat Jan 16 15:42:50 2016 From: fosco.bernasconi at gmail.com (fosco bernasconi) Date: Sat, 16 Jan 2016 15:42:50 +0100 Subject: [FieldTrip] Fwd: ft_statfun_actvsblT & ft_timelockstatistics error In-Reply-To: References: Message-ID: Hi all, I would like to identify ECoG electrodes that are active during my task, by comparing the post-stimulus activity vs. the baseline. I would like to do this on LFP (and not on time-frequency data). Unfortunately, I keep having the error "Inappropriate dimord for the statistics function STATFUN_ACTVSBLT.". My cfg.dimord = 'rpt_chan_time'; I am missing something, any suggestion? Thanks a lot in advance! fosco Here my code: datafldtrp= eeglab2fieldtrip(EEG,'preprocessing'); % define intervals: cfg = []; cfg.channel = {'GA1'}; cfg.toilim = [-.2 0]; dataFIC_baseline = ft_redefinetrial(cfg,datafldtrp); cfg = []; cfg.channel = {'GA1'}; cfg.toilim = [0.05 0.25]; dataFIC_activation = ft_redefinetrial(cfg,datafldtrp); cfg = []; cfg.keeptrials = 'yes'; cfg.removemean = 'no'; [timelock_baseline] = ft_timelockanalysis(cfg,dataFIC_baseline); [timelock_activation] = ft_timelockanalysis(cfg,dataFIC_activation); timelock_activation.time = timelock_baseline.time; cfg = []; ntrials = size(timelock_activation.trial,1); design = zeros(2,2*ntrials); design(1,1:ntrials) = 1; design(1,ntrials+1:2*ntrials) = 2; design(2,1:ntrials) = [1:ntrials]; design(2,ntrials+1:2*ntrials) = [1:ntrials]; cfg.design = design; cfg.statistic = 'ft_statfun_actvsblT'; cfg.method = 'montecarlo'; cfg.numrandomization = 500; cfg.parameter = 'trial'; cfg.ivar = 1; cfg.tail = 0; [stat] = ft_timelockstatistics(cfg,timelock_activation,timelock_baseline); -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Sat Jan 16 18:26:53 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Sat, 16 Jan 2016 17:26:53 +0000 Subject: [FieldTrip] plotting neighbours Message-ID: Hi ! I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243* *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243* however what i see is: *Selected channel MEG0741, which has 0 neighbours: * *Selected channel MEG0731, which has 0 neighbours: * *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243* *Selected channel MEG0711, which has 0 neighbours: * *Selected channel MEG0741, which has 0 neighbours: * It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243* or *Selected channel MEG1031, which has 0 neighbours: * Do you have any suggestions why this happen? Are the channels not grouped correctly? Below is the code starting from the time-frequency analysis of the data. Thank you very much Victoria cfg = []; cfg.output = 'pow'; cfg.channel = 'MEGGRAD'; cfg.method = 'mtmconvol'; cfg.taper = 'hanning'; cfg.foi = [2:2:30]; %cfg.keeptrials = 'yes'; for stats keep trials cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec cfg.toi = [-1.3:0.05:1]; cfg.keeptrials = 'yes'; FreqCon = ft_freqanalysis(cfg, Con_clean); FreqIncon = ft_freqanalysis(cfg, Incon_clean); %combine planar cfg = []; cfg.method ='sum'; ComCon = ft_combineplanar(cfg,FreqCon); ComIncon = ft_combineplanar(cfg, FreqIncon); % plot neighbours cfg=[]; cfg.method = 'triangulation'; cfg.layout = 'neuromag306cmb.lay'; ft_neighbourplot(cfg,ComCon) -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Sat Jan 16 19:00:48 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sat, 16 Jan 2016 19:00:48 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: Dear Victoria, you should remove the ft_combineplanar step from your analysis pipeline. This function takes input from ft_megplanar. The latter is applied only to magnetometers or axial gradiometers. best tzvetan > Hi ! > > I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > > however what i see is: > > Selected channel MEG0741, which has 0 neighbours: > Selected channel MEG0731, which has 0 neighbours: > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > Selected channel MEG0711, which has 0 neighbours: > Selected channel MEG0741, which has 0 neighbours: > > It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > > or > > Selected channel MEG1031, which has 0 neighbours: > > Do you have any suggestions why this happen? Are the channels not grouped correctly? > > Below is the code starting from the time-frequency analysis of the data. > > Thank you very much > Victoria > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEGGRAD'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = [2:2:30]; > %cfg.keeptrials = 'yes'; for stats keep trials > cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec > cfg.toi = [-1.3:0.05:1]; > cfg.keeptrials = 'yes'; > FreqCon = ft_freqanalysis(cfg, Con_clean); > FreqIncon = ft_freqanalysis(cfg, Incon_clean); > > %combine planar > cfg = []; > cfg.method ='sum'; > ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > % plot neighbours > cfg=[]; > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg,ComCon) > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tokimoto at mejiro.ac.jp Sun Jan 17 11:39:24 2016 From: tokimoto at mejiro.ac.jp (Shingo Tokimoto) Date: Sun, 17 Jan 2016 19:39:24 +0900 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> Message-ID: <73BB8BE6-8BC7-40AF-B785-E600CCA77ED6@mejiro.ac.jp> Dear Dr. Tzvetan Popov and FieldTrip users, Thank you for the comment again. I undone the changes, but the same error message appears. The cluster-based permutation test works well for ERP, but it doesn't work for ERSP. Attached is the window of EEGLAB for statistic parameters. I understand you are not familiar with EEGLAB. Could you give me any suggestions for the parameters of FieldTrip statistics? The messages in the command window of Matlab is as follows. Using pre-loaded data. To force rereading data from disk use the 'forceread' flag 1 x 2, paired data, computing T values the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 6 MB Thank you in advance again. ************************************************ Shingo Tokimoto, Ph.D. in Linguistics and Psychology Department of Foreign Languages Mejiro University 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, 161-8539, Japan tokimoto at mejiro.ac.jp ************************************************ On 2016/01/11, at 1:08, Tzvetan Popov wrote: > Dear Shingo, > lets keep it by Tzvetan ;-). I’m not familiar with the way EEGLAB deals with FieldTrip functions at all. So I may not be of any further help. > However as a rule of thumb you should almost never change settings in the FieldTrip functions but provide the appropriate configurations always as cfg.xxx. When you mention your analysis works for ERP I don’t see any reason why it fails with time-freq data. Obviously you have your electrode positions and you were able to generate neighborhood structure. If so the same should work for t-f too. > Maybe if you provide the syntax of your analysis me or others can help you in getting it done. > I will advise to undone any changes you made to the FieldTrip code and try again. Probably a fresh version of EEGLAB, clean math lab path etc. and then do it again. > best > tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Window_EEGLAB.png Type: image/png Size: 79275 bytes Desc: not available URL: From changa5 at mcmaster.ca Sun Jan 17 19:57:03 2016 From: changa5 at mcmaster.ca (Andrew Chang) Date: Sun, 17 Jan 2016 13:57:03 -0500 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) In-Reply-To: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> References: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Message-ID: Hi Dr. Bornfleth, Thanks for your reply very much. I would like to use ICA to remove eye blinks and eye movements, neck movements, as well as cardiac and powerline artifacts. The segment I have is a continuous EEG recording for 10 minutes, which is one block of my experiment including many trials. Before ICA, the segment have been high-pass (0.3 Hz) and low-pass (100 Hz). The components showing activities around the eyes, the back of the neck, and 60 Hz were removed. As for the cardiac artifact, I it is based on visual inspection on the waveform to see whether it looks like an EKG. Any further comments are appreciated! Best, Andrew On Fri, Jan 15, 2016 at 8:35 AM, Harald Bornfleth wrote: > Dear Andrew, > > > > Thanks for bringing this up. I can try to shed some light on the ICA > method used in BESA Research; however, I can not comment on the > implementation in FieldTrip. > > > > The method behind ICA analysis in BESA Research is the extended infomax > ICA algorithm (Lee TW et al.: Independent component analysis using an > extended infomax algorithm for mixed sub-Gaussian and super-Gaussian > sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very > well suited to remove cardiac and powerline artifacts. Depending on the > data, it may also be used to remove ocular (blink) and electrode artifacts. > To assess whether your artifact removal is trustworthy more information > about your processing steps are needed. What types of artifacts are you > trying to correct? What segments are you using to determine the artifact > topographies and what segments are you finally correcting? > > > > Best regards, > > Harald > > > > > > *Dr. Harald Bornfleth* > > Product Manager BESA Research > > > > *BESA GmbH* > > Freihamer Strasse 18 > > 82166 Graefelfing/Germany > > http://www.besa.de > > > > E: Harald.Bornfleth at besa.de > > T: +49 89 8980 9968 > > > > > > HRB Munich 109956 > > CEO: Dr. Tobias Scherg, CFO: Theodor Scherg > > Director of Research: Dr. Michael Scherg > > > > > > > > > > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > mailto:fieldtrip-bounces at science.ru.nl ] *On > Behalf Of *Andrew Chang > *Sent:* Sonntag, 10. Januar 2016 21:18 > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. > Fieldtrip) > > > > Dear Fieldtrip users, > > > > I am wondering whether anyone has compared the performances of the ICA > methods among M/EEG toolboxes. Especially, how is the performance of ICA in > BESA Research 6.0, compared to Fieldtrip? > > I have an EEG data set which has been processed in BESA, including > removing artifact using ICA. I am wondering whether I can trust it, or > I should reprocess it in Fieldtrip. Any comments will be appreciated! > > > > Happy new year! > > > > Best, > > Andrew > > > > -- > > Andrew Chang > Ph.D. Candidate > Auditory Development Lab > > Department of Psychology, Neuroscience & Behaviour > McMaster University > > http://changa5.wordpress.com/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Mon Jan 18 12:38:39 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Mon, 18 Jan 2016 11:38:39 +0000 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: Dear Tzvetan Are you sure about that in the tutorial http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing neuromag data is used and ft_combineplanar is used to combine the gradiometers. This is a paragraph from this tutorial: In fact, we are now plotting the two different gradiometers together. You can see the channel locations being in pairs, one above the other. They are in reality, however, at the same location but oriented differently - radially and axially *with respect to the surface of the helmet*. They can thereby pick up both radial orientations of the magnetic fields. To use them properly for the purpose of plotting, we should therefor combine them first, adding their fields. TFR_left_MEG_comb = ft_combineplanar([],TFR_left_MEG); TFR_right_MEG_comb = ft_combineplanar([],TFR_right_MEG); cfg = []; cfg.baseline = [-0.5 -0.1]; cfg.baselinetype = 'absolute'; cfg.xlim = [0.4 0.8]; cfg.ylim = [15 25]; cfg.zlim = [-4e-24 4e-24]; cfg.marker = 'on'; cfg.layout = 'neuromag306cmb.lay'; figure ; ft_topoplotTFR(cfg, TFR_left_MEG_comb);print -dpng natmeg_freq13.png Thus, it should be possible to use ft_combineplanar for neuromag data. What do you think? Cheers Victoria 2016-01-16 18:00 GMT+00:00 Tzvetan Popov : > Dear Victoria, > you should remove the ft_combineplanar step from your analysis pipeline. > This function takes input from ft_megplanar. The latter is applied only to > magnetometers or axial gradiometers. > > best > tzvetan > > > Hi ! > > I am working with a neuromag system and want to do cluster based > permutation tests with time frequency data. However, before running the > stats i would like to check the clusters which are formed by > ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the > plot and clicking on the channels i would expect to see something like : > > *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, > MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, > MEG1242+1243* > > *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, > MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, > MEG2242+2243* > > however what i see is: > > *Selected channel MEG0741, which has 0 neighbours: * > *Selected channel MEG0731, which has 0 neighbours: * > *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, > MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, > MEG2242+2243* > *Selected channel MEG0711, which has 0 neighbours: * > *Selected channel MEG0741, which has 0 neighbours: * > > It is absolutely random when the correct output occurs. When clicking on a > particular channel it would randomly show me the following results: > > *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, > MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, > MEG1242+1243* > > or > > *Selected channel MEG1031, which has 0 neighbours: * > > Do you have any suggestions why this happen? Are the channels not grouped > correctly? > > Below is the code starting from the time-frequency analysis of the data. > > Thank you very much > Victoria > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEGGRAD'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = [2:2:30]; > %cfg.keeptrials = 'yes'; for stats keep trials > cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window > = 0.5 sec > cfg.toi = [-1.3:0.05:1]; > cfg.keeptrials = 'yes'; > FreqCon = ft_freqanalysis(cfg, Con_clean); > FreqIncon = ft_freqanalysis(cfg, Incon_clean); > > %combine planar > cfg = []; > cfg.method ='sum'; > ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > % plot neighbours > cfg=[]; > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg,ComCon) > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Harald.Bornfleth at besa.de Mon Jan 18 13:49:32 2016 From: Harald.Bornfleth at besa.de (Harald Bornfleth) Date: Mon, 18 Jan 2016 13:49:32 +0100 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) In-Reply-To: References: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Message-ID: Dear Andrew, A couple of questions popped up. 1) The neck movement artifact, is this something with low frequency, or is it a muscle artifact? 2) Did you calculate the ICA on one data screen (e.g. 10 seconds or 20 seconds), or over the whole data set? If you could send us screen shots showing the ICA wave forms and the accompanying topographies, then we could comment on the classification. (In BESA, you right-click on the label of a component and select “Map topography” to show the topography map of that component.) I include my colleague and ICA expert Nicole Ille on CC. Best regards, Harald From: c.andrew123 at gmail.com [mailto:c.andrew123 at gmail.com] On Behalf Of Andrew Chang Sent: 17 January 2016 19:57 To: Harald.Bornfleth at besa.de; FieldTrip discussion list Subject: Re: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Hi Dr. Bornfleth, Thanks for your reply very much. I would like to use ICA to remove eye blinks and eye movements, neck movements, as well as cardiac and powerline artifacts. The segment I have is a continuous EEG recording for 10 minutes, which is one block of my experiment including many trials. Before ICA, the segment have been high-pass (0.3 Hz) and low-pass (100 Hz). The components showing activities around the eyes, the back of the neck, and 60 Hz were removed. As for the cardiac artifact, I it is based on visual inspection on the waveform to see whether it looks like an EKG. Any further comments are appreciated! Best, Andrew On Fri, Jan 15, 2016 at 8:35 AM, Harald Bornfleth > wrote: Dear Andrew, Thanks for bringing this up. I can try to shed some light on the ICA method used in BESA Research; however, I can not comment on the implementation in FieldTrip. The method behind ICA analysis in BESA Research is the extended infomax ICA algorithm (Lee TW et al.: Independent component analysis using an extended infomax algorithm for mixed sub-Gaussian and super-Gaussian sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very well suited to remove cardiac and powerline artifacts. Depending on the data, it may also be used to remove ocular (blink) and electrode artifacts. To assess whether your artifact removal is trustworthy more information about your processing steps are needed. What types of artifacts are you trying to correct? What segments are you using to determine the artifact topographies and what segments are you finally correcting? Best regards, Harald Dr. Harald Bornfleth Product Manager BESA Research BESA GmbH Freihamer Strasse 18 82166 Graefelfing/Germany http://www.besa.de E: Harald.Bornfleth at besa.de T: +49 89 8980 9968 HRB Munich 109956 CEO: Dr. Tobias Scherg, CFO: Theodor Scherg Director of Research: Dr. Michael Scherg From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Andrew Chang Sent: Sonntag, 10. Januar 2016 21:18 To: fieldtrip at science.ru.nl Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Dear Fieldtrip users, I am wondering whether anyone has compared the performances of the ICA methods among M/EEG toolboxes. Especially, how is the performance of ICA in BESA Research 6.0, compared to Fieldtrip? I have an EEG data set which has been processed in BESA, including removing artifact using ICA. I am wondering whether I can trust it, or I should reprocess it in Fieldtrip. Any comments will be appreciated! Happy new year! Best, Andrew -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon Jan 18 13:59:20 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 Jan 2016 13:59:20 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> Hi Victoria, well if you work with the magnetometers yes. Maybe I misunderstood your previous posts. Yet this configuration from your post below cfg.channel = 'MEGGRAD’; results in time-frequency representation of power on the planar gradiometers only. In that case neither ft_megplanar nor ft_combineplanar are appropriate since the data stems from planar gradiometers. The tutorial you mentioned deals only with the magnetometers thus ft_megplanar and ft_combineplanar are used. best tzvetan > Dear Tzvetan > > Are you sure about that in the tutorial http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing neuromag data is used and ft_combineplanar is used to combine the gradiometers. This is a paragraph from this tutorial: > > In fact, we are now plotting the two different gradiometers together. You can see the channel locations being in pairs, one above the other. They are in reality, however, at the same location but oriented differently - radially and axially with respect to the surface of the helmet. They can thereby pick up both radial orientations of the magnetic fields. To use them properly for the purpose of plotting, we should therefor combine them first, adding their fields. > > TFR_left_MEG_comb = ft_combineplanar([],TFR_left_MEG); > TFR_right_MEG_comb = ft_combineplanar([],TFR_right_MEG); > > cfg = []; > cfg.baseline = [-0.5 -0.1]; > cfg.baselinetype = 'absolute'; > cfg.xlim = [0.4 0.8]; > cfg.ylim = [15 25]; > cfg.zlim = [-4e-24 4e-24]; > cfg.marker = 'on'; > cfg.layout = 'neuromag306cmb.lay'; > > figure; > ft_topoplotTFR(cfg, TFR_left_MEG_comb); > print -dpng natmeg_freq13.png > Thus, it should be possible to use ft_combineplanar for neuromag data. > What do you think? > > Cheers > Victoria > > 2016-01-16 18:00 GMT+00:00 Tzvetan Popov : > Dear Victoria, > you should remove the ft_combineplanar step from your analysis pipeline. This function takes input from ft_megplanar. The latter is applied only to magnetometers or axial gradiometers. > > best > tzvetan > > >> Hi ! >> >> I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : >> >> Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 >> Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 >> >> however what i see is: >> >> Selected channel MEG0741, which has 0 neighbours: >> Selected channel MEG0731, which has 0 neighbours: >> Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 >> Selected channel MEG0711, which has 0 neighbours: >> Selected channel MEG0741, which has 0 neighbours: >> >> It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: >> >> Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 >> >> or >> >> Selected channel MEG1031, which has 0 neighbours: >> >> Do you have any suggestions why this happen? Are the channels not grouped correctly? >> >> Below is the code starting from the time-frequency analysis of the data. >> >> Thank you very much >> Victoria >> >> cfg = []; >> cfg.output = 'pow'; >> cfg.channel = 'MEGGRAD'; >> cfg.method = 'mtmconvol'; >> cfg.taper = 'hanning'; >> cfg.foi = [2:2:30]; >> %cfg.keeptrials = 'yes'; for stats keep trials >> cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec >> cfg.toi = [-1.3:0.05:1]; >> cfg.keeptrials = 'yes'; >> FreqCon = ft_freqanalysis(cfg, Con_clean); >> FreqIncon = ft_freqanalysis(cfg, Incon_clean); >> >> %combine planar >> cfg = []; >> cfg.method ='sum'; >> ComCon = ft_combineplanar(cfg,FreqCon); >> ComIncon = ft_combineplanar(cfg, FreqIncon); >> >> % plot neighbours >> cfg=[]; >> cfg.method = 'triangulation'; >> cfg.layout = 'neuromag306cmb.lay'; >> ft_neighbourplot(cfg,ComCon) >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Mon Jan 18 17:45:22 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Mon, 18 Jan 2016 16:45:22 +0000 Subject: [FieldTrip] plotting neighbours In-Reply-To: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> References: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> Message-ID: Dear Tzvetan I get your point. I am only using that gradiometers. However, in the text which i copied into the previous email it is stated that ft_combineplanar is used for 'plotting the two different gradiometers together'. They mention gradiometers specifically. Also when running the code it is clear that the gradiometers not the magnetometers are combined. This is the resulting matrix when running the tutorial : [image: Inline-Bild 1] With this in mind, can you clarify why the toturial only uses magnetometers? As i understand it , it uses gradiometers. Thank you a lot Victoria 2016-01-18 12:59 GMT+00:00 Tzvetan Popov : > Hi Victoria, > well if you work with the magnetometers yes. Maybe I misunderstood your > previous posts. Yet this configuration from your post below cfg.channel = > 'MEGGRAD’; results in time-frequency representation of power on the planar > gradiometers only. In that case neither ft_megplanar nor ft_combineplanar > are appropriate since the data stems from planar gradiometers. The tutorial > you mentioned deals only with the magnetometers thus ft_megplanar and > ft_combineplanar are used. > > best > tzvetan > > > Dear Tzvetan > > Are you sure about that in the tutorial > http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing neuromag > data is used and ft_combineplanar is used to combine the gradiometers. This > is a paragraph from this tutorial: > > In fact, we are now plotting the two different gradiometers together. You > can see the channel locations being in pairs, one above the other. They are > in reality, however, at the same location but oriented differently - > radially and axially *with respect to the surface of the helmet*. They > can thereby pick up both radial orientations of the magnetic fields. To use > them properly for the purpose of plotting, we should therefor combine them > first, adding their fields. > > TFR_left_MEG_comb = ft_combineplanar([],TFR_left_MEG); > TFR_right_MEG_comb = ft_combineplanar([],TFR_right_MEG); > > cfg = []; > cfg.baseline = [-0.5 -0.1]; > cfg.baselinetype = 'absolute'; > cfg.xlim = [0.4 0.8]; > cfg.ylim = [15 25]; > cfg.zlim = [-4e-24 4e-24]; > cfg.marker = 'on'; > cfg.layout = 'neuromag306cmb.lay'; > figure ; > ft_topoplotTFR(cfg, TFR_left_MEG_comb);print -dpng natmeg_freq13.png > > Thus, it should be possible to use ft_combineplanar for neuromag data. > What do you think? > > Cheers > Victoria > > 2016-01-16 18:00 GMT+00:00 Tzvetan Popov : > >> Dear Victoria, >> you should remove the ft_combineplanar step from your analysis pipeline. >> This function takes input from ft_megplanar. The latter is applied only to >> magnetometers or axial gradiometers. >> >> best >> tzvetan >> >> >> Hi ! >> >> I am working with a neuromag system and want to do cluster based >> permutation tests with time frequency data. However, before running the >> stats i would like to check the clusters which are formed by >> ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the >> plot and clicking on the channels i would expect to see something like : >> >> *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, >> MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, >> MEG1242+1243* >> >> *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, >> MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, >> MEG2242+2243* >> >> however what i see is: >> >> *Selected channel MEG0741, which has 0 neighbours: * >> *Selected channel MEG0731, which has 0 neighbours: * >> *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, >> MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, >> MEG2242+2243* >> *Selected channel MEG0711, which has 0 neighbours: * >> *Selected channel MEG0741, which has 0 neighbours: * >> >> It is absolutely random when the correct output occurs. When clicking on >> a particular channel it would randomly show me the following results: >> >> *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, >> MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, >> MEG1242+1243* >> >> or >> >> *Selected channel MEG1031, which has 0 neighbours: * >> >> Do you have any suggestions why this happen? Are the channels not grouped >> correctly? >> >> Below is the code starting from the time-frequency analysis of the data. >> >> Thank you very much >> Victoria >> >> cfg = []; >> cfg.output = 'pow'; >> cfg.channel = 'MEGGRAD'; >> cfg.method = 'mtmconvol'; >> cfg.taper = 'hanning'; >> cfg.foi = [2:2:30]; >> %cfg.keeptrials = 'yes'; for stats keep trials >> cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time >> window = 0.5 sec >> cfg.toi = [-1.3:0.05:1]; >> cfg.keeptrials = 'yes'; >> FreqCon = ft_freqanalysis(cfg, Con_clean); >> FreqIncon = ft_freqanalysis(cfg, Incon_clean); >> >> %combine planar >> cfg = []; >> cfg.method ='sum'; >> ComCon = ft_combineplanar(cfg,FreqCon); >> ComIncon = ft_combineplanar(cfg, FreqIncon); >> >> % plot neighbours >> cfg=[]; >> cfg.method = 'triangulation'; >> cfg.layout = 'neuromag306cmb.lay'; >> ft_neighbourplot(cfg,ComCon) >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Combineplanar.PNG Type: image/png Size: 38714 bytes Desc: not available URL: From mail at philipp-ruhnau.de Mon Jan 18 18:00:59 2016 From: mail at philipp-ruhnau.de (Philipp Ruhnau) Date: Mon, 18 Jan 2016 18:00:59 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: Dear Victoria, I think there might be something odd with the channel selection in your data (or maybe also something that happens in ft_neighborplot) as I see it you have two options 1) I would instead suggest to use ft_prepare neighbors with your data as input cfg = [] cfg.method = ‘triangulation’ cfg.feedback = ‘yes’ % with this you get the feedback plot neigh = ft_prepare_neighbours(cfg, your_data) I am not entirely sure which layout the function uses if you feed in the default layout (which should be fine though), but I think it still uses the data’s for me clicking in the function didn’t work properly, but I think that is a different (gui?) issue, more importantly however the graphical layout and the labels that are grouped make sense that’s also true for what you posted. the only thing odd there is that your neighbor-structure still has magnetometers (MEG***1) that should have been removed, thus my hunch that they are somehow still in the data you feed in to ft_neighbourplot [i just quickly try and I can to a certain extend replicate your problem, but not fully as clicking doesn’t work…but also all the magnetometers with 0 neighbours] and as Tzvetan said, one magnetometer and two gradiometers are in the same position, so I would expect an alternating output between, say, MEG1031 and MEG1032+1033 the easiest thing you can try is use ft_selectdata again before you create the neighbors cfg = []; cfg.channel = ‘MEGGRAD’; data = ft_selectdata(cfg, data) just as a check, if your problem vanishes, the mags were still in there somewhere. 2) just load the default/use the layout field with the function above without the data input. then for me the plotting works and the output is like you predicted cfg = [] cfg.method = ‘triangulation’ cfg.feedback = ‘yes’ % with this you get the feedback plot cfg.layout = ‘neuromag306cmb.lay' neigh = ft_prepare_neighbours(cfg) as for the whether you should use ft_combineplanar. as a neuromag user myself I always use it for plotting but also for statistics, similar to what the wiki says, so I’m a little confused there too. of course you can plot them each of course. I don’t think you need to specify the combination method there though, as ‘sum’ is default for power. cheers philipp > On 16 Jan 2016, at 18:26, victoria schroeder wrote: > > Hi ! > > I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > > however what i see is: > > Selected channel MEG0741, which has 0 neighbours: > Selected channel MEG0731, which has 0 neighbours: > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > Selected channel MEG0711, which has 0 neighbours: > Selected channel MEG0741, which has 0 neighbours: > > It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > > or > > Selected channel MEG1031, which has 0 neighbours: > > Do you have any suggestions why this happen? Are the channels not grouped correctly? > > Below is the code starting from the time-frequency analysis of the data. > > Thank you very much > Victoria > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEGGRAD'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = [2:2:30]; > %cfg.keeptrials = 'yes'; for stats keep trials > cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec > cfg.toi = [-1.3:0.05:1]; > cfg.keeptrials = 'yes'; > FreqCon = ft_freqanalysis(cfg, Con_clean); > FreqIncon = ft_freqanalysis(cfg, Incon_clean); > > %combine planar > cfg = []; > cfg.method ='sum'; > ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > % plot neighbours > cfg=[]; > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg,ComCon) > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon Jan 18 18:57:57 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 Jan 2016 18:57:57 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> Message-ID: <7B5CC5BE-033A-41D6-8112-331FE3B71580@uni-konstanz.de> Hi Victoria, oopsy, I think I confused you dramatically. I’m sorry for this. You are right I was only scrolling up to the part where the mags were analyzed. As for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can threat them separately, as I was naively thinking as non-neuormag user, but indeed combination of both is recommended as I have now learned :-)(thanks Phillip). I ran the following steps and I guess this should work for you. best tzvetan %% cfg = []; ComCon = ft_combineplanar(cfg,FreqCon); %% cfg = [] cfg.method = 'triangulation'; cfg.layout = 'neuromag306cmb.lay'; cfg.senstype = 'MEG'; neighbours = ft_prepare_neighbours(cfg, ComCon) %% % plot neighbours cfg=[]; cfg.neighbours = neighbours; cfg.layout = 'neuromag306cmb.lay'; ft_neighbourplot(cfg); -------------- next part -------------- An HTML attachment was scrubbed... URL: From jim.f.cav at gmail.com Mon Jan 18 20:47:45 2016 From: jim.f.cav at gmail.com (Jim Cavanagh) Date: Mon, 18 Jan 2016 12:47:45 -0700 Subject: [FieldTrip] Restrict source reconstruction to gray matter: Any updates? Message-ID: Has there been any followup on this thread? I'm finding it rather difficult to constrain the source projection to grey matter only - surely someone else has tried this using FT? http://mailman.science.ru.nl/pipermail/fieldtrip/2012-March/004984.html -- Jim Cavanagh Assistant Professor University of New Mexico https://sites.google.com/site/jcavanaghunm/home -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Tue Jan 19 15:35:00 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Tue, 19 Jan 2016 15:35:00 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de> Dear community, My name is Laith Hamid and I am working in the University Medical Complex of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and seizures. Currently I am analysing an EEG data set that was recorded using a 256-channel EGI system and I wanted to ask whether you have a standard BEM or FEM head model that extends enough downwards to accomodate all 256 electrodes. The current standard BEM model in the template folder of Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. Thank you very much in advance for your help! Best, Laith -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Jan 19 16:16:54 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 19 Jan 2016 16:16:54 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps In-Reply-To: <0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de> References: <0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de> Message-ID: Dear Laith, thanks for your question. You could refer to a factory schematic layout such as the one in figure 4 of this publication: http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract and subsequently use the function ft_prepare_layout to manually track the points of the custom design on your own (if you dont want to wait for somebody from the FT to do the same for you). cfg = []; cfg.image = 'figure4_layout_256_Frontiers.png'; lay = ft_prepare_layout(cfg); The following tutorial describes the procedure in more details: http://www.fieldtriptoolbox.org/tutorial/layout Please do not hesitate to get in touch with me for this and other matters. All the best Cris Micheli On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid wrote: > Dear community, > > My name is Laith Hamid and I am working in the University Medical Complex > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > seizures. Currently I am analysing an EEG data set that was recorded using > a 256-channel EGI system and I wanted to ask whether you have a standard > BEM or FEM head model that extends enough downwards to accomodate all 256 > electrodes. The current standard BEM model in the template folder of > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > Thank you very much in advance for your help! > > Best, > > Laith > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Tue Jan 19 17:41:48 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Tue, 19 Jan 2016 17:41:48 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de> Dear Cris, thank you very much for your answer. I am refering to an issue that was discussed in this thread from April 2013: [FieldTrip] source analysis EEG data without MRI The thread however does not offer a segmentation or head model for download. Some electrodes in the EGI 256-electrodes cap are placed on the cheeks or on the back of the neck and these areas are not modeled by the standard BEM skin compartment in the standard BEM model. My question was about a standard segmentation that extends the skin (and skull) compartment downwards to allow these electrodes to sit on the nodes of the skin mesh. Best, Laith -------------- next part -------------- An HTML attachment was scrubbed... URL: From aishwaryaselvaraj1708 at gmail.com Tue Jan 19 17:52:55 2016 From: aishwaryaselvaraj1708 at gmail.com (aishwarya selvaraj) Date: Tue, 19 Jan 2016 16:52:55 +0000 Subject: [FieldTrip] Source Localisation Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> Hi guys, I'm currently working on source localization of EEG signals . Im very new to it . Can Anyone provide any inputs ?? It would be of great help . -- Regards, Aishwarya -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Homolle at donders.ru.nl Tue Jan 19 18:06:13 2016 From: S.Homolle at donders.ru.nl (=?iso-8859-1?Q?Hom=F6lle=2C_S=2E_=28Simon=29?=) Date: Tue, 19 Jan 2016 17:06:13 +0000 Subject: [FieldTrip] Source Localisation In-Reply-To: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> References: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> Message-ID: <2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl> Dear Aishwarya, Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. My recommended start would be: http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate Hopefully this provides you good start working with EEG source reconstruction Best regards, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] Sent: Tuesday, January 19, 2016 5:52 PM To: fieldtrip, donders Subject: [FieldTrip] Source Localisation Hi guys, I'm currently working on source localization of EEG signals . Im very new to it . Can Anyone provide any inputs ?? It would be of great help . -- Regards, Aishwarya -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Tue Jan 19 18:49:21 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Tue, 19 Jan 2016 17:49:21 +0000 Subject: [FieldTrip] plotting neighbours In-Reply-To: <7B5CC5BE-033A-41D6-8112-331FE3B71580@uni-konstanz.de> References: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> <7B5CC5BE-033A-41D6-8112-331FE3B71580@uni-konstanz.de> Message-ID: Thank you very much Philipp and Tzvetan! Things have become much clearer now. I would like to follow up with a very related question. I am trying to replicate the analysis for the cluster based permutation test using the code and the data provided. However, i run into two problems here First, i get the following error if i use the original code: Attempted to access cfg.frequency(2); index out of bounds because numel(cfg.frequency)=1. Error in ft_freqstatistics (line 187) cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. However, then no significant clusters are found. Which becomes clear when trying to plot the cluster or by looking at the output of ft_freqstatistics. Does the change in the code , change the output? How can i avoid the error mentioned above and still get the same output from ft_freqstatistics as the one provided on the webpage? The relevant section of the toturial is provided below. Thank you! Victoria Permutation test Now, run *ft_freqstatistics * to compare freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, the following configuration is identical to the configuration that was used for comparing event-related averages in the cluster-based permutation tests on event related fields tutorial . Also see this tutorial for a detailed explanation of all the configuration settings. You can read more about the *ft_prepare_neighbours * function in the FAQ's . To load the planar gradient TFRs (also available on the FieldTrip FTP servers,freqFIC_planar_cmb.mat and freqFC_planar_cmb.mat ), use: load freqFIC_planar_cmb load freqFC_planar_cmb cfg = []; cfg.channel = {'MEG', '-MLP31', '-MLO12'}; cfg.latency = 'all'; cfg.frequency = 20; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; % prepare_neighbours determines what sensors may form clusters cfg_neighb.method = 'distance'; cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + size(freqFC_planar_cmb.powspctrm,1)); design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... size(freqFC_planar_cmb.powspctrm,1))) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > Hi Victoria, > > oopsy, I think I confused you dramatically. I’m sorry for this. You are > right I was only scrolling up to the part where the mags were analyzed. As > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > threat them separately, as I was naively thinking as non-neuormag user, but > indeed combination of both is recommended as I have now learned :-)(thanks > Phillip). I ran the following steps and I guess this should work for you. > best > tzvetan > > %% > cfg = []; > ComCon = ft_combineplanar(cfg,FreqCon); > %% > cfg = [] > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > cfg.senstype = 'MEG'; > neighbours = ft_prepare_neighbours(cfg, ComCon) > %% > % plot neighbours > cfg=[]; > cfg.neighbours = neighbours; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg); > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Jan 19 20:50:24 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 19 Jan 2016 20:50:24 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps In-Reply-To: <61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de> References: <61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de> Message-ID: Dear Laith, this might be possible if you have the subject-specific MRI by following the tutorial here: http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem and using the function ft_prepare_mesh and the tutorial command: cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); which uses the segmented MRI (see tutorial). The bnd(3) variable should contain your triangulated surface with 1000 vertices. Let me know if that works. Of course you should see the skin and the neck in the original MRI. If you do not have an anatomical MRI that extends down to the chin you could try with a template, such as this: ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri and the corresponding segmented version ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat This goes down to the chin. Then you take care of rearranging the position of the EEG electrodes according to this: http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel I hope this helped Cris On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid wrote: > Dear Cris, > > thank you very much for your answer. I am refering to an issue that was > discussed in this thread from April 2013: > > > [FieldTrip] source analysis EEG data without MRI > > > The thread however does not offer a segmentation or head model for > download. Some electrodes in the EGI 256-electrodes cap are placed on the > cheeks or on the back of the neck and these areas are not modeled by the > standard BEM skin compartment in the standard BEM model. My question was > about a standard segmentation that extends the skin (and skull) compartment > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > Best, > Laith > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From munsif.jatoi at gmail.com Wed Jan 20 05:17:12 2016 From: munsif.jatoi at gmail.com (Munsif Jatoi) Date: Wed, 20 Jan 2016 12:17:12 +0800 Subject: [FieldTrip] Source Localisation In-Reply-To: <2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl> References: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> <2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl> Message-ID: Dear Aishwarya, Please refer to main help tutorials. Also, you can find out the survey papers written in this area. For more, SPM website can provide good help. Best, Munsif. On Wed, Jan 20, 2016 at 1:06 AM, Homölle, S. (Simon) < S.Homolle at donders.ru.nl> wrote: > Dear Aishwarya, > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > My recommended start would be: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > Hopefully this provides you good start working with EEG source > reconstruction > > Best regards, > > Simon Homölle > PhD Candidate > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Phone: +31-(0)24-36-65059 > ------------------------------ > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > *Sent:* Tuesday, January 19, 2016 5:52 PM > *To:* fieldtrip, donders > *Subject:* [FieldTrip] Source Localisation > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Munsif Ali H.Jatoi, Ph D Scholar, Centre for Intelligent Signals and Imaging Research, Universiti Teknologi PETRONAS, Malaysia. http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: From olga.v.sysoeva at gmail.com Wed Jan 20 11:36:16 2016 From: olga.v.sysoeva at gmail.com (Olga Sysoeva) Date: Wed, 20 Jan 2016 13:36:16 +0300 Subject: [FieldTrip] problems with mri interpolation Message-ID: Dear Fieldtrippers, I'm encounter the problem with MRI interpolation and reslicing using FT_VOLUMERESLICE. I have read my MRI from fif.file and this mri variable contains mri_K0012.unit, 'm' mri_K0012.dim, [432, 512, 180] mri_K0012.anatomy, <432, 512, 180 int16> mri_K0012.hdr, (1*1 structure) mri_K0012.transform, (4*4 double) mri_K0012.coordsys 'neuromag'. Than I used mri = ft_volumereslice([], mri); the output is “the input is volume data with dimensions [432 512 180] reslicing from [432 512 180] to [256 256 256] the input is volume data with dimensions [256 256 256] the input is volume data with dimensions [432 512 180] selecting subvolume of 0.0% reslicing and interpolating anatomy interpolating ??? Attempted to access sel(1); index out of bounds because numel(sel)=0. Error in ==> ft_sourceinterpolate>my_interpn at 663 ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ==> ft_sourceinterpolate at 583 av( sel) = my_interpn(fv, ax(sel), ay(sel), az(sel), cfg.interpmethod, cfg.feedback); Error in ==> ft_volumereslice at 176 resliced = ft_sourceinterpolate(tmpcfg, mri, resliced);” I'm using matlab 7.6.0 (R2008a) and recently downloaded fieltrip (also in my previous version of 2013 the error was the same). I'd be thankful for the comments. Best Regards, Olga. P.S.Actually, I can project my sources meaningfully into not interpolated MRI, altoough the images are plotted upside down. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Wed Jan 20 13:39:30 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Wed, 20 Jan 2016 13:39:30 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1@mail.uni-kiel.de> Dear Cris, thank you very much for your answers yesterday. The segmentedmri contained 'white', 'grey' and 'csf' so I needed to repeat the segmentation using 'brain', 'skull' and 'scalp' as described in the tutorial "Creating a BEM volume conduction model of the head for source-reconstruction of EEG data" and everything worked smoothly afterwards. The problem is solved now. Best, Laith -------------- next part -------------- An HTML attachment was scrubbed... URL: From RICHARDS at mailbox.sc.edu Wed Jan 20 15:39:13 2016 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Wed, 20 Jan 2016 14:39:13 +0000 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps (Laith Hamid) Message-ID: Laith: I have a “neurodevelopmental MRI database” (Richards, Sanchez et al., 2015; see my www site) that has average MRI templates that could be used. Each average has the whole head down to about the top of the neck. I did these purposely since I use EEG recording and the MNI template did not even go down far enough for the EGI 128 channel net. The database has average MRI templates for head (T1, T2) and brain. I also have FEM segmented heads for the entire head that could be used for this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, scalp), but ironically, I cut these off about 10% below the EGI 128 channel electrodes. However, you could use the three inner compartments for this and just add the rest of the head below the compartment—or use the whole-head FEM as is for a FEM-model, or use the segmented area below the skull for a whole-head BEM model. I also have average 128-channel EGI electrodes for each template. Additionally, the “developmental” part of the “neurodevelopmental MRI database” is that I have these for a wide range of ages (all ages?). I have a average for young adults (20-24 yrs), and average templates and FEM/BEM models for groups from 3 months through adulthood, and into late adulthood. So if you have specific neuro-pediatric applications you might be interested in using an age appropriate MRI average template rather than an adult template. See my www site for journal article references re this, and http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ Finally… I have been using these head models for FT-based FEM and BEM models. Possibly some of the actually field trip models I have would be useful to you. Some of the parts of the model do not use the electrodes (e.g., grid-dipoles, head-model) whereas the final models (leadfield) requires the electrode locations. The database also includes “virtual” electrodes for the 10-10 system, which might be used to generate the 256 channel locations by knowing the relation between the 10-10 system and the EGI system based on EGI ELP files for the 256 channels. John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: richards-john at sc.edu HTTP: jerlab.psych.sc.edu *********************************************** >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 19 Jan 2016 15:35:00 +0100 >From: Laith Hamid >To: fieldtrip at science.ru.nl >Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> >Content-Type: text/plain; charset="us-ascii" > > > >Dear community, > >My name is Laith Hamid and I am working in the University Medical >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic >spikes and seizures. Currently I am analysing an EEG data set that was >recorded using a 256-channel EGI system and I wanted to ask whether you >have a standard BEM or FEM head model that extends enough downwards to >accomodate all 256 electrodes. The current standard BEM model in the >template folder of Fieldtrip isn't appropriate for source analysis of >256-channel EGI data. > >Thank you very much in advance for your help! > >Best, > >Laith From saeedzahran at hotmail.com Wed Jan 20 18:37:32 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Wed, 20 Jan 2016 19:37:32 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 In-Reply-To: References: Message-ID: Dear Fieldtrip community, I define the volume conductor as: vol = []; vol.bnd(1).pnt=skinpnt vol.bnd(1).tri=skinf vol.bnd(2).pnt=uteruspnt vol.bnd(2).tri=uterusf vol.bnd(3).pnt=uterinecontentpnt vol.bnd(3).tri=uterinecontentf vol.cond = c; But it result with the below error: Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); Thank you very much in advance for your help! Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 18 > To: fieldtrip at science.ru.nl > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 3. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 4. Source Localisation (aishwarya selvaraj) > 5. Re: Source Localisation (Hom?lle) > 6. Re: plotting neighbours (victoria schroeder) > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 8. Re: Source Localisation (Munsif Jatoi) > 9. problems with mri interpolation (Olga Sysoeva) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 19 Jan 2016 15:35:00 +0100 > From: Laith Hamid > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear community, > > My name is Laith Hamid and I am working in the University Medical > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and seizures. Currently I am analysing an EEG data set that was > recorded using a 256-channel EGI system and I wanted to ask whether you > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); model that extends enough downwards to > accomodate all 256 electrodes. The current standard BEM model in the > template folder of Fieldtrip isn't appropriate for source analysis of > 256-channel EGI data. > > Thank you very much in advance for your help! > > Best, > > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Tue, 19 Jan 2016 16:16:54 +0100 > From: Cristiano Micheli > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > thanks for your question. You could refer to a factory schematic layout > such as the one in figure 4 of this publication: > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > and subsequently use the function ft_prepare_layout to manually track the > points of the custom design on your own (if you dont want to wait for > somebody from the FT to do the same for you). > > cfg = []; > cfg.image = 'figure4_layout_256_Frontiers.png'; > lay = ft_prepare_layout(cfg); > > The following tutorial describes the procedure in more details: > http://www.fieldtriptoolbox.org/tutorial/layout > > Please do not hesitate to get in touch with me for this and other matters. > > All the best > Cris Micheli > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > wrote: > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical Complex > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > seizures. Currently I am analysing an EEG data set that was recorded using > > a 256-channel EGI system and I wanted to ask whether you have a standard > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > electrodes. The current standard BEM model in the template folder of > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Tue, 19 Jan 2016 17:41:48 +0100 > From: Laith Hamid > To: Fieldtrip > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear Cris, > > thank you very much for your answer. I am refering to an issue that was > discussed in this thread from April 2013: > > [FieldTrip] source analysis EEG data without MRI > > The thread however does not offer a segmentation or head model for > download. Some electrodes in the EGI 256-electrodes cap are placed on > the cheeks or on the back of the neck and these areas are not modeled by > the standard BEM skin compartment in the standard BEM model. My question > was about a standard segmentation that extends the skin (and skull) > compartment downwards to allow these electrodes to sit on the nodes of > the skin mesh. > > Best, > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Tue, 19 Jan 2016 16:52:55 +0000 > From: aishwarya selvaraj > To: "fieldtrip, donders" > Subject: [FieldTrip] Source Localisation > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 5 > Date: Tue, 19 Jan 2016 17:06:13 +0000 > From: Hom?lle, S. (Simon) > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Aishwarya, > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > My recommended start would be: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > Hopefully this provides you good start working with EEG source reconstruction > > Best regards, > > Simon Hom?lle > PhD Candidate > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Phone: +31-(0)24-36-65059 > ________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > Sent: Tuesday, January 19, 2016 5:52 PM > To: fieldtrip, donders > Subject: [FieldTrip] Source Localisation > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 6 > Date: Tue, 19 Jan 2016 17:49:21 +0000 > From: victoria schroeder > To: FieldTrip discussion list > Subject: Re: [FieldTrip] plotting neighbours > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Thank you very much Philipp and Tzvetan! > > Things have become much clearer now. > > I would like to follow up with a very related question. I am trying to > replicate the analysis for the cluster based permutation test using the > code and the data provided. However, i run into two problems here > > First, i get the following error if i use the original code: > Attempted to access cfg.frequency(2); index out of bounds because > numel(cfg.frequency)=1. > > Error in ft_freqstatistics (line 187) > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > However, then no significant clusters are found. Which becomes clear when > trying to plot the cluster or by looking at the output of > ft_freqstatistics. > > Does the change in the code , change the output? How can i avoid the error > mentioned above and still get the same output from ft_freqstatistics as the > one provided on the webpage? > > > The relevant section of the toturial is provided below. > Thank you! > > Victoria > > Permutation test > > Now, run *ft_freqstatistics > * to compare > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > the following configuration is identical to the configuration that was used > for comparing event-related averages in the cluster-based permutation tests > on event related fields tutorial > . > Also see this tutorial > for > a detailed explanation of all the configuration settings. You can read more > about the *ft_prepare_neighbours > * function > in the FAQ's > . > > To load the planar gradient TFRs (also available on the FieldTrip FTP > servers,freqFIC_planar_cmb.mat > > and freqFC_planar_cmb.mat > ), > use: > > load freqFIC_planar_cmb > load freqFC_planar_cmb > > cfg = []; > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > cfg.latency = 'all'; > cfg.frequency = 20; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > % prepare_neighbours determines what sensors may form clusters > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > size(freqFC_planar_cmb.powspctrm,1)); > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > cfg.design = design; > cfg.ivar = 1; > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > > > > Hi Victoria, > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > right I was only scrolling up to the part where the mags were analyzed. As > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > threat them separately, as I was naively thinking as non-neuormag user, but > > indeed combination of both is recommended as I have now learned :-)(thanks > > Phillip). I ran the following steps and I guess this should work for you. > > best > > tzvetan > > > > %% > > cfg = []; > > ComCon = ft_combineplanar(cfg,FreqCon); > > %% > > cfg = [] > > cfg.method = 'triangulation'; > > cfg.layout = 'neuromag306cmb.lay'; > > cfg.senstype = 'MEG'; > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > %% > > % plot neighbours > > cfg=[]; > > cfg.neighbours = neighbours; > > cfg.layout = 'neuromag306cmb.lay'; > > ft_neighbourplot(cfg); > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 7 > Date: Tue, 19 Jan 2016 20:50:24 +0100 > From: Cristiano Micheli > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > this might be possible if you have the subject-specific MRI by following > the tutorial here: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > and using the function ft_prepare_mesh and the tutorial command: > > cfg=[]; > cfg.tissue={'brain','skull','scalp'}; > cfg.numvertices = [3000 2000 1000]; > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > contain your triangulated surface with 1000 vertices. Let me know if that > works. Of course you should see the skin and the neck in the original MRI. > > If you do not have an anatomical MRI that extends down to the chin you > could try with a template, such as this: > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > and the corresponding segmented version > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > This goes down to the chin. Then you take care of rearranging the position > of the EEG electrodes according to this: > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > I hope this helped > Cris > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > wrote: > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > cheeks or on the back of the neck and these areas are not modeled by the > > standard BEM skin compartment in the standard BEM model. My question was > > about a standard segmentation that extends the skin (and skull) compartment > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > Best, > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 8 > Date: Wed, 20 Jan 2016 12:17:12 +0800 > From: Munsif Jatoi > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Aishwarya, > > Please refer to main help tutorials. > > Also, you can find out the survey papers written in this area. For more, > SPM website can provide good help. > > Best, > Munsif. > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > S.Homolle at donders.ru.nl> wrote: > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source > > reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ------------------------------ > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > *To:* fieldtrip, donders > > *Subject:* [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > Munsif Ali H.Jatoi, > > Ph D Scholar, > Centre for Intelligent Signals and Imaging Research, > Universiti Teknologi PETRONAS, > Malaysia. > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 9 > Date: Wed, 20 Jan 2016 13:36:16 +0300 > From: Olga Sysoeva > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] problems with mri interpolation > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > > I'm encounter the problem with MRI interpolation and reslicing using > > FT_VOLUMERESLICE. > > I have read my MRI from fif.file and this mri variable contains > > mri_K0012.unit, 'm' > > mri_K0012.dim, [432, 512, 180] > > mri_K0012.anatomy, <432, 512, 180 int16> > > mri_K0012.hdr, (1*1 structure) > > mri_K0012.transform, (4*4 double) > > mri_K0012.coordsys 'neuromag'. > > > Than I used > > > mri = ft_volumereslice([], mri); > > > the output is > > > ?the input is volume data with dimensions [432 > 512 180] > > reslicing from [432 512 180] to [256 256 256] > > the input is volume data with dimensions [256 > 256 256] > > the input is volume data with dimensions [432 > 512 180] > > selecting subvolume of 0.0% > > reslicing and interpolating anatomy > > interpolating > > ??? Attempted to access sel(1); index out of > bounds because numel(sel)=0. > > > Error in ==> ft_sourceinterpolate>my_interpn > at 663 > > ft_progress(sel(1)/num, 'interpolating > %.1f%%\n', 100*sel(1)/num); > > > Error in ==> ft_sourceinterpolate at 583 > > av( sel) = my_interpn(fv, ax(sel), > ay(sel), az(sel), cfg.interpmethod, > > cfg.feedback); > > > Error in ==> ft_volumereslice at 176 > > resliced = ft_sourceinterpolate(tmpcfg, mri, > resliced);? > > > I'm using matlab 7.6.0 (R2008a) and recently > downloaded fieltrip (also in my previous version of 2013 the error > was the same). > > > I'd be thankful for the comments. > > > Best Regards, > > Olga. > > P.S.Actually, I can project my sources > meaningfully into not interpolated MRI, altoough the images are > plotted upside down. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 18 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jan 21 09:16:55 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 21 Jan 2016 08:16:55 +0000 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 In-Reply-To: References: Message-ID: Saeed, are you using 0 or 1 indexing for your triangles? You probably want to use 1 indexing. Best, Jan-Mathijs On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: Dear Fieldtrip community, I define the volume conductor as: vol = []; vol.bnd(1).pnt=skinpnt vol.bnd(1).tri=skinf vol.bnd(2).pnt=uteruspnt vol.bnd(2).tri=uterusf vol.bnd(3).pnt=uterinecontentpnt vol.bnd(3).tri=uterinecontentf vol.cond = c; But it result with the below error: Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); Thank you very much in advance for your help! Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 18 > To: fieldtrip at science.ru.nl > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 3. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 4. Source Localisation (aishwarya selvaraj) > 5. Re: Source Localisation (Hom?lle) > 6. Re: plotting neighbours (victoria schroeder) > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 8. Re: Source Localisation (Munsif Jatoi) > 9. problems with mri interpolation (Olga Sysoeva) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 19 Jan 2016 15:35:00 +0100 > From: Laith Hamid > > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear community, > > My name is Laith Hamid and I am working in the University Medical > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and seizures. Currently I am analysing an EEG data set that was > recorded using a 256-channel EGI system and I wanted to ask whether you > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); model that extends enough downwards to > accomodate all 256 electrodes. The current standard BEM model in the > template folder of Fieldtrip isn't appropriate for source analysis of > 256-channel EGI data. > > Thank you very much in advance for your help! > > Best, > > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Tue, 19 Jan 2016 16:16:54 +0100 > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > thanks for your question. You could refer to a factory schematic layout > such as the one in figure 4 of this publication: > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > and subsequently use the function ft_prepare_layout to manually track the > points of the custom design on your own (if you dont want to wait for > somebody from the FT to do the same for you). > > cfg = []; > cfg.image = 'figure4_layout_256_Frontiers.png'; > lay = ft_prepare_layout(cfg); > > The following tutorial describes the procedure in more details: > http://www.fieldtriptoolbox.org/tutorial/layout > > Please do not hesitate to get in touch with me for this and other matters. > > All the best > Cris Micheli > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > wrote: > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical Complex > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > seizures. Currently I am analysing an EEG data set that was recorded using > > a 256-channel EGI system and I wanted to ask whether you have a standard > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > electrodes. The current standard BEM model in the template folder of > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Tue, 19 Jan 2016 17:41:48 +0100 > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear Cris, > > thank you very much for your answer. I am refering to an issue that was > discussed in this thread from April 2013: > > [FieldTrip] source analysis EEG data without MRI > > The thread however does not offer a segmentation or head model for > download. Some electrodes in the EGI 256-electrodes cap are placed on > the cheeks or on the back of the neck and these areas are not modeled by > the standard BEM skin compartment in the standard BEM model. My question > was about a standard segmentation that extends the skin (and skull) > compartment downwards to allow these electrodes to sit on the nodes of > the skin mesh. > > Best, > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Tue, 19 Jan 2016 16:52:55 +0000 > From: aishwarya selvaraj > > To: "fieldtrip, donders" > > Subject: [FieldTrip] Source Localisation > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 5 > Date: Tue, 19 Jan 2016 17:06:13 +0000 > From: Hom?lle, S. (Simon) > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Aishwarya, > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > My recommended start would be: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > Hopefully this provides you good start working with EEG source reconstruction > > Best regards, > > Simon Hom?lle > PhD Candidate > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Phone: +31-(0)24-36-65059 > ________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > Sent: Tuesday, January 19, 2016 5:52 PM > To: fieldtrip, donders > Subject: [FieldTrip] Source Localisation > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 6 > Date: Tue, 19 Jan 2016 17:49:21 +0000 > From: victoria schroeder > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] plotting neighbours > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Thank you very much Philipp and Tzvetan! > > Things have become much clearer now. > > I would like to follow up with a very related question. I am trying to > replicate the analysis for the cluster based permutation test using the > code and the data provided. However, i run into two problems here > > First, i get the following error if i use the original code: > Attempted to access cfg.frequency(2); index out of bounds because > numel(cfg.frequency)=1. > > Error in ft_freqstatistics (line 187) > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > However, then no significant clusters are found. Which becomes clear when > trying to plot the cluster or by looking at the output of > ft_freqstatistics. > > Does the change in the code , change the output? How can i avoid the error > mentioned above and still get the same output from ft_freqstatistics as the > one provided on the webpage? > > > The relevant section of the toturial is provided below. > Thank you! > > Victoria > > Permutation test > > Now, run *ft_freqstatistics > * to compare > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > the following configuration is identical to the configuration that was used > for comparing event-related averages in the cluster-based permutation tests > on event related fields tutorial > . > Also see this tutorial > for > a detailed explanation of all the configuration settings. You can read more > about the *ft_prepare_neighbours > * function > in the FAQ's > . > > To load the planar gradient TFRs (also available on the FieldTrip FTP > servers,freqFIC_planar_cmb.mat > > and freqFC_planar_cmb.mat > ), > use: > > load freqFIC_planar_cmb > load freqFC_planar_cmb > > cfg = []; > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > cfg.latency = 'all'; > cfg.frequency = 20; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > % prepare_neighbours determines what sensors may form clusters > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > size(freqFC_planar_cmb.powspctrm,1)); > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > cfg.design = design; > cfg.ivar = 1; > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > Hi Victoria, > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > right I was only scrolling up to the part where the mags were analyzed. As > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > threat them separately, as I was naively thinking as non-neuormag user, but > > indeed combination of both is recommended as I have now learned :-)(thanks > > Phillip). I ran the following steps and I guess this should work for you. > > best > > tzvetan > > > > %% > > cfg = []; > > ComCon = ft_combineplanar(cfg,FreqCon); > > %% > > cfg = [] > > cfg.method = 'triangulation'; > > cfg.layout = 'neuromag306cmb.lay'; > > cfg.senstype = 'MEG'; > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > %% > > % plot neighbours > > cfg=[]; > > cfg.neighbours = neighbours; > > cfg.layout = 'neuromag306cmb.lay'; > > ft_neighbourplot(cfg); > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 7 > Date: Tue, 19 Jan 2016 20:50:24 +0100 > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > this might be possible if you have the subject-specific MRI by following > the tutorial here: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > and using the function ft_prepare_mesh and the tutorial command: > > cfg=[]; > cfg.tissue={'brain','skull','scalp'}; > cfg.numvertices = [3000 2000 1000]; > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > contain your triangulated surface with 1000 vertices. Let me know if that > works. Of course you should see the skin and the neck in the original MRI. > > If you do not have an anatomical MRI that extends down to the chin you > could try with a template, such as this: > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > and the corresponding segmented version > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > This goes down to the chin. Then you take care of rearranging the position > of the EEG electrodes according to this: > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > I hope this helped > Cris > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > wrote: > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > cheeks or on the back of the neck and these areas are not modeled by the > > standard BEM skin compartment in the standard BEM model. My question was > > about a standard segmentation that extends the skin (and skull) compartment > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > Best, > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 8 > Date: Wed, 20 Jan 2016 12:17:12 +0800 > From: Munsif Jatoi > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Aishwarya, > > Please refer to main help tutorials. > > Also, you can find out the survey papers written in this area. For more, > SPM website can provide good help. > > Best, > Munsif. > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > S.Homolle at donders.ru.nl> wrote: > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source > > reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ------------------------------ > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > *To:* fieldtrip, donders > > *Subject:* [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > Munsif Ali H.Jatoi, > > Ph D Scholar, > Centre for Intelligent Signals and Imaging Research, > Universiti Teknologi PETRONAS, > Malaysia. > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 9 > Date: Wed, 20 Jan 2016 13:36:16 +0300 > From: Olga Sysoeva > > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] problems with mri interpolation > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > > I'm encounter the problem with MRI interpolation and reslicing using > > FT_VOLUMERESLICE. > > I have read my MRI from fif.file and this mri variable contains > > mri_K0012.unit, 'm' > > mri_K0012.dim, [432, 512, 180] > > mri_K0012.anatomy, <432, 512, 180 int16> > > mri_K0012.hdr, (1*1 structure) > > mri_K0012.transform, (4*4 double) > > mri_K0012.coordsys 'neuromag'. > > > Than I used > > > mri = ft_volumereslice([], mri); > > > the output is > > > ?the input is volume data with dimensions [432 > 512 180] > > reslicing from [432 512 180] to [256 256 256] > > the input is volume data with dimensions [256 > 256 256] > > the input is volume data with dimensions [432 > 512 180] > > selecting subvolume of 0.0% > > reslicing and interpolating anatomy > > interpolating > > ??? Attempted to access sel(1); index out of > bounds because numel(sel)=0. > > > Error in ==> ft_sourceinterpolate>my_interpn > at 663 > > ft_progress(sel(1)/num, 'interpolating > %.1f%%\n', 100*sel(1)/num); > > > Error in ==> ft_sourceinterpolate at 583 > > av( sel) = my_interpn(fv, ax(sel), > ay(sel), az(sel), cfg.interpmethod, > > cfg.feedback); > > > Error in ==> ft_volumereslice at 176 > > resliced = ft_sourceinterpolate(tmpcfg, mri, > resliced);? > > > I'm using matlab 7.6.0 (R2008a) and recently > downloaded fieltrip (also in my previous version of 2013 the error > was the same). > > > I'd be thankful for the comments. > > > Best Regards, > > Olga. > > P.S.Actually, I can project my sources > meaningfully into not interpolated MRI, altoough the images are > plotted upside down. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 18 > ***************************************** _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Thu Jan 21 12:06:13 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Thu, 21 Jan 2016 12:06:13 +0100 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 In-Reply-To: References: Message-ID: Hi Saeed, if the content of your triangulation connectivity matrices *skinf, uterusf, **uterinecontentf* is not made of integers you probably get the error you mentioned. Could this be the case? Out of curiosity, are you doing fetal recordings? Cris On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran wrote: > Dear Fieldtrip community, > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > > > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > To: fieldtrip at science.ru.nl > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 4. Source Localisation (aishwarya selvaraj) > > 5. Re: Source Localisation (Hom?lle) > > 6. Re: plotting neighbours (victoria schroeder) > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 8. Re: Source Localisation (Munsif Jatoi) > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > From: Laith Hamid > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > spikes and seizures. Currently I am analysing an EEG data set that was > > recorded using a 256-channel EGI system and I wanted to ask whether you > > have a standard BEM or FEM head Subscript indices must either be real > positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > model that extends enough downwards to > > accomodate all 256 electrodes. The current standard BEM model in the > > template folder of Fieldtrip isn't appropriate for source analysis of > > 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > thanks for your question. You could refer to a factory schematic layout > > such as the one in figure 4 of this publication: > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > and subsequently use the function ft_prepare_layout to manually track the > > points of the custom design on your own (if you dont want to wait for > > somebody from the FT to do the same for you). > > > > cfg = []; > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > lay = ft_prepare_layout(cfg); > > > > The following tutorial describes the procedure in more details: > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > Please do not hesitate to get in touch with me for this and other > matters. > > > > All the best > > Cris Micheli > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > wrote: > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > Complex > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes > and > > > seizures. Currently I am analysing an EEG data set that was recorded > using > > > a 256-channel EGI system and I wanted to ask whether you have a > standard > > > BEM or FEM head model that extends enough downwards to accomodate all > 256 > > > electrodes. The current standard BEM model in the template folder of > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > [FieldTrip] source analysis EEG data without MRI > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the cheeks or on the back of the neck and these areas are not modeled by > > the standard BEM skin compartment in the standard BEM model. My question > > was about a standard segmentation that extends the skin (and skull) > > compartment downwards to allow these electrodes to sit on the nodes of > > the skin mesh. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 4 > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > From: aishwarya selvaraj > > To: "fieldtrip, donders" > > Subject: [FieldTrip] Source Localisation > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > From: Hom?lle, S. (Simon) > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source > reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ________________________________ > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > Sent: Tuesday, January 19, 2016 5:52 PM > > To: fieldtrip, donders > > Subject: [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 6 > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > From: victoria schroeder > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] plotting neighbours > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Thank you very much Philipp and Tzvetan! > > > > Things have become much clearer now. > > > > I would like to follow up with a very related question. I am trying to > > replicate the analysis for the cluster based permutation test using the > > code and the data provided. However, i run into two problems here > > > > First, i get the following error if i use the original code: > > Attempted to access cfg.frequency(2); index out of bounds because > > numel(cfg.frequency)=1. > > > > Error in ft_freqstatistics (line 187) > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > fmax)]; > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > However, then no significant clusters are found. Which becomes clear when > > trying to plot the cluster or by looking at the output of > > ft_freqstatistics. > > > > Does the change in the code , change the output? How can i avoid the > error > > mentioned above and still get the same output from ft_freqstatistics as > the > > one provided on the webpage? > > > > > > The relevant section of the toturial is provided below. > > Thank you! > > > > Victoria > > > > Permutation test > > > > Now, run *ft_freqstatistics > > * to > compare > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > cfg.latency, > > the following configuration is identical to the configuration that was > used > > for comparing event-related averages in the cluster-based permutation > tests > > on event related fields tutorial > > . > > Also see this tutorial > > > for > > a detailed explanation of all the configuration settings. You can read > more > > about the *ft_prepare_neighbours > > * > function > > in the FAQ's > > >. > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > servers,freqFIC_planar_cmb.mat > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > and freqFC_planar_cmb.mat > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > >), > > use: > > > > load freqFIC_planar_cmb > > load freqFC_planar_cmb > > > > cfg = []; > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > cfg.latency = 'all'; > > cfg.frequency = 20; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > cfg.correctm = 'cluster'; > > cfg.clusteralpha = 0.05; > > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.tail = 0; > > cfg.clustertail = 0; > > cfg.alpha = 0.025; > > cfg.numrandomization = 500; > > % prepare_neighbours determines what sensors may form clusters > > cfg_neighb.method = 'distance'; > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > size(freqFC_planar_cmb.powspctrm,1)); > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > cfg.design = design; > > cfg.ivar = 1; > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > > > > Hi Victoria, > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > right I was only scrolling up to the part where the mags were > analyzed. As > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you > can > > > threat them separately, as I was naively thinking as non-neuormag > user, but > > > indeed combination of both is recommended as I have now learned > :-)(thanks > > > Phillip). I ran the following steps and I guess this should work for > you. > > > best > > > tzvetan > > > > > > %% > > > cfg = []; > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > %% > > > cfg = [] > > > cfg.method = 'triangulation'; > > > cfg.layout = 'neuromag306cmb.lay'; > > > cfg.senstype = 'MEG'; > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > %% > > > % plot neighbours > > > cfg=[]; > > > cfg.neighbours = neighbours; > > > cfg.layout = 'neuromag306cmb.lay'; > > > ft_neighbourplot(cfg); > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 7 > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > this might be possible if you have the subject-specific MRI by following > > the tutorial here: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > cfg=[]; > > cfg.tissue={'brain','skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > contain your triangulated surface with 1000 vertices. Let me know if that > > works. Of course you should see the skin and the neck in the original > MRI. > > > > If you do not have an anatomical MRI that extends down to the chin you > > could try with a template, such as this: > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > and the corresponding segmented version > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > This goes down to the chin. Then you take care of rearranging the > position > > of the EEG electrodes according to this: > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > I hope this helped > > Cris > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > wrote: > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > the > > > cheeks or on the back of the neck and these areas are not modeled by > the > > > standard BEM skin compartment in the standard BEM model. My question > was > > > about a standard segmentation that extends the skin (and skull) > compartment > > > downwards to allow these electrodes to sit on the nodes of the skin > mesh. > > > > > > Best, > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 8 > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > From: Munsif Jatoi > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Aishwarya, > > > > Please refer to main help tutorials. > > > > Also, you can find out the survey papers written in this area. For more, > > SPM website can provide good help. > > > > Best, > > Munsif. > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > S.Homolle at donders.ru.nl> wrote: > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ------------------------------ > > > *From:* fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > *To:* fieldtrip, donders > > > *Subject:* [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > -- > > Munsif Ali H.Jatoi, > > > > Ph D Scholar, > > Centre for Intelligent Signals and Imaging Research, > > Universiti Teknologi PETRONAS, > > Malaysia. > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 9 > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > From: Olga Sysoeva > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] problems with mri interpolation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Fieldtrippers, > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > FT_VOLUMERESLICE. > > > > I have read my MRI from fif.file and this mri variable contains > > > > mri_K0012.unit, 'm' > > > > mri_K0012.dim, [432, 512, 180] > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > mri_K0012.hdr, (1*1 structure) > > > > mri_K0012.transform, (4*4 double) > > > > mri_K0012.coordsys 'neuromag'. > > > > > > Than I used > > > > > > mri = ft_volumereslice([], mri); > > > > > > the output is > > > > > > ?the input is volume data with dimensions [432 > > 512 180] > > > > reslicing from [432 512 180] to [256 256 256] > > > > the input is volume data with dimensions [256 > > 256 256] > > > > the input is volume data with dimensions [432 > > 512 180] > > > > selecting subvolume of 0.0% > > > > reslicing and interpolating anatomy > > > > interpolating > > > > ??? Attempted to access sel(1); index out of > > bounds because numel(sel)=0. > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > at 663 > > > > ft_progress(sel(1)/num, 'interpolating > > %.1f%%\n', 100*sel(1)/num); > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > av( sel) = my_interpn(fv, ax(sel), > > ay(sel), az(sel), cfg.interpmethod, > > > > cfg.feedback); > > > > > > Error in ==> ft_volumereslice at 176 > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > resliced);? > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > downloaded fieltrip (also in my previous version of 2013 the error > > was the same). > > > > > > I'd be thankful for the comments. > > > > > > Best Regards, > > > > Olga. > > > > P.S.Actually, I can project my sources > > meaningfully into not interpolated MRI, altoough the images are > > plotted upside down. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mniqureshi at gist.ac.kr Thu Jan 21 13:59:06 2016 From: mniqureshi at gist.ac.kr (Muhammad Naveed Iqbal Qureshi) Date: Thu, 21 Jan 2016 21:59:06 +0900 Subject: [FieldTrip] difficulty in loading BCI-IV-2a dataset into fieldtrip for preprocessing Message-ID: <000b01d1544b$8323d8e0$896b8aa0$@gist.ac.kr> Hi, I am using BCI competition IV dataset 2a for my experiment. I want to preprocess it with field trip. I have written the following code for this task. addpath(genpath('E:\bbci_data\fieldtrip-20160118\fieldtrip-20160118')); cd 'E:\bbci_data\BCICIV_2a_gdf\'; %% Field Trip preprocessing code for i=1:9 file=num2str(i); file=strcat('A0',file,'T.gdf'); cfg = []; cfg.dataset = file ; cfg.trialdef.eventtype = 'Stimulus'; cfg.trialdef.eventvalue = {'left', 'right', 'both feet', 'tongue'}; cfg.trialdef.triallength = 8; % duration in seconds cfg.trialdef.ntrials = inf; % number of trials, inf results in as many as possible cfg.trialdef.prestim = 3; cfg.trialdef.poststim = 6; cfg = ft_definetrial(cfg); cfg.bpfilter = 'yes'; cfg.bpfreq = [0.5 100]; cfg.bpfilttype = 'but'; cfg.bpfiltord = 5; cfg.demean = 'yes'; cfg.detrend = 'yes'; trialdata_EO{i} = ft_preprocessing(cfg); end However, this code does not import the event and trigger information from the header file of the data. I will be highly obliged if anyone can help me in this regard. Thank in advance. Best Regards, Muhammad Naveed Iqbal Qureshi -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Thu Jan 21 19:14:01 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Thu, 21 Jan 2016 20:14:01 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 19 In-Reply-To: References: Message-ID: Thank you Jan and Cristiano; I downloaded another version of Fieldtrip thus the below error disappear: Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); But now I have another error: Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example (line 100) vol = ft_prepare_headmodel(cfg, vol); Thank you for any suggestion Cristiano, I record the contraction of the uterus; Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 19 > To: fieldtrip at science.ru.nl > Date: Thu, 21 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) (RICHARDS, JOHN) > 3. Re: fieldtrip Digest, Vol 62, Issue 18 (saeed zahran) > 4. Re: fieldtrip Digest, Vol 62, Issue 18 > (Schoffelen, J.M. (Jan Mathijs)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Jan 2016 13:39:30 +0100 > From: Laith Hamid > To: Fieldtrip > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1 at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear Cris, > > thank you very much for your answers yesterday. The segmentedmri > contained 'white', 'grey' and 'csf' so I needed to repeat the > segmentation using 'brain', 'skull' and 'scalp' as described in the > tutorial "Creating a BEM volume conduction model of the head for > source-reconstruction of EEG data" and everything worked smoothly > afterwards. The problem is solved now. > > Best, > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Wed, 20 Jan 2016 14:39:13 +0000 > From: "RICHARDS, JOHN" > To: "fieldtrip at science.ru.nl" , > "lah at pedneuro.uni-kiel.de" > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps (Laith Hamid) > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Laith: > > I have a ?neurodevelopmental MRI database? (Richards, Sanchez et al., 2015; see my www site) that has average MRI templates that could be used. Each average has the whole head down to about the top of the neck. I did these purposely since I use EEG recording and the MNI template did not even go down far enough for the EGI 128 channel net. > > The database has average MRI templates for head (T1, T2) and brain. I also have FEM segmented heads for the entire head that could be used for this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, scalp), but ironically, I cut these off about 10% below the EGI 128 channel electrodes. However, you could use the three inner compartments for this and just add the rest of the head below the compartment?or use the whole-head FEM as is for a FEM-model, or use the segmented area below the skull for a whole-head BEM model. I also have average 128-channel EGI electrodes for each template. > > Additionally, the ?developmental? part of the ?neurodevelopmental MRI database? is that I have these for a wide range of ages (all ages?). I have a average for young adults (20-24 yrs), and average templates and FEM/BEM models for groups from 3 months through adulthood, and into late adulthood. So if you have specific neuro-pediatric applications you might be interested in using an age appropriate MRI average template rather than an adult template. > > See my www site for journal article references re this, and http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > Finally? I have been using these head models for FT-based FEM and BEM models. Possibly some of the actually field trip models I have would be useful to you. Some of the parts of the model do not use the electrodes (e.g., grid-dipoles, head-model) whereas the final models (leadfield) requires the electrode locations. The database also includes ?virtual? electrodes for the 10-10 system, which might be used to generate the 256 channel locations by knowing the relation between the 10-10 system and the EGI system based on EGI ELP files for the 256 channels. > > John > > *********************************************** > John E. Richards Carolina Distinguished Professor > Department of Psychology > University of South Carolina > Columbia, SC 29208 > Dept Phone: 803 777 2079 > Fax: 803 777 9558 > Email: richards-john at sc.edu > HTTP: jerlab.psych.sc.edu > *********************************************** > > > > > >---------------------------------------------------------------------- > > > >Message: 1 > >Date: Tue, 19 Jan 2016 15:35:00 +0100 > >From: Laith Hamid > >To: fieldtrip at science.ru.nl > >Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > >Content-Type: text/plain; charset="us-ascii" > > > > > > > >Dear community, > > > >My name is Laith Hamid and I am working in the University Medical > >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > >spikes and seizures. Currently I am analysing an EEG data set that was > >recorded using a 256-channel EGI system and I wanted to ask whether you > >have a standard BEM or FEM head model that extends enough downwards to > >accomodate all 256 electrodes. The current standard BEM model in the > >template folder of Fieldtrip isn't appropriate for source analysis of > >256-channel EGI data. > > > >Thank you very much in advance for your help! > > > >Best, > > > >Laith > > > > ------------------------------ > > Message: 3 > Date: Wed, 20 Jan 2016 19:37:32 +0200 > From: saeed zahran > To: "fieldtrip at science.ru.nl" > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Dear Fieldtrip community, > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > > > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > To: fieldtrip at science.ru.nl > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 4. Source Localisation (aishwarya selvaraj) > > 5. Re: Source Localisation (Hom?lle) > > 6. Re: plotting neighbours (victoria schroeder) > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 8. Re: Source Localisation (Munsif Jatoi) > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > From: Laith Hamid > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > spikes and seizures. Currently I am analysing an EEG data set that was > > recorded using a 256-channel EGI system and I wanted to ask whether you > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > model that extends enough downwards to > > accomodate all 256 electrodes. The current standard BEM model in the > > template folder of Fieldtrip isn't appropriate for source analysis of > > 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > thanks for your question. You could refer to a factory schematic layout > > such as the one in figure 4 of this publication: > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > and subsequently use the function ft_prepare_layout to manually track the > > points of the custom design on your own (if you dont want to wait for > > somebody from the FT to do the same for you). > > > > cfg = []; > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > lay = ft_prepare_layout(cfg); > > > > The following tutorial describes the procedure in more details: > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > All the best > > Cris Micheli > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > wrote: > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > electrodes. The current standard BEM model in the template folder of > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > [FieldTrip] source analysis EEG data without MRI > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the cheeks or on the back of the neck and these areas are not modeled by > > the standard BEM skin compartment in the standard BEM model. My question > > was about a standard segmentation that extends the skin (and skull) > > compartment downwards to allow these electrodes to sit on the nodes of > > the skin mesh. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 4 > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > From: aishwarya selvaraj > > To: "fieldtrip, donders" > > Subject: [FieldTrip] Source Localisation > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > From: Hom?lle, S. (Simon) > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ________________________________ > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > Sent: Tuesday, January 19, 2016 5:52 PM > > To: fieldtrip, donders > > Subject: [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 6 > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > From: victoria schroeder > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] plotting neighbours > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Thank you very much Philipp and Tzvetan! > > > > Things have become much clearer now. > > > > I would like to follow up with a very related question. I am trying to > > replicate the analysis for the cluster based permutation test using the > > code and the data provided. However, i run into two problems here > > > > First, i get the following error if i use the original code: > > Attempted to access cfg.frequency(2); index out of bounds because > > numel(cfg.frequency)=1. > > > > Error in ft_freqstatistics (line 187) > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > However, then no significant clusters are found. Which becomes clear when > > trying to plot the cluster or by looking at the output of > > ft_freqstatistics. > > > > Does the change in the code , change the output? How can i avoid the error > > mentioned above and still get the same output from ft_freqstatistics as the > > one provided on the webpage? > > > > > > The relevant section of the toturial is provided below. > > Thank you! > > > > Victoria > > > > Permutation test > > > > Now, run *ft_freqstatistics > > * to compare > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > the following configuration is identical to the configuration that was used > > for comparing event-related averages in the cluster-based permutation tests > > on event related fields tutorial > > . > > Also see this tutorial > > for > > a detailed explanation of all the configuration settings. You can read more > > about the *ft_prepare_neighbours > > * function > > in the FAQ's > > . > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > servers,freqFIC_planar_cmb.mat > > > > and freqFC_planar_cmb.mat > > ), > > use: > > > > load freqFIC_planar_cmb > > load freqFC_planar_cmb > > > > cfg = []; > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > cfg.latency = 'all'; > > cfg.frequency = 20; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > cfg.correctm = 'cluster'; > > cfg.clusteralpha = 0.05; > > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.tail = 0; > > cfg.clustertail = 0; > > cfg.alpha = 0.025; > > cfg.numrandomization = 500; > > % prepare_neighbours determines what sensors may form clusters > > cfg_neighb.method = 'distance'; > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > size(freqFC_planar_cmb.powspctrm,1)); > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > cfg.design = design; > > cfg.ivar = 1; > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > > > > > > > Hi Victoria, > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > right I was only scrolling up to the part where the mags were analyzed. As > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > Phillip). I ran the following steps and I guess this should work for you. > > > best > > > tzvetan > > > > > > %% > > > cfg = []; > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > %% > > > cfg = [] > > > cfg.method = 'triangulation'; > > > cfg.layout = 'neuromag306cmb.lay'; > > > cfg.senstype = 'MEG'; > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > %% > > > % plot neighbours > > > cfg=[]; > > > cfg.neighbours = neighbours; > > > cfg.layout = 'neuromag306cmb.lay'; > > > ft_neighbourplot(cfg); > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 7 > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > this might be possible if you have the subject-specific MRI by following > > the tutorial here: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > cfg=[]; > > cfg.tissue={'brain','skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > contain your triangulated surface with 1000 vertices. Let me know if that > > works. Of course you should see the skin and the neck in the original MRI. > > > > If you do not have an anatomical MRI that extends down to the chin you > > could try with a template, such as this: > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > and the corresponding segmented version > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > This goes down to the chin. Then you take care of rearranging the position > > of the EEG electrodes according to this: > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > I hope this helped > > Cris > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > wrote: > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > cheeks or on the back of the neck and these areas are not modeled by the > > > standard BEM skin compartment in the standard BEM model. My question was > > > about a standard segmentation that extends the skin (and skull) compartment > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 8 > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > From: Munsif Jatoi > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Aishwarya, > > > > Please refer to main help tutorials. > > > > Also, you can find out the survey papers written in this area. For more, > > SPM website can provide good help. > > > > Best, > > Munsif. > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > S.Homolle at donders.ru.nl> wrote: > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ------------------------------ > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > *To:* fieldtrip, donders > > > *Subject:* [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > -- > > Munsif Ali H.Jatoi, > > > > Ph D Scholar, > > Centre for Intelligent Signals and Imaging Research, > > Universiti Teknologi PETRONAS, > > Malaysia. > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 9 > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > From: Olga Sysoeva > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] problems with mri interpolation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Fieldtrippers, > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > FT_VOLUMERESLICE. > > > > I have read my MRI from fif.file and this mri variable contains > > > > mri_K0012.unit, 'm' > > > > mri_K0012.dim, [432, 512, 180] > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > mri_K0012.hdr, (1*1 structure) > > > > mri_K0012.transform, (4*4 double) > > > > mri_K0012.coordsys 'neuromag'. > > > > > > Than I used > > > > > > mri = ft_volumereslice([], mri); > > > > > > the output is > > > > > > ?the input is volume data with dimensions [432 > > 512 180] > > > > reslicing from [432 512 180] to [256 256 256] > > > > the input is volume data with dimensions [256 > > 256 256] > > > > the input is volume data with dimensions [432 > > 512 180] > > > > selecting subvolume of 0.0% > > > > reslicing and interpolating anatomy > > > > interpolating > > > > ??? Attempted to access sel(1); index out of > > bounds because numel(sel)=0. > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > at 663 > > > > ft_progress(sel(1)/num, 'interpolating > > %.1f%%\n', 100*sel(1)/num); > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > av( sel) = my_interpn(fv, ax(sel), > > ay(sel), az(sel), cfg.interpmethod, > > > > cfg.feedback); > > > > > > Error in ==> ft_volumereslice at 176 > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > resliced);? > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > downloaded fieltrip (also in my previous version of 2013 the error > > was the same). > > > > > > I'd be thankful for the comments. > > > > > > Best Regards, > > > > Olga. > > > > P.S.Actually, I can project my sources > > meaningfully into not interpolated MRI, altoough the images are > > plotted upside down. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > ***************************************** > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Thu, 21 Jan 2016 08:16:55 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Saeed, > > are you using 0 or 1 indexing for your triangles? You probably want to use 1 indexing. > > Best, > Jan-Mathijs > > > On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: > > Dear Fieldtrip community, > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > > > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > To: fieldtrip at science.ru.nl > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 4. Source Localisation (aishwarya selvaraj) > > 5. Re: Source Localisation (Hom?lle) > > 6. Re: plotting neighbours (victoria schroeder) > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 8. Re: Source Localisation (Munsif Jatoi) > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > From: Laith Hamid > > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > spikes and seizures. Currently I am analysing an EEG data set that was > > recorded using a 256-channel EGI system and I wanted to ask whether you > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > model that extends enough downwards to > > accomodate all 256 electrodes. The current standard BEM model in the > > template folder of Fieldtrip isn't appropriate for source analysis of > > 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > thanks for your question. You could refer to a factory schematic layout > > such as the one in figure 4 of this publication: > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > and subsequently use the function ft_prepare_layout to manually track the > > points of the custom design on your own (if you dont want to wait for > > somebody from the FT to do the same for you). > > > > cfg = []; > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > lay = ft_prepare_layout(cfg); > > > > The following tutorial describes the procedure in more details: > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > All the best > > Cris Micheli > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > wrote: > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > electrodes. The current standard BEM model in the template folder of > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > [FieldTrip] source analysis EEG data without MRI > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the cheeks or on the back of the neck and these areas are not modeled by > > the standard BEM skin compartment in the standard BEM model. My question > > was about a standard segmentation that extends the skin (and skull) > > compartment downwards to allow these electrodes to sit on the nodes of > > the skin mesh. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 4 > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > From: aishwarya selvaraj > > > To: "fieldtrip, donders" > > > Subject: [FieldTrip] Source Localisation > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > From: Hom?lle, S. (Simon) > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ________________________________ > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > Sent: Tuesday, January 19, 2016 5:52 PM > > To: fieldtrip, donders > > Subject: [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 6 > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > From: victoria schroeder > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] plotting neighbours > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Thank you very much Philipp and Tzvetan! > > > > Things have become much clearer now. > > > > I would like to follow up with a very related question. I am trying to > > replicate the analysis for the cluster based permutation test using the > > code and the data provided. However, i run into two problems here > > > > First, i get the following error if i use the original code: > > Attempted to access cfg.frequency(2); index out of bounds because > > numel(cfg.frequency)=1. > > > > Error in ft_freqstatistics (line 187) > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > However, then no significant clusters are found. Which becomes clear when > > trying to plot the cluster or by looking at the output of > > ft_freqstatistics. > > > > Does the change in the code , change the output? How can i avoid the error > > mentioned above and still get the same output from ft_freqstatistics as the > > one provided on the webpage? > > > > > > The relevant section of the toturial is provided below. > > Thank you! > > > > Victoria > > > > Permutation test > > > > Now, run *ft_freqstatistics > > * to compare > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > the following configuration is identical to the configuration that was used > > for comparing event-related averages in the cluster-based permutation tests > > on event related fields tutorial > > . > > Also see this tutorial > > for > > a detailed explanation of all the configuration settings. You can read more > > about the *ft_prepare_neighbours > > * function > > in the FAQ's > > . > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > servers,freqFIC_planar_cmb.mat > > > > and freqFC_planar_cmb.mat > > ), > > use: > > > > load freqFIC_planar_cmb > > load freqFC_planar_cmb > > > > cfg = []; > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > cfg.latency = 'all'; > > cfg.frequency = 20; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > cfg.correctm = 'cluster'; > > cfg.clusteralpha = 0.05; > > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.tail = 0; > > cfg.clustertail = 0; > > cfg.alpha = 0.025; > > cfg.numrandomization = 500; > > % prepare_neighbours determines what sensors may form clusters > > cfg_neighb.method = 'distance'; > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > size(freqFC_planar_cmb.powspctrm,1)); > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > cfg.design = design; > > cfg.ivar = 1; > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > > > > Hi Victoria, > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > right I was only scrolling up to the part where the mags were analyzed. As > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > Phillip). I ran the following steps and I guess this should work for you. > > > best > > > tzvetan > > > > > > %% > > > cfg = []; > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > %% > > > cfg = [] > > > cfg.method = 'triangulation'; > > > cfg.layout = 'neuromag306cmb.lay'; > > > cfg.senstype = 'MEG'; > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > %% > > > % plot neighbours > > > cfg=[]; > > > cfg.neighbours = neighbours; > > > cfg.layout = 'neuromag306cmb.lay'; > > > ft_neighbourplot(cfg); > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 7 > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > this might be possible if you have the subject-specific MRI by following > > the tutorial here: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > cfg=[]; > > cfg.tissue={'brain','skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > contain your triangulated surface with 1000 vertices. Let me know if that > > works. Of course you should see the skin and the neck in the original MRI. > > > > If you do not have an anatomical MRI that extends down to the chin you > > could try with a template, such as this: > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > and the corresponding segmented version > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > This goes down to the chin. Then you take care of rearranging the position > > of the EEG electrodes according to this: > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > I hope this helped > > Cris > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > wrote: > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > cheeks or on the back of the neck and these areas are not modeled by the > > > standard BEM skin compartment in the standard BEM model. My question was > > > about a standard segmentation that extends the skin (and skull) compartment > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 8 > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > From: Munsif Jatoi > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Aishwarya, > > > > Please refer to main help tutorials. > > > > Also, you can find out the survey papers written in this area. For more, > > SPM website can provide good help. > > > > Best, > > Munsif. > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > S.Homolle at donders.ru.nl> wrote: > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ------------------------------ > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > *To:* fieldtrip, donders > > > *Subject:* [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > -- > > Munsif Ali H.Jatoi, > > > > Ph D Scholar, > > Centre for Intelligent Signals and Imaging Research, > > Universiti Teknologi PETRONAS, > > Malaysia. > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 9 > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > From: Olga Sysoeva > > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] problems with mri interpolation > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Fieldtrippers, > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > FT_VOLUMERESLICE. > > > > I have read my MRI from fif.file and this mri variable contains > > > > mri_K0012.unit, 'm' > > > > mri_K0012.dim, [432, 512, 180] > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > mri_K0012.hdr, (1*1 structure) > > > > mri_K0012.transform, (4*4 double) > > > > mri_K0012.coordsys 'neuromag'. > > > > > > Than I used > > > > > > mri = ft_volumereslice([], mri); > > > > > > the output is > > > > > > ?the input is volume data with dimensions [432 > > 512 180] > > > > reslicing from [432 512 180] to [256 256 256] > > > > the input is volume data with dimensions [256 > > 256 256] > > > > the input is volume data with dimensions [432 > > 512 180] > > > > selecting subvolume of 0.0% > > > > reslicing and interpolating anatomy > > > > interpolating > > > > ??? Attempted to access sel(1); index out of > > bounds because numel(sel)=0. > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > at 663 > > > > ft_progress(sel(1)/num, 'interpolating > > %.1f%%\n', 100*sel(1)/num); > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > av( sel) = my_interpn(fv, ax(sel), > > ay(sel), az(sel), cfg.interpmethod, > > > > cfg.feedback); > > > > > > Error in ==> ft_volumereslice at 176 > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > resliced);? > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > downloaded fieltrip (also in my previous version of 2013 the error > > was the same). > > > > > > I'd be thankful for the comments. > > > > > > Best Regards, > > > > Olga. > > > > P.S.Actually, I can project my sources > > meaningfully into not interpolated MRI, altoough the images are > > plotted upside down. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > ***************************************** > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 19 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Thu Jan 21 19:22:42 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Thu, 21 Jan 2016 20:22:42 +0200 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Dear Fieldtrip Community, Dear Fieldtrip community, What does the error of the surface nesting means; I define the volume conductor as: vol = []; vol.bnd(1).pnt=skinpnt vol.bnd(1).tri=skinf vol.bnd(2).pnt=uteruspnt vol.bnd(2).tri=uterusf vol.bnd(3).pnt=uterinecontentpnt vol.bnd(3).tri=uterinecontentf vol.cond = c; But it result with the below error: Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example (line 100) vol = ft_prepare_headmodel(cfg, vol); Thank you very much in advance for your help! Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 20 > To: fieldtrip at science.ru.nl > Date: Thu, 21 Jan 2016 19:14:24 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: fieldtrip Digest, Vol 62, Issue 18 (Cristiano Micheli) > 2. difficulty in loading BCI-IV-2a dataset into fieldtrip for > preprocessing (Muhammad Naveed Iqbal Qureshi) > 3. Re: fieldtrip Digest, Vol 62, Issue 19 (saeed zahran) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Jan 2016 12:06:13 +0100 > From: Cristiano Micheli > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Saeed, > if the content of your triangulation connectivity matrices *skinf, > uterusf, **uterinecontentf* is not made of integers you probably get the > error you mentioned. Could this be the case? > Out of curiosity, are you doing fetal recordings? > > Cris > > > On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran > wrote: > > > Dear Fieldtrip community, > > > > I define the volume conductor as: > > > > vol = []; > > vol.bnd(1).pnt=skinpnt > > vol.bnd(1).tri=skinf > > > > vol.bnd(2).pnt=uteruspnt > > vol.bnd(2).tri=uterusf > > > > vol.bnd(3).pnt=uterinecontentpnt > > vol.bnd(3).tri=uterinecontentf > > > > vol.cond = c; > > > > > > But it result with the below error: > > > > Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > Thank you very much in advance for your help! > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > To: fieldtrip at science.ru.nl > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 4. Source Localisation (aishwarya selvaraj) > > > 5. Re: Source Localisation (Hom?lle) > > > 6. Re: plotting neighbours (victoria schroeder) > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 8. Re: Source Localisation (Munsif Jatoi) > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > From: Laith Hamid > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > spikes and seizures. Currently I am analysing an EEG data set that was > > > recorded using a 256-channel EGI system and I wanted to ask whether you > > > have a standard BEM or FEM head Subscript indices must either be real > > positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > model that extends enough downwards to > > > accomodate all 256 electrodes. The current standard BEM model in the > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > thanks for your question. You could refer to a factory schematic layout > > > such as the one in figure 4 of this publication: > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > and subsequently use the function ft_prepare_layout to manually track the > > > points of the custom design on your own (if you dont want to wait for > > > somebody from the FT to do the same for you). > > > > > > cfg = []; > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > lay = ft_prepare_layout(cfg); > > > > > > The following tutorial describes the procedure in more details: > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > Please do not hesitate to get in touch with me for this and other > > matters. > > > > > > All the best > > > Cris Micheli > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > wrote: > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > Complex > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes > > and > > > > seizures. Currently I am analysing an EEG data set that was recorded > > using > > > > a 256-channel EGI system and I wanted to ask whether you have a > > standard > > > > BEM or FEM head model that extends enough downwards to accomodate all > > 256 > > > > electrodes. The current standard BEM model in the template folder of > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > > data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > the cheeks or on the back of the neck and these areas are not modeled by > > > the standard BEM skin compartment in the standard BEM model. My question > > > was about a standard segmentation that extends the skin (and skull) > > > compartment downwards to allow these electrodes to sit on the nodes of > > > the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > From: aishwarya selvaraj > > > To: "fieldtrip, donders" > > > Subject: [FieldTrip] Source Localisation > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > From: Hom?lle, S. (Simon) > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ________________________________ > > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > To: fieldtrip, donders > > > Subject: [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 6 > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > From: victoria schroeder > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] plotting neighbours > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > Things have become much clearer now. > > > > > > I would like to follow up with a very related question. I am trying to > > > replicate the analysis for the cluster based permutation test using the > > > code and the data provided. However, i run into two problems here > > > > > > First, i get the following error if i use the original code: > > > Attempted to access cfg.frequency(2); index out of bounds because > > > numel(cfg.frequency)=1. > > > > > > Error in ft_freqstatistics (line 187) > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > > fmax)]; > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > > However, then no significant clusters are found. Which becomes clear when > > > trying to plot the cluster or by looking at the output of > > > ft_freqstatistics. > > > > > > Does the change in the code , change the output? How can i avoid the > > error > > > mentioned above and still get the same output from ft_freqstatistics as > > the > > > one provided on the webpage? > > > > > > > > > The relevant section of the toturial is provided below. > > > Thank you! > > > > > > Victoria > > > > > > Permutation test > > > > > > Now, run *ft_freqstatistics > > > * to > > compare > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > > cfg.latency, > > > the following configuration is identical to the configuration that was > > used > > > for comparing event-related averages in the cluster-based permutation > > tests > > > on event related fields tutorial > > > . > > > Also see this tutorial > > > > > for > > > a detailed explanation of all the configuration settings. You can read > > more > > > about the *ft_prepare_neighbours > > > * > > function > > > in the FAQ's > > > > >. > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > servers,freqFIC_planar_cmb.mat > > > < > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > < > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > > >), > > > use: > > > > > > load freqFIC_planar_cmb > > > load freqFC_planar_cmb > > > > > > cfg = []; > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > cfg.latency = 'all'; > > > cfg.frequency = 20; > > > cfg.method = 'montecarlo'; > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > cfg.correctm = 'cluster'; > > > cfg.clusteralpha = 0.05; > > > cfg.clusterstatistic = 'maxsum'; > > > cfg.minnbchan = 2; > > > cfg.tail = 0; > > > cfg.clustertail = 0; > > > cfg.alpha = 0.025; > > > cfg.numrandomization = 500; > > > % prepare_neighbours determines what sensors may form clusters > > > cfg_neighb.method = 'distance'; > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > size(freqFC_planar_cmb.powspctrm,1)); > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > cfg.design = design; > > > cfg.ivar = 1; > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov > >: > > > > > > > > > > > Hi Victoria, > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > > right I was only scrolling up to the part where the mags were > > analyzed. As > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you > > can > > > > threat them separately, as I was naively thinking as non-neuormag > > user, but > > > > indeed combination of both is recommended as I have now learned > > :-)(thanks > > > > Phillip). I ran the following steps and I guess this should work for > > you. > > > > best > > > > tzvetan > > > > > > > > %% > > > > cfg = []; > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > %% > > > > cfg = [] > > > > cfg.method = 'triangulation'; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > cfg.senstype = 'MEG'; > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > %% > > > > % plot neighbours > > > > cfg=[]; > > > > cfg.neighbours = neighbours; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 7 > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > this might be possible if you have the subject-specific MRI by following > > > the tutorial here: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > cfg=[]; > > > cfg.tissue={'brain','skull','scalp'}; > > > cfg.numvertices = [3000 2000 1000]; > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > > contain your triangulated surface with 1000 vertices. Let me know if that > > > works. Of course you should see the skin and the neck in the original > > MRI. > > > > > > If you do not have an anatomical MRI that extends down to the chin you > > > could try with a template, such as this: > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > and the corresponding segmented version > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > This goes down to the chin. Then you take care of rearranging the > > position > > > of the EEG electrodes according to this: > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > I hope this helped > > > Cris > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > wrote: > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that was > > > > discussed in this thread from April 2013: > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the > > > > cheeks or on the back of the neck and these areas are not modeled by > > the > > > > standard BEM skin compartment in the standard BEM model. My question > > was > > > > about a standard segmentation that extends the skin (and skull) > > compartment > > > > downwards to allow these electrodes to sit on the nodes of the skin > > mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 8 > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > From: Munsif Jatoi > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Aishwarya, > > > > > > Please refer to main help tutorials. > > > > > > Also, you can find out the survey papers written in this area. For more, > > > SPM website can provide good help. > > > > > > Best, > > > Munsif. > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ------------------------------ > > > > *From:* fieldtrip-bounces at science.ru.nl [ > > fieldtrip-bounces at science.ru.nl] > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > *To:* fieldtrip, donders > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > -- > > > Munsif Ali H.Jatoi, > > > > > > Ph D Scholar, > > > Centre for Intelligent Signals and Imaging Research, > > > Universiti Teknologi PETRONAS, > > > Malaysia. > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 9 > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > From: Olga Sysoeva > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] problems with mri interpolation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Fieldtrippers, > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > FT_VOLUMERESLICE. > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > mri_K0012.unit, 'm' > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > mri_K0012.transform, (4*4 double) > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > Than I used > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > the output is > > > > > > > > > ?the input is volume data with dimensions [432 > > > 512 180] > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > the input is volume data with dimensions [256 > > > 256 256] > > > > > > the input is volume data with dimensions [432 > > > 512 180] > > > > > > selecting subvolume of 0.0% > > > > > > reslicing and interpolating anatomy > > > > > > interpolating > > > > > > ??? Attempted to access sel(1); index out of > > > bounds because numel(sel)=0. > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > at 663 > > > > > > ft_progress(sel(1)/num, 'interpolating > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > cfg.feedback); > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > resliced);? > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > downloaded fieltrip (also in my previous version of 2013 the error > > > was the same). > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > Best Regards, > > > > > > Olga. > > > > > > P.S.Actually, I can project my sources > > > meaningfully into not interpolated MRI, altoough the images are > > > plotted upside down. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > ***************************************** > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Thu, 21 Jan 2016 21:59:06 +0900 > From: "Muhammad Naveed Iqbal Qureshi" > To: > Subject: [FieldTrip] difficulty in loading BCI-IV-2a dataset into > fieldtrip for preprocessing > Message-ID: <000b01d1544b$8323d8e0$896b8aa0$@gist.ac.kr> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > > > I am using BCI competition IV dataset 2a for my experiment. > > I want to preprocess it with field trip. > > > > I have written the following code for this task. > > > > addpath(genpath('E:\bbci_data\fieldtrip-20160118\fieldtrip-20160118')); > > cd 'E:\bbci_data\BCICIV_2a_gdf\'; > > > > %% Field Trip preprocessing code > > for i=1:9 > > file=num2str(i); > > file=strcat('A0',file,'T.gdf'); > > cfg = []; > > cfg.dataset = file ; > > cfg.trialdef.eventtype = 'Stimulus'; > > cfg.trialdef.eventvalue = {'left', 'right', 'both feet', 'tongue'}; > > cfg.trialdef.triallength = 8; % duration in seconds > > cfg.trialdef.ntrials = inf; % number of trials, inf > results in as many as possible > > cfg.trialdef.prestim = 3; > > cfg.trialdef.poststim = 6; > > cfg = ft_definetrial(cfg); > > > > cfg.bpfilter = 'yes'; > > cfg.bpfreq = [0.5 100]; > > cfg.bpfilttype = 'but'; > > cfg.bpfiltord = 5; > > cfg.demean = 'yes'; > > cfg.detrend = 'yes'; > > trialdata_EO{i} = ft_preprocessing(cfg); > > end > > > > However, this code does not import the event and trigger information from > the header file of the data. > > I will be highly obliged if anyone can help me in this regard. > > > > Thank in advance. > > > > Best Regards, > Muhammad Naveed Iqbal Qureshi > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Thu, 21 Jan 2016 20:14:01 +0200 > From: saeed zahran > To: "fieldtrip at science.ru.nl" > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 19 > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Thank you Jan and Cristiano; > > I downloaded another version of Fieldtrip thus the below error disappear: > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > But now I have another error: > > Error using surface_nesting (line 26) > the compartment nesting cannot be determined > > Error in ft_headmodel_bemcp (line 66) > order = surface_nesting(vol.bnd, 'insidefirst'); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example (line 100) > vol = ft_prepare_headmodel(cfg, vol); > Thank you for any suggestion > > Cristiano, I record the contraction of the uterus; > > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 19 > > To: fieldtrip at science.ru.nl > > Date: Thu, 21 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) (RICHARDS, JOHN) > > 3. Re: fieldtrip Digest, Vol 62, Issue 18 (saeed zahran) > > 4. Re: fieldtrip Digest, Vol 62, Issue 18 > > (Schoffelen, J.M. (Jan Mathijs)) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 20 Jan 2016 13:39:30 +0100 > > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1 at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answers yesterday. The segmentedmri > > contained 'white', 'grey' and 'csf' so I needed to repeat the > > segmentation using 'brain', 'skull' and 'scalp' as described in the > > tutorial "Creating a BEM volume conduction model of the head for > > source-reconstruction of EEG data" and everything worked smoothly > > afterwards. The problem is solved now. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 2 > > Date: Wed, 20 Jan 2016 14:39:13 +0000 > > From: "RICHARDS, JOHN" > > To: "fieldtrip at science.ru.nl" , > > "lah at pedneuro.uni-kiel.de" > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps (Laith Hamid) > > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > > > Laith: > > > > I have a ?neurodevelopmental MRI database? (Richards, Sanchez et al., 2015; see my www site) that has average MRI templates that could be used. Each average has the whole head down to about the top of the neck. I did these purposely since I use EEG recording and the MNI template did not even go down far enough for the EGI 128 channel net. > > > > The database has average MRI templates for head (T1, T2) and brain. I also have FEM segmented heads for the entire head that could be used for this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, scalp), but ironically, I cut these off about 10% below the EGI 128 channel electrodes. However, you could use the three inner compartments for this and just add the rest of the head below the compartment?or use the whole-head FEM as is for a FEM-model, or use the segmented area below the skull for a whole-head BEM model. I also have average 128-channel EGI electrodes for each template. > > > > Additionally, the ?developmental? part of the ?neurodevelopmental MRI database? is that I have these for a wide range of ages (all ages?). I have a average for young adults (20-24 yrs), and average templates and FEM/BEM models for groups from 3 months through adulthood, and into late adulthood. So if you have specific neuro-pediatric applications you might be interested in using an age appropriate MRI average template rather than an adult template. > > > > See my www site for journal article references re this, and http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > > > Finally? I have been using these head models for FT-based FEM and BEM models. Possibly some of the actually field trip models I have would be useful to you. Some of the parts of the model do not use the electrodes (e.g., grid-dipoles, head-model) whereas the final models (leadfield) requires the electrode locations. The database also includes ?virtual? electrodes for the 10-10 system, which might be used to generate the 256 channel locations by knowing the relation between the 10-10 system and the EGI system based on EGI ELP files for the 256 channels. > > > > John > > > > *********************************************** > > John E. Richards Carolina Distinguished Professor > > Department of Psychology > > University of South Carolina > > Columbia, SC 29208 > > Dept Phone: 803 777 2079 > > Fax: 803 777 9558 > > Email: richards-john at sc.edu > > HTTP: jerlab.psych.sc.edu > > *********************************************** > > > > > > > > > > >---------------------------------------------------------------------- > > > > > >Message: 1 > > >Date: Tue, 19 Jan 2016 15:35:00 +0100 > > >From: Laith Hamid > > >To: fieldtrip at science.ru.nl > > >Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > >Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > >Dear community, > > > > > >My name is Laith Hamid and I am working in the University Medical > > >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > >spikes and seizures. Currently I am analysing an EEG data set that was > > >recorded using a 256-channel EGI system and I wanted to ask whether you > > >have a standard BEM or FEM head model that extends enough downwards to > > >accomodate all 256 electrodes. The current standard BEM model in the > > >template folder of Fieldtrip isn't appropriate for source analysis of > > >256-channel EGI data. > > > > > >Thank you very much in advance for your help! > > > > > >Best, > > > > > >Laith > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Wed, 20 Jan 2016 19:37:32 +0200 > > From: saeed zahran > > To: "fieldtrip at science.ru.nl" > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Fieldtrip community, > > > > I define the volume conductor as: > > > > vol = []; > > vol.bnd(1).pnt=skinpnt > > vol.bnd(1).tri=skinf > > > > vol.bnd(2).pnt=uteruspnt > > vol.bnd(2).tri=uterusf > > > > vol.bnd(3).pnt=uterinecontentpnt > > vol.bnd(3).tri=uterinecontentf > > > > vol.cond = c; > > > > > > But it result with the below error: > > > > Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > Thank you very much in advance for your help! > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > To: fieldtrip at science.ru.nl > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 4. Source Localisation (aishwarya selvaraj) > > > 5. Re: Source Localisation (Hom?lle) > > > 6. Re: plotting neighbours (victoria schroeder) > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 8. Re: Source Localisation (Munsif Jatoi) > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > From: Laith Hamid > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > spikes and seizures. Currently I am analysing an EEG data set that was > > > recorded using a 256-channel EGI system and I wanted to ask whether you > > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > model that extends enough downwards to > > > accomodate all 256 electrodes. The current standard BEM model in the > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > thanks for your question. You could refer to a factory schematic layout > > > such as the one in figure 4 of this publication: > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > and subsequently use the function ft_prepare_layout to manually track the > > > points of the custom design on your own (if you dont want to wait for > > > somebody from the FT to do the same for you). > > > > > > cfg = []; > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > lay = ft_prepare_layout(cfg); > > > > > > The following tutorial describes the procedure in more details: > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > > > All the best > > > Cris Micheli > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > wrote: > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > > electrodes. The current standard BEM model in the template folder of > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > the cheeks or on the back of the neck and these areas are not modeled by > > > the standard BEM skin compartment in the standard BEM model. My question > > > was about a standard segmentation that extends the skin (and skull) > > > compartment downwards to allow these electrodes to sit on the nodes of > > > the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > From: aishwarya selvaraj > > > To: "fieldtrip, donders" > > > Subject: [FieldTrip] Source Localisation > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > From: Hom?lle, S. (Simon) > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ________________________________ > > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > To: fieldtrip, donders > > > Subject: [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 6 > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > From: victoria schroeder > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] plotting neighbours > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > Things have become much clearer now. > > > > > > I would like to follow up with a very related question. I am trying to > > > replicate the analysis for the cluster based permutation test using the > > > code and the data provided. However, i run into two problems here > > > > > > First, i get the following error if i use the original code: > > > Attempted to access cfg.frequency(2); index out of bounds because > > > numel(cfg.frequency)=1. > > > > > > Error in ft_freqstatistics (line 187) > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > > However, then no significant clusters are found. Which becomes clear when > > > trying to plot the cluster or by looking at the output of > > > ft_freqstatistics. > > > > > > Does the change in the code , change the output? How can i avoid the error > > > mentioned above and still get the same output from ft_freqstatistics as the > > > one provided on the webpage? > > > > > > > > > The relevant section of the toturial is provided below. > > > Thank you! > > > > > > Victoria > > > > > > Permutation test > > > > > > Now, run *ft_freqstatistics > > > * to compare > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > > the following configuration is identical to the configuration that was used > > > for comparing event-related averages in the cluster-based permutation tests > > > on event related fields tutorial > > > . > > > Also see this tutorial > > > for > > > a detailed explanation of all the configuration settings. You can read more > > > about the *ft_prepare_neighbours > > > * function > > > in the FAQ's > > > . > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > servers,freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > ), > > > use: > > > > > > load freqFIC_planar_cmb > > > load freqFC_planar_cmb > > > > > > cfg = []; > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > cfg.latency = 'all'; > > > cfg.frequency = 20; > > > cfg.method = 'montecarlo'; > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > cfg.correctm = 'cluster'; > > > cfg.clusteralpha = 0.05; > > > cfg.clusterstatistic = 'maxsum'; > > > cfg.minnbchan = 2; > > > cfg.tail = 0; > > > cfg.clustertail = 0; > > > cfg.alpha = 0.025; > > > cfg.numrandomization = 500; > > > % prepare_neighbours determines what sensors may form clusters > > > cfg_neighb.method = 'distance'; > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > size(freqFC_planar_cmb.powspctrm,1)); > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > cfg.design = design; > > > cfg.ivar = 1; > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > > > > > > > > > > Hi Victoria, > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > > right I was only scrolling up to the part where the mags were analyzed. As > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > > Phillip). I ran the following steps and I guess this should work for you. > > > > best > > > > tzvetan > > > > > > > > %% > > > > cfg = []; > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > %% > > > > cfg = [] > > > > cfg.method = 'triangulation'; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > cfg.senstype = 'MEG'; > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > %% > > > > % plot neighbours > > > > cfg=[]; > > > > cfg.neighbours = neighbours; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 7 > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > this might be possible if you have the subject-specific MRI by following > > > the tutorial here: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > cfg=[]; > > > cfg.tissue={'brain','skull','scalp'}; > > > cfg.numvertices = [3000 2000 1000]; > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > > contain your triangulated surface with 1000 vertices. Let me know if that > > > works. Of course you should see the skin and the neck in the original MRI. > > > > > > If you do not have an anatomical MRI that extends down to the chin you > > > could try with a template, such as this: > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > and the corresponding segmented version > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > This goes down to the chin. Then you take care of rearranging the position > > > of the EEG electrodes according to this: > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > I hope this helped > > > Cris > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > wrote: > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that was > > > > discussed in this thread from April 2013: > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > > cheeks or on the back of the neck and these areas are not modeled by the > > > > standard BEM skin compartment in the standard BEM model. My question was > > > > about a standard segmentation that extends the skin (and skull) compartment > > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 8 > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > From: Munsif Jatoi > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Aishwarya, > > > > > > Please refer to main help tutorials. > > > > > > Also, you can find out the survey papers written in this area. For more, > > > SPM website can provide good help. > > > > > > Best, > > > Munsif. > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ------------------------------ > > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > *To:* fieldtrip, donders > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > -- > > > Munsif Ali H.Jatoi, > > > > > > Ph D Scholar, > > > Centre for Intelligent Signals and Imaging Research, > > > Universiti Teknologi PETRONAS, > > > Malaysia. > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 9 > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > From: Olga Sysoeva > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] problems with mri interpolation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Fieldtrippers, > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > FT_VOLUMERESLICE. > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > mri_K0012.unit, 'm' > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > mri_K0012.transform, (4*4 double) > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > Than I used > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > the output is > > > > > > > > > ?the input is volume data with dimensions [432 > > > 512 180] > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > the input is volume data with dimensions [256 > > > 256 256] > > > > > > the input is volume data with dimensions [432 > > > 512 180] > > > > > > selecting subvolume of 0.0% > > > > > > reslicing and interpolating anatomy > > > > > > interpolating > > > > > > ??? Attempted to access sel(1); index out of > > > bounds because numel(sel)=0. > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > at 663 > > > > > > ft_progress(sel(1)/num, 'interpolating > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > cfg.feedback); > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > resliced);? > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > downloaded fieltrip (also in my previous version of 2013 the error > > > was the same). > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > Best Regards, > > > > > > Olga. > > > > > > P.S.Actually, I can project my sources > > > meaningfully into not interpolated MRI, altoough the images are > > > plotted upside down. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > ***************************************** > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 4 > > Date: Thu, 21 Jan 2016 08:16:55 +0000 > > From: "Schoffelen, J.M. (Jan Mathijs)" > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Saeed, > > > > are you using 0 or 1 indexing for your triangles? You probably want to use 1 indexing. > > > > Best, > > Jan-Mathijs > > > > > > On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: > > > > Dear Fieldtrip community, > > > > I define the volume conductor as: > > > > vol = []; > > vol.bnd(1).pnt=skinpnt > > vol.bnd(1).tri=skinf > > > > vol.bnd(2).pnt=uteruspnt > > vol.bnd(2).tri=uterusf > > > > vol.bnd(3).pnt=uterinecontentpnt > > vol.bnd(3).tri=uterinecontentf > > > > vol.cond = c; > > > > > > But it result with the below error: > > > > Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > Thank you very much in advance for your help! > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > To: fieldtrip at science.ru.nl > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 4. Source Localisation (aishwarya selvaraj) > > > 5. Re: Source Localisation (Hom?lle) > > > 6. Re: plotting neighbours (victoria schroeder) > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 8. Re: Source Localisation (Munsif Jatoi) > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > From: Laith Hamid > > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > spikes and seizures. Currently I am analysing an EEG data set that was > > > recorded using a 256-channel EGI system and I wanted to ask whether you > > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > model that extends enough downwards to > > > accomodate all 256 electrodes. The current standard BEM model in the > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > thanks for your question. You could refer to a factory schematic layout > > > such as the one in figure 4 of this publication: > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > and subsequently use the function ft_prepare_layout to manually track the > > > points of the custom design on your own (if you dont want to wait for > > > somebody from the FT to do the same for you). > > > > > > cfg = []; > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > lay = ft_prepare_layout(cfg); > > > > > > The following tutorial describes the procedure in more details: > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > > > All the best > > > Cris Micheli > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > > wrote: > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > > electrodes. The current standard BEM model in the template folder of > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > From: Laith Hamid > > > > To: Fieldtrip > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > the cheeks or on the back of the neck and these areas are not modeled by > > > the standard BEM skin compartment in the standard BEM model. My question > > > was about a standard segmentation that extends the skin (and skull) > > > compartment downwards to allow these electrodes to sit on the nodes of > > > the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > From: aishwarya selvaraj > > > > To: "fieldtrip, donders" > > > > Subject: [FieldTrip] Source Localisation > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > From: Hom?lle, S. (Simon) > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ________________________________ > > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > To: fieldtrip, donders > > > Subject: [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 6 > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > From: victoria schroeder > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] plotting neighbours > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > Things have become much clearer now. > > > > > > I would like to follow up with a very related question. I am trying to > > > replicate the analysis for the cluster based permutation test using the > > > code and the data provided. However, i run into two problems here > > > > > > First, i get the following error if i use the original code: > > > Attempted to access cfg.frequency(2); index out of bounds because > > > numel(cfg.frequency)=1. > > > > > > Error in ft_freqstatistics (line 187) > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > > However, then no significant clusters are found. Which becomes clear when > > > trying to plot the cluster or by looking at the output of > > > ft_freqstatistics. > > > > > > Does the change in the code , change the output? How can i avoid the error > > > mentioned above and still get the same output from ft_freqstatistics as the > > > one provided on the webpage? > > > > > > > > > The relevant section of the toturial is provided below. > > > Thank you! > > > > > > Victoria > > > > > > Permutation test > > > > > > Now, run *ft_freqstatistics > > > * to compare > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > > the following configuration is identical to the configuration that was used > > > for comparing event-related averages in the cluster-based permutation tests > > > on event related fields tutorial > > > . > > > Also see this tutorial > > > for > > > a detailed explanation of all the configuration settings. You can read more > > > about the *ft_prepare_neighbours > > > * function > > > in the FAQ's > > > . > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > servers,freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > ), > > > use: > > > > > > load freqFIC_planar_cmb > > > load freqFC_planar_cmb > > > > > > cfg = []; > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > cfg.latency = 'all'; > > > cfg.frequency = 20; > > > cfg.method = 'montecarlo'; > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > cfg.correctm = 'cluster'; > > > cfg.clusteralpha = 0.05; > > > cfg.clusterstatistic = 'maxsum'; > > > cfg.minnbchan = 2; > > > cfg.tail = 0; > > > cfg.clustertail = 0; > > > cfg.alpha = 0.025; > > > cfg.numrandomization = 500; > > > % prepare_neighbours determines what sensors may form clusters > > > cfg_neighb.method = 'distance'; > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > size(freqFC_planar_cmb.powspctrm,1)); > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > cfg.design = design; > > > cfg.ivar = 1; > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > > > > > > > Hi Victoria, > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > > right I was only scrolling up to the part where the mags were analyzed. As > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > > Phillip). I ran the following steps and I guess this should work for you. > > > > best > > > > tzvetan > > > > > > > > %% > > > > cfg = []; > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > %% > > > > cfg = [] > > > > cfg.method = 'triangulation'; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > cfg.senstype = 'MEG'; > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > %% > > > > % plot neighbours > > > > cfg=[]; > > > > cfg.neighbours = neighbours; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 7 > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > this might be possible if you have the subject-specific MRI by following > > > the tutorial here: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > cfg=[]; > > > cfg.tissue={'brain','skull','scalp'}; > > > cfg.numvertices = [3000 2000 1000]; > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > > contain your triangulated surface with 1000 vertices. Let me know if that > > > works. Of course you should see the skin and the neck in the original MRI. > > > > > > If you do not have an anatomical MRI that extends down to the chin you > > > could try with a template, such as this: > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > and the corresponding segmented version > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > This goes down to the chin. Then you take care of rearranging the position > > > of the EEG electrodes according to this: > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > I hope this helped > > > Cris > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > > wrote: > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that was > > > > discussed in this thread from April 2013: > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > > cheeks or on the back of the neck and these areas are not modeled by the > > > > standard BEM skin compartment in the standard BEM model. My question was > > > > about a standard segmentation that extends the skin (and skull) compartment > > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 8 > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > From: Munsif Jatoi > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Aishwarya, > > > > > > Please refer to main help tutorials. > > > > > > Also, you can find out the survey papers written in this area. For more, > > > SPM website can provide good help. > > > > > > Best, > > > Munsif. > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ------------------------------ > > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > *To:* fieldtrip, donders > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > -- > > > Munsif Ali H.Jatoi, > > > > > > Ph D Scholar, > > > Centre for Intelligent Signals and Imaging Research, > > > Universiti Teknologi PETRONAS, > > > Malaysia. > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 9 > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > From: Olga Sysoeva > > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] problems with mri interpolation > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Fieldtrippers, > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > FT_VOLUMERESLICE. > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > mri_K0012.unit, 'm' > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > mri_K0012.transform, (4*4 double) > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > Than I used > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > the output is > > > > > > > > > ?the input is volume data with dimensions [432 > > > 512 180] > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > the input is volume data with dimensions [256 > > > 256 256] > > > > > > the input is volume data with dimensions [432 > > > 512 180] > > > > > > selecting subvolume of 0.0% > > > > > > reslicing and interpolating anatomy > > > > > > interpolating > > > > > > ??? Attempted to access sel(1); index out of > > > bounds because numel(sel)=0. > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > at 663 > > > > > > ft_progress(sel(1)/num, 'interpolating > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > cfg.feedback); > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > resliced);? > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > downloaded fieltrip (also in my previous version of 2013 the error > > > was the same). > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > Best Regards, > > > > > > Olga. > > > > > > P.S.Actually, I can project my sources > > > meaningfully into not interpolated MRI, altoough the images are > > > plotted upside down. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > ***************************************** > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 19 > > ***************************************** > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 20 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.thomas at nin.knaw.nl Fri Jan 22 12:16:59 2016 From: r.thomas at nin.knaw.nl (Rajat Thomas) Date: Fri, 22 Jan 2016 11:16:59 +0000 Subject: [FieldTrip] ROI based analysis Message-ID: <1453461419134.82627@nin.knaw.nl> ?Dear Fieldtrippers, Has anyone fixed with problem with ROI based analysis in Fieldtrip. I see that it says ROI analysis needs to be fixed for new implementation. Are there newer functions that do this? Any help would be highly appreciated. Thanks Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam -------------- next part -------------- An HTML attachment was scrubbed... URL: From mortaheb.sepehr at yahoo.com Sat Jan 23 13:39:07 2016 From: mortaheb.sepehr at yahoo.com (Sepehr Mortaheb) Date: Sat, 23 Jan 2016 12:39:07 +0000 (UTC) Subject: [FieldTrip] Synthetic EEG References: <814709100.138411.1453552747072.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <814709100.138411.1453552747072.JavaMail.yahoo@mail.yahoo.com> Hi, How can I generate a synthetic EEG signal using forward models of FieldTrip?  -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Sat Jan 23 17:14:06 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Sat, 23 Jan 2016 17:14:06 +0100 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Dear Saeed, it might depend on the boundaries. If they are not nested (one is inside another, which is inside another, etc... like chinese boxes) then you have a fundamental problem. This is a constraint of the BEM algorithm in order for it to work properly. Have you tried plotting the triangulated meshes? Do they look nested? I hope this helps for now, Cris On Thu, Jan 21, 2016 at 7:22 PM, saeed zahran wrote: > Dear Fieldtrip Community, > > Dear Fieldtrip community, > > > What does the error of the surface nesting means; > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Error using surface_nesting (line 26) > the compartment nesting cannot be determined > > Error in ft_headmodel_bemcp (line 66) > order = surface_nesting(vol.bnd, 'insidefirst'); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example (line 100) > vol = ft_prepare_headmodel(cfg, vol); > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 20 > > To: fieldtrip at science.ru.nl > > Date: Thu, 21 Jan 2016 19:14:24 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Re: fieldtrip Digest, Vol 62, Issue 18 (Cristiano Micheli) > > 2. difficulty in loading BCI-IV-2a dataset into fieldtrip for > > preprocessing (Muhammad Naveed Iqbal Qureshi) > > 3. Re: fieldtrip Digest, Vol 62, Issue 19 (saeed zahran) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 21 Jan 2016 12:06:13 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Hi Saeed, > > if the content of your triangulation connectivity matrices *skinf, > > uterusf, **uterinecontentf* is not made of integers you probably get the > > error you mentioned. Could this be the case? > > Out of curiosity, are you doing fetal recordings? > > > > Cris > > > > > > On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran > > wrote: > > > > > Dear Fieldtrip community, > > > > > > I define the volume conductor as: > > > > > > vol = []; > > > vol.bnd(1).pnt=skinpnt > > > vol.bnd(1).tri=skinf > > > > > > vol.bnd(2).pnt=uteruspnt > > > vol.bnd(2).tri=uterusf > > > > > > vol.bnd(3).pnt=uterinecontentpnt > > > vol.bnd(3).tri=uterinecontentf > > > > > > vol.cond = c; > > > > > > > > > But it result with the below error: > > > > > > Subscript indices must either be real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > > > > Thank you very much in advance for your help! > > > > > > Best regards > > > Saeed Zahran > > > > > > > From: fieldtrip-request at science.ru.nl > > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > > To: fieldtrip at science.ru.nl > > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > > > Send fieldtrip mailing list submissions to > > > > fieldtrip at science.ru.nl > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > or, via email, send a message with subject or body 'help' to > > > > fieldtrip-request at science.ru.nl > > > > > > > > You can reach the person managing the list at > > > > fieldtrip-owner at science.ru.nl > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 4. Source Localisation (aishwarya selvaraj) > > > > 5. Re: Source Localisation (Hom?lle) > > > > 6. Re: plotting neighbours (victoria schroeder) > > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 8. Re: Source Localisation (Munsif Jatoi) > > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > > From: Laith Hamid > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > > spikes and seizures. Currently I am analysing an EEG data set that > was > > > > recorded using a 256-channel EGI system and I wanted to ask whether > you > > > > have a standard BEM or FEM head Subscript indices must either be real > > > positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > model that extends enough downwards to > > > > accomodate all 256 electrodes. The current standard BEM model in the > > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > > 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > thanks for your question. You could refer to a factory schematic > layout > > > > such as the one in figure 4 of this publication: > > > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > > > and subsequently use the function ft_prepare_layout to manually > track the > > > > points of the custom design on your own (if you dont want to wait for > > > > somebody from the FT to do the same for you). > > > > > > > > cfg = []; > > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > > lay = ft_prepare_layout(cfg); > > > > > > > > The following tutorial describes the procedure in more details: > > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > > > Please do not hesitate to get in touch with me for this and other > > > matters. > > > > > > > > All the best > > > > Cris Micheli > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear community, > > > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex > > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes > > > and > > > > > seizures. Currently I am analysing an EEG data set that was > recorded > > > using > > > > > a 256-channel EGI system and I wanted to ask whether you have a > > > standard > > > > > BEM or FEM head model that extends enough downwards to accomodate > all > > > 256 > > > > > electrodes. The current standard BEM model in the template folder > of > > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > > > data. > > > > > > > > > > Thank you very much in advance for your help! > > > > > > > > > > Best, > > > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > > From: Laith Hamid > > > > To: Fieldtrip > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that > was > > > > discussed in this thread from April 2013: > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > > the cheeks or on the back of the neck and these areas are not > modeled by > > > > the standard BEM skin compartment in the standard BEM model. My > question > > > > was about a standard segmentation that extends the skin (and skull) > > > > compartment downwards to allow these electrodes to sit on the nodes > of > > > > the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 4 > > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > > From: aishwarya selvaraj > > > > To: "fieldtrip, donders" > > > > Subject: [FieldTrip] Source Localisation > > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 5 > > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > > From: Hom?lle, S. (Simon) > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ________________________________ > > > > From: fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > > To: fieldtrip, donders > > > > Subject: [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 6 > > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > > From: victoria schroeder > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] plotting neighbours > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > > > Things have become much clearer now. > > > > > > > > I would like to follow up with a very related question. I am trying > to > > > > replicate the analysis for the cluster based permutation test using > the > > > > code and the data provided. However, i run into two problems here > > > > > > > > First, i get the following error if i use the original code: > > > > Attempted to access cfg.frequency(2); index out of bounds because > > > > numel(cfg.frequency)=1. > > > > > > > > Error in ft_freqstatistics (line 187) > > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > > > fmax)]; > > > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 > 20]. > > > > However, then no significant clusters are found. Which becomes clear > when > > > > trying to plot the cluster or by looking at the output of > > > > ft_freqstatistics. > > > > > > > > Does the change in the code , change the output? How can i avoid the > > > error > > > > mentioned above and still get the same output from ft_freqstatistics > as > > > the > > > > one provided on the webpage? > > > > > > > > > > > > The relevant section of the toturial is provided below. > > > > Thank you! > > > > > > > > Victoria > > > > > > > > Permutation test > > > > > > > > Now, run *ft_freqstatistics > > > > * to > > > compare > > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > > > cfg.latency, > > > > the following configuration is identical to the configuration that > was > > > used > > > > for comparing event-related averages in the cluster-based permutation > > > tests > > > > on event related fields tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>. > > > > Also see this tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> > > > for > > > > a detailed explanation of all the configuration settings. You can > read > > > more > > > > about the *ft_prepare_neighbours > > > > * > > > function > > > > in the FAQ's > > > > < > http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work > > > >. > > > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > > servers,freqFIC_planar_cmb.mat > > > > < > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > > > and freqFC_planar_cmb.mat > > > > < > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > > > >), > > > > use: > > > > > > > > load freqFIC_planar_cmb > > > > load freqFC_planar_cmb > > > > > > > > cfg = []; > > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > > cfg.latency = 'all'; > > > > cfg.frequency = 20; > > > > cfg.method = 'montecarlo'; > > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > > cfg.correctm = 'cluster'; > > > > cfg.clusteralpha = 0.05; > > > > cfg.clusterstatistic = 'maxsum'; > > > > cfg.minnbchan = 2; > > > > cfg.tail = 0; > > > > cfg.clustertail = 0; > > > > cfg.alpha = 0.025; > > > > cfg.numrandomization = 500; > > > > % prepare_neighbours determines what sensors may form clusters > > > > cfg_neighb.method = 'distance'; > > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > > size(freqFC_planar_cmb.powspctrm,1)); > > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > > > cfg.design = design; > > > > cfg.ivar = 1; > > > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, > freqFC_planar_cmb); > > > > > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov < > tzvetan.popov at uni-konstanz.de > > > >: > > > > > > > > > > > > > > Hi Victoria, > > > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. > You are > > > > > right I was only scrolling up to the part where the mags were > > > analyzed. As > > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course > you > > > can > > > > > threat them separately, as I was naively thinking as non-neuormag > > > user, but > > > > > indeed combination of both is recommended as I have now learned > > > :-)(thanks > > > > > Phillip). I ran the following steps and I guess this should work > for > > > you. > > > > > best > > > > > tzvetan > > > > > > > > > > %% > > > > > cfg = []; > > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > > %% > > > > > cfg = [] > > > > > cfg.method = 'triangulation'; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > cfg.senstype = 'MEG'; > > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > > %% > > > > > % plot neighbours > > > > > cfg=[]; > > > > > cfg.neighbours = neighbours; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 7 > > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > this might be possible if you have the subject-specific MRI by > following > > > > the tutorial here: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > > > cfg=[]; > > > > cfg.tissue={'brain','skull','scalp'}; > > > > cfg.numvertices = [3000 2000 1000]; > > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable > should > > > > contain your triangulated surface with 1000 vertices. Let me know if > that > > > > works. Of course you should see the skin and the neck in the original > > > MRI. > > > > > > > > If you do not have an anatomical MRI that extends down to the chin > you > > > > could try with a template, such as this: > > > > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > > and the corresponding segmented version > > > > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > > > This goes down to the chin. Then you take care of rearranging the > > > position > > > > of the EEG electrodes according to this: > > > > > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > > > I hope this helped > > > > Cris > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear Cris, > > > > > > > > > > thank you very much for your answer. I am refering to an issue > that was > > > > > discussed in this thread from April 2013: > > > > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > > download. Some electrodes in the EGI 256-electrodes cap are placed > on > > > the > > > > > cheeks or on the back of the neck and these areas are not modeled > by > > > the > > > > > standard BEM skin compartment in the standard BEM model. My > question > > > was > > > > > about a standard segmentation that extends the skin (and skull) > > > compartment > > > > > downwards to allow these electrodes to sit on the nodes of the skin > > > mesh. > > > > > > > > > > Best, > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 8 > > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > > From: Munsif Jatoi > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Aishwarya, > > > > > > > > Please refer to main help tutorials. > > > > > > > > Also, you can find out the survey papers written in this area. For > more, > > > > SPM website can provide good help. > > > > > > > > Best, > > > > Munsif. > > > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > > > Dear Aishwarya, > > > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > > tutorials about source reconstruction. > > > > > > > > > > My recommended start would be: > > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > > reconstruction > > > > > > > > > > Best regards, > > > > > > > > > > Simon Hom?lle > > > > > PhD Candidate > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > Centre for Cognitive Neuroimaging > > > > > Radboud University Nijmegen > > > > > Phone: +31-(0)24-36-65059 > > > > > ------------------------------ > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > > > fieldtrip-bounces at science.ru.nl] > > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > > *To:* fieldtrip, donders > > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > > > Hi guys, > > > > > I'm currently working on source localization of EEG signals . > > > > > Im very new to it . > > > > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > > It would be of great help . > > > > > > > > > > -- > > > > > Regards, > > > > > Aishwarya > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > > > > > > -- > > > > Munsif Ali H.Jatoi, > > > > > > > > Ph D Scholar, > > > > Centre for Intelligent Signals and Imaging Research, > > > > Universiti Teknologi PETRONAS, > > > > Malaysia. > > > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 9 > > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > > From: Olga Sysoeva > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] problems with mri interpolation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Fieldtrippers, > > > > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > > > FT_VOLUMERESLICE. > > > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > > > mri_K0012.unit, 'm' > > > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > > > mri_K0012.transform, (4*4 double) > > > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > > > > Than I used > > > > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > > > > the output is > > > > > > > > > > > > ?the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > > > the input is volume data with dimensions [256 > > > > 256 256] > > > > > > > > the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > selecting subvolume of 0.0% > > > > > > > > reslicing and interpolating anatomy > > > > > > > > interpolating > > > > > > > > ??? Attempted to access sel(1); index out of > > > > bounds because numel(sel)=0. > > > > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > > at 663 > > > > > > > > ft_progress(sel(1)/num, 'interpolating > > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > > > cfg.feedback); > > > > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > > resliced);? > > > > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > > downloaded fieltrip (also in my previous version of 2013 the error > > > > was the same). > > > > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > > > > Best Regards, > > > > > > > > Olga. > > > > > > > > P.S.Actually, I can project my sources > > > > meaningfully into not interpolated MRI, altoough the images are > > > > plotted upside down. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > > ***************************************** > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/5f4a716a/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 2 > > Date: Thu, 21 Jan 2016 21:59:06 +0900 > > From: "Muhammad Naveed Iqbal Qureshi" > > To: > > Subject: [FieldTrip] difficulty in loading BCI-IV-2a dataset into > > fieldtrip for preprocessing > > Message-ID: <000b01d1544b$8323d8e0$896b8aa0$@gist.ac.kr> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi, > > > > > > > > I am using BCI competition IV dataset 2a for my experiment. > > > > I want to preprocess it with field trip. > > > > > > > > I have written the following code for this task. > > > > > > > > addpath(genpath('E:\bbci_data\fieldtrip-20160118\fieldtrip-20160118')); > > > > cd 'E:\bbci_data\BCICIV_2a_gdf\'; > > > > > > > > %% Field Trip preprocessing code > > > > for i=1:9 > > > > file=num2str(i); > > > > file=strcat('A0',file,'T.gdf'); > > > > cfg = []; > > > > cfg.dataset = file ; > > > > cfg.trialdef.eventtype = 'Stimulus'; > > > > cfg.trialdef.eventvalue = {'left', 'right', 'both feet', 'tongue'}; > > > > cfg.trialdef.triallength = 8; % duration in seconds > > > > cfg.trialdef.ntrials = inf; % number of trials, inf > > results in as many as possible > > > > cfg.trialdef.prestim = 3; > > > > cfg.trialdef.poststim = 6; > > > > cfg = ft_definetrial(cfg); > > > > > > > > cfg.bpfilter = 'yes'; > > > > cfg.bpfreq = [0.5 100]; > > > > cfg.bpfilttype = 'but'; > > > > cfg.bpfiltord = 5; > > > > cfg.demean = 'yes'; > > > > cfg.detrend = 'yes'; > > > > trialdata_EO{i} = ft_preprocessing(cfg); > > > > end > > > > > > > > However, this code does not import the event and trigger information from > > the header file of the data. > > > > I will be highly obliged if anyone can help me in this regard. > > > > > > > > Thank in advance. > > > > > > > > Best Regards, > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/1dbb2d2d/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 21 Jan 2016 20:14:01 +0200 > > From: saeed zahran > > To: "fieldtrip at science.ru.nl" > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 19 > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Thank you Jan and Cristiano; > > > > I downloaded another version of Fieldtrip thus the below error disappear: > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > But now I have another error: > > > > Error using surface_nesting (line 26) > > the compartment nesting cannot be determined > > > > Error in ft_headmodel_bemcp (line 66) > > order = surface_nesting(vol.bnd, 'insidefirst'); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example (line 100) > > vol = ft_prepare_headmodel(cfg, vol); > > Thank you for any suggestion > > > > Cristiano, I record the contraction of the uterus; > > > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 19 > > > To: fieldtrip at science.ru.nl > > > Date: Thu, 21 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) (RICHARDS, JOHN) > > > 3. Re: fieldtrip Digest, Vol 62, Issue 18 (saeed zahran) > > > 4. Re: fieldtrip Digest, Vol 62, Issue 18 > > > (Schoffelen, J.M. (Jan Mathijs)) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Wed, 20 Jan 2016 13:39:30 +0100 > > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1 at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answers yesterday. The segmentedmri > > > contained 'white', 'grey' and 'csf' so I needed to repeat the > > > segmentation using 'brain', 'skull' and 'scalp' as described in the > > > tutorial "Creating a BEM volume conduction model of the head for > > > source-reconstruction of EEG data" and everything worked smoothly > > > afterwards. The problem is solved now. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/e700c8d6/attachment-0001.html > > > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Wed, 20 Jan 2016 14:39:13 +0000 > > > From: "RICHARDS, JOHN" > > > To: "fieldtrip at science.ru.nl" , > > > "lah at pedneuro.uni-kiel.de" > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps (Laith Hamid) > > > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > > > > > Laith: > > > > > > I have a ?neurodevelopmental MRI database? (Richards, Sanchez et al., > 2015; see my www site) that has average MRI templates that could be used. > Each average has the whole head down to about the top of the neck. I did > these purposely since I use EEG recording and the MNI template did not even > go down far enough for the EGI 128 channel net. > > > > > > The database has average MRI templates for head (T1, T2) and brain. I > also have FEM segmented heads for the entire head that could be used for > this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, > scalp), but ironically, I cut these off about 10% below the EGI 128 channel > electrodes. However, you could use the three inner compartments for this > and just add the rest of the head below the compartment?or use the > whole-head FEM as is for a FEM-model, or use the segmented area below the > skull for a whole-head BEM model. I also have average 128-channel EGI > electrodes for each template. > > > > > > Additionally, the ?developmental? part of the ?neurodevelopmental MRI > database? is that I have these for a wide range of ages (all ages?). I have > a average for young adults (20-24 yrs), and average templates and FEM/BEM > models for groups from 3 months through adulthood, and into late adulthood. > So if you have specific neuro-pediatric applications you might be > interested in using an age appropriate MRI average template rather than an > adult template. > > > > > > See my www site for journal article references re this, and > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > > > > > Finally? I have been using these head models for FT-based FEM and BEM > models. Possibly some of the actually field trip models I have would be > useful to you. Some of the parts of the model do not use the electrodes > (e.g., grid-dipoles, head-model) whereas the final models (leadfield) > requires the electrode locations. The database also includes ?virtual? > electrodes for the 10-10 system, which might be used to generate the 256 > channel locations by knowing the relation between the 10-10 system and the > EGI system based on EGI ELP files for the 256 channels. > > > > > > John > > > > > > *********************************************** > > > John E. Richards Carolina Distinguished Professor > > > Department of Psychology > > > University of South Carolina > > > Columbia, SC 29208 > > > Dept Phone: 803 777 2079 > > > Fax: 803 777 9558 > > > Email: richards-john at sc.edu > > > HTTP: jerlab.psych.sc.edu > > > *********************************************** > > > > > > > > > > > > > > > >---------------------------------------------------------------------- > > > > > > > >Message: 1 > > > >Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > >From: Laith Hamid > > > >To: fieldtrip at science.ru.nl > > > >Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > >Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > >Dear community, > > > > > > > >My name is Laith Hamid and I am working in the University Medical > > > >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > >spikes and seizures. Currently I am analysing an EEG data set that was > > > >recorded using a 256-channel EGI system and I wanted to ask whether > you > > > >have a standard BEM or FEM head model that extends enough downwards to > > > >accomodate all 256 electrodes. The current standard BEM model in the > > > >template folder of Fieldtrip isn't appropriate for source analysis of > > > >256-channel EGI data. > > > > > > > >Thank you very much in advance for your help! > > > > > > > >Best, > > > > > > > >Laith > > > > > > > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Wed, 20 Jan 2016 19:37:32 +0200 > > > From: saeed zahran > > > To: "fieldtrip at science.ru.nl" > > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Fieldtrip community, > > > > > > I define the volume conductor as: > > > > > > vol = []; > > > vol.bnd(1).pnt=skinpnt > > > vol.bnd(1).tri=skinf > > > > > > vol.bnd(2).pnt=uteruspnt > > > vol.bnd(2).tri=uterusf > > > > > > vol.bnd(3).pnt=uterinecontentpnt > > > vol.bnd(3).tri=uterinecontentf > > > > > > vol.cond = c; > > > > > > > > > But it result with the below error: > > > > > > Subscript indices must either be real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > > > > Thank you very much in advance for your help! > > > > > > Best regards > > > Saeed Zahran > > > > > > > From: fieldtrip-request at science.ru.nl > > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > > To: fieldtrip at science.ru.nl > > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > > > Send fieldtrip mailing list submissions to > > > > fieldtrip at science.ru.nl > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > or, via email, send a message with subject or body 'help' to > > > > fieldtrip-request at science.ru.nl > > > > > > > > You can reach the person managing the list at > > > > fieldtrip-owner at science.ru.nl > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 4. Source Localisation (aishwarya selvaraj) > > > > 5. Re: Source Localisation (Hom?lle) > > > > 6. Re: plotting neighbours (victoria schroeder) > > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 8. Re: Source Localisation (Munsif Jatoi) > > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > > From: Laith Hamid > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > > spikes and seizures. Currently I am analysing an EEG data set that > was > > > > recorded using a 256-channel EGI system and I wanted to ask whether > you > > > > have a standard BEM or FEM head Subscript indices must either be > real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > model that extends enough downwards to > > > > accomodate all 256 electrodes. The current standard BEM model in the > > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > > 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > thanks for your question. You could refer to a factory schematic > layout > > > > such as the one in figure 4 of this publication: > > > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > > > and subsequently use the function ft_prepare_layout to manually > track the > > > > points of the custom design on your own (if you dont want to wait for > > > > somebody from the FT to do the same for you). > > > > > > > > cfg = []; > > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > > lay = ft_prepare_layout(cfg); > > > > > > > > The following tutorial describes the procedure in more details: > > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > > > Please do not hesitate to get in touch with me for this and other > matters. > > > > > > > > All the best > > > > Cris Micheli > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear community, > > > > > > > > > > My name is Laith Hamid and I am working in the University Medical > Complex > > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and > > > > > seizures. Currently I am analysing an EEG data set that was > recorded using > > > > > a 256-channel EGI system and I wanted to ask whether you have a > standard > > > > > BEM or FEM head model that extends enough downwards to accomodate > all 256 > > > > > electrodes. The current standard BEM model in the template folder > of > > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > data. > > > > > > > > > > Thank you very much in advance for your help! > > > > > > > > > > Best, > > > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > > From: Laith Hamid > > > > To: Fieldtrip > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that > was > > > > discussed in this thread from April 2013: > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > > the cheeks or on the back of the neck and these areas are not > modeled by > > > > the standard BEM skin compartment in the standard BEM model. My > question > > > > was about a standard segmentation that extends the skin (and skull) > > > > compartment downwards to allow these electrodes to sit on the nodes > of > > > > the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 4 > > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > > From: aishwarya selvaraj > > > > To: "fieldtrip, donders" > > > > Subject: [FieldTrip] Source Localisation > > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 5 > > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > > From: Hom?lle, S. (Simon) > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ________________________________ > > > > From: fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [ > aishwaryaselvaraj1708 at gmail.com] > > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > > To: fieldtrip, donders > > > > Subject: [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 6 > > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > > From: victoria schroeder > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] plotting neighbours > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > > > Things have become much clearer now. > > > > > > > > I would like to follow up with a very related question. I am trying > to > > > > replicate the analysis for the cluster based permutation test using > the > > > > code and the data provided. However, i run into two problems here > > > > > > > > First, i get the following error if i use the original code: > > > > Attempted to access cfg.frequency(2); index out of bounds because > > > > numel(cfg.frequency)=1. > > > > > > > > Error in ft_freqstatistics (line 187) > > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > fmax)]; > > > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 > 20]. > > > > However, then no significant clusters are found. Which becomes clear > when > > > > trying to plot the cluster or by looking at the output of > > > > ft_freqstatistics. > > > > > > > > Does the change in the code , change the output? How can i avoid the > error > > > > mentioned above and still get the same output from ft_freqstatistics > as the > > > > one provided on the webpage? > > > > > > > > > > > > The relevant section of the toturial is provided below. > > > > Thank you! > > > > > > > > Victoria > > > > > > > > Permutation test > > > > > > > > Now, run *ft_freqstatistics > > > > * to > compare > > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > cfg.latency, > > > > the following configuration is identical to the configuration that > was used > > > > for comparing event-related averages in the cluster-based > permutation tests > > > > on event related fields tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>. > > > > Also see this tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> for > > > > a detailed explanation of all the configuration settings. You can > read more > > > > about the *ft_prepare_neighbours > > > > * > function > > > > in the FAQ's > > > > < > http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work>. > > > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > > servers,freqFIC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > >), > > > > use: > > > > > > > > load freqFIC_planar_cmb > > > > load freqFC_planar_cmb > > > > > > > > cfg = []; > > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > > cfg.latency = 'all'; > > > > cfg.frequency = 20; > > > > cfg.method = 'montecarlo'; > > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > > cfg.correctm = 'cluster'; > > > > cfg.clusteralpha = 0.05; > > > > cfg.clusterstatistic = 'maxsum'; > > > > cfg.minnbchan = 2; > > > > cfg.tail = 0; > > > > cfg.clustertail = 0; > > > > cfg.alpha = 0.025; > > > > cfg.numrandomization = 500; > > > > % prepare_neighbours determines what sensors may form clusters > > > > cfg_neighb.method = 'distance'; > > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > > size(freqFC_planar_cmb.powspctrm,1)); > > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > > > cfg.design = design; > > > > cfg.ivar = 1; > > > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, > freqFC_planar_cmb); > > > > > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov < > tzvetan.popov at uni-konstanz.de>: > > > > > > > > > > > > > > Hi Victoria, > > > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. > You are > > > > > right I was only scrolling up to the part where the mags were > analyzed. As > > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course > you can > > > > > threat them separately, as I was naively thinking as non-neuormag > user, but > > > > > indeed combination of both is recommended as I have now learned > :-)(thanks > > > > > Phillip). I ran the following steps and I guess this should work > for you. > > > > > best > > > > > tzvetan > > > > > > > > > > %% > > > > > cfg = []; > > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > > %% > > > > > cfg = [] > > > > > cfg.method = 'triangulation'; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > cfg.senstype = 'MEG'; > > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > > %% > > > > > % plot neighbours > > > > > cfg=[]; > > > > > cfg.neighbours = neighbours; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 7 > > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > this might be possible if you have the subject-specific MRI by > following > > > > the tutorial here: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > > > cfg=[]; > > > > cfg.tissue={'brain','skull','scalp'}; > > > > cfg.numvertices = [3000 2000 1000]; > > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable > should > > > > contain your triangulated surface with 1000 vertices. Let me know if > that > > > > works. Of course you should see the skin and the neck in the > original MRI. > > > > > > > > If you do not have an anatomical MRI that extends down to the chin > you > > > > could try with a template, such as this: > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > > and the corresponding segmented version > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > > > This goes down to the chin. Then you take care of rearranging the > position > > > > of the EEG electrodes according to this: > > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > > > I hope this helped > > > > Cris > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear Cris, > > > > > > > > > > thank you very much for your answer. I am refering to an issue > that was > > > > > discussed in this thread from April 2013: > > > > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > > download. Some electrodes in the EGI 256-electrodes cap are placed > on the > > > > > cheeks or on the back of the neck and these areas are not modeled > by the > > > > > standard BEM skin compartment in the standard BEM model. My > question was > > > > > about a standard segmentation that extends the skin (and skull) > compartment > > > > > downwards to allow these electrodes to sit on the nodes of the > skin mesh. > > > > > > > > > > Best, > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 8 > > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > > From: Munsif Jatoi > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Aishwarya, > > > > > > > > Please refer to main help tutorials. > > > > > > > > Also, you can find out the survey papers written in this area. For > more, > > > > SPM website can provide good help. > > > > > > > > Best, > > > > Munsif. > > > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > > > Dear Aishwarya, > > > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > > tutorials about source reconstruction. > > > > > > > > > > My recommended start would be: > > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > > reconstruction > > > > > > > > > > Best regards, > > > > > > > > > > Simon Hom?lle > > > > > PhD Candidate > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > Centre for Cognitive Neuroimaging > > > > > Radboud University Nijmegen > > > > > Phone: +31-(0)24-36-65059 > > > > > ------------------------------ > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] > > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > > *To:* fieldtrip, donders > > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > > > Hi guys, > > > > > I'm currently working on source localization of EEG signals . > > > > > Im very new to it . > > > > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > > It would be of great help . > > > > > > > > > > -- > > > > > Regards, > > > > > Aishwarya > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > > > > > > -- > > > > Munsif Ali H.Jatoi, > > > > > > > > Ph D Scholar, > > > > Centre for Intelligent Signals and Imaging Research, > > > > Universiti Teknologi PETRONAS, > > > > Malaysia. > > > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 9 > > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > > From: Olga Sysoeva > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] problems with mri interpolation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Fieldtrippers, > > > > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > > > FT_VOLUMERESLICE. > > > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > > > mri_K0012.unit, 'm' > > > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > > > mri_K0012.transform, (4*4 double) > > > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > > > > Than I used > > > > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > > > > the output is > > > > > > > > > > > > ?the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > > > the input is volume data with dimensions [256 > > > > 256 256] > > > > > > > > the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > selecting subvolume of 0.0% > > > > > > > > reslicing and interpolating anatomy > > > > > > > > interpolating > > > > > > > > ??? Attempted to access sel(1); index out of > > > > bounds because numel(sel)=0. > > > > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > > at 663 > > > > > > > > ft_progress(sel(1)/num, 'interpolating > > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > > > cfg.feedback); > > > > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > > resliced);? > > > > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > > downloaded fieltrip (also in my previous version of 2013 the error > > > > was the same). > > > > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > > > > Best Regards, > > > > > > > > Olga. > > > > > > > > P.S.Actually, I can project my sources > > > > meaningfully into not interpolated MRI, altoough the images are > > > > plotted upside down. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > > ***************************************** > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/0d8cf652/attachment-0001.html > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Thu, 21 Jan 2016 08:16:55 +0000 > > > From: "Schoffelen, J.M. (Jan Mathijs)" > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Saeed, > > > > > > are you using 0 or 1 indexing for your triangles? You probably want to > use 1 indexing. > > > > > > Best, > > > Jan-Mathijs > > > > > > > > > On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: > > > > > > Dear Fieldtrip community, > > > > > > I define the volume conductor as: > > > > > > vol = []; > > > vol.bnd(1).pnt=skinpnt > > > vol.bnd(1).tri=skinf > > > > > > vol.bnd(2).pnt=uteruspnt > > > vol.bnd(2).tri=uterusf > > > > > > vol.bnd(3).pnt=uterinecontentpnt > > > vol.bnd(3).tri=uterinecontentf > > > > > > vol.cond = c; > > > > > > > > > But it result with the below error: > > > > > > Subscript indices must either be real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > > > > Thank you very much in advance for your help! > > > > > > Best regards > > > Saeed Zahran > > > > > > > From: fieldtrip-request at science.ru.nl fieldtrip-request at science.ru.nl> > > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > > To: fieldtrip at science.ru.nl > > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > > > Send fieldtrip mailing list submissions to > > > > fieldtrip at science.ru.nl > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > or, via email, send a message with subject or body 'help' to > > > > fieldtrip-request at science.ru.nl fieldtrip-request at science.ru.nl> > > > > > > > > You can reach the person managing the list at > > > > fieldtrip-owner at science.ru.nl > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 4. Source Localisation (aishwarya selvaraj) > > > > 5. Re: Source Localisation (Hom?lle) > > > > 6. Re: plotting neighbours (victoria schroeder) > > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 8. Re: Source Localisation (Munsif Jatoi) > > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > > From: Laith Hamid lah at pedneuro.uni-kiel.de>> > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > > spikes and seizures. Currently I am analysing an EEG data set that > was > > > > recorded using a 256-channel EGI system and I wanted to ask whether > you > > > > have a standard BEM or FEM head Subscript indices must either be > real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > model that extends enough downwards to > > > > accomodate all 256 electrodes. The current standard BEM model in the > > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > > 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > > From: Cristiano Micheli michelic72 at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > thanks for your question. You could refer to a factory schematic > layout > > > > such as the one in figure 4 of this publication: > > > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > > > and subsequently use the function ft_prepare_layout to manually > track the > > > > points of the custom design on your own (if you dont want to wait for > > > > somebody from the FT to do the same for you). > > > > > > > > cfg = []; > > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > > lay = ft_prepare_layout(cfg); > > > > > > > > The following tutorial describes the procedure in more details: > > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > > > Please do not hesitate to get in touch with me for this and other > matters. > > > > > > > > All the best > > > > Cris Micheli > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear community, > > > > > > > > > > My name is Laith Hamid and I am working in the University Medical > Complex > > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and > > > > > seizures. Currently I am analysing an EEG data set that was > recorded using > > > > > a 256-channel EGI system and I wanted to ask whether you have a > standard > > > > > BEM or FEM head model that extends enough downwards to accomodate > all 256 > > > > > electrodes. The current standard BEM model in the template folder > of > > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > data. > > > > > > > > > > Thank you very much in advance for your help! > > > > > > > > > > Best, > > > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > > From: Laith Hamid lah at pedneuro.uni-kiel.de>> > > > > To: Fieldtrip fieldtrip at science.ru.nl>> > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that > was > > > > discussed in this thread from April 2013: > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > > the cheeks or on the back of the neck and these areas are not > modeled by > > > > the standard BEM skin compartment in the standard BEM model. My > question > > > > was about a standard segmentation that extends the skin (and skull) > > > > compartment downwards to allow these electrodes to sit on the nodes > of > > > > the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 4 > > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > > From: aishwarya selvaraj aishwaryaselvaraj1708 at gmail.com>> > > > > To: "fieldtrip, donders" fieldtrip at donders.ru.nl>> > > > > Subject: [FieldTrip] Source Localisation > > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 5 > > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > > From: Hom?lle, S. (Simon) S.Homolle at donders.ru.nl>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ________________________________ > > > > From: fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl>] on behalf of aishwarya selvaraj [ > aishwaryaselvaraj1708 at gmail.com] > > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > > To: fieldtrip, donders > > > > Subject: [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 6 > > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > > From: victoria schroeder vic.schroeder2 at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] plotting neighbours > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > > > Things have become much clearer now. > > > > > > > > I would like to follow up with a very related question. I am trying > to > > > > replicate the analysis for the cluster based permutation test using > the > > > > code and the data provided. However, i run into two problems here > > > > > > > > First, i get the following error if i use the original code: > > > > Attempted to access cfg.frequency(2); index out of bounds because > > > > numel(cfg.frequency)=1. > > > > > > > > Error in ft_freqstatistics (line 187) > > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > fmax)]; > > > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 > 20]. > > > > However, then no significant clusters are found. Which becomes clear > when > > > > trying to plot the cluster or by looking at the output of > > > > ft_freqstatistics. > > > > > > > > Does the change in the code , change the output? How can i avoid the > error > > > > mentioned above and still get the same output from ft_freqstatistics > as the > > > > one provided on the webpage? > > > > > > > > > > > > The relevant section of the toturial is provided below. > > > > Thank you! > > > > > > > > Victoria > > > > > > > > Permutation test > > > > > > > > Now, run *ft_freqstatistics > > > > * to > compare > > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > cfg.latency, > > > > the following configuration is identical to the configuration that > was used > > > > for comparing event-related averages in the cluster-based > permutation tests > > > > on event related fields tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>. > > > > Also see this tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> for > > > > a detailed explanation of all the configuration settings. You can > read more > > > > about the *ft_prepare_neighbours > > > > * > function > > > > in the FAQ's > > > > < > http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work>. > > > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > > servers,freqFIC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > >), > > > > use: > > > > > > > > load freqFIC_planar_cmb > > > > load freqFC_planar_cmb > > > > > > > > cfg = []; > > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > > cfg.latency = 'all'; > > > > cfg.frequency = 20; > > > > cfg.method = 'montecarlo'; > > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > > cfg.correctm = 'cluster'; > > > > cfg.clusteralpha = 0.05; > > > > cfg.clusterstatistic = 'maxsum'; > > > > cfg.minnbchan = 2; > > > > cfg.tail = 0; > > > > cfg.clustertail = 0; > > > > cfg.alpha = 0.025; > > > > cfg.numrandomization = 500; > > > > % prepare_neighbours determines what sensors may form clusters > > > > cfg_neighb.method = 'distance'; > > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > > size(freqFC_planar_cmb.powspctrm,1)); > > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > > > cfg.design = design; > > > > cfg.ivar = 1; > > > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, > freqFC_planar_cmb); > > > > > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov < > tzvetan.popov at uni-konstanz.de>: > > > > > > > > > > > > > > Hi Victoria, > > > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. > You are > > > > > right I was only scrolling up to the part where the mags were > analyzed. As > > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course > you can > > > > > threat them separately, as I was naively thinking as non-neuormag > user, but > > > > > indeed combination of both is recommended as I have now learned > :-)(thanks > > > > > Phillip). I ran the following steps and I guess this should work > for you. > > > > > best > > > > > tzvetan > > > > > > > > > > %% > > > > > cfg = []; > > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > > %% > > > > > cfg = [] > > > > > cfg.method = 'triangulation'; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > cfg.senstype = 'MEG'; > > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > > %% > > > > > % plot neighbours > > > > > cfg=[]; > > > > > cfg.neighbours = neighbours; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 7 > > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > > From: Cristiano Micheli michelic72 at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > this might be possible if you have the subject-specific MRI by > following > > > > the tutorial here: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > > > cfg=[]; > > > > cfg.tissue={'brain','skull','scalp'}; > > > > cfg.numvertices = [3000 2000 1000]; > > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable > should > > > > contain your triangulated surface with 1000 vertices. Let me know if > that > > > > works. Of course you should see the skin and the neck in the > original MRI. > > > > > > > > If you do not have an anatomical MRI that extends down to the chin > you > > > > could try with a template, such as this: > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > > and the corresponding segmented version > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > > > This goes down to the chin. Then you take care of rearranging the > position > > > > of the EEG electrodes according to this: > > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > > > I hope this helped > > > > Cris > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear Cris, > > > > > > > > > > thank you very much for your answer. I am refering to an issue > that was > > > > > discussed in this thread from April 2013: > > > > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > > download. Some electrodes in the EGI 256-electrodes cap are placed > on the > > > > > cheeks or on the back of the neck and these areas are not modeled > by the > > > > > standard BEM skin compartment in the standard BEM model. My > question was > > > > > about a standard segmentation that extends the skin (and skull) > compartment > > > > > downwards to allow these electrodes to sit on the nodes of the > skin mesh. > > > > > > > > > > Best, > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 8 > > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > > From: Munsif Jatoi munsif.jatoi at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Aishwarya, > > > > > > > > Please refer to main help tutorials. > > > > > > > > Also, you can find out the survey papers written in this area. For > more, > > > > SPM website can provide good help. > > > > > > > > Best, > > > > Munsif. > > > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > > > Dear Aishwarya, > > > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > > tutorials about source reconstruction. > > > > > > > > > > My recommended start would be: > > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > > reconstruction > > > > > > > > > > Best regards, > > > > > > > > > > Simon Hom?lle > > > > > PhD Candidate > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > Centre for Cognitive Neuroimaging > > > > > Radboud University Nijmegen > > > > > Phone: +31-(0)24-36-65059 > > > > > ------------------------------ > > > > > *From:* fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl>] > > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com > ] > > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > > *To:* fieldtrip, donders > > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > > > Hi guys, > > > > > I'm currently working on source localization of EEG signals . > > > > > Im very new to it . > > > > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > > It would be of great help . > > > > > > > > > > -- > > > > > Regards, > > > > > Aishwarya > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > > > > > > -- > > > > Munsif Ali H.Jatoi, > > > > > > > > Ph D Scholar, > > > > Centre for Intelligent Signals and Imaging Research, > > > > Universiti Teknologi PETRONAS, > > > > Malaysia. > > > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 9 > > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > > From: Olga Sysoeva olga.v.sysoeva at gmail.com>> > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] problems with mri interpolation > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Fieldtrippers, > > > > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > > > FT_VOLUMERESLICE. > > > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > > > mri_K0012.unit, 'm' > > > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > > > mri_K0012.transform, (4*4 double) > > > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > > > > Than I used > > > > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > > > > the output is > > > > > > > > > > > > ?the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > > > the input is volume data with dimensions [256 > > > > 256 256] > > > > > > > > the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > selecting subvolume of 0.0% > > > > > > > > reslicing and interpolating anatomy > > > > > > > > interpolating > > > > > > > > ??? Attempted to access sel(1); index out of > > > > bounds because numel(sel)=0. > > > > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > > at 663 > > > > > > > > ft_progress(sel(1)/num, 'interpolating > > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > > > cfg.feedback); > > > > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > > resliced);? > > > > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > > downloaded fieltrip (also in my previous version of 2013 the error > > > > was the same). > > > > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > > > > Best Regards, > > > > > > > > Olga. > > > > > > > > P.S.Actually, I can project my sources > > > > meaningfully into not interpolated MRI, altoough the images are > > > > plotted upside down. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > > ***************************************** > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/d9124654/attachment-0001.html > > > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 19 > > > ***************************************** > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/043a7628/attachment.html > > > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 20 > > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.roux at bcbl.eu Mon Jan 25 11:55:27 2016 From: f.roux at bcbl.eu (=?utf-8?B?RnLDqWTDqXJpYw==?= Roux) Date: Mon, 25 Jan 2016 11:55:27 +0100 (CET) Subject: [FieldTrip] cross-frequency coupling between MEG planar channel twins? Message-ID: <1957967079.822957.1453719327381.JavaMail.zimbra@bcbl.eu> Dear all, in my MEG-data (Elekta Vectorview System) I am observing that the amplitude of higher frequencies over one planar gradient channel is coupled to the phase of lower frequencies on its corresponding twin-channel . I am attaching a figure to illustrate this. The upper row shows a low-frequency oscillation for one planar-channel and the bottom row shows the amplitude of a higher-frequency oscillation on its corresponding twin channel. Note that this separation is fairly consistent across other channels as well. My question relates to what could explain such a coupling of low and high freq activity over channel-pairs with different gradient orientations (ie vertical vs. horizontal)? Could this be an indicator of two separate sources which are being picked up by the different spatial sensitivity of the planar gradients and where the phase of one source modulates the amplitude of the other source? Any comments or suggestions on this would be highly appreciated. Fred -- Frédéric Roux Postdoctoral Scientist, Marie-Curie fellow BCBL. Basque Center on Cognition, Brain & Language. f.roux at bcbl.eu Tel: +34 943 309 300 Ext 211 Fax: +34 943 309 052 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer --------------------------------------------------------------------------- “The probability of success is difficult to estimate; but if we never search the chance of success is zero.” -------------- next part -------------- A non-text attachment was scrubbed... Name: low_high_coupling_planar_grads_TFR.png Type: image/png Size: 26838 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: low_high_coupling_planar_grads.png Type: image/png Size: 11179 bytes Desc: not available URL: From saeedzahran at hotmail.com Mon Jan 25 18:08:07 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Mon, 25 Jan 2016 19:08:07 +0200 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Thank you Cris, but I am sure that the meshes is nested, does it require to calculate the normal for each vertices? Best regards Saeed. > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 24 > To: fieldtrip at science.ru.nl > Date: Mon, 25 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. cross-frequency coupling between MEG planar channel twins? > (Fr?d?ric Roux) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 25 Jan 2016 11:55:27 +0100 (CET) > From: Fr?d?ric Roux > To: FieldTrip discussion list > Subject: [FieldTrip] cross-frequency coupling between MEG planar > channel twins? > Message-ID: <1957967079.822957.1453719327381.JavaMail.zimbra at bcbl.eu> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > in my MEG-data (Elekta Vectorview System) I am observing that the amplitude of higher frequencies over one planar gradient channel is coupled to the > phase of lower frequencies on its corresponding twin-channel . I am attaching a figure to illustrate this. The upper row shows a low-frequency oscillation for one planar-channel and the bottom row shows the amplitude of a higher-frequency oscillation on its corresponding twin channel. Note that this separation is fairly consistent across other channels as well. > > My question relates to what could explain such a coupling of low and high freq activity over channel-pairs with different gradient orientations (ie vertical vs. horizontal)? > > Could this be an indicator of two separate sources which are being picked up by the different spatial sensitivity of the planar gradients and where the phase of one source modulates the amplitude of the other source? > > Any comments or suggestions on this would be highly appreciated. > > Fred > > > > > > > > -- > Fr?d?ric Roux > Postdoctoral Scientist, Marie-Curie fellow > BCBL. Basque Center on Cognition, Brain & Language. > > f.roux at bcbl.eu > Tel: +34 943 309 300 Ext 211 > Fax: +34 943 309 052 > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > --------------------------------------------------------------------------- > > ?The probability of success is difficult to estimate; but if we never search the chance of success is zero.? > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: low_high_coupling_planar_grads_TFR.png > Type: image/png > Size: 26838 bytes > Desc: not available > URL: > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: low_high_coupling_planar_grads.png > Type: image/png > Size: 11179 bytes > Desc: not available > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 24 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From toni.rbaena at gmail.com Mon Jan 25 18:15:55 2016 From: toni.rbaena at gmail.com (Antonio Rodriguez) Date: Mon, 25 Jan 2016 18:15:55 +0100 Subject: [FieldTrip] =?utf-8?q?Can=C2=B4t_read_CFS_files=2E?= Message-ID: Dear Fieldtrippers, My name is Antonio Rodriguez, i´m very new with fieldtrip., We´re trying to open a file with CFS extension (Cambridge Electronic Design), which is the format that Signal Software returns, but i can´t read the file. I´m trying to load the file "dataset.cfs"; no error is prompted but nothing is loaded in the Workspace, I found in the tutorial that fieldtrip is able to open this kind of files. Am i doing anything wrong? Thank you. Antonio Rodriguez, University of Seville. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Mon Jan 25 18:57:04 2016 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Mon, 25 Jan 2016 09:57:04 -0800 Subject: [FieldTrip] =?utf-8?q?Can=C2=B4t_read_CFS_files=2E?= In-Reply-To: References: Message-ID: Hi Antonio, How are you trying to load the file? To see whether your format is supported, try: hdr = ft_read_header('dataset.cfs') Hope that gets you started, Arjen 2016-01-25 9:15 GMT-08:00 Antonio Rodriguez : > Dear Fieldtrippers, > > My name is Antonio Rodriguez, i´m very new with fieldtrip., We´re trying > to open a file with CFS extension (Cambridge Electronic Design), which is > the format that Signal Software returns, but i can´t read the file. > > I´m trying to load the file "dataset.cfs"; no error is prompted but > nothing is loaded in the Workspace, I found in the tutorial that fieldtrip > is able to open this kind of files. > > Am i doing anything wrong? > > Thank you. > > > Antonio Rodriguez, University of Seville. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Mon Jan 25 19:41:53 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Mon, 25 Jan 2016 19:41:53 +0100 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Hi Saeed, could you be more specific by attaching the nesting matrix? You find it by typing: dbstop if error in the matlab workspace. and then by running your script again. The script will stop at the line where it fails and at that point you will be able to look inside the local variables of the subfunction that is returning the error (in your case it is the private function surface_nesting.m). Please copy the content of the variables *nesting* and * numboundaries* in the next email. At that point I will have enough information to help you. I don't think the normals are a problem here. Best regards, Cris On Mon, Jan 25, 2016 at 6:08 PM, saeed zahran wrote: > Thank you Cris, but I am sure that the meshes is nested, > does it require to calculate the normal for each vertices? > > Best regards > Saeed. > > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 24 > > To: fieldtrip at science.ru.nl > > Date: Mon, 25 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. cross-frequency coupling between MEG planar channel twins? > > (Fr?d?ric Roux) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 25 Jan 2016 11:55:27 +0100 (CET) > > From: Fr?d?ric Roux > > To: FieldTrip discussion list > > Subject: [FieldTrip] cross-frequency coupling between MEG planar > > channel twins? > > Message-ID: <1957967079.822957.1453719327381.JavaMail.zimbra at bcbl.eu> > > Content-Type: text/plain; charset="utf-8" > > > > Dear all, > > > > in my MEG-data (Elekta Vectorview System) I am observing that the > amplitude of higher frequencies over one planar gradient channel is coupled > to the > > phase of lower frequencies on its corresponding twin-channel . I am > attaching a figure to illustrate this. The upper row shows a low-frequency > oscillation for one planar-channel and the bottom row shows the amplitude > of a higher-frequency oscillation on its corresponding twin channel. Note > that this separation is fairly consistent across other channels as well. > > > > My question relates to what could explain such a coupling of low and > high freq activity over channel-pairs with different gradient orientations > (ie vertical vs. horizontal)? > > > > Could this be an indicator of two separate sources which are being > picked up by the different spatial sensitivity of the planar gradients and > where the phase of one source modulates the amplitude of the other source? > > > > Any comments or suggestions on this would be highly appreciated. > > > > Fred > > > > > > > > > > > > > > > > -- > > Fr?d?ric Roux > > Postdoctoral Scientist, Marie-Curie fellow > > BCBL. Basque Center on Cognition, Brain & Language. > > > > f.roux at bcbl.eu > > Tel: +34 943 309 300 Ext 211 > > Fax: +34 943 309 052 > > > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > --------------------------------------------------------------------------- > > > > ?The probability of success is difficult to estimate; but if we never > search the chance of success is zero.? > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: low_high_coupling_planar_grads_TFR.png > > Type: image/png > > Size: 26838 bytes > > Desc: not available > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160125/c41f609c/attachment-0002.png > > > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: low_high_coupling_planar_grads.png > > Type: image/png > > Size: 11179 bytes > > Desc: not available > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160125/c41f609c/attachment-0003.png > > > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 24 > > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Tue Jan 26 00:25:13 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Tue, 26 Jan 2016 00:25:13 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: Message-ID: Dear FieldTrip users, I'm looking for the best method to analyse the relationship between ERP and behavioural data but all I've been able to find so far are methods to compare ERPs (or more generally time-series). Consider the following example: 20 participants performed a memory-related task in which they had to respond based on the difference between the target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 samples at 200 Hz) and responses were recorded; ERPs were then created based on epochs in which the responses were correct. Similarly, response accuracy was averaged over all successful epochs per each subject. The resulting data are therefore: 20 participants x 50 channels x 1000 samples (ERP) and 20 averages of accuracy (one value per participant). My objective is to identify which portion of the ERP data best explains (or predicts) the changes in accuracy. In other words, in which time interval is the most significant difference between people who do well in the task and those who don't. So far I've been doing correlations between ERP at each time point and overall accuracy, which is unreliable due to multiple comparisons (correction methods are reportedly too conservative). Nevertheless, certain channels show quite strong correlations in multiple time intervals. How would you approach this problem, please? Many thanks! Best regards, Harold -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue Jan 26 06:35:58 2016 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 26 Jan 2016 06:35:58 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: Message-ID: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Dear Harold, have you checked out ft_statfun_correlationT? This sounds like the function you're looking for. Use cfg.statistic = 'ft_statfun_correlationT' in your call to ft_timelockstatistics. Plus you can use all the correction methods available in FT. See the FAQ for more info: http://www.fieldtriptoolbox.org/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables Good luck, Julian ******************** Dr. Julian Keil AG Multisensorische Integration Psychiatrische Universitätsklinik der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11, Raum A007 10115 Berlin Telefon: +49-30-2311-1879 Fax: +49-30-2311-2209 http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration Am 26.01.2016 um 00:25 schrieb Harold Cavendish: > Dear FieldTrip users, > > I'm looking for the best method to analyse the relationship between ERP and behavioural data but all I've been able to find so far are methods to compare ERPs (or more generally time-series). > > Consider the following example: 20 participants performed a memory-related task in which they had to respond based on the difference between the target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 samples at 200 Hz) and responses were recorded; ERPs were then created based on epochs in which the responses were correct. Similarly, response accuracy was averaged over all successful epochs per each subject. > > The resulting data are therefore: 20 participants x 50 channels x 1000 samples (ERP) and 20 averages of accuracy (one value per participant). > > My objective is to identify which portion of the ERP data best explains (or predicts) the changes in accuracy. In other words, in which time interval is the most significant difference between people who do well in the task and those who don't. > > So far I've been doing correlations between ERP at each time point and overall accuracy, which is unreliable due to multiple comparisons (correction methods are reportedly too conservative). Nevertheless, certain channels show quite strong correlations in multiple time intervals. > > How would you approach this problem, please? > > Many thanks! > > Best regards, > Harold > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From stephen.politzer-ahles at ling-phil.ox.ac.uk Tue Jan 26 12:08:32 2016 From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles) Date: Tue, 26 Jan 2016 11:08:32 +0000 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data Message-ID: Hi Harold, If you're only interested in identifying which timepoints have the best correlation, multiple comparisons aren't really an issue; if you're not worried about testing for significance, then the place where you see the highest estimate is the highest. See e.g., Hauk et al. 2006 in NeuroImage, and Smith & Kutas 2015 in Psychophysiology, for similar analyses. If you're interested in finding a part of the waveform where the correlation is significantly different from zero while also dealing with multiple comparisons, you could use [spatio]temporal clustering (Maris & Oostenveld 2007). Just make an event-related regression coefficient (as described in Hauk et al.; just do a regression at each timepoint, and then rather than plotting the ERP amplitude at each timepoint, plot the regression estimate (*b*) at each timepoint, to derive a similar waveform) and then test that waveform against 0 using temporal clustering. Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/ > Message: 5 > Date: Tue, 26 Jan 2016 00:25:13 +0100 > From: Harold Cavendish > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Fwd: Identify a window of best correlation > between ERP and behavioural data > Message-ID: > < > CALOTjvZXPNWHLefXrG6uss7uF3kkXie7qjiWqEcesOUqWay6qA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear FieldTrip users, > > I'm looking for the best method to analyse the relationship between ERP and > behavioural data but all I've been able to find so far are methods to > compare ERPs (or more generally time-series). > > Consider the following example: 20 participants performed a memory-related > task in which they had to respond based on the difference between the > target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 > samples at 200 Hz) and responses were recorded; ERPs were then created > based on epochs in which the responses were correct. Similarly, response > accuracy was averaged over all successful epochs per each subject. > > The resulting data are therefore: 20 participants x 50 channels x 1000 > samples (ERP) and 20 averages of accuracy (one value per participant). > > My objective is to identify which portion of the ERP data best explains (or > predicts) the changes in accuracy. In other words, in which time interval > is the most significant difference between people who do well in the task > and those who don't. > > So far I've been doing correlations between ERP at each time point and > overall accuracy, which is unreliable due to multiple comparisons > (correction methods are reportedly too conservative). Nevertheless, certain > channels show quite strong correlations in multiple time intervals. > > How would you approach this problem, please? > > Many thanks! > > Best regards, > Harold > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160126/b5769634/attachment-0001.html > > > > ------------------------------ > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Wed Jan 27 10:51:13 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Wed, 27 Jan 2016 10:51:13 +0100 Subject: [FieldTrip] Two questions regarding source analysis in Fieldtrip Message-ID: <4fcc207813cc3640c68f3d637e011a79@mail.uni-kiel.de> Dear Community, I have two questions regarding source analysis in Fieldtrip. 1- Is it possible to estimate the regularization parameter (lambda) in ft_timelockanalysis or ft_sourceanalysis? How is it automatically determined if it is not specified by the user? 2- The source analysis results of ft_sourceanalysis contain information aobut time series of the sources. How can I show a specific point in time (e.g. the epileptic spike's peak) in ft_sourceplot? or is this information lost in ft_sourceinterpolate? Thank you very much for your help. Best, Laith Hamid -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Wed Jan 27 14:04:21 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Wed, 27 Jan 2016 14:04:21 +0100 Subject: [FieldTrip] Two questions regarding source analysis in Fieldtrip In-Reply-To: <4fcc207813cc3640c68f3d637e011a79@mail.uni-kiel.de> References: <4fcc207813cc3640c68f3d637e011a79@mail.uni-kiel.de> Message-ID: Hi Laith On Wed, Jan 27, 2016 at 10:51 AM, Laith Hamid wrote: > > Dear Community, > > I have two questions regarding source analysis in Fieldtrip. > > 1- Is it possible to estimate the regularization parameter (lambda) in > ft_timelockanalysis or ft_sourceanalysis? How is it automatically > determined if it is not specified by the user? > > I am reporting a mail by M Wibral (2-3-2009) from the FieldTrip mailing list here below: *Hi Marco,in a nutshell the effect of the lambda parameter is to smoothe your solution in space, it also makes it more stable in the presence of noise. You might know that the estimation of the covariance matrix for beamforming requires quite a lot of data. CTF/VSM (a MEG manufacturer) used to suggest to have your data satisfy the following relationship:3000 < BW[Hz] * #trials *EffectLength[s]Where BW[Hz] is the bandwidth of your effect of interest in Hz, #trials is the number of trials that contain that effect, and EffectLength[s] is the length of your effect in seconds (NOT ms!).Here's an example: You have an effect between 30 and 60Hz, so the bandwidth of that effect is 30Hz. The effect is visible (say at the electrode level) for 400ms=0.4s in each trial. Now you calculate the number of trials to be:#trials > 3000 / ( BW[Hz] * EffectLength[s]) = 3000/(0.4*30)= 250. This means that you would need 250 artifact free, valid trials. Choosing a larger lambda can help to reduce the amount of data necessary, but you get a more smeared out solution.A good introduction and simulation results for various values of lambda can be found in:Neuroimage. 2008 Feb 15;39(4):1788-802. Epub 2007 Oct 10Optimising experimental design for MEG beamformer imaging.Brookes MJ, Vrba J, Robinson SE, Stevenson CM, Peters AM, Barnes GR, Hillebrand A, Morris PG.Hope this helps,* *Michael* In short, if you have enough trials you do not need to smoothe your solution. If not, then apply the rule of thumb described above. I believe you have an option to declare lambda in percentages as well (e.g. lambda = '5%'; ) You can refer to this tutorial too: http://www.fieldtriptoolbox.org/tutorial/beamformer 2- The source analysis results of ft_sourceanalysis contain information > aobut time series of the sources. How can I show a specific point in time > (e.g. the epileptic spike's peak) in ft_sourceplot? or is this information > lost in ft_sourceinterpolate? > Can you add your scripts/code? This will add context to the conversation and allow users to help you further. If I understand your question, you can try to use the ft_sourcemovie function, for example like in this tutorial: http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate Here it is applied to minimum norm solutions, but the same concept holds for LCMV beamformer (which you are using right?) I hope this helps Cris > Thank you very much for your help. > > Best, > > Laith Hamid > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From adamaron at ucsd.edu Wed Jan 27 22:22:39 2016 From: adamaron at ucsd.edu (Adam Aron) Date: Wed, 27 Jan 2016 13:22:39 -0800 Subject: [FieldTrip] Postdoc position in simultaneous electrophysiology of frontal cortex and basal ganglia during action control in humans Message-ID: A funded postdoctoral position is available in the lab of Adam Aron (PhD) at University of California San Diego (www.aronlab.org ) to work collaboratively with Nader Pouratian (MD, PhD) at University of California Los Angeles (http://tinyurl.com/gwuvbja ). The studies will be done in the operating room in patients with Parkinson’s disease who are having electrodes implanted in global pallidus or subthalamic nucleus. The project is to design behavioral tasks, acquire simultaneous local field potential data from basal ganglia and frontal cortex (ECoG) while patients perform the tasks, and to analyze the data using time frequency methods and measures of connectivity and causal flow. The candidate will be based in San Diego with occasional travel to Los Angeles for data collection. This is a substantial postdoctoral training opportunity either for candidates with signal processing expertise (engineering/computer science/neuroscience) who want to branch out into cognition (especially as it pertains to action control); or for cognitive neuroscience candidates who already have cognitive (and frontal-basal-ganglia) expertise and want to learn human electrophysiological analysis methods. Candidates must have a PhD, or be about to be awarded one. Applications (and enquiries) should be sent to adamaron at ucsd.edu and should consist in: - a subject line “electrophysiology of frontal cortex and basal ganglia” - a cover letter describing research interests and how those are a match for the lab - a CV - contact info for references Salary is commensurate with NIH-rates. Non US Citizens are welcome. Full University of California benefits are provided. Applications for the position are open until March 15th 2016. The position is available immediately and for ~3 years. A delayed start time is also possible. --------------------------------------- Adam R. Aron Professor, Department of Psychology Neuroscience Graduate Program University of California, San Diego www.aronlab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From hayes.brenner at gmail.com Thu Jan 28 03:57:20 2016 From: hayes.brenner at gmail.com (Hayes Brenner) Date: Wed, 27 Jan 2016 20:57:20 -0600 Subject: [FieldTrip] How to select trials based on their timing Message-ID: Hello everyone! I'm fairly new to Fieldtrip, so I apologize if this question seems trivial, but I've been stuck for a while and I would greatly appreciate everyone's help. I have a set of data that I'm working on to get a better sense of how to process EEG data. I'm having trouble with this part when given these instructions: "let's only grab trials in which a '30' also appeared along side the '20'. [These labels are a part of cfg.trialdef.eventtype]. This '30' event code denotes a certain kind of trial in the experiment in which only the colored square was presented. The '30' event code should onset at the same time or within just a few milliseconds of the onset of the '20'. Third, let's also only grab trials in which subjects correctly responded with a button press to the stimulus (i.e., the colored square). To do this, you'll need to make sure there is a '90' following the '20'. The button press (or event code '90') should appear within 1000 ms of the onset of the '20'. My question is: how can I designate my code so that I can have a data set that meets the following conditions? I know I should use an 'if' or 'for' but I'm not sure how to write it exactly. Any advice? I've included my code as is without including the file upload. As of now, I created 3 data sets, each one with the required markers (20, 30, and 90). ft_defaults; cfg = []; cfg.trialdef.eventtype = '?'; ft_definetrial(cfg); cfg.trialdef.eventtype = 'Stim'; cfg.trialdef.prestim = 0.2; cfg.trialdef.poststim = .8; cfg.trialdef.eventvalue = '20'; cfg1=ft_definetrial(cfg); cfg.trialdef.eventvalue = '30'; cfg2=ft_definetrial(cfg); cfg.trialdef.eventvalue = '90'; cfg3=ft_definetrial(cfg); cfg.lpfilter='yes'; cfg.lpfreq = 30; cfg.reref = 'yes'; cfg.implicitref = 'REF'; cfg.refchannel = {'LM' 'REF'}; trialdata1 = ft_preprocessing(cfg1); trialdata2 = ft_preprocessing(cfg2); trialdata3 = ft_preprocessing(cfg3); Thank you all so much! Hayes Brenner -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Thu Jan 28 12:06:34 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Thu, 28 Jan 2016 13:06:34 +0200 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: , Message-ID: Dear Cris, Thank you for your time and consideration. I have solved the problem, after I add 1 to all the faces, since there was zeros in the faces, Faces=load('Faces.mat'); Faces=Faces.Faces; Points=load('Points.mat'); Points=Points.Points; Rfaces=load('Rfaces.mat'); Rfaces=Rfaces.Rfaces; Rpoints=load('Rpoints.mat'); Rpoints=Rpoints.Rpoints; RRfaces=load('RRfaces.mat'); RRfaces=RRfaces.RRfaces; RRpoints=load('RRpoints.mat'); RRpoints=RRpoints.RRpoints; Faces=Faces+1; Rfaces=Rfaces+1; RRfaces=RRfaces+1; vol = []; vol.bnd(1).pnt=Points; vol.bnd(1).tri=Faces; vol.bnd(2).pnt=Rpoints; vol.bnd(2).tri=Rfaces; vol.bnd(3).pnt=RRpoints; vol.bnd(3).tri=RRfaces; vol.cond = c; but I have the below error:Attempted to access vol.cond(4); index out of bounds because numel(vol.cond)=3. Error in ft_headmodel_bemcp (line 154) weight = (vol.cond(2)-vol.cond(3))/((vol.cond(3)+vol.cond(4)));%*2*pi); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 167) vol = ft_prepare_headmodel(cfg, vol); With two boundaries I have the below error: Attempted to access vol.cond(3); index out of bounds because numel(vol.cond)=2. Error in ft_headmodel_bemcp (line 129) weight = (vol.cond(1)-vol.cond(2))/((vol.cond(2)+vol.cond(3)));%*2*pi); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 167) vol = ft_prepare_headmodel(cfg, vol); Best regards Saeed. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.politzer-ahles at ling-phil.ox.ac.uk Thu Jan 28 12:10:16 2016 From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles) Date: Thu, 28 Jan 2016 11:10:16 +0000 Subject: [FieldTrip] How to select trials based on their timing Message-ID: Hi Hayes, This isn't really about Fieldtrip specifically, but is a MATLAB programming issue; that is to say, the solution isn't a special Fieldtrip function or anything like that, just basic MATLAB coding. (There might be a Fieldtrip-internal solution, like there is in ERPLAB for relatively complex trial selection, but I'm not aware of it.) All you really need to do is rewrite the trigger numbers so they distinguish the kinds of triggers you actually need. For example, rather than all trials of a given condition being coded as 30, you might want correct trials in that condition to be 31 and incorrect trials 32; the same logic also goes for recoding the trials based on whether or not there was a 20 nearby. All this information about trial timing is available in the 'cfg.trl' matrix that is created after you run ft_definetrial (see http://www.fieldtriptoolbox.org/reference/definetrial for details about how this matrix is organized). So all you need to do is write a FOR loop that iterates through each row of the trl matrix, and for each row checks (using an IF statement) whether that row meets the various conditions you outlined, and rewrites that row's trigger code if it meets those conditions. Then you can pull out a list of which trials you want (this is doable with basic MATLAB code, e.g., find(cfg.trl(:,3)==31) gives you a list of the row numbers of every trial with a code of 31) and use that list with ft_preprocessing to process just the trials you want. Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/ > Message: 3 > Date: Wed, 27 Jan 2016 20:57:20 -0600 > From: Hayes Brenner > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] How to select trials based on their timing > Message-ID: > < > CAB--YMYoCGP7KKCW-a7DwP2iZgyCVO-D_SJh1dmjUP79NtcLow at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello everyone! I'm fairly new to Fieldtrip, so I apologize if this > question seems trivial, but I've been stuck for a while and I would greatly > appreciate everyone's help. > > I have a set of data that I'm working on to get a better sense of how to > process EEG data. I'm having trouble with this part when given these > instructions: > > "let's only grab trials in which a '30' also appeared along side the '20'. > [These labels are a part of cfg.trialdef.eventtype]. This '30' event code > denotes a certain kind of trial in the experiment in which only the colored > square was presented. The '30' event code should onset at the same time or > within just a few milliseconds of the onset of the '20'. Third, let's also > only grab trials in which subjects correctly responded with a button press > to the stimulus (i.e., the colored square). To do this, you'll need to make > sure there is a '90' following the '20'. The button press (or event code > '90') should appear within 1000 ms of the onset of the '20'. > > My question is: how can I designate my code so that I can have a data set > that meets the following conditions? I know I should use an 'if' or 'for' > but I'm not sure how to write it exactly. Any advice? I've included my code > as is without including the file upload. As of now, I created 3 data sets, > each one with the required markers (20, 30, and 90). > > ft_defaults; > cfg = []; > cfg.trialdef.eventtype = '?'; > ft_definetrial(cfg); > cfg.trialdef.eventtype = 'Stim'; > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = .8; > cfg.trialdef.eventvalue = '20'; > cfg1=ft_definetrial(cfg); > cfg.trialdef.eventvalue = '30'; > cfg2=ft_definetrial(cfg); > cfg.trialdef.eventvalue = '90'; > cfg3=ft_definetrial(cfg); > cfg.lpfilter='yes'; > cfg.lpfreq = 30; > cfg.reref = 'yes'; > cfg.implicitref = 'REF'; > cfg.refchannel = {'LM' 'REF'}; > trialdata1 = ft_preprocessing(cfg1); > trialdata2 = ft_preprocessing(cfg2); > trialdata3 = ft_preprocessing(cfg3); > > Thank you all so much! > > Hayes Brenner > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160127/b0726da2/attachment-0001.html > > > > ------------------------------ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Thu Jan 28 13:31:37 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Thu, 28 Jan 2016 13:31:37 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> References: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Message-ID: Dear Julian, thank you for your help, I believe I read the same page but I didn't realise it could be used with ft_timelockstatistics – the way certain ft_ functions fit others is still a bit unclear to me (it's practically my first contact with FT). Now, it appears to be exactly what I'm looking for. I took me some time to figure out how to import my already processed data (ERPs averaged per subject) into FieldTrip and run the test but it seems I've succeeded. However, ft_timelockstatistics(cfg, data) gave me the following warnings: *1. Warning: the data does not contain a trial definition* *2. Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous* *recording* *3. Warning: doing a two-sided test without correcting p-values or alpha-level, p-values and alpha-level* *will reflect one-sided tests per tail* Should I be worried about these? (Here's the full output: https://gist.github.com/anonymous/1866a2b1a424dd9f0ac9) Finally, the resulting *stat* structure contains 10 fields but I'm not sure what *mask*, *stat* and *ref* represent. Is there any guidance on how to report the results like in the case of comparisons between conditions ( http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test )? Many thanks! Harold 2016-01-26 6:35 GMT+01:00 Julian Keil : > Dear Harold, > > have you checked out ft_statfun_correlationT? > This sounds like the function you're looking for. Use cfg.statistic = > 'ft_statfun_correlationT' in your call to ft_timelockstatistics. > Plus you can use all the correction methods available in FT. > See the FAQ for more info: > http://www.fieldtriptoolbox.org/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables > > Good luck, > > Julian > > ******************** > *Dr. Julian Keil* > > AG Multisensorische Integration > Psychiatrische Universitätsklinik > der Charité im St. Hedwig-Krankenhaus > Große Hamburger Straße 5-11, Raum A007 > 10115 Berlin > > Telefon: +49-30-2311-1879 > Fax: +49-30-2311-2209 > > http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration > > Am 26.01.2016 um 00:25 schrieb Harold Cavendish: > > Dear FieldTrip users, > > I'm looking for the best method to analyse the relationship between ERP > and behavioural data but all I've been able to find so far are methods to > compare ERPs (or more generally time-series). > > Consider the following example: 20 participants performed a memory-related > task in which they had to respond based on the difference between the > target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 > samples at 200 Hz) and responses were recorded; ERPs were then created > based on epochs in which the responses were correct. Similarly, response > accuracy was averaged over all successful epochs per each subject. > > The resulting data are therefore: 20 participants x 50 channels x 1000 > samples (ERP) and 20 averages of accuracy (one value per participant). > > My objective is to identify which portion of the ERP data best explains > (or predicts) the changes in accuracy. In other words, in which time > interval is the most significant difference between people who do well in > the task and those who don't. > > So far I've been doing correlations between ERP at each time point and > overall accuracy, which is unreliable due to multiple comparisons > (correction methods are reportedly too conservative). Nevertheless, certain > channels show quite strong correlations in multiple time intervals. > > How would you approach this problem, please? > > Many thanks! > > Best regards, > Harold > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Thu Jan 28 13:37:38 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Thu, 28 Jan 2016 13:37:38 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: Message-ID: Dear Steve, thank you for your help, the references are greatly appreciated! Indeed, I'd like to extend the analysis to identifying parts where the correlation is significantly different; I am going to try this approach. Best regards, Harold 2016-01-26 12:08 GMT+01:00 Stephen Politzer-Ahles < stephen.politzer-ahles at ling-phil.ox.ac.uk>: > Hi Harold, > > If you're only interested in identifying which timepoints have the best > correlation, multiple comparisons aren't really an issue; if you're not > worried about testing for significance, then the place where you see the > highest estimate is the highest. See e.g., Hauk et al. 2006 in NeuroImage, > and Smith & Kutas 2015 in Psychophysiology, for similar analyses. > > If you're interested in finding a part of the waveform where the > correlation is significantly different from zero while also dealing with > multiple comparisons, you could use [spatio]temporal clustering (Maris & > Oostenveld 2007). Just make an event-related regression coefficient (as > described in Hauk et al.; just do a regression at each timepoint, and then > rather than plotting the ERP amplitude at each timepoint, plot the > regression estimate (*b*) at each timepoint, to derive a similar > waveform) and then test that waveform against 0 using temporal clustering. > > Best, > Steve > > > > > --- > Stephen Politzer-Ahles > University of Oxford > Language and Brain Lab > Faculty of Linguistics, Phonetics & Philology > http://users.ox.ac.uk/~cpgl0080/ > > > >> Message: 5 >> Date: Tue, 26 Jan 2016 00:25:13 +0100 >> From: Harold Cavendish >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] Fwd: Identify a window of best correlation >> between ERP and behavioural data >> Message-ID: >> < >> CALOTjvZXPNWHLefXrG6uss7uF3kkXie7qjiWqEcesOUqWay6qA at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Dear FieldTrip users, >> >> I'm looking for the best method to analyse the relationship between ERP >> and >> behavioural data but all I've been able to find so far are methods to >> compare ERPs (or more generally time-series). >> >> Consider the following example: 20 participants performed a memory-related >> task in which they had to respond based on the difference between the >> target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 >> samples at 200 Hz) and responses were recorded; ERPs were then created >> based on epochs in which the responses were correct. Similarly, response >> accuracy was averaged over all successful epochs per each subject. >> >> The resulting data are therefore: 20 participants x 50 channels x 1000 >> samples (ERP) and 20 averages of accuracy (one value per participant). >> >> My objective is to identify which portion of the ERP data best explains >> (or >> predicts) the changes in accuracy. In other words, in which time interval >> is the most significant difference between people who do well in the task >> and those who don't. >> >> So far I've been doing correlations between ERP at each time point and >> overall accuracy, which is unreliable due to multiple comparisons >> (correction methods are reportedly too conservative). Nevertheless, >> certain >> channels show quite strong correlations in multiple time intervals. >> >> How would you approach this problem, please? >> >> Many thanks! >> >> Best regards, >> Harold >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160126/b5769634/attachment-0001.html >> > >> >> ------------------------------ >> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Thu Jan 28 14:25:42 2016 From: julian.keil at gmail.com (Julian Keil) Date: Thu, 28 Jan 2016 14:25:42 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Message-ID: Dear Harold, as far as the warnings go, maybe someone closer to the development team can chime in here. I think you can safely ignore warnings 1 and 2. With respect to warning 3, you actually need to set cfg.correcttail = 'alpha'; to set the alpha from e.g. .05 to 0.025 for a two sided test. As for your output, mask is a binary mask corrected for multiple comparisons, i.e. values of 1 designate the significant elements. stat contains the actual t-values. Depending on the method you used, the output will vary. If you also paste your code and the output, it's a bit easier to explain. I suggest to look at some papers in which fieldtrip-stats have been reported to get an idea what is appropriate. I'll blatantly advertise my own work here: Keil, J., Müller, N., Hartmann, T., & Weisz, N. (2014). Prestimulus beta power and phase synchrony influence the sound-induced flash illusion. Cerebral Cortex, 24(5), 1278–1288. http://doi.org/10.1093/cercor/bhs409 Keil, J., Müller, N., Ihssen, N., & Weisz, N. (2012). On the variability of the McGurk effect: audiovisual integration depends on prestimulus brain states. Cerebral Cortex, 22(1), 221–231. http://doi.org/10.1093/cercor/bhr125 And an excellent tutorial by Joachim Gross et al.: Gross, J., Baillet, S., Barnes, G. R., Henson, R. N., Hillebrand, A., Jensen, O., et al. (2012). Good practice for conducting and reporting MEG research. NeuroImage, 1–15. http://doi.org/10.1016/j.neuroimage.2012.10.001 Good luck, Julian Am 28.01.2016 um 13:31 schrieb Harold Cavendish: > Dear Julian, > > thank you for your help, I believe I read the same page but I didn't realise it could be used with ft_timelockstatistics – the way certain ft_ functions fit others is still a bit unclear to me (it's practically my first contact with FT). Now, it appears to be exactly what I'm looking for. > > I took me some time to figure out how to import my already processed data (ERPs averaged per subject) into FieldTrip and run the test but it seems I've succeeded. However, ft_timelockstatistics(cfg, data) gave me the following warnings: > > 1. Warning: the data does not contain a trial definition > 2. Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous > recording > 3. Warning: doing a two-sided test without correcting p-values or alpha-level, p-values and alpha-level > will reflect one-sided tests per tail > > Should I be worried about these? (Here's the full output: https://gist.github.com/anonymous/1866a2b1a424dd9f0ac9) > > Finally, the resulting stat structure contains 10 fields but I'm not sure what mask, stat and ref represent. Is there any guidance on how to report the results like in the case of comparisons between conditions (http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test)? > > Many thanks! > Harold > > > 2016-01-26 6:35 GMT+01:00 Julian Keil : > Dear Harold, > > have you checked out ft_statfun_correlationT? > This sounds like the function you're looking for. Use cfg.statistic = 'ft_statfun_correlationT' in your call to ft_timelockstatistics. > Plus you can use all the correction methods available in FT. > See the FAQ for more info: http://www.fieldtriptoolbox.org/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables > > Good luck, > > Julian > > ******************** > Dr. Julian Keil > > AG Multisensorische Integration > Psychiatrische Universitätsklinik > der Charité im St. Hedwig-Krankenhaus > Große Hamburger Straße 5-11, Raum A007 > 10115 Berlin > > Telefon: +49-30-2311-1879 > Fax: +49-30-2311-2209 > http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration > > Am 26.01.2016 um 00:25 schrieb Harold Cavendish: > >> Dear FieldTrip users, >> >> I'm looking for the best method to analyse the relationship between ERP and behavioural data but all I've been able to find so far are methods to compare ERPs (or more generally time-series). >> >> Consider the following example: 20 participants performed a memory-related task in which they had to respond based on the difference between the target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 samples at 200 Hz) and responses were recorded; ERPs were then created based on epochs in which the responses were correct. Similarly, response accuracy was averaged over all successful epochs per each subject. >> >> The resulting data are therefore: 20 participants x 50 channels x 1000 samples (ERP) and 20 averages of accuracy (one value per participant). >> >> My objective is to identify which portion of the ERP data best explains (or predicts) the changes in accuracy. In other words, in which time interval is the most significant difference between people who do well in the task and those who don't. >> >> So far I've been doing correlations between ERP at each time point and overall accuracy, which is unreliable due to multiple comparisons (correction methods are reportedly too conservative). Nevertheless, certain channels show quite strong correlations in multiple time intervals. >> >> How would you approach this problem, please? >> >> Many thanks! >> >> Best regards, >> Harold >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From changa5 at mcmaster.ca Fri Jan 29 04:25:47 2016 From: changa5 at mcmaster.ca (Andrew Chang) Date: Thu, 28 Jan 2016 22:25:47 -0500 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) In-Reply-To: References: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Message-ID: Hi Harald, I did the ICA based on the continuos recorded block (~7 minutes), including 100 trials, with PCA option on. The attached file is the ICA topography and waveform (ICA 22). The spectrum showed that the peak power was at ~11Hz. I suspected it is a neck movement artifact, because the generator seems to be in the front of the neck. Also, I got another similar ICA component from another subject, and the topography seems to be centered at the back of the neck, would it be considered as neck movement too. Thank you very much once again! Best, Andrew On Mon, Jan 18, 2016 at 7:49 AM, Harald Bornfleth wrote: > Dear Andrew, > > > > A couple of questions popped up. > > 1) The neck movement artifact, is this something with low frequency, > or is it a muscle artifact? > > 2) Did you calculate the ICA on one data screen (e.g. 10 seconds or > 20 seconds), or over the whole data set? > > > > If you could send us screen shots showing the ICA wave forms and the > accompanying topographies, then we could comment on the classification. (In > BESA, you right-click on the label of a component and select “Map > topography” to show the topography map of that component.) > > I include my colleague and ICA expert Nicole Ille on CC. > > > > Best regards, > > Harald > > > > > > *From:* c.andrew123 at gmail.com [mailto:c.andrew123 at gmail.com] *On Behalf > Of *Andrew Chang > *Sent:* 17 January 2016 19:57 > *To:* Harald.Bornfleth at besa.de; FieldTrip discussion list < > fieldtrip at science.ru.nl> > *Subject:* Re: [FieldTrip] Comparing ICA methods between toolboxes (BESA > vs. Fieldtrip) > > > > Hi Dr. Bornfleth, > > > > Thanks for your reply very much. > > I would like to use ICA to remove eye blinks and eye movements, neck > movements, as well as cardiac and powerline artifacts. The segment I have > is a continuous EEG recording for 10 minutes, which is one block of my > experiment including many trials. > > Before ICA, the segment have been high-pass (0.3 Hz) and low-pass (100 > Hz). The components showing activities around the eyes, the back of the > neck, and 60 Hz were removed. As for the cardiac artifact, I it is based on > visual inspection on the waveform to see whether it looks like an EKG. > > Any further comments are appreciated! > > > > Best, > > Andrew > > > > On Fri, Jan 15, 2016 at 8:35 AM, Harald Bornfleth < > Harald.Bornfleth at besa.de> wrote: > > Dear Andrew, > > > > Thanks for bringing this up. I can try to shed some light on the ICA > method used in BESA Research; however, I can not comment on the > implementation in FieldTrip. > > > > The method behind ICA analysis in BESA Research is the extended infomax > ICA algorithm (Lee TW et al.: Independent component analysis using an > extended infomax algorithm for mixed sub-Gaussian and super-Gaussian > sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very > well suited to remove cardiac and powerline artifacts. Depending on the > data, it may also be used to remove ocular (blink) and electrode artifacts. > To assess whether your artifact removal is trustworthy more information > about your processing steps are needed. What types of artifacts are you > trying to correct? What segments are you using to determine the artifact > topographies and what segments are you finally correcting? > > > > Best regards, > > Harald > > > > > > *Dr. Harald Bornfleth* > > Product Manager BESA Research > > > > *BESA GmbH* > > Freihamer Strasse 18 > > 82166 Graefelfing/Germany > > http://www.besa.de > > > > E: Harald.Bornfleth at besa.de > > T: +49 89 8980 9968 > > > > > > HRB Munich 109956 > > CEO: Dr. Tobias Scherg, CFO: Theodor Scherg > > Director of Research: Dr. Michael Scherg > > > > > > > > > > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > mailto:fieldtrip-bounces at science.ru.nl ] *On > Behalf Of *Andrew Chang > *Sent:* Sonntag, 10. Januar 2016 21:18 > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. > Fieldtrip) > > > > Dear Fieldtrip users, > > > > I am wondering whether anyone has compared the performances of the ICA > methods among M/EEG toolboxes. Especially, how is the performance of ICA in > BESA Research 6.0, compared to Fieldtrip? > > I have an EEG data set which has been processed in BESA, including > removing artifact using ICA. I am wondering whether I can trust it, or > I should reprocess it in Fieldtrip. Any comments will be appreciated! > > > > Happy new year! > > > > Best, > > Andrew > > > > -- > > Andrew Chang > Ph.D. Candidate > Auditory Development Lab > > Department of Psychology, Neuroscience & Behaviour > McMaster University > > http://changa5.wordpress.com/ > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > > Andrew Chang > Ph.D. Candidate > Auditory Development Lab > > Department of Psychology, Neuroscience & Behaviour > McMaster University > > http://changa5.wordpress.com/ > -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 螢幕快照 2016-01-28 下午10.14.20.png Type: image/png Size: 694915 bytes Desc: not available URL: From labdipsco at unitn.it Fri Jan 29 12:28:02 2016 From: labdipsco at unitn.it (Laboratori_Didattici Rovereto) Date: Fri, 29 Jan 2016 12:28:02 +0100 Subject: [FieldTrip] Problem importing cfg structure from eeg lab Message-ID: Dear FieldTripers, we are new in the field of Frequency Analysis. We have some problem in importing data from eeglab into ft (we are using the eeglab2fieldtrip function). data=eeglab2fieldtrip(EEG,'preprocessing','none'); data.label=data.label'; data.trialinfo=repmat(condition,1,length(data.trial))'; After the import, we checked the data with ft_databroswer([],data) and we see all the trials and the channels. However our cfg contains only "version" and then when we run ft_freqanalysis the function works but is applied only to 1 trial. Do we make a mistake in the importing phase or in applying ft_freqanalysis?? Thanks a lot, Paolo and Simone -------------- next part -------------- An HTML attachment was scrubbed... URL: From Darren.Kadis at cchmc.org Fri Jan 29 18:46:34 2016 From: Darren.Kadis at cchmc.org (Kadis, Darren) Date: Fri, 29 Jan 2016 17:46:34 +0000 Subject: [FieldTrip] Post-doctoral research position in language MEG (Cincinnati OH) Message-ID: <927408BECA23304AA310FCEDD94A02651110E1C8@MCEXMB1.chmccorp.cchmc.org> Post Doc, Cincinnati, USA Post-doctoral research position in language MEG We invite applications for a post-doctoral research position in Neurology at Cincinnati Children's Hospital Medical Center (CCHMC). The successful applicant will contribute to ongoing MEG studies of pediatric language and epilepsy. This is a two-year position focused in one or more of the following areas: * Methods for multimodal neuroimaging, with a focus on integration of fMRI and MEG data * Source-space connectivity techniques, designed to overcome challenges related to leakage, impact of inverse solution, etc. * Validation of integrated imaging and analysis protocols for mapping language in children undergoing epilepsy surgery (MEG, fMRI, EEG, ECoG, stimulation mapping, pathology, and outcome data available) The post-doctoral fellow will regularly interact with clinical and research faculty, other post-docs, graduate students, and research staff in the Divisions of Neurology and Radiology, the Pediatric Neuroimaging Research Consortium (PNRC) and the Imaging Research Center (IRC). He/she is expected to contribute to our regular research discussions, and to present at research meetings within CCHMC and at major conferences (e.g., BIOMAG, OHBM). The successful candidate will have completed their PhD in biomedical or electrical engineering, physics, computer science, psychology, neuroscience, or a related discipline. He/she will have experience in collection and analysis of electrophysiological data, expertise in signal processing, with strong programming skills (MATLAB or a similar environment). The ideal candidate would also have prior experience in neuroimaging and a solid background in neuroanatomy, and familiarity with M/EEG analysis software (e.g., FieldTrip/SPM, Brainstorm, Brainwave, BESA, MNE). All qualified recent graduates, or those nearing completion of their PhD, are encouraged to apply. CCHMC is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, age, genetic information, physical or mental disability, military or veteran status, sexual orientation, or other protected status in accordance with applicable federal, state, and local laws and regulations. Applicants should submit a cover letter and current CV (including a list of scholarly publications), along with the names and contact information for three referees to: Darren S. Kadis, PhD Assistant Professor, Division of Neurology Pediatric Neuroimaging Research Consortium Cincinnati Children's Hospital Medical Center c/o Kimra Smith Kimra.Smith at cchmc.org Review of applications will begin immediately. We anticipate a start date in the spring, 2016. -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Sat Jan 30 22:24:22 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Sat, 30 Jan 2016 22:24:22 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Message-ID: Dear Julian, thank you for your help so far! I've read the papers and I'm starting to piece it all together. I've ran into some issues with FieldTrip (hence my delay) which are still persistent but I don't want to come here with every problem I encounter so I'm going to give it a couple more days on my own. My original question has been fully answered and the rest is another matter. Best wishes, Harold -------------- next part -------------- An HTML attachment was scrubbed... URL: From moessing at uni-muenster.de Fri Jan 1 16:20:53 2016 From: moessing at uni-muenster.de (=?utf-8?Q?Wanja_M=C3=B6ssing?=) Date: Fri, 1 Jan 2016 16:20:53 +0100 Subject: [FieldTrip] =?utf-8?q?Vacant_Postdoc_Position_in_Visual_Cognition?= =?utf-8?q?/Cognitive_Neuroscience_at_the_University_of_M=C3=BCnster=2C_Ge?= =?utf-8?q?rmany?= Message-ID: <20160101152051.CE178BF402@SECMAIL.UNI-MUENSTER.DE> Our lab at the Institute of Psychology/University of Muenster, Germany, is currently looking for a postdoctoral researcher (TVL13 Mitarbeiterstelle). The initial appointment is for 3 years (extension possible). In brief, the successful applicant will contribute to the group's research projects and teaching in the Bachelor in Psychology program. Research in the lab focuses on visual cognition and cognitive neuroscience. Our research topics include visual masking, scene perception, and the role of brain oscillations in perception, attention and visual memory. Our arsenal of research methods includes psychophysics, EEG, and eye tracking (fMRI, MEG, and brain stimulation are available at other institutions in Muenster). Applicants should have strong interest in our research topics and solid experience with any of these research methods. Most of the teaching at our institute is in German; thus, good command of German is also a requirement. Application deadline is January 31 2016; we would like to fill this position until April 1. The detailed job ad is available (only in German; see requirement above) here: http://www.uni-muenster.de/Rektorat/Stellen/ausschreibungen/st_20150412_sk19.html If you are potentially interested in this position, I would be glad to answer any informal questions about the position, research, or application requirements (niko.busch at uni-muenster.de). Furthermore, I would be grateful if you could pass this information on to potentially interested colleagues. -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Sun Jan 3 00:49:25 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Sun, 3 Jan 2016 01:49:25 +0200 Subject: [FieldTrip] Fieldtrip compatibility Message-ID: Dear Fieldtrip team, Hope you are well and in good health, I am a PhD student in Compiegne University, working on "source localization and connectivity study of the sources of uterine activity for the prediction of the preterm labor''. The uterine electrical activity, measured noninvasively on the woman's abdomen by means of surface electrodes is referred to as the electrohysterogram (EHG= uterine electromyogram). We have the meshes of the uterus layers segmented from MRI, and we have a database for real pregnancy and labor signal. My question is does Fieldtrip toolbox able to deal with my data? Best regards, Saeed Zahran -------------- next part -------------- An HTML attachment was scrubbed... URL: From senakahks at gmail.com Sun Jan 3 04:38:49 2016 From: senakahks at gmail.com (Senaka Amarakeerthi) Date: Sun, 3 Jan 2016 09:08:49 +0530 Subject: [FieldTrip] Ft_databrowser layout error Message-ID: I am trying to visualise data from databrowser. But I end up with following error message. reading layout from file horizontal.lay Attempted to access laysels(14); index out of bounds because numel(laysels)=13. Error in ft_databrowser>redraw_cb (line 1821) laysel = laysels(i); Error in ft_databrowser (line 725) redraw_cb(h); Error in main (line 29) fg = ft_databrowser(cfg,data); script: cfg = []; cfg.dataset = 'Thilina.edf'; cfg.trl = [4 10 0; 12 20 0; 18 20 0; 22 110 0]; cfg.continuous = 'yes'; cfg.channel = {'all', '-COUNTER', '-INTERPOLATED', '-RAW_CQ', '-GYROX', '-GYROY', '-MARKER', '-SYNC', '-TIME_STAMP_s', '-TIME_STAMP_ms', '-CQ_AF3', '-CQ_F7', '-CQ_F3', '-CQ_FC5', '-CQ_T7', '-CQ_P7', '-CQ_O1', '-CQ_O2', '-CQ_P8', '-CQ_T8', '-CQ_FC6', '-CQ_F4', '-CQ_F8', '-CQ_AF4', '-CQ_CMS', '-CQ_DRL'}; data = ft_preprocessing(cfg); cfg.viewmode = 'horizontal'; fg = ft_databrowser(cfg,data); horizontal.lay file: 1 -0.545830 1.170536 0.290000 0.230000 AF3 2 -0.659023 0.813825 0.290000 0.230000 F3 3 -1.299041 0.943808 0.290000 0.230000 F7 4 -1.173172 0.450338 0.290000 0.230000 FC5 5 -1.299041 -0.943808 0.290000 0.230000 P7 6 -1.605703 -0.000000 0.290000 0.230000 T7 7 -0.496189 -1.527114 0.290000 0.230000 O1 8 0.545830 1.170536 0.290000 0.230000 AF4 9 0.659023 0.813825 0.290000 0.230000 F4 10 1.299041 0.943808 0.290000 0.230000 F8 11 1.173172 0.450338 0.290000 0.230000 FC6 12 1.299041 -0.943808 0.290000 0.230000 P8 13 1.527114 -0.496189 0.290000 0.230000 TP8 14 0.496189 -1.527114 0.290000 0.230000 O2 Your support to get this error fixed is highly appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Sun Jan 3 20:20:12 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Sun, 3 Jan 2016 19:20:12 +0000 Subject: [FieldTrip] (no subject) Message-ID: Dear Fieldtrip team, I am currently working on data acquired from an elektra system (neuromag). I have done all the preprocessing and the ft_freqanalysis with the gradiometers only. I combined the gradiometers to create planar gradients.However , later when doing the statistics problems occur when i want to specify the channels. The error tells me that no degrees of freedom are found for the analysis. However, when i remove the cfg.channel form the script it runs through without an error. (please see code below). My question is whether the output of the stastistic is correct without specifying the channels? If not, does anybody have suggestions how to fix the problem? I have run into similar problems when wanting to plot the time frequency data from the planar gradients after having used ft_combineplanar. Here i cannot find a layout file that suits the output of ft_combineplanar. Thus, i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, however, the layouts provided by fieldtrip does not fit that number. Has anybody run into similar problems? Or does anybody know a possible solution? Thank you very much for any suggestions Victoria %combine planar cfg = []; cfg.method ='sum'; %ComCon = ft_combineplanar(cfg,FreqCon); ComIncon = ft_combineplanar(cfg, FreqIncon); cfg = []; %cfg.channel = {'MEG'}; cfg.latency = 'all'; cfg.frequency = [14.5 16]; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; cfg_neighb.method = 'distance'; cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); design = zeros(1,size(ComGrad_con.powspctrm,1) + size(ComGrad_incon.powspctrm,1)); design(1,1:size(ComGrad_con.powspctrm,1)) = 1; design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... size(ComGrad_incon.powspctrm,1))) = 2; -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Sun Jan 3 21:18:22 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 3 Jan 2016 21:18:22 +0100 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: Dear Victoria, the system you are working with is already equipped with two orthogonal planar gradiometer sensors. Thus you should not try to create planar gradients on the basis of the planar gradients. Yet you might want to use the magnetometers only. There you can represent the activity as if it was picked up by planar gradients. Could you please skip the planar transformation bit and redo your analysis? FieldTrip provides three types of layouts for the Neuromag system: NM306all.lay NM306mag.lay NM306grad.lay. For example if you want to plot magnetometers only you’d specify cfg.layout = 'neuromag306mag.lay’; cfg.channel = 'MEG*1’; Here MEG*1 refers to magnetometers and MEG*2 and MEG*3 would be the two orthogonal planar gradients respectively. Also the neighbours are provided as neuromag306cmb_neighb.mat; neuromag306mag_neighb.mat; neuromag306planar_neighb.mat;. You might consider loading the structure of your choice directly. Here is an example tutorial that might help: http://www.fieldtriptoolbox.org/tutorial/natmeg/timefrequency Good luck, tzvetan > Dear Fieldtrip team, > > I am currently working on data acquired from an elektra system (neuromag). I have done all the preprocessing and the ft_freqanalysis with the gradiometers only. I combined the gradiometers to create planar gradients.However , later when doing the statistics problems occur when i want to specify the channels. The error tells me that no degrees of freedom are found for the analysis. However, when i remove the cfg.channel form the script it runs through without an error. (please see code below). > My question is whether the output of the stastistic is correct without specifying the channels? If not, does anybody have suggestions how to fix the problem? > > I have run into similar problems when wanting to plot the time frequency data from the planar gradients after having used ft_combineplanar. Here i cannot find a layout file that suits the output of ft_combineplanar. Thus, i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, however, the layouts provided by fieldtrip does not fit that number. > Has anybody run into similar problems? Or does anybody know a possible solution? > > Thank you very much for any suggestions > Victoria > > %combine planar > cfg = []; > cfg.method ='sum'; > %ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > cfg = []; > %cfg.channel = {'MEG'}; > cfg.latency = 'all'; > cfg.frequency = [14.5 16]; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); > > design = zeros(1,size(ComGrad_con.powspctrm,1) + size(ComGrad_incon.powspctrm,1)); > design(1,1:size(ComGrad_con.powspctrm,1)) = 1; > design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... > size(ComGrad_incon.powspctrm,1))) = 2; > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From slama at berkeley.edu Mon Jan 4 02:22:43 2016 From: slama at berkeley.edu (Katarina Slama) Date: Sun, 3 Jan 2016 17:22:43 -0800 Subject: [FieldTrip] Inferential statistics on connectivity data? Message-ID: Dear Fieldtrip community, My name is Katarina Slama. I’m a graduate student in the Knight lab at UC Berkeley, and I use ECoG to study visual attention. I am currently examining connectivity in ECoG data using ft_connectivityanalysis (cfg and data structures below). I have computed partial coherence values for a network of electrodes. Now I would like to assess the statistical significance of each of the edges by computing a non-parametric equivalent of a one-sample t-test on the coherence values over trials. I have two questions: 1. Is there a way to obtain a separate partial coherence value for each trial? At present, the partial coherence structure that ft_connectivityanalysis creates has the dimord “chan_chan_freq”. 2. Is there a fieldtrip function that is designed for computing statistics on connectivity metrics? I have been advised to look into ft_freqstatistics, but this function does not seem to be designed for the output of ft_connectivityanalysis. — input structure (freq): label: {'34' '35' '36' '37' '38' '39' '44' '45' '47' '48' '49' '50' '51' '52' '53' '54' '55' '56' '57' '62' '63' '64' '76' '77' '80' '99' '100' '101'} dimord: 'rpttap_chan_freq' freq: [2.0000 3.0000 4.0000] fourierspctrm: [220x28x3 double] cumsumcnt: [220x1 double] cumtapcnt: [220x1 double] trialinfo: [220x1 double] cfg: [1x1 struct] configuration (cfg): cfg = []; cfg.method = 'coh'; cfg.partchannel = freq.label(1); cfg.keeptrials = 'yes'; partcoh = ft_connectivityanalysis(cfg,freq); output structure (partcoh) label: {27x1 cell} dimord: 'chan_chan_freq' cohspctrm: [27x27x3 double] freq: [2.0000 3.0000 4.0000] cfg: [1x1 struct] — Thank you and best wishes, Kata -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Jan 4 09:16:28 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 4 Jan 2016 09:16:28 +0100 Subject: [FieldTrip] Fieldtrip compatibility In-Reply-To: References: Message-ID: <5E6A3CD3-4736-4AD6-B815-78713B323FC6@donders.ru.nl> Dear Saeed, Happy New Year. FieldTrip can be used for channel level time series analysis and forward and inverse volume conduction modelling of ExG. The typical application (besides MEG, i.e. magnetic measurements of brain activity) is EEG, but we also use if for intracranial EEG and for EMG. I see no reason why EHG would not work. The way you have your data represented in files on disk might be different than what is common for EEG, but see here http://www.fieldtriptoolbox.org/dataformat. This should not be too hard to deal with. The more important difference might be in the assumptions on the sources that are required for the inverse modelling. In EHG I presume you will be interested in localizing the contractions of the uterus. That is muscle activity which propagates (i.e. changes spatially over time), which may have different characteristics than the activity that we model in the brain. Also this is something that can be dealt with, but it is not merely a technical detail and it requires careful consideration of the inverse model assumptions. I know that Ahmad Diab (who I suppose is a colleague of yours) used FieldTrip for his thesis https://tel.archives-ouvertes.fr/tel-01237525/document. I suggest you look at details there and consult Ahmad. best regards, Robert On 03 Jan 2016, at 00:49, saeed zahran wrote: > Dear Fieldtrip team, > > Hope you are well and in good health, > > I am a PhD student in Compiegne University, working on "source localization and connectivity study of the sources of uterine activity for the prediction of the preterm labor''. > > The uterine electrical activity, measured noninvasively on the woman's abdomen by means of surface electrodes is referred to as the electrohysterogram (EHG= uterine electromyogram). > > We have the meshes of the uterus layers segmented from MRI, and we have a database for real pregnancy and labor signal. My question is does Fieldtrip toolbox able to deal with my data? > > Best regards, > Saeed Zahran > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Mon Jan 4 10:27:31 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 4 Jan 2016 10:27:31 +0100 Subject: [FieldTrip] clarification on beam forming evoked fields in MEG In-Reply-To: <7E884835-8D6B-47E6-987E-7C174A828C07@gmail.com> References: <7E884835-8D6B-47E6-987E-7C174A828C07@gmail.com> Message-ID: Hi Russ, The units that are used by FieldTrip in data processing are not always consistent. The problem already starts at the level of reading (where we sometimes use our own FT code, and sometimes code from other projects). MEG data might be represented in T or fT, but for Eleka there are also gradiometers that have their data expressed as T/m or fT/cm or T/mm or … Then the anatomical MRi is read in, coregistered and used to construct a volume conduction model. In that volume conduction model there is again geometrical units (m, cm, mm) but also units of conductivity. You can imagine that combining data (in algorithms) that has different units will lead to unexpected results. Hence I usually play it safe and report on the results of computations as “arbitrary units”. Mostly in statistics and interpretation it does not matter anyway. If you use SI units throughout, then the low-level FieldTrip code will work as expected and also represent the output of all computations in SI units. For anatomical models you can use ft_convert_units to scale it to meters. For electrode and gradiometer arrays you should use the distance and amplitude option in ft_datatype_sens (see the code, it is not mentioned in the help) and for Elekta the scaling should be specified as ‘amplitude/distance’. The unit handling is a known issue and we have a number of ideas on http://bugzilla.fieldtriptoolbox.org to improve it, but to little resources to actually get it resolved. best regards, Robert PS Note that for spectral analysis it is again different, since spectral power or density can be differently normalized. Also in that aspect the FT code is not 100% consistent. But since you mention ERFs that does not apply. On 31 Dec 2015, at 22:51, russ port wrote: > Dear Robert and Jan-Mathijs > > I was hoping for someone to help me with a point of clarification concerning the fieldtrip wiki. I have followed Fieldtrip’s example of creating virtual sensor ERFs for MEG data using LMCV beamforming (e.g. http://www.fieldtriptoolbox.org/tutorial/aarhus/beamformingerf). I get great ERFs for auditory responses that I’m happy with. There is a point on contention left between my lab mates and I though. Following what was discuss previously (http://mailman.science.ru.nl/pipermail/fieldtrip/2015-September/009609.html), I think that the ERF are in a “unit-less” unit. They suggest however, that these (as mentioned in the wiki) are related to equivalent current dipoles for the chosen sources (and so the unit would be A/m [or since we used cm in the head model, A/cm]). Please can you help clear up this point of contention? > > Thanks > Russ -------------- next part -------------- An HTML attachment was scrubbed... URL: From marta.bortoletto at cognitiveneuroscience.it Mon Jan 4 14:33:44 2016 From: marta.bortoletto at cognitiveneuroscience.it (Marta Bortoletto) Date: Mon, 4 Jan 2016 13:33:44 +0000 (UTC) Subject: [FieldTrip] Applying wPLI to sLORETA-derived sources? References: <1782756321.10177641.1451914424709.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <1782756321.10177641.1451914424709.JavaMail.yahoo@mail.yahoo.com> Dear Community,I have resting-state data obtained by 70-channel EEGrecording. I have calculated EEG sources and obtained estimated signal in 88 Brodmannareas (BAs) by means of sLORETA. Now I would like to measure connectivitybetween these BAs. I have seen that many connectivity measures have beendeveloped in fieldtrip, including the weighted Phase Lag Index (wPLI). Giventhat wPLI estimates time-lagged interdependences, is it appropriate to apply wPLIto sLORETA estimated sources? Thank you for your help! Marta Marta Bortoletto, PhD Cognitive Neuroscience Section, IRCCS Centro San Giovanni di Dio Fatebenefratelli Via Pilastroni 4, 25125 Brescia, Italy Phone number: (+39) 0303501594 E-mail: marta.bortoletto at cognitiveneuroscience.it web: http://www.cognitiveneuroscience.it/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon Jan 4 17:02:49 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 4 Jan 2016 17:02:49 +0100 Subject: [FieldTrip] Applying wPLI to sLORETA-derived sources? In-Reply-To: <1782756321.10177641.1451914424709.JavaMail.yahoo@mail.yahoo.com> References: <1782756321.10177641.1451914424709.JavaMail.yahoo.ref@mail.yahoo.com> <1782756321.10177641.1451914424709.JavaMail.yahoo@mail.yahoo.com> Message-ID: <269EB91B-FE42-4B47-A470-8AD7A5C71EC0@uni-konstanz.de> Dear Marta, the applicability of connectivity metrics in FieldTrip (including wPLI) is independent of the inverse operator. So the answer is yes and no. It is appropriate if you have the single observations (i.e. epochs that you cut the data into) kept in the output of your source reconstruction analysis. I guess you have 88 source waveforms and not 88 x Ntrials time series. If this is correct wPLI or any phase metric is rather inappropriate. Good luck, tzvetan > Dear Community, > I have resting-state data obtained by 70-channel EEG recording. I have calculated EEG sources and obtained estimated signal in 88 Brodmann areas (BAs) by means of sLORETA. Now I would like to measure connectivity between these BAs. I have seen that many connectivity measures have been developed in fieldtrip, including the weighted Phase Lag Index (wPLI). Given that wPLI estimates time-lagged interdependences, is it appropriate to apply wPLI to sLORETA estimated sources? > > Thank you for your help! > > Marta > > Marta Bortoletto, PhD > Cognitive Neuroscience Section, > IRCCS Centro San Giovanni di Dio Fatebenefratelli > Via Pilastroni 4, 25125 Brescia, Italy > Phone number: (+39) 0303501594 > E-mail: marta.bortoletto at cognitiveneuroscience.it > web: http://www.cognitiveneuroscience.it/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tmadsen at emory.edu Mon Jan 4 21:29:55 2016 From: tmadsen at emory.edu (Teresa Madsen) Date: Mon, 4 Jan 2016 15:29:55 -0500 Subject: [FieldTrip] How are bugs triaged? Message-ID: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 -------------- next part -------------- An HTML attachment was scrubbed... URL: From slama at berkeley.edu Tue Jan 5 01:14:42 2016 From: slama at berkeley.edu (Katarina Slama) Date: Mon, 4 Jan 2016 16:14:42 -0800 Subject: [FieldTrip] How to interpret content of partial PLV-spectrum when dimensionality is inconsistent with dimord? Message-ID: Dear Fieldtrip community, Happy new year! I have a question about computing partial PLV-values using ft_connectivityanalysis: When I try to compute PLV-values, and request that one channel be partialized, the resulting PLV-spectrum has the dimensionality 27 x 27 x 28 x 3, while dimord reports it to be: chan_chan_freq. Why this inconsistency, and how should I interpret the contents of this PLV-spectrum? I provide information about my input and output structures below. — input structure (freq): label: {'34' '35' '36' '37' '38' '39' '44' '45' '47' '48' '49' '50' '51' '52' '53' '54' '55' '56' '57' '62' '63' '64' '76' '77' '80' '99' '100' '101'} dimord: 'rpttap_chan_freq' freq: [2.0000 3.0000 4.0000] fourierspctrm: [220x28x3 double] cumsumcnt: [220x1 double] cumtapcnt: [220x1 double] trialinfo: [220x1 double] cfg: [1x1 struct] configuration structure (cfg): method: 'plv' partchannel: {'34'} plv_struct = ft_connectivityanalysis(cfg,freq); output structure (plv_struct): label: {27x1 cell} dimord: 'chan_chan_freq' plvspctrm: [4-D double] freq: [2.0000 3.0000 4.0000] dof: 220 cfg: [1x1 struct] — Thank you very much for your help! Best, Kata -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jan 5 09:10:21 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 5 Jan 2016 08:10:21 +0000 Subject: [FieldTrip] How to interpret content of partial PLV-spectrum when dimensionality is inconsistent with dimord? In-Reply-To: References: Message-ID: <0AE94B5A-16C1-40C1-8FD3-4523B25FC6FF@fcdonders.ru.nl> Hi Katarina, Good question. Could be a bug. Could you file this on bugzilla.fieldtriptoolbox.org, and upload the necessary data so that we can try and reproduce it? Thanks and best, Jan-Mathijs On Jan 5, 2016, at 1:14 AM, Katarina Slama wrote: > Dear Fieldtrip community, > > Happy new year! > > I have a question about computing partial PLV-values using ft_connectivityanalysis: > > When I try to compute PLV-values, and request that one channel be partialized, the resulting PLV-spectrum has the dimensionality 27 x 27 x 28 x 3, while dimord reports it to be: chan_chan_freq. Why this inconsistency, and how should I interpret the contents of this PLV-spectrum? > > I provide information about my input and output structures below. > > — > input structure (freq): > label: {'34' '35' '36' '37' '38' '39' '44' '45' '47' '48' '49' '50' '51' '52' '53' '54' '55' '56' '57' '62' '63' '64' '76' '77' '80' '99' '100' '101'} > dimord: 'rpttap_chan_freq' > freq: [2.0000 3.0000 4.0000] > fourierspctrm: [220x28x3 double] > cumsumcnt: [220x1 double] > cumtapcnt: [220x1 double] > trialinfo: [220x1 double] > cfg: [1x1 struct] > > configuration structure (cfg): > method: 'plv' > partchannel: {'34'} > > plv_struct = ft_connectivityanalysis(cfg,freq); > > output structure (plv_struct): > label: {27x1 cell} > dimord: 'chan_chan_freq' > plvspctrm: [4-D double] > freq: [2.0000 3.0000 4.0000] > dof: 220 > cfg: [1x1 struct] > — > > Thank you very much for your help! > > Best, > Kata > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Tue Jan 5 09:27:18 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 5 Jan 2016 08:27:18 +0000 Subject: [FieldTrip] How are bugs triaged? In-Reply-To: References: Message-ID: Hi Teresa, Generally, we don’t have an ‘official’ triage system for the bugs that are filed. The speed with which a bug is considered/resolved depends on a combination of things: 1) the quality of the bug report. 2) the perceived urgency by the people who would be able to resolve it. 3) the estimated cost-benefit relationship for the people who would be able to resolve it. 4) the amount of other piled-up work for the people who would be able to resolve it. 5) the level of serotonin. 6) the prospect of compensation in kind (beer/chocolate/formal involvement in projects etc). Thus, in general, there may be things that the bug filer can do to increase the probability for consideration/resolution, including adding code snippets and data that allow for a reproduction of a genuine bug, or by including code snippets that implement a new feature. Note that in general feature requests that are not a priority for the daily scientific work of the development/fixing team will get a low priority. In addition it should be noted that anybody who is on the list is allowed to contribute fixes/patches/features, and that it is not the responsibility of the core development team (which nowadays extends far beyond the people at the Donders Centre). Also, it should be noted that nobody has a formal requirement to provide fieldtrip/bugzilla support, it’s all pro bono. This means that we have to squeeze it in besides our daily scientific work and additional chores. Anyway, the problem is that we are just short-handed, which indeed sometimes results in bugs already being ‘open’ for a long time. Our oldest one still open dates from 2010, so the 2013 you mention is not that bad :o). With regard to the NEX file reader error you mentioned, if you think your workaround might be of benefit of other users, don’t hesitate to contribute! Best wishes, Jan-Mathijs On Jan 4, 2016, at 9:29 PM, Teresa Madsen > wrote: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tmadsen at emory.edu Tue Jan 5 18:39:14 2016 From: tmadsen at emory.edu (Teresa Madsen) Date: Tue, 5 Jan 2016 12:39:14 -0500 Subject: [FieldTrip] How are bugs triaged? (Schoffelen, J.M. (Jan Mathijs)) Message-ID: Thanks for the insight, Jan-Mathijs. I'm not exactly sure how to contribute... I'm not familiar with SVN or GIT, and it would likely be small improvements that I would suggest, not whole new functions or anything. So could I just post the applicable snippets of code as a comment on the bug report? Will anyone see it there? When I update a previously posted bug, I see this message: Changes submitted for bug 2093 Email sent to:no oneExcluding:fieldtrip-bugs at donders.ru.nl, braingirl at gmail.com So I'm assuming no one knows. Is there a way to send it back to the bug listserv? Or should I really just learn how to use GIT (which seems more straightforward than SVN - is that true?)? ;-) Thanks again, Teresa ------------------------------ > > Message: 6 > Date: Tue, 5 Jan 2016 08:27:18 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] How are bugs triaged? > Message-ID: > Content-Type: text/plain; charset="windows-1252" > > Hi Teresa, > > Generally, we don?t have an ?official? triage system for the bugs that are > filed. The speed with which a bug is considered/resolved depends on a > combination of things: > > 1) the quality of the bug report. > 2) the perceived urgency by the people who would be able to resolve it. > 3) the estimated cost-benefit relationship for the people who would be > able to resolve it. > 4) the amount of other piled-up work for the people who would be able to > resolve it. > 5) the level of serotonin. > 6) the prospect of compensation in kind (beer/chocolate/formal involvement > in projects etc). > > Thus, in general, there may be things that the bug filer can do to > increase the probability for consideration/resolution, including adding > code snippets and data that allow for a reproduction of a genuine bug, or > by including code snippets that implement a new feature. Note that in > general feature requests that are not a priority for the daily scientific > work of the development/fixing team will get a low priority. > > In addition it should be noted that anybody who is on the list is allowed > to contribute fixes/patches/features, and that it is not the responsibility > of the core development team (which nowadays extends far beyond the people > at the Donders Centre). Also, it should be noted that nobody has a formal > requirement to provide fieldtrip/bugzilla support, it?s all pro bono. > This means that we have to squeeze it in besides our daily scientific work > and additional chores. > > Anyway, the problem is that we are just short-handed, which indeed > sometimes results in bugs already being ?open? for a long time. Our oldest > one still open dates from 2010, so the 2013 you mention is not that bad > :o). With regard to the NEX file reader error you mentioned, if you think > your workaround might be of benefit of other users, don?t hesitate to > contribute! > > Best wishes, > Jan-Mathijs > > > > > On Jan 4, 2016, at 9:29 PM, Teresa Madsen tmadsen at emory.edu>> wrote: > > I'm just curious because I've gotten such quick responses and fixes on > some bugs, while others sit around for long periods of time without any > feedback. Luckily, they're not anything stopping me from doing my work, > but I was just curious if they've been seen and determined to be of low > priority, or simply overlooked. > > Examples: > http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" > button on GUI for ft_rejectvisual (summary mode) plots average of all > trials instead of the single trial requested - first posted in October > http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file > reader errors - posted in 2013 - Obviously, I've worked around it, but it's > still there with a status of "new"! > > Hope I'm not being a pest. > Thanks, > Teresa > > -- > Teresa E. Madsen, PhD > Division of Behavioral Neuroscience and Psychiatric Disorders > Yerkes National Primate Research Center > Emory University > Rainnie Lab, NSB 5233 > 954 Gatewood Rd. NE > Atlanta, GA 30329 > (770) 296-9119 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160105/9b0ab1ac/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 4 > **************************************** > -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Jan 6 09:09:12 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 6 Jan 2016 08:09:12 +0000 Subject: [FieldTrip] How are bugs triaged? In-Reply-To: References: Message-ID: <9670C70F-D4E8-4445-865C-5B41FAF81D3E@fcdonders.ru.nl> Hi Teresa, Yes, one way of contributing would be to add snippets of code to the bug. In order to attract other people’s attention, you could add (judiciously) people to the CC-list of the bug. That way you ensure that these people receive an e-mail message once the bug is updated. Note, that people then can remove themselves again if they don’t like to be updated, which is a thing that needs to be respected. Note also, that adding a group e-mail address, such as fieldtrip-bugs at donders.ru.nl is likely less efficient than adding named persons, because members of the group may feel less inclined to be actively involved if addressed as a group, rather than as an individual. Best, Jan-Mathijs On Jan 5, 2016, at 6:39 PM, Teresa Madsen > wrote: Thanks for the insight, Jan-Mathijs. I'm not exactly sure how to contribute... I'm not familiar with SVN or GIT, and it would likely be small improvements that I would suggest, not whole new functions or anything. So could I just post the applicable snippets of code as a comment on the bug report? Will anyone see it there? When I update a previously posted bug, I see this message: Changes submitted for bug 2093 Email sent to: no one Excluding: fieldtrip-bugs at donders.ru.nl, braingirl at gmail.com So I'm assuming no one knows. Is there a way to send it back to the bug listserv? Or should I really just learn how to use GIT (which seems more straightforward than SVN - is that true?)? ;-) Thanks again, Teresa ------------------------------ Message: 6 Date: Tue, 5 Jan 2016 08:27:18 +0000 From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] How are bugs triaged? Message-ID: > Content-Type: text/plain; charset="windows-1252" Hi Teresa, Generally, we don?t have an ?official? triage system for the bugs that are filed. The speed with which a bug is considered/resolved depends on a combination of things: 1) the quality of the bug report. 2) the perceived urgency by the people who would be able to resolve it. 3) the estimated cost-benefit relationship for the people who would be able to resolve it. 4) the amount of other piled-up work for the people who would be able to resolve it. 5) the level of serotonin. 6) the prospect of compensation in kind (beer/chocolate/formal involvement in projects etc). Thus, in general, there may be things that the bug filer can do to increase the probability for consideration/resolution, including adding code snippets and data that allow for a reproduction of a genuine bug, or by including code snippets that implement a new feature. Note that in general feature requests that are not a priority for the daily scientific work of the development/fixing team will get a low priority. In addition it should be noted that anybody who is on the list is allowed to contribute fixes/patches/features, and that it is not the responsibility of the core development team (which nowadays extends far beyond the people at the Donders Centre). Also, it should be noted that nobody has a formal requirement to provide fieldtrip/bugzilla support, it?s all pro bono. This means that we have to squeeze it in besides our daily scientific work and additional chores. Anyway, the problem is that we are just short-handed, which indeed sometimes results in bugs already being ?open? for a long time. Our oldest one still open dates from 2010, so the 2013 you mention is not that bad :o). With regard to the NEX file reader error you mentioned, if you think your workaround might be of benefit of other users, don?t hesitate to contribute! Best wishes, Jan-Mathijs On Jan 4, 2016, at 9:29 PM, Teresa Madsen >> wrote: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 62, Issue 4 **************************************** -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jorn at artinis.com Wed Jan 6 09:28:16 2016 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 Jan 2016 09:28:16 +0100 Subject: [FieldTrip] How are bugs triaged? In-Reply-To: <9670C70F-D4E8-4445-865C-5B41FAF81D3E@fcdonders.ru.nl> References: <9670C70F-D4E8-4445-865C-5B41FAF81D3E@fcdonders.ru.nl> Message-ID: <001d01d1485c$3128bec0$937a3c40$@artinis.com> Hi Teresa, Adding to JM’s last mail, it might be important to note that every new bug is automatically sent out to fieldtrip-bugs at donders.ru.nl , so that the core dev team will get notified, so the dev team is aware of new bugs being posted. But as JM said, depending on subjective prioritization, it might get ignored anyhow. Best, Jörn -- Jörn M. Horschig, PhD, Software Engineer Artinis Medical Systems | +31 481 350 980 From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Schoffelen, J.M. (Jan Mathijs) Sent: Wednesday, January 6, 2016 9:09 To: FieldTrip discussion list Subject: Re: [FieldTrip] How are bugs triaged? Hi Teresa, Yes, one way of contributing would be to add snippets of code to the bug. In order to attract other people’s attention, you could add (judiciously) people to the CC-list of the bug. That way you ensure that these people receive an e-mail message once the bug is updated. Note, that people then can remove themselves again if they don’t like to be updated, which is a thing that needs to be respected. Note also, that adding a group e-mail address, such as fieldtrip-bugs at donders.ru.nl is likely less efficient than adding named persons, because members of the group may feel less inclined to be actively involved if addressed as a group, rather than as an individual. Best, Jan-Mathijs On Jan 5, 2016, at 6:39 PM, Teresa Madsen > wrote: Thanks for the insight, Jan-Mathijs. I'm not exactly sure how to contribute... I'm not familiar with SVN or GIT, and it would likely be small improvements that I would suggest, not whole new functions or anything. So could I just post the applicable snippets of code as a comment on the bug report? Will anyone see it there? When I update a previously posted bug, I see this message: Changes submitted for bug 2093 Email sent to: no one Excluding: fieldtrip-bugs at donders.ru.nl , braingirl at gmail.com So I'm assuming no one knows. Is there a way to send it back to the bug listserv? Or should I really just learn how to use GIT (which seems more straightforward than SVN - is that true?)? ;-) Thanks again, Teresa ------------------------------ Message: 6 Date: Tue, 5 Jan 2016 08:27:18 +0000 From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] How are bugs triaged? Message-ID: > Content-Type: text/plain; charset="windows-1252" Hi Teresa, Generally, we don?t have an ?official? triage system for the bugs that are filed. The speed with which a bug is considered/resolved depends on a combination of things: 1) the quality of the bug report. 2) the perceived urgency by the people who would be able to resolve it. 3) the estimated cost-benefit relationship for the people who would be able to resolve it. 4) the amount of other piled-up work for the people who would be able to resolve it. 5) the level of serotonin. 6) the prospect of compensation in kind (beer/chocolate/formal involvement in projects etc). Thus, in general, there may be things that the bug filer can do to increase the probability for consideration/resolution, including adding code snippets and data that allow for a reproduction of a genuine bug, or by including code snippets that implement a new feature. Note that in general feature requests that are not a priority for the daily scientific work of the development/fixing team will get a low priority. In addition it should be noted that anybody who is on the list is allowed to contribute fixes/patches/features, and that it is not the responsibility of the core development team (which nowadays extends far beyond the people at the Donders Centre). Also, it should be noted that nobody has a formal requirement to provide fieldtrip/bugzilla support, it?s all pro bono. This means that we have to squeeze it in besides our daily scientific work and additional chores. Anyway, the problem is that we are just short-handed, which indeed sometimes results in bugs already being ?open? for a long time. Our oldest one still open dates from 2010, so the 2013 you mention is not that bad :o). With regard to the NEX file reader error you mentioned, if you think your workaround might be of benefit of other users, don?t hesitate to contribute! Best wishes, Jan-Mathijs On Jan 4, 2016, at 9:29 PM, Teresa Madsen >> wrote: I'm just curious because I've gotten such quick responses and fixes on some bugs, while others sit around for long periods of time without any feedback. Luckily, they're not anything stopping me from doing my work, but I was just curious if they've been seen and determined to be of low priority, or simply overlooked. Examples: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2978 - "Plot Trial" button on GUI for ft_rejectvisual (summary mode) plots average of all trials instead of the single trial requested - first posted in October http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2093 - NEX file reader errors - posted in 2013 - Obviously, I've worked around it, but it's still there with a status of "new"! Hope I'm not being a pest. Thanks, Teresa -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 62, Issue 4 **************************************** -- Teresa E. Madsen, PhD Division of Behavioral Neuroscience and Psychiatric Disorders Yerkes National Primate Research Center Emory University Rainnie Lab, NSB 5233 954 Gatewood Rd. NE Atlanta, GA 30329 (770) 296-9119 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From frsantos at fpce.up.pt Wed Jan 6 19:57:31 2016 From: frsantos at fpce.up.pt (Fernando Ferreira-Santos) Date: Wed, 6 Jan 2016 18:57:31 +0000 Subject: [FieldTrip] =?windows-1252?q?3rd_ESCAN_Porto_CONFERENCE_=96_EXTEN?= =?windows-1252?q?DED_SUBMISSION_DEADLINE_=96_22nd_January_2016?= Message-ID: <2BAB036A9BAEA44984A131DFCE446108010BFDAB11@SRVMBX01.fpceup.psi.up.pt> Dear colleagues, In order to allow for a full recovery from the holiday season the submission deadline for the 3rd International Conference of the European Society for Cognitive and Affective Neuroscience (ESCAN) in Porto has been extended to the 22nd of January, 2016. To submit your abstract for a symposium or oral/poster presentation and for all details on the conference please visit the website: www.escan2016.eu We would appreciate it if you could pass this information along to other colleagues and students. We are looking forward to seeing you in Porto in 2016! ESCAN 2016 Porto Local Organizing Committee -------------- next part -------------- An HTML attachment was scrubbed... URL: From mbj0310 at gmail.com Thu Jan 7 14:23:03 2016 From: mbj0310 at gmail.com (Beom Jun Min) Date: Thu, 7 Jan 2016 22:23:03 +0900 Subject: [FieldTrip] Using loreta2fieldtrip Message-ID: Dear community, I tried to load sLORETA data into the fieldtrip. My experiment is a kind of ERP experiment. And currently I have 5 subjects' data with 6 different conditions. With the related instructions ( http://www.fieldtriptoolbox.org/integrating_with/integrating_with_loreta), I made the volume structures of each condition (averaged over trials) for each subject (30 files). My converted volume structures have the following contents. dim [37,44,36] transform <44 double> inside <6239x1 double> outside <52369x1 double> {mom} <37x44x36 cell> cfg <1x1 struct> Is this structure is compatible with the up-to-date version of fieldtrip? It seems the ft_sourcegrandaverage function requires parameters such as pow, nai or coh. Best regards -- BeomJun Min, M.D. Department of Medical System Engineering (DMSE) Gwangju Institute of Science and Technology (GIST) 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 500-712, Republic of Korea (South) Phone: +82-62-715-3266 / Fax: +82-62-715-3244 E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Jan 7 17:58:09 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 7 Jan 2016 17:58:09 +0100 Subject: [FieldTrip] Job vacancies MRI/MEG physicists/engineers in Oldenburg References: <568E815B.7080205@uni-oldenburg.de> Message-ID: On 07 Jan 2016, at 16:16, Stefan Debener wrote: > The European Medical School is a cooperation project between the Universities of Oldenburg and Groningen and three local hospitals. > The newly founded Neuroimaging Center at the University of Oldenburg, Germany, offers the following two positions > > 1. MEG-Physicist/Engineer (E13/TV-L, initially 3 years) > > 2. MRI-Physicist/Engineer (E13/TV-L, initially 3 years) > > The positions are suitable for part-time work. > > The Neuroimaging Center hosts a state of the art magnetoencephalograph (ElektaTriux) and a magnetic resonance tomograph (Siemens Prisma 3T) and is embedded in an excellent interdisciplinary scientific environment with a strong research focus on neurosensory, neurocognitive, and medicalresearch. > > We seek for highly motivated post-doctoral candidates (with PhD) with an academic university degree in physics, engineering or related fields, with documented research experience in magnetoencephalography (position 1) or magnetic resonance imaging (position 2). For both positions, fluency in English is necessary. German and experience in the design of neurocognitive experiments are desirable. > > Successful candidates will be responsible for the operation and administration of the MEG system and MRI system respectively, their infrastructure, the development and improvement of measurement and analyses techniques and user consultancy. > > The University of Oldenburg is rapidly growing and offers a vibrant scientific environment with strong foci on cognitive and sensory neuroscience and a new medical school. Oldenburg is an attractive city in Germany's northwest with excellent quality of life. It is close to Bremen, Hamburg, Groningen, and approx. 1 h from the north sea. > > The University of Oldenburg is dedicated to increasing the percentage of women in science. Therefore, female candidates are particularly encouraged to apply and will be given preference in cases of equal qualification. Handicapped applicants will be given preference if equally qualified. > > Electronic applications (one pdf file) are preferred and can be send to: > Professor Dr. JochemRieger: Jochem.rieger at uni-oldenburg.de > Applications by mail should be sent to > Prof. Jochem Rieger > Universität Oldenburg > Kuepkersweg 74 (W30) > 26129 Oldenburg > Germany > > The application process is open until January 31st 2016. Applications should include your CV, a list of most recent publications, and a statement (max. 3 pages). > From RICHARDS at mailbox.sc.edu Fri Jan 8 18:15:01 2016 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Fri, 8 Jan 2016 17:15:01 +0000 Subject: [FieldTrip] Using loreta2fieldtrip (Beom Jun Min) Message-ID: <2215ED56-32F8-491B-9CD4-87B8D820A719@mailbox.sc.edu> Beom Jun Min: I am not sure of the exact answer, but…. Many of FT procedures require a pos (position) matrix, which is the s/c/a x/y/z positions of each dipole, and some other position information (e.g., mm; name of space; ft volume realign). This may not be necessary for a specific proc (ft_sourcegrandaverage) but is for other (ft_sourceinterpolate). pow can be calculated from mom, either with 3-dipole-moment or single-dipole-moment. Alternatively. I have been using the Nutmeg sLORETA procedure from the FT structures and data. If you have all your data in the FT format (head model, electrodes, lf), there is a routine that “almost” works to translate your FT LF to Nutmeg, and the sLORETA and dSPM routines from Nutmeg seem to work well. One advantage of FT/Nutmeg over LORETA or sLORETA packages is the FT is oriented to single participant head models. John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: richards-john at sc.edu HTTP: jerlab.psych.sc.edu *********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From zjyao at bu.edu Fri Jan 8 20:31:15 2016 From: zjyao at bu.edu (Zhaojie Yao) Date: Fri, 8 Jan 2016 14:31:15 -0500 Subject: [FieldTrip] Question about least-square FIR filter Message-ID: <247430E1-5A73-4DAD-8A8A-8FE5A8C430F3@bu.edu> Hi I am trying to process my data through Hilbert transform. I am used to the EEGLAB package, so I tried to use the same filter recommended by EEGLAB, which is least-square FIR filter in fieldtrip. However, I got a warning, when running the function ft_specest_hilbert, that least-square FIR 'is not recommended for neural signals, only proceed if you know what you are doing’. I am curious why least-square FIR is not appropriate for neural signals? Zhaojie Yao From tokimoto at mejiro.ac.jp Sun Jan 10 12:30:14 2016 From: tokimoto at mejiro.ac.jp (Shingo Tokimoto) Date: Sun, 10 Jan 2016 20:30:14 +0900 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB Message-ID: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> Dear Fieldtrip users, I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. -------------- EEGLAB error in function ft_checkconfig() at line 147: Error: ft_checkconfig (line 147) The field cfg.neighbours is required This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. ------------ I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. ************************************************ Shingo Tokimoto, Ph.D. in Linguistics and Psychology Department of Foreign Languages Mejiro University 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, 161-8539, Japan tokimoto at mejiro.ac.jp ************************************************ From tzvetan.popov at uni-konstanz.de Sun Jan 10 13:08:58 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 10 Jan 2016 13:08:58 +0100 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> Message-ID: Dear Shingo, You get this error because of a missing neighborhood structure with respect to your electrodes. Since you mention one electrode I suggest to specify cfg.neighbours = []. Thus you perform cluster based analysis over time and frequency within the electrode of your interest. Good luck Tzvetan > Am 10.01.2016 um 12:30 schrieb Shingo Tokimoto : > > Dear Fieldtrip users, > > I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. > > -------------- > EEGLAB error in function ft_checkconfig() at line 147: > > Error: ft_checkconfig (line 147) > The field cfg.neighbours is required > > This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. > ------------ > > I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. > > ************************************************ > Shingo Tokimoto, Ph.D. > in Linguistics and Psychology > Department of Foreign Languages > Mejiro University > 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, > 161-8539, Japan > tokimoto at mejiro.ac.jp > ************************************************ > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tokimoto at mejiro.ac.jp Sun Jan 10 16:27:30 2016 From: tokimoto at mejiro.ac.jp (Shingo Tokimoto) Date: Mon, 11 Jan 2016 00:27:30 +0900 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> Message-ID: <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> Dear Dr. Tzvetan Popov, Thank you very much for the quick reply. I edited "cfg.neighbours = neighbors;" in ft_prepare_neighbours.m to be "cfg.neighbours = [];." However, the same error message appears. I am sorry, but I am new to Fieldtrip. I am not sticking to one electrode. I want to specify the electrodes where their power are significantly different from those of the control condition in some specific time-windows and frequencies. The cluster-based analysis works well for ERP. Should I edit other m files? Thank you in advance again. ************************************************ Shingo Tokimoto, Ph.D. in Linguistics and Psychology Department of Foreign Languages Mejiro University 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, 161-8539, Japan tokimoto at mejiro.ac.jp ************************************************ On 2016/01/10, at 21:08, Tzvetan Popov wrote: > Dear Shingo, > You get this error because of a missing neighborhood structure with respect to your electrodes. Since you mention one electrode I suggest to specify cfg.neighbours = []. Thus you perform cluster based analysis over time and frequency within the electrode of your interest. > Good luck > Tzvetan > >> Am 10.01.2016 um 12:30 schrieb Shingo Tokimoto : >> >> Dear Fieldtrip users, >> >> I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. >> >> -------------- >> EEGLAB error in function ft_checkconfig() at line 147: >> >> Error: ft_checkconfig (line 147) >> The field cfg.neighbours is required >> >> This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. >> ------------ >> >> I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. >> >> ************************************************ >> Shingo Tokimoto, Ph.D. >> in Linguistics and Psychology >> Department of Foreign Languages >> Mejiro University >> 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, >> 161-8539, Japan >> tokimoto at mejiro.ac.jp >> ************************************************ >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From tzvetan.popov at uni-konstanz.de Sun Jan 10 17:08:19 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sun, 10 Jan 2016 17:08:19 +0100 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> Message-ID: Dear Shingo, lets keep it by Tzvetan ;-). I’m not familiar with the way EEGLAB deals with FieldTrip functions at all. So I may not be of any further help. However as a rule of thumb you should almost never change settings in the FieldTrip functions but provide the appropriate configurations always as cfg.xxx. When you mention your analysis works for ERP I don’t see any reason why it fails with time-freq data. Obviously you have your electrode positions and you were able to generate neighborhood structure. If so the same should work for t-f too. Maybe if you provide the syntax of your analysis me or others can help you in getting it done. I will advise to undone any changes you made to the FieldTrip code and try again. Probably a fresh version of EEGLAB, clean math lab path etc. and then do it again. best tzvetan > Dear Dr. Tzvetan Popov, > > Thank you very much for the quick reply. I edited "cfg.neighbours = neighbors;" in ft_prepare_neighbours.m to be "cfg.neighbours = [];." However, the same error message appears. I am sorry, but I am new to Fieldtrip. I am not sticking to one electrode. I want to specify the electrodes where their power are significantly different from those of the control condition in some specific time-windows and frequencies. The cluster-based analysis works well for ERP. Should I edit other m files? Thank you in advance again. > > ************************************************ > Shingo Tokimoto, Ph.D. > in Linguistics and Psychology > Department of Foreign Languages > Mejiro University > 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, > 161-8539, Japan > tokimoto at mejiro.ac.jp > ************************************************ > > > On 2016/01/10, at 21:08, Tzvetan Popov wrote: > >> Dear Shingo, >> You get this error because of a missing neighborhood structure with respect to your electrodes. Since you mention one electrode I suggest to specify cfg.neighbours = []. Thus you perform cluster based analysis over time and frequency within the electrode of your interest. >> Good luck >> Tzvetan >> >>> Am 10.01.2016 um 12:30 schrieb Shingo Tokimoto : >>> >>> Dear Fieldtrip users, >>> >>> I am trying to apply a cluster-based permutation test on my EEG data. When I try the time-frequency analysis on a channel from the command window of EEGLAB, the error message appears, as follows. >>> >>> -------------- >>> EEGLAB error in function ft_checkconfig() at line 147: >>> >>> Error: ft_checkconfig (line 147) >>> The field cfg.neighbours is required >>> >>> This is a problem with FIELDTRIP. The Fieldtrip version you downloaded is corrupted. Please manually replace Fieldtrip with an earlier version and/or email the Fieldtrip developers so they can fix the issue. >>> ------------ >>> >>> I am running EEGLAB (eeglab13_5_4b) on Matlab 2013b. I tried Fieldtrip-lite ver. 151020 first, and replaced it with fieldtrip-20160104. However, the same message appears. It is my pleasure if anyone tell me the proper "earlier version" of Fieldtrip. I appreciate any suggestions. Thank you in advance. >>> >>> ************************************************ >>> Shingo Tokimoto, Ph.D. >>> in Linguistics and Psychology >>> Department of Foreign Languages >>> Mejiro University >>> 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, >>> 161-8539, Japan >>> tokimoto at mejiro.ac.jp >>> ************************************************ >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From changa5 at mcmaster.ca Sun Jan 10 21:17:40 2016 From: changa5 at mcmaster.ca (Andrew Chang) Date: Sun, 10 Jan 2016 15:17:40 -0500 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Message-ID: Dear Fieldtrip users, I am wondering whether anyone has compared the performances of the ICA methods among M/EEG toolboxes. Especially, how is the performance of ICA in BESA Research 6.0, compared to Fieldtrip? I have an EEG data set which has been processed in BESA, including removing artifact using ICA. I am wondering whether I can trust it, or I should reprocess it in Fieldtrip. Any comments will be appreciated! Happy new year! Best, Andrew -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From leilayou_54 at yahoo.com Mon Jan 11 11:50:01 2016 From: leilayou_54 at yahoo.com (Leila Ayoubian) Date: Mon, 11 Jan 2016 10:50:01 +0000 (UTC) Subject: [FieldTrip] loading data in GUI References: <253366430.2575220.1452509401650.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <253366430.2575220.1452509401650.JavaMail.yahoo@mail.yahoo.com> Good morning everyone: I am new to fieldtrip am having trouble loading EEG data in a GUI . While there is no trouble loading the same file in a script , when the same file is being loaded inside a simple GUI , Matlab hangs, and I have to press ctrl C to exit! I am really puzzled! I understand it could be the GUI issue and not fieldtrip function issue.I thought if someone have come across this problem can save me time. I attached the two codes to compare. This is the script that works ************************************ clear all; clc; close all; [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename) cfg1 = []; cfg1.trl = [1 61440 0]; cfg1.dataset = filename%'K_S_Event_Marker_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1);  display('Finished') ***************************** Here is the GUI code, which does not work function varargout = loadDataGUI(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @loadDataGUI_OpeningFcn, ...                    'gui_OutputFcn',  @loadDataGUI_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before loadDataGUI is made visible. function loadDataGUI_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to loadDataGUI (see VARARGIN) % Choose default command line output for loadDataGUI handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes loadDataGUI wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = loadDataGUI_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in loadData. function loadData_Callback(hObject, eventdata, handles) % hObject    handle to loadData (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %Load the EEG file if isempty(handles)     disp('ERROR:::Please select a valid Montage'); end [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename) cfg1 = []; % beginSample=1; %The indice of sample to begin % endSample=61440; %The indice of sample to end (1 min data to load, 60*1024=61440) % cfg1.trl = [1 61440 0]; cfg1.dataset = filename%'K_S_Event_Marker_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1); %set(handles.filePath,'string',file ); function filePath_Callback(hObject, eventdata, handles) % hObject    handle to filePath (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of filePath as text %        str2double(get(hObject,'String')) returns contents of filePath as a double % global handles; % display(handles.file)  set(handles.filePath,'string',handles.file ); ************************************************************* __________________________________________________ Leila Ayoubian, PhD. Institute of Psychiatry, Psychology and Neuroscience King's College London -------------- next part -------------- An HTML attachment was scrubbed... URL: From leilayou_54 at yahoo.com Mon Jan 11 16:19:25 2016 From: leilayou_54 at yahoo.com (Leila Ayoubian) Date: Mon, 11 Jan 2016 15:19:25 +0000 (UTC) Subject: [FieldTrip] GUi issue with ft_preprocessing References: <1162479313.2666505.1452525565497.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <1162479313.2666505.1452525565497.JavaMail.yahoo@mail.yahoo.com> Why Data do not load in GUI, but it loads in a script using fieldtrip ft-preprocessing function?  Look a the two code below. One which is a script work perfectly fine.The other one is inside a simple gui and Matlab crashes.....Can anyone enlighten me?! Thanks in advance function varargout = trial5(varargin) % TRIAL5 MATLAB code for trial5.fig %      TRIAL5, by itself, creates a new TRIAL5 or raises the existing %      singleton*. % %      H = TRIAL5 returns the handle to a new TRIAL5 or the handle to %      the existing singleton*. % %      TRIAL5('CALLBACK',hObject,eventData,handles,...) calls the local %      function named CALLBACK in TRIAL5.M with the given input arguments. % %      TRIAL5('Property','Value',...) creates a new TRIAL5 or raises the %      existing singleton*.  Starting from the left, property value pairs are %      applied to the GUI before trial5_OpeningFcn gets called.  An %      unrecognized property name or invalid value makes property application %      stop.  All inputs are passed to trial5_OpeningFcn via varargin. % %      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one %      instance to run (singleton)". % % See also: GUIDE, GUIDATA, GUIHANDLES % Edit the above text to modify the response to help trial5 % Last Modified by GUIDE v2.5 11-Jan-2016 13:20:07 % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @trial5_OpeningFcn, ...                    'gui_OutputFcn',  @trial5_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before trial5 is made visible. function trial5_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to trial5 (see VARARGIN) % Choose default command line output for trial5 handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes trial5 wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = trial5_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in pushbutton1. function pushbutton1_Callback(hObject, eventdata, handles) % hObject    handle to pushbutton1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %file = fullfile(pathname, filename) cfg1 = []; cfg1.trl = [1 61440 0]; cfg1.dataset = 'Event06_Interictal_Background_Sleep_Segment_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1); function edit1_Callback(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit1 as text %        str2double(get(hObject,'String')) returns contents of edit1 as a double % --- Executes during object creation, after setting all properties. function edit1_CreateFcn(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. %       See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))     set(hObject,'BackgroundColor','white'); end *************************************************************************** function varargout = trial5(varargin) % TRIAL5 MATLAB code for trial5.fig %      TRIAL5, by itself, creates a new TRIAL5 or raises the existing %      singleton*. % %      H = TRIAL5 returns the handle to a new TRIAL5 or the handle to %      the existing singleton*. % %      TRIAL5('CALLBACK',hObject,eventData,handles,...) calls the local %      function named CALLBACK in TRIAL5.M with the given input arguments. % %      TRIAL5('Property','Value',...) creates a new TRIAL5 or raises the %      existing singleton*.  Starting from the left, property value pairs are %      applied to the GUI before trial5_OpeningFcn gets called.  An %      unrecognized property name or invalid value makes property application %      stop.  All inputs are passed to trial5_OpeningFcn via varargin. % %      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one %      instance to run (singleton)". % % See also: GUIDE, GUIDATA, GUIHANDLES % Edit the above text to modify the response to help trial5 % Last Modified by GUIDE v2.5 11-Jan-2016 13:20:07 % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @trial5_OpeningFcn, ...                    'gui_OutputFcn',  @trial5_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before trial5 is made visible. function trial5_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to trial5 (see VARARGIN) % Choose default command line output for trial5 handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes trial5 wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = trial5_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in pushbutton1. function pushbutton1_Callback(hObject, eventdata, handles) % hObject    handle to pushbutton1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %file = fullfile(pathname, filename) cfg1 = []; cfg1.trl = [1 61440 0]; cfg1.dataset = 'Event06_Interictal_Background_Sleep_Segment_1.edf';  cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes';  data1 = ft_preprocessing(cfg1); function edit1_Callback(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit1 as text %        str2double(get(hObject,'String')) returns contents of edit1 as a double % --- Executes during object creation, after setting all properties. function edit1_CreateFcn(hObject, eventdata, handles) % hObject    handle to edit1 (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. %       See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))     set(hObject,'BackgroundColor','white'); end -------------- next part -------------- An HTML attachment was scrubbed... URL: From widmann at uni-leipzig.de Mon Jan 11 17:42:07 2016 From: widmann at uni-leipzig.de (Andreas Widmann) Date: Mon, 11 Jan 2016 17:42:07 +0100 Subject: [FieldTrip] Question about least-square FIR filter In-Reply-To: <247430E1-5A73-4DAD-8A8A-8FE5A8C430F3@bu.edu> References: <247430E1-5A73-4DAD-8A8A-8FE5A8C430F3@bu.edu> Message-ID: <9BABEA1A-A464-41E0-BBA2-5ABE35D540DB@uni-leipzig.de> Hi, > I am trying to process my data through Hilbert transform. I am used to the EEGLAB package, so I tried to use the same filter recommended by EEGLAB, which is least-square FIR filter in fieldtrip. However, I got a warning, when running the function ft_specest_hilbert, that least-square FIR 'is not recommended for neural signals, only proceed if you know what you are doing’. I am curious why least-square FIR is not appropriate for neural signals? Short version: See http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2453 Point (3) and first attachment (png). Long version: firls filters are also NOT recommended in EEGLAB. Where did you get this information? The EEGLAB firls filter are marked legacy/deprecated since 2012. See http://journal.frontiersin.org/article/10.3389/fpsyg.2012.00233/full for a more detailed description of the problem, in particular footnote 1. Filter roll-off/transition width is a function of the filter order. However, with MATLAB firls filters roll-off/transition width is defined independently from filter order. This might work if the selected parameters for both are appropriate, however, commonly it does not work resulting in various artifacts in the filter’s frequency and/or time domain responses, bad attenuation, non-unity DC gain etc. In Fieldtrip the problem was/is particularly problematic as a zero transition width (rectangular frequency response) filter is requested combined with an incorrect estimation of required filter order (actually infinite). Hope this helps! Best, Andreas From leilayou_54 at yahoo.com Tue Jan 12 11:42:27 2016 From: leilayou_54 at yahoo.com (Leila Ayoubian) Date: Tue, 12 Jan 2016 10:42:27 +0000 (UTC) Subject: [FieldTrip] importing large edf data In-Reply-To: References: Message-ID: <2128658446.3021319.1452595347079.JavaMail.yahoo@mail.yahoo.com>  Hi Steve:Happy new year. Following the code you sent me to import large  EDF data sets, I designed a simple GUI to select data and display the path.I simplified the GUI for convenience so you can have a look at it. When I run this GUI Matlab crashes, meaning it will be busy until I quite the execution by pressing ctrl C. The same code on a script is absolutely fine! I am really puzzled and not underestanding why this is happening. Could it be a bug of ft_preprocessing function? I have copied both files beow. Can you please have a look. I have been hanging around for couple days wondering and not getting to any conclusion. I appreciate if you can enlighten me.Thanks ******** THE GUI CODE***************** function varargout = loadDataGUI(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name',       mfilename, ...                    'gui_Singleton',  gui_Singleton, ...                    'gui_OpeningFcn', @loadDataGUI_OpeningFcn, ...                    'gui_OutputFcn',  @loadDataGUI_OutputFcn, ...                    'gui_LayoutFcn',  [] , ...                    'gui_Callback',   []); if nargin && ischar(varargin{1})     gui_State.gui_Callback = str2func(varargin{1}); end if nargout     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else     gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before loadDataGUI is made visible. function loadDataGUI_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % varargin   command line arguments to loadDataGUI (see VARARGIN) % Choose default command line output for loadDataGUI handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes loadDataGUI wait for user response (see UIRESUME) % uiwait(handles.figure1); % --- Outputs from this function are returned to the command line. function varargout = loadDataGUI_OutputFcn(hObject, eventdata, handles) % varargout  cell array for returning output args (see VARARGOUT); % hObject    handle to figure % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes on button press in loadData. function loadData_Callback(hObject, eventdata, handles) % hObject    handle to loadData (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) %Load the EEG file if isempty(handles)     disp('ERROR:::Please select a valid Montage'); end [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename)  cfg = [];  cfg.trl = [1 61440 0];  cfg.dataset = filename%'K_S_Event_Marker_1.edf';  cfg= ft_definetrial( cfg );  cfg.continuous = 'yes'; data = ft_preprocessing(cfg); % [hdr, record] = edfread(file); set(handles.filePath,'string',file ); function filePath_Callback(hObject, eventdata, handles) % hObject    handle to filePath (see GCBO) % eventdata  reserved - to be defined in a future version of MATLAB % handles    structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of filePath as text %        str2double(get(hObject,'String')) returns contents of filePath as a double % global handles; % display(handles.file)  set(handles.filePath,'string',handles.file ); *************** THE SCRIPT************ clear all; clc; close all; %% [filename, pathname] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file'); if isequal(filename, 0) || isequal(pathname, 0)     disp('Exiting...');     return; end file = fullfile(pathname, filename) %% cfg1 = []; cfg1.trl = [1 61440 0]; %cfg1.dataset = filename%'K_S_Event_Marker_1.edf'; cfg1.dataset = 'Event06_Interictal_Background_Sleep_Segment_1.edf' cfg1 = ft_definetrial( cfg1 ); cfg1.continuous = 'yes'; data1 = ft_preprocessing(cfg1); %% %[hdr, record] = edfread(file); %%  display('Finished') __________________________________________________ Leila Ayoubian, PhD. Institute of Psychiatry, Psychology and Neuroscience King's College London From: Stephen Politzer-Ahles To: fieldtrip at science.ru.nl Sent: Saturday, December 19, 2015 2:06 PM Subject: Re: [FieldTrip] importing large edf data Hi Leila, I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me: cfg = []; cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf'; cfg.trl = [1 500 0]; cfg.continuous = 'yes'; data_500samples = ft_preprocessing(cfg); cfg = []; cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf'; cfg.trl = [1 1000 0]; cfg.continuous = 'yes'; data_1000samples = ft_preprocessing(cfg); Here's the output: >> data_500samples data_500samples =            hdr: [1x1 struct]          label: {37x1 cell}           time: {[1x500 double]}          trial: {[37x500 double]}        fsample: 200     sampleinfo: [1 500]            cfg: [1x1 struct] >> data_1000samples data_1000samples =            hdr: [1x1 struct]          label: {37x1 cell}           time: {[1x1000 double]}          trial: {[37x1000 double]}        fsample: 200     sampleinfo: [1 1000]            cfg: [1x1 struct] Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/  ------------------------------ Message: 5 Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC) From: Leila Ayoubian To: FieldTrip discussion list Subject: Re: [FieldTrip] importing large edf data Message-ID:         <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com> Content-Type: text/plain; charset="utf-8" ?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same! So this is what I get: ?? hdr: [1x1 struct] ???????? label: {51x1 cell} ????????? time: {1x50710 cell} ???????? trial: {1x50710 cell} ?????? fsample: 1024 ??? sampleinfo: [50710x2 double] ?????????? cfg: [1x1 struct] so the actual data which is in data.trial? is this in both cases! size(data.trial) ans = ?????????? 1?????? 50710 How could that happen if you are segmenting it in two different chunks? Best regards ___________________________________________________ Leila Ayoubian       From: Stephen Politzer-Ahles  To: fieldtrip at science.ru.nl  Sent: Friday, December 18, 2015 12:37 PM  Subject: Re: [FieldTrip] importing large edf data Hello Leila, I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size. If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add: cfg.trl = [1 1000 0]; and then use ft_preprocessing. By way of example, here is code that reads in raw data as a series of 1-second "trials": cfg = []; cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr'; cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters cfg.trialdef.ntrials = Inf; cfg = ft_definetrial( cfg ); cfg.continuous = 'yes'; data = ft_preprocessing(cfg); After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details). Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/ On Fri, Dec 18, 2015 at 11:00 AM, wrote: Send fieldtrip mailing list submissions to ? ? ? ? fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit ? ? ? ? http://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to ? ? ? ? fieldtrip-request at science.ru.nl You can reach the person managing the list at ? ? ? ? fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: ? ?1. importing large edf data (Leila Ayoubian) ---------------------------------------------------------------------- Message: 1 Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC) From: Leila Ayoubian To: "fieldtrip at science.ru.nl" Subject: [FieldTrip] importing large edf data Message-ID: ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com> Content-Type: text/plain; charset="utf-8" Hi:Thanks for providing us with this amazing toolbox. I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.? So trying to load the data like this: cfg.dataset= ('mydata.edf'); rawdata=ft_preprocessing(cfg); This is the error message I get : %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Error using zeros Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information. Error in read_edf (line 403) ? dat = zeros(length(chanindx),nepochs*epochlength); Error in ft_read_data (line 622) ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx); Error in ft_preprocessing (line 566) ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat); Error in ReadFedfiles (line 8) rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf' ?hdr?? = ft_read_header(filename); ?sample.start=1 ?sample.end=100 dat = ft_read_data(filename,'sample.start','1','sample.end','100') and here is again the error message: Error using zeros Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information. Error in read_edf (line 403) ? dat = zeros(length(chanindx),nepochs*epochlength); Error in ft_read_data (line 622) ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx); Error in ReadFedfiles (line 31) dat = ft_read_data(filename,'sample.start','1','sample.end','100') ? >> Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful. Thanks again for your support and assistance. We appreciate your effort. Kind regards ___________________________________________________ Dr. Leila Ayoubian -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lorenzomagazzini at gmail.com Tue Jan 12 15:46:44 2016 From: lorenzomagazzini at gmail.com (Lorenzo Magazzini) Date: Tue, 12 Jan 2016 14:46:44 +0000 Subject: [FieldTrip] Help understanding the lcmv beamformer output Message-ID: Hi, I hope someone can help me to understand the use of the lcmv beamformer, because either I am using it incorrectly, or I misunderstood the meaning of its output. I am trying to get source-level power estimates of 'baseline' and 'active' time-windows. I first compute a common filter, and then apply it separately to the two conditions. I thought the power estimates would be stored, voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. However, the values I get in the '.pow' field for the analysis of 'baseline' and 'active' windows are identical. Furthermore, the '.pow' values are identical to the '.noise' values when using cfg.projectnoise = 'yes';. I have checked if the sensor-level data that passed on to ft_sourceanalysis is different between baseline and active - it is. Also, if I do the following... 1. reconstruct virtual sensors by applying the common filter separately to baseline and active, 2. average the single-trial (virtual sensor) power estimates, 3. replace the '.pow' value for each voxel, ...then the contrast between baseline and active is correct. Can anyone please help me figure out what I'm doing wrong here? Below I copied part of the code. Many thanks in advance! Lorenzo %compute the leadfield cfg = []; cfg.channel = {'MEG'}; cfg.grid = sourcemodel; cfg.vol = hdm; cfg.grad = grad; cfg.normalize = 'yes'; leadfield = ft_prepare_leadfield(cfg); %compute covariance matrix cfg = []; cfg.channel = {'MEG'}; cfg.removemean = 'no'; cfg.covariance = 'yes'; cfg.covariancewindow = [-1.5 1.5]; tlck = ft_timelockanalysis(cfg, data); %get the common spatial filter cfg = []; cfg.method = 'lcmv'; cfg.grid = leadfield; cfg.vol = hdm; cfg.grad = grad; cfg.lcmv.fixedori = 'yes'; cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.projectnoise = 'yes'; cfg.lcmv.lambda = '5%'; src = ft_sourceanalysis(cfg, tlck); %store the filter wts = src.avg.filter; %separate baseline and active windows of bandpass-filtered data cfg = []; cfg.toilim = [-1.5 -0.3]; data_bsln = ft_redefinetrial(cfg, data); cfg = []; cfg.toilim = [0.3 1.5]; data_actv = ft_redefinetrial(cfg, data); %timelock analysis of baseline and active cfg = []; cfg.channel = {'MEG'}; cfg.keeptrials = 'yes'; tlck_bsln = ft_timelockanalysis(cfg, data_bsln); tlck_actv = ft_timelockanalysis(cfg, data_actv); %get source-power estimates of bsln and actv separately using the pre-computed common filter (wts) cfg = []; cfg.method = 'lcmv'; cfg.vol = hdm; cfg.grid = leadfield; cfg.grid.filter = wts; % cfg.keepfilter = 'no'; cfg.lcmv.fixedori = 'yes'; cfg.projectnoise = 'yes'; cfg.lambda = '5%'; cfg.keeptrials = 'yes'; src_bsln = ft_sourceanalysis(cfg, tlck_bsln); src_actv = ft_sourceanalysis(cfg, tlck_actv); -------------- next part -------------- An HTML attachment was scrubbed... URL: From ervin.poljac at donders.ru.nl Tue Jan 12 16:32:52 2016 From: ervin.poljac at donders.ru.nl (Poljac, E. (Ervin)) Date: Tue, 12 Jan 2016 15:32:52 +0000 Subject: [FieldTrip] Help understanding the lcmv beamformer output In-Reply-To: References: Message-ID: Hi Marjolein, Even een snelle vraag, wat is de risingedge(mask)? Groetjes, Ervin -- Ervin Poljac, PhD Donders Institute for Brain, Cognition and Behaviour Centre for Cognition (DCC) Radboud University Nijmegen Room B.00.78A Montessorilaan 3 6500 HE Nijmegen T. 024 36 15457 ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Lorenzo Magazzini [lorenzomagazzini at gmail.com] Sent: Tuesday, January 12, 2016 3:46 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Help understanding the lcmv beamformer output Hi, I hope someone can help me to understand the use of the lcmv beamformer, because either I am using it incorrectly, or I misunderstood the meaning of its output. I am trying to get source-level power estimates of 'baseline' and 'active' time-windows. I first compute a common filter, and then apply it separately to the two conditions. I thought the power estimates would be stored, voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. However, the values I get in the '.pow' field for the analysis of 'baseline' and 'active' windows are identical. Furthermore, the '.pow' values are identical to the '.noise' values when using cfg.projectnoise = 'yes';. I have checked if the sensor-level data that passed on to ft_sourceanalysis is different between baseline and active - it is. Also, if I do the following... 1. reconstruct virtual sensors by applying the common filter separately to baseline and active, 2. average the single-trial (virtual sensor) power estimates, 3. replace the '.pow' value for each voxel, ...then the contrast between baseline and active is correct. Can anyone please help me figure out what I'm doing wrong here? Below I copied part of the code. Many thanks in advance! Lorenzo %compute the leadfield cfg = []; cfg.channel = {'MEG'}; cfg.grid = sourcemodel; cfg.vol = hdm; cfg.grad = grad; cfg.normalize = 'yes'; leadfield = ft_prepare_leadfield(cfg); %compute covariance matrix cfg = []; cfg.channel = {'MEG'}; cfg.removemean = 'no'; cfg.covariance = 'yes'; cfg.covariancewindow = [-1.5 1.5]; tlck = ft_timelockanalysis(cfg, data); %get the common spatial filter cfg = []; cfg.method = 'lcmv'; cfg.grid = leadfield; cfg.vol = hdm; cfg.grad = grad; cfg.lcmv.fixedori = 'yes'; cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.projectnoise = 'yes'; cfg.lcmv.lambda = '5%'; src = ft_sourceanalysis(cfg, tlck); %store the filter wts = src.avg.filter; %separate baseline and active windows of bandpass-filtered data cfg = []; cfg.toilim = [-1.5 -0.3]; data_bsln = ft_redefinetrial(cfg, data); cfg = []; cfg.toilim = [0.3 1.5]; data_actv = ft_redefinetrial(cfg, data); %timelock analysis of baseline and active cfg = []; cfg.channel = {'MEG'}; cfg.keeptrials = 'yes'; tlck_bsln = ft_timelockanalysis(cfg, data_bsln); tlck_actv = ft_timelockanalysis(cfg, data_actv); %get source-power estimates of bsln and actv separately using the pre-computed common filter (wts) cfg = []; cfg.method = 'lcmv'; cfg.vol = hdm; cfg.grid = leadfield; cfg.grid.filter = wts; % cfg.keepfilter = 'no'; cfg.lcmv.fixedori = 'yes'; cfg.projectnoise = 'yes'; cfg.lambda = '5%'; cfg.keeptrials = 'yes'; src_bsln = ft_sourceanalysis(cfg, tlck_bsln); src_actv = ft_sourceanalysis(cfg, tlck_actv); -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Wed Jan 13 16:23:22 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Wed, 13 Jan 2016 17:23:22 +0200 Subject: [FieldTrip] Fieldtrip compatibility In-Reply-To: References: Message-ID: Dear Robert, Thank you to put in our problem from the first question, yes we want to localize the contractions of the uterus, and thank you to provide me with the careful consideration of the inverse model assumptions for this case. I have looked at http://www.fieldtriptoolbox.org/dataformat, but the data what I have is: 1- a real signal generated from 16 electrodes saved as ".mat", 2- the meshes as ".off"( I seperated the points and faces and I saved each one on ".mat") it is already segmented, and 3- the simulated potential (99084x201) given from our team who works on the model and I want to convert it to in the form of signal collected from the 16 electrode (16x201). The algorithm of my colleague was as below, but I didn't convinced in the computation of the inverse problem using the gain matrix not the lead field, it is possible to use the gain matrix as done below in the bold inverse problem part or in another word what does gain represent? % Set the radius and conductivities of each of the compartments addpath(cd) % 3 Layers r = [0 0.936 2.068 2.268]; c = [0.2 0.3 0.04 0.5]; %% Description of the spherical mesh pnt=point_square(:,2:4); tri=faces_square(:,3:5); %% Create a set of electrodes on the outer surface % sensor = [pnt(10201,:);pnt(17376,:);pnt(24756,:);pnt(31931,:);pnt(10166,:);pnt(17341,:);pnt(24721,:);pnt(31896,:);pnt(10130,:);pnt(17305,:);pnt(24685,:);pnt(31860,:);pnt(10095,:);pnt(17270,:);pnt(24650,:);pnt(31825,:)]; sensor = [pnt(664,:);pnt(1080,:);pnt(1600,:);pnt(2016,:);pnt(656,:);pnt(1072,:);pnt(1592,:);pnt(2008,:);pnt(646,:);pnt(1062,:);pnt(1582,:);pnt(1998,:);pnt(638,:);pnt(1054,:);pnt(1574,:);pnt(1990,:)]; sensor(:,3)=sensor(:,3)+max(r)+0.1; sens.elecpos = sensor; sens.label = {}; nsens = size(sens.elecpos,1); for ii=1:nsens sens.label{ii} = sprintf('vertex%03d', ii); end %% Set the position of the probe dipole %%Un source pos = pnt(1326,:);%[5 5 0] maillage complet pos(:,3) = pos(:,3)+0.1; %%Deux source % S1 = pnt(10609,:);%[2.5 2.5 0] maillage complet % S1(:,3) = S1(:,3)+0.1; % S2 = pnt(31417,:);%[7.5 7.5 0] maillage complet % S2(:,3) = S2(:,3)+0.1; % pos=[S1;S2]; %%All the uterine muscle mesh %S=pnt(:,:,:); %S(:,3) = S(:,3)+0.1; %pos=S; %% Create a BEM volume conduction model vol = []; for ii=1:length(r) uterus=pnt; uterus(:,3)=uterus(:,3)+r(ii)+0.1; vol.bnd(ii).pnt = uterus; vol.bnd(ii).tri = fliplr(tri); % pointing inwards!!! end vol.cond = c; %% Compute the BEM cfg=[]; cfg.method = 'bemcp'; vol = ft_prepare_headmodel(cfg, vol); cfg.vol = vol; cfg.grid.pos = pos; cfg.elec = sens; [grid,gain] = ft_prepare_leadfield(cfg); lf_openmeeg = grid.leadfield{1}; %% Inverse problem %load data data_simulated = hdf5read('Sources_EHG_1.hdf5','/surface/EHG'); %real=load('W4_P_27_07_10_CTMono3_deb.mat'); %data_real=real.XXF2D1; %MNE lambda = 1e-1; % MNE_1 = inverse_operator_MNE(gain,lambda); % A: Gain matrix S_MNE_1 = bayesian_inverse_solution(data_simulated',MNE_1); % X: Signal mean_S_MNE_1=mean(S_MNE_1,2); % % MNE_2 = inverse_operator_MNE(gain,lambda); % A: Gain matrix % S_MNE_2 = bayesian_inverse_solution(data_real',MNE_2); % X: Signal % mean_S_MNE_2=mean(S_MNE_2,2); bnd = struct('pnt', pnt, 'tri', tri); figure;ft_plot_mesh(bnd, 'vertexcolor', mean_S_MNE_1(1:size(pnt,1))); % figure;ft_plot_mesh(bnd, 'vertexcolor', mean_S_MNE_2(1:size(pnt,1))); To be more accurate I want to use your algorithm in: http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate?s[]=mne but my obstacle was cfg.dataset = 'Subject01.ds'; I didn't know in our cases what is the "Subject01.ds", and also the same in: http://www.fieldtriptoolbox.org/tutorial/beamformer,... Thank you very much for any suggestions Best regards Saeed -------------- next part -------------- An HTML attachment was scrubbed... URL: From mail at philipp-ruhnau.de Wed Jan 13 16:46:09 2016 From: mail at philipp-ruhnau.de (Philipp Ruhnau) Date: Wed, 13 Jan 2016 16:46:09 +0100 Subject: [FieldTrip] Help understanding the lcmv beamformer output In-Reply-To: References: Message-ID: <9EDB2B94-3D95-4084-82F2-71968FF04217@philipp-ruhnau.de> Dear Lorenzo and others, I’ve just looked into this, can reproduce the issue (same result with two different conditions/activity-baseline) The issue arises because power is calculated based on the filter and the covariance of the input data (following VanVeen or a slight change for precomputed filters), yet in the example below no covariance is precomputed for activity/baseline timelock structures (only for the common dataset) and in that case fieldtrip creates an identity matrix for both activity and baseline (around line 713 in ft_sourceanalysis). there is actually a warning about this, yet just from this warning (No covariance matrix found - will assume identity covariance matrix (mininum-norm solution)) it might to hard to get that this explains the results: in essence from what I understand, the input data is ignored in the formula (for those interested this is line 278 in beamformer_lcmv) to compute the time series power, because the covariance is an identity matrix, and only the filter determines what ends up in the .pow field. and as the filter is the same for activity and baseline, the difference between the .pow output is zero. now, computing covariances for the to-be-beamed segments (add a cfg.covariance = ‘yes’ to the timelock step for baseline and activity in the example) produces different power values (just tested with a simple auditory ERF dataset). I suppose this is desired behavior (the identity matrix covariance), otherwise I would suggest to produce an error. how well the ERF/timeseries is reconstructed of course depends on the data (time window) you use to create the filters. still it seems to me using the .mom field or creating virtual sensors yields better (in a sense of more focused) results. I still wonder why virtual sensors/.mom averages and .pow results are quite different, maybe one of the more knowledgeable ft developers could comment on at some point, but this might exceed the limit of this list… cheers philipp > On 12 Jan 2016, at 15:46, Lorenzo Magazzini wrote: > > Hi, > > I hope someone can help me to understand the use of the lcmv beamformer, because either I am using it incorrectly, or I misunderstood the meaning of its output. > > I am trying to get source-level power estimates of 'baseline' and 'active' time-windows. I first compute a common filter, and then apply it separately to the two conditions. I thought the power estimates would be stored, voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. However, the values I get in the '.pow' field for the analysis of 'baseline' and 'active' windows are identical. Furthermore, the '.pow' values are identical to the '.noise' values when using cfg.projectnoise = 'yes';. > > I have checked if the sensor-level data that passed on to ft_sourceanalysis is different between baseline and active - it is. > > Also, if I do the following... > 1. reconstruct virtual sensors by applying the common filter separately to baseline and active, > 2. average the single-trial (virtual sensor) power estimates, > 3. replace the '.pow' value for each voxel, > ...then the contrast between baseline and active is correct. > > Can anyone please help me figure out what I'm doing wrong here? Below I copied part of the code. > > Many thanks in advance! > > Lorenzo > > > %compute the leadfield > cfg = []; > cfg.channel = {'MEG'}; > cfg.grid = sourcemodel; > cfg.vol = hdm; > cfg.grad = grad; > cfg.normalize = 'yes'; > leadfield = ft_prepare_leadfield(cfg); > > %compute covariance matrix > cfg = []; > cfg.channel = {'MEG'}; > cfg.removemean = 'no'; > cfg.covariance = 'yes'; > cfg.covariancewindow = [-1.5 1.5]; > tlck = ft_timelockanalysis(cfg, data); > > %get the common spatial filter > cfg = []; > cfg.method = 'lcmv'; > cfg.grid = leadfield; > cfg.vol = hdm; > cfg.grad = grad; > cfg.lcmv.fixedori = 'yes'; > cfg.lcmv.keepfilter = 'yes'; > cfg.lcmv.projectnoise = 'yes'; > cfg.lcmv.lambda = '5%'; > src = ft_sourceanalysis(cfg, tlck); > > %store the filter > wts = src.avg.filter; > > %separate baseline and active windows of bandpass-filtered data > cfg = []; > cfg.toilim = [-1.5 -0.3]; > data_bsln = ft_redefinetrial(cfg, data); > cfg = []; > cfg.toilim = [0.3 1.5]; > data_actv = ft_redefinetrial(cfg, data); > > %timelock analysis of baseline and active > cfg = []; > cfg.channel = {'MEG'}; > cfg.keeptrials = 'yes'; > tlck_bsln = ft_timelockanalysis(cfg, data_bsln); > tlck_actv = ft_timelockanalysis(cfg, data_actv); > > %get source-power estimates of bsln and actv separately using the pre-computed common filter (wts) > cfg = []; > cfg.method = 'lcmv'; > cfg.vol = hdm; > cfg.grid = leadfield; > cfg.grid.filter = wts; > % cfg.keepfilter = 'no'; > cfg.lcmv.fixedori = 'yes'; > cfg.projectnoise = 'yes'; > cfg.lambda = '5%'; > cfg.keeptrials = 'yes'; > src_bsln = ft_sourceanalysis(cfg, tlck_bsln); > src_actv = ft_sourceanalysis(cfg, tlck_actv); > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lorenzomagazzini at gmail.com Wed Jan 13 19:44:26 2016 From: lorenzomagazzini at gmail.com (Lorenzo Magazzini) Date: Wed, 13 Jan 2016 18:44:26 +0000 Subject: [FieldTrip] Help understanding the lcmv beamformer output Message-ID: Hi Philipp, Thanks so much for your answer, it does indeed solve the problem! I thought the covariance matrix was no longer necessary after computation of the (common) filter, but, as you showed by pointing to the code, this is clearly not the case. Now, I compared the results of a) calculating power from the virtual sensors time-series (data multiplied by the filter, estimated using the 'common' covariance), and b) power taken from the output of ft_sourceanalysis, using two different 'condition-specific' covariance matrices. Results are pretty identical in my case, apart from minor differences in the power values. I wonder if anyone could help me figure out if there is a mathematical difference between these two approaches? Anyway, many thanks again for your help! Best wishes, Lorenzo > *From: *Philipp Ruhnau > *Subject: **Re: [FieldTrip] Help understanding the lcmv beamformer output* > *Date: *13 January 2016 at 16:46:09 GMT+1 > *To: *FieldTrip discussion list > > Dear Lorenzo and others, > I’ve just looked into this, can reproduce the issue (same result with two > different conditions/activity-baseline) > > The issue arises because power is calculated based on the filter and the > covariance of the input data (following VanVeen or a slight change for > precomputed filters), yet in the example below no covariance is precomputed > for activity/baseline timelock structures (only for the common dataset) and > in that case fieldtrip creates an identity matrix for both activity and > baseline (around line 713 in ft_sourceanalysis). > there is actually a warning about this, yet just from this warning (No > covariance matrix found - will assume identity covariance matrix > (mininum-norm solution)) it might to hard to get that this explains the > results: > > in essence from what I understand, the input data is ignored in the > formula (for those interested this is line 278 in beamformer_lcmv) to > compute the time series power, because the covariance is an identity > matrix, and only the filter determines what ends up in the .pow field. and > as the filter is the same for activity and baseline, the difference between > the .pow output is zero. > > now, computing covariances for the to-be-beamed segments (add a > cfg.covariance = ‘yes’ to the timelock step for baseline and activity in > the example) produces different power values (just tested with a simple > auditory ERF dataset). > > I suppose this is desired behavior (the identity matrix covariance), > otherwise I would suggest to produce an error. > > how well the ERF/timeseries is reconstructed of course depends on the data > (time window) you use to create the filters. still it seems to me using the > .mom field or creating virtual sensors yields better (in a sense of more > focused) results. I still wonder why virtual sensors/.mom averages and .pow > results are quite different, maybe one of the more knowledgeable ft > developers could comment on at some point, but this might exceed the limit > of this list… > > cheers > philipp > > On 12 Jan 2016, at 15:46, Lorenzo Magazzini > wrote: > > Hi, > > I hope someone can help me to understand the use of the lcmv beamformer, > because either I am using it incorrectly, or I misunderstood the meaning of > its output. > > I am trying to get source-level power estimates of 'baseline' and 'active' > time-windows. I first compute a common filter, and then apply it separately > to the two conditions. I thought the power estimates would be stored, > voxel-wise, in the '.avg.pow' field of the ft_sourceanalysis output. > However, the values I get in the '.pow' field for the analysis of > 'baseline' and 'active' windows are identical. Furthermore, the '.pow' > values are identical to the '.noise' values when using cfg.projectnoise = > 'yes';. > > I have checked if the sensor-level data that passed on to > ft_sourceanalysis is different between baseline and active - it is. > > Also, if I do the following... > 1. reconstruct virtual sensors by applying the common filter separately to > baseline and active, > 2. average the single-trial (virtual sensor) power estimates, > 3. replace the '.pow' value for each voxel, > ...then the contrast between baseline and active is correct. > > Can anyone please help me figure out what I'm doing wrong here? Below I > copied part of the code. > > Many thanks in advance! > > Lorenzo > > > %compute the leadfield > cfg = []; > cfg.channel = {'MEG'}; > cfg.grid = sourcemodel; > cfg.vol = hdm; > cfg.grad = grad; > cfg.normalize = 'yes'; > leadfield = ft_prepare_leadfield(cfg); > > %compute covariance matrix > cfg = []; > cfg.channel = {'MEG'}; > cfg.removemean = 'no'; > cfg.covariance = 'yes'; > cfg.covariancewindow = [-1.5 1.5]; > tlck = ft_timelockanalysis(cfg, data); > > %get the common spatial filter > cfg = []; > cfg.method = 'lcmv'; > cfg.grid = leadfield; > cfg.vol = hdm; > cfg.grad = grad; > cfg.lcmv.fixedori = 'yes'; > cfg.lcmv.keepfilter = 'yes'; > cfg.lcmv.projectnoise = 'yes'; > cfg.lcmv.lambda = '5%'; > src = ft_sourceanalysis(cfg, tlck); > > %store the filter > wts = src.avg.filter; > > %separate baseline and active windows of bandpass-filtered data > cfg = []; > cfg.toilim = [-1.5 -0.3]; > data_bsln = ft_redefinetrial(cfg, data); > cfg = []; > cfg.toilim = [0.3 1.5]; > data_actv = ft_redefinetrial(cfg, data); > > %timelock analysis of baseline and active > cfg = []; > cfg.channel = {'MEG'}; > cfg.keeptrials = 'yes'; > tlck_bsln = ft_timelockanalysis(cfg, data_bsln); > tlck_actv = ft_timelockanalysis(cfg, data_actv); > > %get source-power estimates of bsln and actv separately using the > pre-computed common filter (wts) > cfg = []; > cfg.method = 'lcmv'; > cfg.vol = hdm; > cfg.grid = leadfield; > cfg.grid.filter = wts; > % cfg.keepfilter = 'no'; > cfg.lcmv.fixedori = 'yes'; > cfg.projectnoise = 'yes'; > cfg.lambda = '5%'; > cfg.keeptrials = 'yes'; > src_bsln = ft_sourceanalysis(cfg, tlck_bsln); > src_actv = ft_sourceanalysis(cfg, tlck_actv); > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dlozanosoldevilla at gmail.com Thu Jan 14 11:41:09 2016 From: dlozanosoldevilla at gmail.com (dlozanosoldevilla .) Date: Thu, 14 Jan 2016 11:41:09 +0100 Subject: [FieldTrip] Fieldtrip tutor WANTED: Coimbra workshop Message-ID: Dear Fieldtrippers, I am organizing a Fieldtrip workshop at Coimbra (Portugal) with talented alumni from Coimbra University, Champalimaud Center for the Unknown and Imperial College of London. I am looking for a highly motivated researcher that would like to be a tutor that available on any of the following dates: - May 9th - 11th - June 6th - 9th The workshop is two and a half days long and a draft of the program can be found here: http://www.fieldtriptoolbox.org/workshop/coimbra There will be around 12-13 people, most of them with EEG and/or MEG experience. The audience has a special interest in connectivity and source space analysis so a tutor with experience on these topics is mandatory. - Tutor activities: 1. Teach one or two lecture sessions. The tutor need to teach two lecture sessions; see program above. Besides the teaching material (slides + video ) is available and will be provided. In addition, the preparation of the lectures includes that the tutor will have a videoconferencing session with the main developers in Nijmegen to ensure that all aspects that are not clear in the slides are resolved. 2. Support hands-on sessions. After each theory session there is a hands-on session using tested tutorial data and code. The last day, the alumni bring their on data and the mission is to help the users with their analysis goals as much as time allows. All costs associated to travel and accommodation are covered (Only restricted to researchers working within Europe). If you are interested and/or you want to know more about it, please do not hesitate to contact me (dlozanosoldevilla at gmail.com). Preparing and teaching in such a workshop is a great opportunity to increase your own skills and to boost your CV! Looking forward to hear from you, Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Jan 15 09:16:20 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 15 Jan 2016 09:16:20 +0100 Subject: [FieldTrip] MEG/EEG FieldTrip toolkit course in Nijmegen: pre-registration now open Message-ID: Dear All, — Please disseminate to PhD students and postdoctoral researchers working with MEG, EEG and ECoG data analysis. --- On April 18-21, 2016 we will host the "Toolkit of Cognitive Neuroscience: advanced data analysis and source modelling of EEG and MEG data" at the Donders Institute in Nijmegen. This intense 4-day toolkit course will teach you advanced MEG and EEG data analysis skills. Preprocessing, frequency analysis, source reconstruction, connectivity and various statistical methods will be covered. The toolkit will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG data set using the FieldTrip toolbox. The lectures and tutoring will be provided by the core FieldTrip development team, and there will also be plenty of opportunity to interact and ask questions to us about your research and data. On the final day you will have the opportunity to work on your own dataset under supervision of the tutors. We can host a limited number of participants. From past experience we expect the course to be oversubscribed, hence we will start with pre-registration. The final selection of the participants will be based on the motivation, background experience and research interests that are provided in the registration form. The deadline for pre-registration is March 1, 2016. More information, including a preliminary program, can be found at http://www.ru.nl/donders/agenda-news/tool-kits-cognitive/toolkit-meg/ Looking forward to welcoming you in Nijmegen, Robert Oostenveld and Jan-Mathijs Schoffelen. ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Radboud University, Nijmegen, The Netherlands Visiting Professor NatMEG - the Swedish National MEG facility Karolinska Institute, Stockholm, Sweden tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/donders skype: r.oostenveld ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri Jan 15 11:18:31 2016 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 15 Jan 2016 11:18:31 +0100 Subject: [FieldTrip] fixed bug in MEG localspheres forward model Message-ID: <8543B5C2-731C-4AEA-9CFE-894B5E35D40D@donders.ru.nl> Dear FieldTrip users, We found (and fixed) a bug in the MEG localspheres forward model, which may have affected your recent analyses. The consequence is that MEG source reconstructions would have been of very poor quaility. This was pointed out to me by Fraincois Tadel (thanks!) who noticed that dipole fits of clean topographies ended up in completely unexpected locations. Also MNE and beamformer results will have been wrong, although there it was less obvious to detect the flaw. I have included the fix in SVN revision 11061, which you can also find on https://github.com/fieldtrip/fieldtrip. If you use the download version from our FTP server: the version that is released this evening will include the fix. Further details can be found on http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3037 Sorry for the inconvenience, Robert PS If you use singlesphere, BEM or singleshell models, you have not been affected by this. From vic.schroeder2 at gmail.com Fri Jan 15 11:26:14 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Fri, 15 Jan 2016 10:26:14 +0000 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: Thank you Tzvetan. 2016-01-03 20:18 GMT+00:00 Tzvetan Popov : > > Dear Victoria, > the system you are working with is already equipped with two orthogonal > planar gradiometer sensors. Thus you should not try to create planar > gradients on the basis of the planar gradients. Yet you might want to use > the magnetometers only. There you can represent the activity as if it was > picked up by planar gradients. Could you please skip the planar > transformation bit and redo your analysis? > FieldTrip provides three types of layouts for the Neuromag system: *NM306all.lay > NM306mag.lay NM306grad.lay*. For example if you want to plot > magnetometers only you’d specify *cfg.layout = 'neuromag306mag.lay’; > cfg.channel = 'MEG*1’*; Here MEG*1 refers to magnetometers and MEG*2 and > MEG*3 would be the two orthogonal planar gradients respectively. Also the > neighbours are provided as* neuromag306cmb_neighb.mat; > neuromag306mag_neighb.mat; neuromag306planar_neighb.ma > *t;. You might consider loading the > structure of your choice directly. > Here is an example tutorial that might help: > http://www.fieldtriptoolbox.org/tutorial/natmeg/timefrequency > Good luck, > tzvetan > > Dear Fieldtrip team, > > I am currently working on data acquired from an elektra system (neuromag). > I have done all the preprocessing and the ft_freqanalysis with the > gradiometers only. I combined the gradiometers to create planar > gradients.However , later when doing the statistics problems occur when i > want to specify the channels. The error tells me that no degrees of freedom > are found for the analysis. However, when i remove the cfg.channel form the > script it runs through without an error. (please see code below). > My question is whether the output of the stastistic is correct without > specifying the channels? If not, does anybody have suggestions how to fix > the problem? > > I have run into similar problems when wanting to plot the time frequency > data from the planar gradients after having used ft_combineplanar. Here i > cannot find a layout file that suits the output of ft_combineplanar. Thus, > i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, > however, the layouts provided by fieldtrip does not fit that number. > Has anybody run into similar problems? Or does anybody know a possible > solution? > > Thank you very much for any suggestions > Victoria > > %combine planar > cfg = []; > cfg.method ='sum'; > %ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > cfg = []; > %cfg.channel = {'MEG'}; > cfg.latency = 'all'; > cfg.frequency = [14.5 16]; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); > > design = zeros(1,size(ComGrad_con.powspctrm,1) + > size(ComGrad_incon.powspctrm,1)); > design(1,1:size(ComGrad_con.powspctrm,1)) = 1; > > design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... > size(ComGrad_incon.powspctrm,1))) = 2; > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Fri Jan 15 12:09:07 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Fri, 15 Jan 2016 11:09:07 +0000 Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: Dear Tzvetan, I did not do any planar transformation with the gradiometers. I only did the ft_combineplanar. Should i also omit that? Cheers Victoria 2016-01-15 10:26 GMT+00:00 victoria schroeder : > Thank you Tzvetan. > > 2016-01-03 20:18 GMT+00:00 Tzvetan Popov : > >> >> Dear Victoria, >> the system you are working with is already equipped with two orthogonal >> planar gradiometer sensors. Thus you should not try to create planar >> gradients on the basis of the planar gradients. Yet you might want to use >> the magnetometers only. There you can represent the activity as if it was >> picked up by planar gradients. Could you please skip the planar >> transformation bit and redo your analysis? >> FieldTrip provides three types of layouts for the Neuromag system: *NM306all.lay >> NM306mag.lay NM306grad.lay*. For example if you want to plot >> magnetometers only you’d specify *cfg.layout = 'neuromag306mag.lay’; >> cfg.channel = 'MEG*1’*; Here MEG*1 refers to magnetometers and MEG*2 and >> MEG*3 would be the two orthogonal planar gradients respectively. Also the >> neighbours are provided as* neuromag306cmb_neighb.mat; >> neuromag306mag_neighb.mat; neuromag306planar_neighb.ma >> *t;. You might consider loading the >> structure of your choice directly. >> Here is an example tutorial that might help: >> http://www.fieldtriptoolbox.org/tutorial/natmeg/timefrequency >> Good luck, >> tzvetan >> >> Dear Fieldtrip team, >> >> I am currently working on data acquired from an elektra system >> (neuromag). I have done all the preprocessing and the ft_freqanalysis with >> the gradiometers only. I combined the gradiometers to create planar >> gradients.However , later when doing the statistics problems occur when i >> want to specify the channels. The error tells me that no degrees of freedom >> are found for the analysis. However, when i remove the cfg.channel form the >> script it runs through without an error. (please see code below). >> My question is whether the output of the stastistic is correct without >> specifying the channels? If not, does anybody have suggestions how to fix >> the problem? >> >> I have run into similar problems when wanting to plot the time frequency >> data from the planar gradients after having used ft_combineplanar. Here i >> cannot find a layout file that suits the output of ft_combineplanar. Thus, >> i cannot specify a cfg.layout. After ft_combineplanar i have 102 channels, >> however, the layouts provided by fieldtrip does not fit that number. >> Has anybody run into similar problems? Or does anybody know a possible >> solution? >> >> Thank you very much for any suggestions >> Victoria >> >> %combine planar >> cfg = []; >> cfg.method ='sum'; >> %ComCon = ft_combineplanar(cfg,FreqCon); >> ComIncon = ft_combineplanar(cfg, FreqIncon); >> >> cfg = []; >> %cfg.channel = {'MEG'}; >> cfg.latency = 'all'; >> cfg.frequency = [14.5 16]; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'ft_statfun_indepsamplesT'; >> cfg.correctm = 'cluster'; >> cfg.clusteralpha = 0.05; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan = 2; >> cfg.tail = 0; >> cfg.clustertail = 0; >> cfg.alpha = 0.025; >> cfg.numrandomization = 500; >> cfg_neighb.method = 'distance'; >> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, data_orig); >> >> design = zeros(1,size(ComGrad_con.powspctrm,1) + >> size(ComGrad_incon.powspctrm,1)); >> design(1,1:size(ComGrad_con.powspctrm,1)) = 1; >> >> design(1,(size(ComGrad_con.powspctrm,1)+1):(size(ComGrad_con.powspctrm,1)+... >> size(ComGrad_incon.powspctrm,1))) = 2; >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Harald.Bornfleth at besa.de Fri Jan 15 14:35:11 2016 From: Harald.Bornfleth at besa.de (Harald Bornfleth) Date: Fri, 15 Jan 2016 14:35:11 +0100 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Message-ID: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Dear Andrew, Thanks for bringing this up. I can try to shed some light on the ICA method used in BESA Research; however, I can not comment on the implementation in FieldTrip. The method behind ICA analysis in BESA Research is the extended infomax ICA algorithm (Lee TW et al.: Independent component analysis using an extended infomax algorithm for mixed sub-Gaussian and super-Gaussian sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very well suited to remove cardiac and powerline artifacts. Depending on the data, it may also be used to remove ocular (blink) and electrode artifacts. To assess whether your artifact removal is trustworthy more information about your processing steps are needed. What types of artifacts are you trying to correct? What segments are you using to determine the artifact topographies and what segments are you finally correcting? Best regards, Harald Dr. Harald Bornfleth Product Manager BESA Research BESA GmbH Freihamer Strasse 18 82166 Graefelfing/Germany http://www.besa.de E: Harald.Bornfleth at besa.de T: +49 89 8980 9968 HRB Munich 109956 CEO: Dr. Tobias Scherg, CFO: Theodor Scherg Director of Research: Dr. Michael Scherg From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Andrew Chang Sent: Sonntag, 10. Januar 2016 21:18 To: fieldtrip at science.ru.nl Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Dear Fieldtrip users, I am wondering whether anyone has compared the performances of the ICA methods among M/EEG toolboxes. Especially, how is the performance of ICA in BESA Research 6.0, compared to Fieldtrip? I have an EEG data set which has been processed in BESA, including removing artifact using ICA. I am wondering whether I can trust it, or I should reprocess it in Fieldtrip. Any comments will be appreciated! Happy new year! Best, Andrew -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ATT00004.txt URL: From michele.scaltritti at gmail.com Fri Jan 15 16:03:18 2016 From: michele.scaltritti at gmail.com (Michele Scaltritti) Date: Fri, 15 Jan 2016 16:03:18 +0100 Subject: [FieldTrip] unexpected boundary effects using Morlet wavelets Message-ID: Dears, I am Michele Scaltritti, and this is my first post on this mailing list. I work on ERPs in the context of psycholinguistics, and I just recently started working with Fieldtrip to perform time-frequency analyses. I am encountering a problem with respect to boundary effects, as these affects time windows that I didn't expect. More precisely, I' running my analysis on epochs going from -1.1s before stimulus onset (0 s), to 4 s afterwards (for a total length of 5.1s). In order to do that, I am using Morlet wavelets of 7 cycles, with 50 milliseconds time-steps. I am estimating frequencies ranging from 10 to 35 Hz. At 10Hz frequency, the length of my wavelet should be 7/10/pi, so around 222 ms. As such, I would expect to be able to estimate frequency power at -800 ms in my epoch (which corresponds to the starting time of what I would like to be my baseline): in fact, I would expect to be able to estimate 10Hz frequency power as soon as the third time-step (150 ms), corresponding to -950 in my epochs. However, I don't get any value for 10Hz frequency at -800 ms. Clearly, my reasoning is wrong, but I can't figure out what I am missing. In the following lines, I'll post the code of the configuration I used to run the frequency decomposition cfg = [] cfg.channel = 'all'; cfg.method = 'wavelet'; cfg.width = 7; cfg.output = 'pow'; cfg.foi = 10:1:35; cfg.toi = -1.1:0.05:4 TF_data = ft_freqanalysis(cfg,data) Thank you very much for the attention, and please excuse eventual gross mistakes in my arguments. michele -------------- next part -------------- An HTML attachment was scrubbed... URL: From fosco.bernasconi at gmail.com Sat Jan 16 15:42:50 2016 From: fosco.bernasconi at gmail.com (fosco bernasconi) Date: Sat, 16 Jan 2016 15:42:50 +0100 Subject: [FieldTrip] Fwd: ft_statfun_actvsblT & ft_timelockstatistics error In-Reply-To: References: Message-ID: Hi all, I would like to identify ECoG electrodes that are active during my task, by comparing the post-stimulus activity vs. the baseline. I would like to do this on LFP (and not on time-frequency data). Unfortunately, I keep having the error "Inappropriate dimord for the statistics function STATFUN_ACTVSBLT.". My cfg.dimord = 'rpt_chan_time'; I am missing something, any suggestion? Thanks a lot in advance! fosco Here my code: datafldtrp= eeglab2fieldtrip(EEG,'preprocessing'); % define intervals: cfg = []; cfg.channel = {'GA1'}; cfg.toilim = [-.2 0]; dataFIC_baseline = ft_redefinetrial(cfg,datafldtrp); cfg = []; cfg.channel = {'GA1'}; cfg.toilim = [0.05 0.25]; dataFIC_activation = ft_redefinetrial(cfg,datafldtrp); cfg = []; cfg.keeptrials = 'yes'; cfg.removemean = 'no'; [timelock_baseline] = ft_timelockanalysis(cfg,dataFIC_baseline); [timelock_activation] = ft_timelockanalysis(cfg,dataFIC_activation); timelock_activation.time = timelock_baseline.time; cfg = []; ntrials = size(timelock_activation.trial,1); design = zeros(2,2*ntrials); design(1,1:ntrials) = 1; design(1,ntrials+1:2*ntrials) = 2; design(2,1:ntrials) = [1:ntrials]; design(2,ntrials+1:2*ntrials) = [1:ntrials]; cfg.design = design; cfg.statistic = 'ft_statfun_actvsblT'; cfg.method = 'montecarlo'; cfg.numrandomization = 500; cfg.parameter = 'trial'; cfg.ivar = 1; cfg.tail = 0; [stat] = ft_timelockstatistics(cfg,timelock_activation,timelock_baseline); -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Sat Jan 16 18:26:53 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Sat, 16 Jan 2016 17:26:53 +0000 Subject: [FieldTrip] plotting neighbours Message-ID: Hi ! I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243* *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243* however what i see is: *Selected channel MEG0741, which has 0 neighbours: * *Selected channel MEG0731, which has 0 neighbours: * *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243* *Selected channel MEG0711, which has 0 neighbours: * *Selected channel MEG0741, which has 0 neighbours: * It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243* or *Selected channel MEG1031, which has 0 neighbours: * Do you have any suggestions why this happen? Are the channels not grouped correctly? Below is the code starting from the time-frequency analysis of the data. Thank you very much Victoria cfg = []; cfg.output = 'pow'; cfg.channel = 'MEGGRAD'; cfg.method = 'mtmconvol'; cfg.taper = 'hanning'; cfg.foi = [2:2:30]; %cfg.keeptrials = 'yes'; for stats keep trials cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec cfg.toi = [-1.3:0.05:1]; cfg.keeptrials = 'yes'; FreqCon = ft_freqanalysis(cfg, Con_clean); FreqIncon = ft_freqanalysis(cfg, Incon_clean); %combine planar cfg = []; cfg.method ='sum'; ComCon = ft_combineplanar(cfg,FreqCon); ComIncon = ft_combineplanar(cfg, FreqIncon); % plot neighbours cfg=[]; cfg.method = 'triangulation'; cfg.layout = 'neuromag306cmb.lay'; ft_neighbourplot(cfg,ComCon) -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Sat Jan 16 19:00:48 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Sat, 16 Jan 2016 19:00:48 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: Dear Victoria, you should remove the ft_combineplanar step from your analysis pipeline. This function takes input from ft_megplanar. The latter is applied only to magnetometers or axial gradiometers. best tzvetan > Hi ! > > I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > > however what i see is: > > Selected channel MEG0741, which has 0 neighbours: > Selected channel MEG0731, which has 0 neighbours: > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > Selected channel MEG0711, which has 0 neighbours: > Selected channel MEG0741, which has 0 neighbours: > > It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > > or > > Selected channel MEG1031, which has 0 neighbours: > > Do you have any suggestions why this happen? Are the channels not grouped correctly? > > Below is the code starting from the time-frequency analysis of the data. > > Thank you very much > Victoria > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEGGRAD'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = [2:2:30]; > %cfg.keeptrials = 'yes'; for stats keep trials > cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec > cfg.toi = [-1.3:0.05:1]; > cfg.keeptrials = 'yes'; > FreqCon = ft_freqanalysis(cfg, Con_clean); > FreqIncon = ft_freqanalysis(cfg, Incon_clean); > > %combine planar > cfg = []; > cfg.method ='sum'; > ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > % plot neighbours > cfg=[]; > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg,ComCon) > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tokimoto at mejiro.ac.jp Sun Jan 17 11:39:24 2016 From: tokimoto at mejiro.ac.jp (Shingo Tokimoto) Date: Sun, 17 Jan 2016 19:39:24 +0900 Subject: [FieldTrip] Cluster-based permutation test from EEGLAB In-Reply-To: References: <535ED12E-E28C-4704-900C-4B3F0A2FB4C8@mejiro.ac.jp> <0AE563A7-9F8A-4EC3-A136-1132CBDB3F41@mejiro.ac.jp> Message-ID: <73BB8BE6-8BC7-40AF-B785-E600CCA77ED6@mejiro.ac.jp> Dear Dr. Tzvetan Popov and FieldTrip users, Thank you for the comment again. I undone the changes, but the same error message appears. The cluster-based permutation test works well for ERP, but it doesn't work for ERSP. Attached is the window of EEGLAB for statistic parameters. I understand you are not familiar with EEGLAB. Could you give me any suggestions for the parameters of FieldTrip statistics? The messages in the command window of Matlab is as follows. Using pre-loaded data. To force rereading data from disk use the 'forceread' flag 1 x 2, paired data, computing T values the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 6 MB Thank you in advance again. ************************************************ Shingo Tokimoto, Ph.D. in Linguistics and Psychology Department of Foreign Languages Mejiro University 4-31-1, Naka-Ochiai, Shinjuku, Tokyo, 161-8539, Japan tokimoto at mejiro.ac.jp ************************************************ On 2016/01/11, at 1:08, Tzvetan Popov wrote: > Dear Shingo, > lets keep it by Tzvetan ;-). I’m not familiar with the way EEGLAB deals with FieldTrip functions at all. So I may not be of any further help. > However as a rule of thumb you should almost never change settings in the FieldTrip functions but provide the appropriate configurations always as cfg.xxx. When you mention your analysis works for ERP I don’t see any reason why it fails with time-freq data. Obviously you have your electrode positions and you were able to generate neighborhood structure. If so the same should work for t-f too. > Maybe if you provide the syntax of your analysis me or others can help you in getting it done. > I will advise to undone any changes you made to the FieldTrip code and try again. Probably a fresh version of EEGLAB, clean math lab path etc. and then do it again. > best > tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Window_EEGLAB.png Type: image/png Size: 79275 bytes Desc: not available URL: From changa5 at mcmaster.ca Sun Jan 17 19:57:03 2016 From: changa5 at mcmaster.ca (Andrew Chang) Date: Sun, 17 Jan 2016 13:57:03 -0500 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) In-Reply-To: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> References: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Message-ID: Hi Dr. Bornfleth, Thanks for your reply very much. I would like to use ICA to remove eye blinks and eye movements, neck movements, as well as cardiac and powerline artifacts. The segment I have is a continuous EEG recording for 10 minutes, which is one block of my experiment including many trials. Before ICA, the segment have been high-pass (0.3 Hz) and low-pass (100 Hz). The components showing activities around the eyes, the back of the neck, and 60 Hz were removed. As for the cardiac artifact, I it is based on visual inspection on the waveform to see whether it looks like an EKG. Any further comments are appreciated! Best, Andrew On Fri, Jan 15, 2016 at 8:35 AM, Harald Bornfleth wrote: > Dear Andrew, > > > > Thanks for bringing this up. I can try to shed some light on the ICA > method used in BESA Research; however, I can not comment on the > implementation in FieldTrip. > > > > The method behind ICA analysis in BESA Research is the extended infomax > ICA algorithm (Lee TW et al.: Independent component analysis using an > extended infomax algorithm for mixed sub-Gaussian and super-Gaussian > sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very > well suited to remove cardiac and powerline artifacts. Depending on the > data, it may also be used to remove ocular (blink) and electrode artifacts. > To assess whether your artifact removal is trustworthy more information > about your processing steps are needed. What types of artifacts are you > trying to correct? What segments are you using to determine the artifact > topographies and what segments are you finally correcting? > > > > Best regards, > > Harald > > > > > > *Dr. Harald Bornfleth* > > Product Manager BESA Research > > > > *BESA GmbH* > > Freihamer Strasse 18 > > 82166 Graefelfing/Germany > > http://www.besa.de > > > > E: Harald.Bornfleth at besa.de > > T: +49 89 8980 9968 > > > > > > HRB Munich 109956 > > CEO: Dr. Tobias Scherg, CFO: Theodor Scherg > > Director of Research: Dr. Michael Scherg > > > > > > > > > > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > mailto:fieldtrip-bounces at science.ru.nl ] *On > Behalf Of *Andrew Chang > *Sent:* Sonntag, 10. Januar 2016 21:18 > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. > Fieldtrip) > > > > Dear Fieldtrip users, > > > > I am wondering whether anyone has compared the performances of the ICA > methods among M/EEG toolboxes. Especially, how is the performance of ICA in > BESA Research 6.0, compared to Fieldtrip? > > I have an EEG data set which has been processed in BESA, including > removing artifact using ICA. I am wondering whether I can trust it, or > I should reprocess it in Fieldtrip. Any comments will be appreciated! > > > > Happy new year! > > > > Best, > > Andrew > > > > -- > > Andrew Chang > Ph.D. Candidate > Auditory Development Lab > > Department of Psychology, Neuroscience & Behaviour > McMaster University > > http://changa5.wordpress.com/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Mon Jan 18 12:38:39 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Mon, 18 Jan 2016 11:38:39 +0000 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: Dear Tzvetan Are you sure about that in the tutorial http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing neuromag data is used and ft_combineplanar is used to combine the gradiometers. This is a paragraph from this tutorial: In fact, we are now plotting the two different gradiometers together. You can see the channel locations being in pairs, one above the other. They are in reality, however, at the same location but oriented differently - radially and axially *with respect to the surface of the helmet*. They can thereby pick up both radial orientations of the magnetic fields. To use them properly for the purpose of plotting, we should therefor combine them first, adding their fields. TFR_left_MEG_comb = ft_combineplanar([],TFR_left_MEG); TFR_right_MEG_comb = ft_combineplanar([],TFR_right_MEG); cfg = []; cfg.baseline = [-0.5 -0.1]; cfg.baselinetype = 'absolute'; cfg.xlim = [0.4 0.8]; cfg.ylim = [15 25]; cfg.zlim = [-4e-24 4e-24]; cfg.marker = 'on'; cfg.layout = 'neuromag306cmb.lay'; figure ; ft_topoplotTFR(cfg, TFR_left_MEG_comb);print -dpng natmeg_freq13.png Thus, it should be possible to use ft_combineplanar for neuromag data. What do you think? Cheers Victoria 2016-01-16 18:00 GMT+00:00 Tzvetan Popov : > Dear Victoria, > you should remove the ft_combineplanar step from your analysis pipeline. > This function takes input from ft_megplanar. The latter is applied only to > magnetometers or axial gradiometers. > > best > tzvetan > > > Hi ! > > I am working with a neuromag system and want to do cluster based > permutation tests with time frequency data. However, before running the > stats i would like to check the clusters which are formed by > ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the > plot and clicking on the channels i would expect to see something like : > > *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, > MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, > MEG1242+1243* > > *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, > MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, > MEG2242+2243* > > however what i see is: > > *Selected channel MEG0741, which has 0 neighbours: * > *Selected channel MEG0731, which has 0 neighbours: * > *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, > MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, > MEG2242+2243* > *Selected channel MEG0711, which has 0 neighbours: * > *Selected channel MEG0741, which has 0 neighbours: * > > It is absolutely random when the correct output occurs. When clicking on a > particular channel it would randomly show me the following results: > > *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, > MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, > MEG1242+1243* > > or > > *Selected channel MEG1031, which has 0 neighbours: * > > Do you have any suggestions why this happen? Are the channels not grouped > correctly? > > Below is the code starting from the time-frequency analysis of the data. > > Thank you very much > Victoria > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEGGRAD'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = [2:2:30]; > %cfg.keeptrials = 'yes'; for stats keep trials > cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window > = 0.5 sec > cfg.toi = [-1.3:0.05:1]; > cfg.keeptrials = 'yes'; > FreqCon = ft_freqanalysis(cfg, Con_clean); > FreqIncon = ft_freqanalysis(cfg, Incon_clean); > > %combine planar > cfg = []; > cfg.method ='sum'; > ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > % plot neighbours > cfg=[]; > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg,ComCon) > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Harald.Bornfleth at besa.de Mon Jan 18 13:49:32 2016 From: Harald.Bornfleth at besa.de (Harald Bornfleth) Date: Mon, 18 Jan 2016 13:49:32 +0100 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) In-Reply-To: References: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Message-ID: Dear Andrew, A couple of questions popped up. 1) The neck movement artifact, is this something with low frequency, or is it a muscle artifact? 2) Did you calculate the ICA on one data screen (e.g. 10 seconds or 20 seconds), or over the whole data set? If you could send us screen shots showing the ICA wave forms and the accompanying topographies, then we could comment on the classification. (In BESA, you right-click on the label of a component and select “Map topography” to show the topography map of that component.) I include my colleague and ICA expert Nicole Ille on CC. Best regards, Harald From: c.andrew123 at gmail.com [mailto:c.andrew123 at gmail.com] On Behalf Of Andrew Chang Sent: 17 January 2016 19:57 To: Harald.Bornfleth at besa.de; FieldTrip discussion list Subject: Re: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Hi Dr. Bornfleth, Thanks for your reply very much. I would like to use ICA to remove eye blinks and eye movements, neck movements, as well as cardiac and powerline artifacts. The segment I have is a continuous EEG recording for 10 minutes, which is one block of my experiment including many trials. Before ICA, the segment have been high-pass (0.3 Hz) and low-pass (100 Hz). The components showing activities around the eyes, the back of the neck, and 60 Hz were removed. As for the cardiac artifact, I it is based on visual inspection on the waveform to see whether it looks like an EKG. Any further comments are appreciated! Best, Andrew On Fri, Jan 15, 2016 at 8:35 AM, Harald Bornfleth > wrote: Dear Andrew, Thanks for bringing this up. I can try to shed some light on the ICA method used in BESA Research; however, I can not comment on the implementation in FieldTrip. The method behind ICA analysis in BESA Research is the extended infomax ICA algorithm (Lee TW et al.: Independent component analysis using an extended infomax algorithm for mixed sub-Gaussian and super-Gaussian sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very well suited to remove cardiac and powerline artifacts. Depending on the data, it may also be used to remove ocular (blink) and electrode artifacts. To assess whether your artifact removal is trustworthy more information about your processing steps are needed. What types of artifacts are you trying to correct? What segments are you using to determine the artifact topographies and what segments are you finally correcting? Best regards, Harald Dr. Harald Bornfleth Product Manager BESA Research BESA GmbH Freihamer Strasse 18 82166 Graefelfing/Germany http://www.besa.de E: Harald.Bornfleth at besa.de T: +49 89 8980 9968 HRB Munich 109956 CEO: Dr. Tobias Scherg, CFO: Theodor Scherg Director of Research: Dr. Michael Scherg From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Andrew Chang Sent: Sonntag, 10. Januar 2016 21:18 To: fieldtrip at science.ru.nl Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) Dear Fieldtrip users, I am wondering whether anyone has compared the performances of the ICA methods among M/EEG toolboxes. Especially, how is the performance of ICA in BESA Research 6.0, compared to Fieldtrip? I have an EEG data set which has been processed in BESA, including removing artifact using ICA. I am wondering whether I can trust it, or I should reprocess it in Fieldtrip. Any comments will be appreciated! Happy new year! Best, Andrew -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon Jan 18 13:59:20 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 Jan 2016 13:59:20 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> Hi Victoria, well if you work with the magnetometers yes. Maybe I misunderstood your previous posts. Yet this configuration from your post below cfg.channel = 'MEGGRAD’; results in time-frequency representation of power on the planar gradiometers only. In that case neither ft_megplanar nor ft_combineplanar are appropriate since the data stems from planar gradiometers. The tutorial you mentioned deals only with the magnetometers thus ft_megplanar and ft_combineplanar are used. best tzvetan > Dear Tzvetan > > Are you sure about that in the tutorial http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing neuromag data is used and ft_combineplanar is used to combine the gradiometers. This is a paragraph from this tutorial: > > In fact, we are now plotting the two different gradiometers together. You can see the channel locations being in pairs, one above the other. They are in reality, however, at the same location but oriented differently - radially and axially with respect to the surface of the helmet. They can thereby pick up both radial orientations of the magnetic fields. To use them properly for the purpose of plotting, we should therefor combine them first, adding their fields. > > TFR_left_MEG_comb = ft_combineplanar([],TFR_left_MEG); > TFR_right_MEG_comb = ft_combineplanar([],TFR_right_MEG); > > cfg = []; > cfg.baseline = [-0.5 -0.1]; > cfg.baselinetype = 'absolute'; > cfg.xlim = [0.4 0.8]; > cfg.ylim = [15 25]; > cfg.zlim = [-4e-24 4e-24]; > cfg.marker = 'on'; > cfg.layout = 'neuromag306cmb.lay'; > > figure; > ft_topoplotTFR(cfg, TFR_left_MEG_comb); > print -dpng natmeg_freq13.png > Thus, it should be possible to use ft_combineplanar for neuromag data. > What do you think? > > Cheers > Victoria > > 2016-01-16 18:00 GMT+00:00 Tzvetan Popov : > Dear Victoria, > you should remove the ft_combineplanar step from your analysis pipeline. This function takes input from ft_megplanar. The latter is applied only to magnetometers or axial gradiometers. > > best > tzvetan > > >> Hi ! >> >> I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : >> >> Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 >> Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 >> >> however what i see is: >> >> Selected channel MEG0741, which has 0 neighbours: >> Selected channel MEG0731, which has 0 neighbours: >> Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 >> Selected channel MEG0711, which has 0 neighbours: >> Selected channel MEG0741, which has 0 neighbours: >> >> It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: >> >> Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 >> >> or >> >> Selected channel MEG1031, which has 0 neighbours: >> >> Do you have any suggestions why this happen? Are the channels not grouped correctly? >> >> Below is the code starting from the time-frequency analysis of the data. >> >> Thank you very much >> Victoria >> >> cfg = []; >> cfg.output = 'pow'; >> cfg.channel = 'MEGGRAD'; >> cfg.method = 'mtmconvol'; >> cfg.taper = 'hanning'; >> cfg.foi = [2:2:30]; >> %cfg.keeptrials = 'yes'; for stats keep trials >> cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec >> cfg.toi = [-1.3:0.05:1]; >> cfg.keeptrials = 'yes'; >> FreqCon = ft_freqanalysis(cfg, Con_clean); >> FreqIncon = ft_freqanalysis(cfg, Incon_clean); >> >> %combine planar >> cfg = []; >> cfg.method ='sum'; >> ComCon = ft_combineplanar(cfg,FreqCon); >> ComIncon = ft_combineplanar(cfg, FreqIncon); >> >> % plot neighbours >> cfg=[]; >> cfg.method = 'triangulation'; >> cfg.layout = 'neuromag306cmb.lay'; >> ft_neighbourplot(cfg,ComCon) >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Mon Jan 18 17:45:22 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Mon, 18 Jan 2016 16:45:22 +0000 Subject: [FieldTrip] plotting neighbours In-Reply-To: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> References: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> Message-ID: Dear Tzvetan I get your point. I am only using that gradiometers. However, in the text which i copied into the previous email it is stated that ft_combineplanar is used for 'plotting the two different gradiometers together'. They mention gradiometers specifically. Also when running the code it is clear that the gradiometers not the magnetometers are combined. This is the resulting matrix when running the tutorial : [image: Inline-Bild 1] With this in mind, can you clarify why the toturial only uses magnetometers? As i understand it , it uses gradiometers. Thank you a lot Victoria 2016-01-18 12:59 GMT+00:00 Tzvetan Popov : > Hi Victoria, > well if you work with the magnetometers yes. Maybe I misunderstood your > previous posts. Yet this configuration from your post below cfg.channel = > 'MEGGRAD’; results in time-frequency representation of power on the planar > gradiometers only. In that case neither ft_megplanar nor ft_combineplanar > are appropriate since the data stems from planar gradiometers. The tutorial > you mentioned deals only with the magnetometers thus ft_megplanar and > ft_combineplanar are used. > > best > tzvetan > > > Dear Tzvetan > > Are you sure about that in the tutorial > http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing neuromag > data is used and ft_combineplanar is used to combine the gradiometers. This > is a paragraph from this tutorial: > > In fact, we are now plotting the two different gradiometers together. You > can see the channel locations being in pairs, one above the other. They are > in reality, however, at the same location but oriented differently - > radially and axially *with respect to the surface of the helmet*. They > can thereby pick up both radial orientations of the magnetic fields. To use > them properly for the purpose of plotting, we should therefor combine them > first, adding their fields. > > TFR_left_MEG_comb = ft_combineplanar([],TFR_left_MEG); > TFR_right_MEG_comb = ft_combineplanar([],TFR_right_MEG); > > cfg = []; > cfg.baseline = [-0.5 -0.1]; > cfg.baselinetype = 'absolute'; > cfg.xlim = [0.4 0.8]; > cfg.ylim = [15 25]; > cfg.zlim = [-4e-24 4e-24]; > cfg.marker = 'on'; > cfg.layout = 'neuromag306cmb.lay'; > figure ; > ft_topoplotTFR(cfg, TFR_left_MEG_comb);print -dpng natmeg_freq13.png > > Thus, it should be possible to use ft_combineplanar for neuromag data. > What do you think? > > Cheers > Victoria > > 2016-01-16 18:00 GMT+00:00 Tzvetan Popov : > >> Dear Victoria, >> you should remove the ft_combineplanar step from your analysis pipeline. >> This function takes input from ft_megplanar. The latter is applied only to >> magnetometers or axial gradiometers. >> >> best >> tzvetan >> >> >> Hi ! >> >> I am working with a neuromag system and want to do cluster based >> permutation tests with time frequency data. However, before running the >> stats i would like to check the clusters which are formed by >> ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the >> plot and clicking on the channels i would expect to see something like : >> >> *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, >> MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, >> MEG1242+1243* >> >> *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, >> MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, >> MEG2242+2243* >> >> however what i see is: >> >> *Selected channel MEG0741, which has 0 neighbours: * >> *Selected channel MEG0731, which has 0 neighbours: * >> *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, >> MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, >> MEG2242+2243* >> *Selected channel MEG0711, which has 0 neighbours: * >> *Selected channel MEG0741, which has 0 neighbours: * >> >> It is absolutely random when the correct output occurs. When clicking on >> a particular channel it would randomly show me the following results: >> >> *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, >> MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, >> MEG1242+1243* >> >> or >> >> *Selected channel MEG1031, which has 0 neighbours: * >> >> Do you have any suggestions why this happen? Are the channels not grouped >> correctly? >> >> Below is the code starting from the time-frequency analysis of the data. >> >> Thank you very much >> Victoria >> >> cfg = []; >> cfg.output = 'pow'; >> cfg.channel = 'MEGGRAD'; >> cfg.method = 'mtmconvol'; >> cfg.taper = 'hanning'; >> cfg.foi = [2:2:30]; >> %cfg.keeptrials = 'yes'; for stats keep trials >> cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time >> window = 0.5 sec >> cfg.toi = [-1.3:0.05:1]; >> cfg.keeptrials = 'yes'; >> FreqCon = ft_freqanalysis(cfg, Con_clean); >> FreqIncon = ft_freqanalysis(cfg, Incon_clean); >> >> %combine planar >> cfg = []; >> cfg.method ='sum'; >> ComCon = ft_combineplanar(cfg,FreqCon); >> ComIncon = ft_combineplanar(cfg, FreqIncon); >> >> % plot neighbours >> cfg=[]; >> cfg.method = 'triangulation'; >> cfg.layout = 'neuromag306cmb.lay'; >> ft_neighbourplot(cfg,ComCon) >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: Combineplanar.PNG Type: image/png Size: 38714 bytes Desc: not available URL: From mail at philipp-ruhnau.de Mon Jan 18 18:00:59 2016 From: mail at philipp-ruhnau.de (Philipp Ruhnau) Date: Mon, 18 Jan 2016 18:00:59 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: Message-ID: Dear Victoria, I think there might be something odd with the channel selection in your data (or maybe also something that happens in ft_neighborplot) as I see it you have two options 1) I would instead suggest to use ft_prepare neighbors with your data as input cfg = [] cfg.method = ‘triangulation’ cfg.feedback = ‘yes’ % with this you get the feedback plot neigh = ft_prepare_neighbours(cfg, your_data) I am not entirely sure which layout the function uses if you feed in the default layout (which should be fine though), but I think it still uses the data’s for me clicking in the function didn’t work properly, but I think that is a different (gui?) issue, more importantly however the graphical layout and the labels that are grouped make sense that’s also true for what you posted. the only thing odd there is that your neighbor-structure still has magnetometers (MEG***1) that should have been removed, thus my hunch that they are somehow still in the data you feed in to ft_neighbourplot [i just quickly try and I can to a certain extend replicate your problem, but not fully as clicking doesn’t work…but also all the magnetometers with 0 neighbours] and as Tzvetan said, one magnetometer and two gradiometers are in the same position, so I would expect an alternating output between, say, MEG1031 and MEG1032+1033 the easiest thing you can try is use ft_selectdata again before you create the neighbors cfg = []; cfg.channel = ‘MEGGRAD’; data = ft_selectdata(cfg, data) just as a check, if your problem vanishes, the mags were still in there somewhere. 2) just load the default/use the layout field with the function above without the data input. then for me the plotting works and the output is like you predicted cfg = [] cfg.method = ‘triangulation’ cfg.feedback = ‘yes’ % with this you get the feedback plot cfg.layout = ‘neuromag306cmb.lay' neigh = ft_prepare_neighbours(cfg) as for the whether you should use ft_combineplanar. as a neuromag user myself I always use it for plotting but also for statistics, similar to what the wiki says, so I’m a little confused there too. of course you can plot them each of course. I don’t think you need to specify the combination method there though, as ‘sum’ is default for power. cheers philipp > On 16 Jan 2016, at 18:26, victoria schroeder wrote: > > Hi ! > > I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like : > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > > however what i see is: > > Selected channel MEG0741, which has 0 neighbours: > Selected channel MEG0731, which has 0 neighbours: > Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243 > Selected channel MEG0711, which has 0 neighbours: > Selected channel MEG0741, which has 0 neighbours: > > It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results: > > Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243 > > or > > Selected channel MEG1031, which has 0 neighbours: > > Do you have any suggestions why this happen? Are the channels not grouped correctly? > > Below is the code starting from the time-frequency analysis of the data. > > Thank you very much > Victoria > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEGGRAD'; > cfg.method = 'mtmconvol'; > cfg.taper = 'hanning'; > cfg.foi = [2:2:30]; > %cfg.keeptrials = 'yes'; for stats keep trials > cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec > cfg.toi = [-1.3:0.05:1]; > cfg.keeptrials = 'yes'; > FreqCon = ft_freqanalysis(cfg, Con_clean); > FreqIncon = ft_freqanalysis(cfg, Incon_clean); > > %combine planar > cfg = []; > cfg.method ='sum'; > ComCon = ft_combineplanar(cfg,FreqCon); > ComIncon = ft_combineplanar(cfg, FreqIncon); > > % plot neighbours > cfg=[]; > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg,ComCon) > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon Jan 18 18:57:57 2016 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 Jan 2016 18:57:57 +0100 Subject: [FieldTrip] plotting neighbours In-Reply-To: References: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> Message-ID: <7B5CC5BE-033A-41D6-8112-331FE3B71580@uni-konstanz.de> Hi Victoria, oopsy, I think I confused you dramatically. I’m sorry for this. You are right I was only scrolling up to the part where the mags were analyzed. As for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can threat them separately, as I was naively thinking as non-neuormag user, but indeed combination of both is recommended as I have now learned :-)(thanks Phillip). I ran the following steps and I guess this should work for you. best tzvetan %% cfg = []; ComCon = ft_combineplanar(cfg,FreqCon); %% cfg = [] cfg.method = 'triangulation'; cfg.layout = 'neuromag306cmb.lay'; cfg.senstype = 'MEG'; neighbours = ft_prepare_neighbours(cfg, ComCon) %% % plot neighbours cfg=[]; cfg.neighbours = neighbours; cfg.layout = 'neuromag306cmb.lay'; ft_neighbourplot(cfg); -------------- next part -------------- An HTML attachment was scrubbed... URL: From jim.f.cav at gmail.com Mon Jan 18 20:47:45 2016 From: jim.f.cav at gmail.com (Jim Cavanagh) Date: Mon, 18 Jan 2016 12:47:45 -0700 Subject: [FieldTrip] Restrict source reconstruction to gray matter: Any updates? Message-ID: Has there been any followup on this thread? I'm finding it rather difficult to constrain the source projection to grey matter only - surely someone else has tried this using FT? http://mailman.science.ru.nl/pipermail/fieldtrip/2012-March/004984.html -- Jim Cavanagh Assistant Professor University of New Mexico https://sites.google.com/site/jcavanaghunm/home -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Tue Jan 19 15:35:00 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Tue, 19 Jan 2016 15:35:00 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de> Dear community, My name is Laith Hamid and I am working in the University Medical Complex of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and seizures. Currently I am analysing an EEG data set that was recorded using a 256-channel EGI system and I wanted to ask whether you have a standard BEM or FEM head model that extends enough downwards to accomodate all 256 electrodes. The current standard BEM model in the template folder of Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. Thank you very much in advance for your help! Best, Laith -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Jan 19 16:16:54 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 19 Jan 2016 16:16:54 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps In-Reply-To: <0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de> References: <0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de> Message-ID: Dear Laith, thanks for your question. You could refer to a factory schematic layout such as the one in figure 4 of this publication: http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract and subsequently use the function ft_prepare_layout to manually track the points of the custom design on your own (if you dont want to wait for somebody from the FT to do the same for you). cfg = []; cfg.image = 'figure4_layout_256_Frontiers.png'; lay = ft_prepare_layout(cfg); The following tutorial describes the procedure in more details: http://www.fieldtriptoolbox.org/tutorial/layout Please do not hesitate to get in touch with me for this and other matters. All the best Cris Micheli On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid wrote: > Dear community, > > My name is Laith Hamid and I am working in the University Medical Complex > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > seizures. Currently I am analysing an EEG data set that was recorded using > a 256-channel EGI system and I wanted to ask whether you have a standard > BEM or FEM head model that extends enough downwards to accomodate all 256 > electrodes. The current standard BEM model in the template folder of > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > Thank you very much in advance for your help! > > Best, > > Laith > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Tue Jan 19 17:41:48 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Tue, 19 Jan 2016 17:41:48 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de> Dear Cris, thank you very much for your answer. I am refering to an issue that was discussed in this thread from April 2013: [FieldTrip] source analysis EEG data without MRI The thread however does not offer a segmentation or head model for download. Some electrodes in the EGI 256-electrodes cap are placed on the cheeks or on the back of the neck and these areas are not modeled by the standard BEM skin compartment in the standard BEM model. My question was about a standard segmentation that extends the skin (and skull) compartment downwards to allow these electrodes to sit on the nodes of the skin mesh. Best, Laith -------------- next part -------------- An HTML attachment was scrubbed... URL: From aishwaryaselvaraj1708 at gmail.com Tue Jan 19 17:52:55 2016 From: aishwaryaselvaraj1708 at gmail.com (aishwarya selvaraj) Date: Tue, 19 Jan 2016 16:52:55 +0000 Subject: [FieldTrip] Source Localisation Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> Hi guys, I'm currently working on source localization of EEG signals . Im very new to it . Can Anyone provide any inputs ?? It would be of great help . -- Regards, Aishwarya -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Homolle at donders.ru.nl Tue Jan 19 18:06:13 2016 From: S.Homolle at donders.ru.nl (=?iso-8859-1?Q?Hom=F6lle=2C_S=2E_=28Simon=29?=) Date: Tue, 19 Jan 2016 17:06:13 +0000 Subject: [FieldTrip] Source Localisation In-Reply-To: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> References: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> Message-ID: <2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl> Dear Aishwarya, Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. My recommended start would be: http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate Hopefully this provides you good start working with EEG source reconstruction Best regards, Simon Homölle PhD Candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Phone: +31-(0)24-36-65059 ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] Sent: Tuesday, January 19, 2016 5:52 PM To: fieldtrip, donders Subject: [FieldTrip] Source Localisation Hi guys, I'm currently working on source localization of EEG signals . Im very new to it . Can Anyone provide any inputs ?? It would be of great help . -- Regards, Aishwarya -------------- next part -------------- An HTML attachment was scrubbed... URL: From vic.schroeder2 at gmail.com Tue Jan 19 18:49:21 2016 From: vic.schroeder2 at gmail.com (victoria schroeder) Date: Tue, 19 Jan 2016 17:49:21 +0000 Subject: [FieldTrip] plotting neighbours In-Reply-To: <7B5CC5BE-033A-41D6-8112-331FE3B71580@uni-konstanz.de> References: <251E09FD-F885-4A5E-83B7-60AA33531A2B@uni-konstanz.de> <7B5CC5BE-033A-41D6-8112-331FE3B71580@uni-konstanz.de> Message-ID: Thank you very much Philipp and Tzvetan! Things have become much clearer now. I would like to follow up with a very related question. I am trying to replicate the analysis for the cluster based permutation test using the code and the data provided. However, i run into two problems here First, i get the following error if i use the original code: Attempted to access cfg.frequency(2); index out of bounds because numel(cfg.frequency)=1. Error in ft_freqstatistics (line 187) cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. However, then no significant clusters are found. Which becomes clear when trying to plot the cluster or by looking at the output of ft_freqstatistics. Does the change in the code , change the output? How can i avoid the error mentioned above and still get the same output from ft_freqstatistics as the one provided on the webpage? The relevant section of the toturial is provided below. Thank you! Victoria Permutation test Now, run *ft_freqstatistics * to compare freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, the following configuration is identical to the configuration that was used for comparing event-related averages in the cluster-based permutation tests on event related fields tutorial . Also see this tutorial for a detailed explanation of all the configuration settings. You can read more about the *ft_prepare_neighbours * function in the FAQ's . To load the planar gradient TFRs (also available on the FieldTrip FTP servers,freqFIC_planar_cmb.mat and freqFC_planar_cmb.mat ), use: load freqFIC_planar_cmb load freqFC_planar_cmb cfg = []; cfg.channel = {'MEG', '-MLP31', '-MLO12'}; cfg.latency = 'all'; cfg.frequency = 20; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; % prepare_neighbours determines what sensors may form clusters cfg_neighb.method = 'distance'; cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + size(freqFC_planar_cmb.powspctrm,1)); design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... size(freqFC_planar_cmb.powspctrm,1))) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > Hi Victoria, > > oopsy, I think I confused you dramatically. I’m sorry for this. You are > right I was only scrolling up to the part where the mags were analyzed. As > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > threat them separately, as I was naively thinking as non-neuormag user, but > indeed combination of both is recommended as I have now learned :-)(thanks > Phillip). I ran the following steps and I guess this should work for you. > best > tzvetan > > %% > cfg = []; > ComCon = ft_combineplanar(cfg,FreqCon); > %% > cfg = [] > cfg.method = 'triangulation'; > cfg.layout = 'neuromag306cmb.lay'; > cfg.senstype = 'MEG'; > neighbours = ft_prepare_neighbours(cfg, ComCon) > %% > % plot neighbours > cfg=[]; > cfg.neighbours = neighbours; > cfg.layout = 'neuromag306cmb.lay'; > ft_neighbourplot(cfg); > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Jan 19 20:50:24 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 19 Jan 2016 20:50:24 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps In-Reply-To: <61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de> References: <61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de> Message-ID: Dear Laith, this might be possible if you have the subject-specific MRI by following the tutorial here: http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem and using the function ft_prepare_mesh and the tutorial command: cfg=[]; cfg.tissue={'brain','skull','scalp'}; cfg.numvertices = [3000 2000 1000]; bnd=ft_prepare_mesh(cfg,segmentedmri); which uses the segmented MRI (see tutorial). The bnd(3) variable should contain your triangulated surface with 1000 vertices. Let me know if that works. Of course you should see the skin and the neck in the original MRI. If you do not have an anatomical MRI that extends down to the chin you could try with a template, such as this: ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri and the corresponding segmented version ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat This goes down to the chin. Then you take care of rearranging the position of the EEG electrodes according to this: http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel I hope this helped Cris On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid wrote: > Dear Cris, > > thank you very much for your answer. I am refering to an issue that was > discussed in this thread from April 2013: > > > [FieldTrip] source analysis EEG data without MRI > > > The thread however does not offer a segmentation or head model for > download. Some electrodes in the EGI 256-electrodes cap are placed on the > cheeks or on the back of the neck and these areas are not modeled by the > standard BEM skin compartment in the standard BEM model. My question was > about a standard segmentation that extends the skin (and skull) compartment > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > Best, > Laith > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From munsif.jatoi at gmail.com Wed Jan 20 05:17:12 2016 From: munsif.jatoi at gmail.com (Munsif Jatoi) Date: Wed, 20 Jan 2016 12:17:12 +0800 Subject: [FieldTrip] Source Localisation In-Reply-To: <2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl> References: <3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl> <2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl> Message-ID: Dear Aishwarya, Please refer to main help tutorials. Also, you can find out the survey papers written in this area. For more, SPM website can provide good help. Best, Munsif. On Wed, Jan 20, 2016 at 1:06 AM, Homölle, S. (Simon) < S.Homolle at donders.ru.nl> wrote: > Dear Aishwarya, > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > My recommended start would be: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > Hopefully this provides you good start working with EEG source > reconstruction > > Best regards, > > Simon Homölle > PhD Candidate > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Phone: +31-(0)24-36-65059 > ------------------------------ > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > *Sent:* Tuesday, January 19, 2016 5:52 PM > *To:* fieldtrip, donders > *Subject:* [FieldTrip] Source Localisation > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Munsif Ali H.Jatoi, Ph D Scholar, Centre for Intelligent Signals and Imaging Research, Universiti Teknologi PETRONAS, Malaysia. http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: From olga.v.sysoeva at gmail.com Wed Jan 20 11:36:16 2016 From: olga.v.sysoeva at gmail.com (Olga Sysoeva) Date: Wed, 20 Jan 2016 13:36:16 +0300 Subject: [FieldTrip] problems with mri interpolation Message-ID: Dear Fieldtrippers, I'm encounter the problem with MRI interpolation and reslicing using FT_VOLUMERESLICE. I have read my MRI from fif.file and this mri variable contains mri_K0012.unit, 'm' mri_K0012.dim, [432, 512, 180] mri_K0012.anatomy, <432, 512, 180 int16> mri_K0012.hdr, (1*1 structure) mri_K0012.transform, (4*4 double) mri_K0012.coordsys 'neuromag'. Than I used mri = ft_volumereslice([], mri); the output is “the input is volume data with dimensions [432 512 180] reslicing from [432 512 180] to [256 256 256] the input is volume data with dimensions [256 256 256] the input is volume data with dimensions [432 512 180] selecting subvolume of 0.0% reslicing and interpolating anatomy interpolating ??? Attempted to access sel(1); index out of bounds because numel(sel)=0. Error in ==> ft_sourceinterpolate>my_interpn at 663 ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ==> ft_sourceinterpolate at 583 av( sel) = my_interpn(fv, ax(sel), ay(sel), az(sel), cfg.interpmethod, cfg.feedback); Error in ==> ft_volumereslice at 176 resliced = ft_sourceinterpolate(tmpcfg, mri, resliced);” I'm using matlab 7.6.0 (R2008a) and recently downloaded fieltrip (also in my previous version of 2013 the error was the same). I'd be thankful for the comments. Best Regards, Olga. P.S.Actually, I can project my sources meaningfully into not interpolated MRI, altoough the images are plotted upside down. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Wed Jan 20 13:39:30 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Wed, 20 Jan 2016 13:39:30 +0100 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1@mail.uni-kiel.de> Dear Cris, thank you very much for your answers yesterday. The segmentedmri contained 'white', 'grey' and 'csf' so I needed to repeat the segmentation using 'brain', 'skull' and 'scalp' as described in the tutorial "Creating a BEM volume conduction model of the head for source-reconstruction of EEG data" and everything worked smoothly afterwards. The problem is solved now. Best, Laith -------------- next part -------------- An HTML attachment was scrubbed... URL: From RICHARDS at mailbox.sc.edu Wed Jan 20 15:39:13 2016 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Wed, 20 Jan 2016 14:39:13 +0000 Subject: [FieldTrip] Standard BEM or FEM models for use with 256-electrode EEG data recorded with EGI caps (Laith Hamid) Message-ID: Laith: I have a “neurodevelopmental MRI database” (Richards, Sanchez et al., 2015; see my www site) that has average MRI templates that could be used. Each average has the whole head down to about the top of the neck. I did these purposely since I use EEG recording and the MNI template did not even go down far enough for the EGI 128 channel net. The database has average MRI templates for head (T1, T2) and brain. I also have FEM segmented heads for the entire head that could be used for this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, scalp), but ironically, I cut these off about 10% below the EGI 128 channel electrodes. However, you could use the three inner compartments for this and just add the rest of the head below the compartment—or use the whole-head FEM as is for a FEM-model, or use the segmented area below the skull for a whole-head BEM model. I also have average 128-channel EGI electrodes for each template. Additionally, the “developmental” part of the “neurodevelopmental MRI database” is that I have these for a wide range of ages (all ages?). I have a average for young adults (20-24 yrs), and average templates and FEM/BEM models for groups from 3 months through adulthood, and into late adulthood. So if you have specific neuro-pediatric applications you might be interested in using an age appropriate MRI average template rather than an adult template. See my www site for journal article references re this, and http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ Finally… I have been using these head models for FT-based FEM and BEM models. Possibly some of the actually field trip models I have would be useful to you. Some of the parts of the model do not use the electrodes (e.g., grid-dipoles, head-model) whereas the final models (leadfield) requires the electrode locations. The database also includes “virtual” electrodes for the 10-10 system, which might be used to generate the 256 channel locations by knowing the relation between the 10-10 system and the EGI system based on EGI ELP files for the 256 channels. John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: richards-john at sc.edu HTTP: jerlab.psych.sc.edu *********************************************** >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 19 Jan 2016 15:35:00 +0100 >From: Laith Hamid >To: fieldtrip at science.ru.nl >Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> >Content-Type: text/plain; charset="us-ascii" > > > >Dear community, > >My name is Laith Hamid and I am working in the University Medical >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic >spikes and seizures. Currently I am analysing an EEG data set that was >recorded using a 256-channel EGI system and I wanted to ask whether you >have a standard BEM or FEM head model that extends enough downwards to >accomodate all 256 electrodes. The current standard BEM model in the >template folder of Fieldtrip isn't appropriate for source analysis of >256-channel EGI data. > >Thank you very much in advance for your help! > >Best, > >Laith From saeedzahran at hotmail.com Wed Jan 20 18:37:32 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Wed, 20 Jan 2016 19:37:32 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 In-Reply-To: References: Message-ID: Dear Fieldtrip community, I define the volume conductor as: vol = []; vol.bnd(1).pnt=skinpnt vol.bnd(1).tri=skinf vol.bnd(2).pnt=uteruspnt vol.bnd(2).tri=uterusf vol.bnd(3).pnt=uterinecontentpnt vol.bnd(3).tri=uterinecontentf vol.cond = c; But it result with the below error: Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); Thank you very much in advance for your help! Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 18 > To: fieldtrip at science.ru.nl > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 3. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 4. Source Localisation (aishwarya selvaraj) > 5. Re: Source Localisation (Hom?lle) > 6. Re: plotting neighbours (victoria schroeder) > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 8. Re: Source Localisation (Munsif Jatoi) > 9. problems with mri interpolation (Olga Sysoeva) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 19 Jan 2016 15:35:00 +0100 > From: Laith Hamid > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear community, > > My name is Laith Hamid and I am working in the University Medical > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and seizures. Currently I am analysing an EEG data set that was > recorded using a 256-channel EGI system and I wanted to ask whether you > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); model that extends enough downwards to > accomodate all 256 electrodes. The current standard BEM model in the > template folder of Fieldtrip isn't appropriate for source analysis of > 256-channel EGI data. > > Thank you very much in advance for your help! > > Best, > > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Tue, 19 Jan 2016 16:16:54 +0100 > From: Cristiano Micheli > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > thanks for your question. You could refer to a factory schematic layout > such as the one in figure 4 of this publication: > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > and subsequently use the function ft_prepare_layout to manually track the > points of the custom design on your own (if you dont want to wait for > somebody from the FT to do the same for you). > > cfg = []; > cfg.image = 'figure4_layout_256_Frontiers.png'; > lay = ft_prepare_layout(cfg); > > The following tutorial describes the procedure in more details: > http://www.fieldtriptoolbox.org/tutorial/layout > > Please do not hesitate to get in touch with me for this and other matters. > > All the best > Cris Micheli > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > wrote: > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical Complex > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > seizures. Currently I am analysing an EEG data set that was recorded using > > a 256-channel EGI system and I wanted to ask whether you have a standard > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > electrodes. The current standard BEM model in the template folder of > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Tue, 19 Jan 2016 17:41:48 +0100 > From: Laith Hamid > To: Fieldtrip > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear Cris, > > thank you very much for your answer. I am refering to an issue that was > discussed in this thread from April 2013: > > [FieldTrip] source analysis EEG data without MRI > > The thread however does not offer a segmentation or head model for > download. Some electrodes in the EGI 256-electrodes cap are placed on > the cheeks or on the back of the neck and these areas are not modeled by > the standard BEM skin compartment in the standard BEM model. My question > was about a standard segmentation that extends the skin (and skull) > compartment downwards to allow these electrodes to sit on the nodes of > the skin mesh. > > Best, > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Tue, 19 Jan 2016 16:52:55 +0000 > From: aishwarya selvaraj > To: "fieldtrip, donders" > Subject: [FieldTrip] Source Localisation > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 5 > Date: Tue, 19 Jan 2016 17:06:13 +0000 > From: Hom?lle, S. (Simon) > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Aishwarya, > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > My recommended start would be: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > Hopefully this provides you good start working with EEG source reconstruction > > Best regards, > > Simon Hom?lle > PhD Candidate > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Phone: +31-(0)24-36-65059 > ________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > Sent: Tuesday, January 19, 2016 5:52 PM > To: fieldtrip, donders > Subject: [FieldTrip] Source Localisation > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 6 > Date: Tue, 19 Jan 2016 17:49:21 +0000 > From: victoria schroeder > To: FieldTrip discussion list > Subject: Re: [FieldTrip] plotting neighbours > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Thank you very much Philipp and Tzvetan! > > Things have become much clearer now. > > I would like to follow up with a very related question. I am trying to > replicate the analysis for the cluster based permutation test using the > code and the data provided. However, i run into two problems here > > First, i get the following error if i use the original code: > Attempted to access cfg.frequency(2); index out of bounds because > numel(cfg.frequency)=1. > > Error in ft_freqstatistics (line 187) > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > However, then no significant clusters are found. Which becomes clear when > trying to plot the cluster or by looking at the output of > ft_freqstatistics. > > Does the change in the code , change the output? How can i avoid the error > mentioned above and still get the same output from ft_freqstatistics as the > one provided on the webpage? > > > The relevant section of the toturial is provided below. > Thank you! > > Victoria > > Permutation test > > Now, run *ft_freqstatistics > * to compare > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > the following configuration is identical to the configuration that was used > for comparing event-related averages in the cluster-based permutation tests > on event related fields tutorial > . > Also see this tutorial > for > a detailed explanation of all the configuration settings. You can read more > about the *ft_prepare_neighbours > * function > in the FAQ's > . > > To load the planar gradient TFRs (also available on the FieldTrip FTP > servers,freqFIC_planar_cmb.mat > > and freqFC_planar_cmb.mat > ), > use: > > load freqFIC_planar_cmb > load freqFC_planar_cmb > > cfg = []; > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > cfg.latency = 'all'; > cfg.frequency = 20; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > % prepare_neighbours determines what sensors may form clusters > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > size(freqFC_planar_cmb.powspctrm,1)); > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > cfg.design = design; > cfg.ivar = 1; > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > > > > Hi Victoria, > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > right I was only scrolling up to the part where the mags were analyzed. As > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > threat them separately, as I was naively thinking as non-neuormag user, but > > indeed combination of both is recommended as I have now learned :-)(thanks > > Phillip). I ran the following steps and I guess this should work for you. > > best > > tzvetan > > > > %% > > cfg = []; > > ComCon = ft_combineplanar(cfg,FreqCon); > > %% > > cfg = [] > > cfg.method = 'triangulation'; > > cfg.layout = 'neuromag306cmb.lay'; > > cfg.senstype = 'MEG'; > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > %% > > % plot neighbours > > cfg=[]; > > cfg.neighbours = neighbours; > > cfg.layout = 'neuromag306cmb.lay'; > > ft_neighbourplot(cfg); > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 7 > Date: Tue, 19 Jan 2016 20:50:24 +0100 > From: Cristiano Micheli > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > this might be possible if you have the subject-specific MRI by following > the tutorial here: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > and using the function ft_prepare_mesh and the tutorial command: > > cfg=[]; > cfg.tissue={'brain','skull','scalp'}; > cfg.numvertices = [3000 2000 1000]; > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > contain your triangulated surface with 1000 vertices. Let me know if that > works. Of course you should see the skin and the neck in the original MRI. > > If you do not have an anatomical MRI that extends down to the chin you > could try with a template, such as this: > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > and the corresponding segmented version > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > This goes down to the chin. Then you take care of rearranging the position > of the EEG electrodes according to this: > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > I hope this helped > Cris > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > wrote: > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > cheeks or on the back of the neck and these areas are not modeled by the > > standard BEM skin compartment in the standard BEM model. My question was > > about a standard segmentation that extends the skin (and skull) compartment > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > Best, > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 8 > Date: Wed, 20 Jan 2016 12:17:12 +0800 > From: Munsif Jatoi > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Aishwarya, > > Please refer to main help tutorials. > > Also, you can find out the survey papers written in this area. For more, > SPM website can provide good help. > > Best, > Munsif. > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > S.Homolle at donders.ru.nl> wrote: > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source > > reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ------------------------------ > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > *To:* fieldtrip, donders > > *Subject:* [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > Munsif Ali H.Jatoi, > > Ph D Scholar, > Centre for Intelligent Signals and Imaging Research, > Universiti Teknologi PETRONAS, > Malaysia. > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 9 > Date: Wed, 20 Jan 2016 13:36:16 +0300 > From: Olga Sysoeva > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] problems with mri interpolation > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > > I'm encounter the problem with MRI interpolation and reslicing using > > FT_VOLUMERESLICE. > > I have read my MRI from fif.file and this mri variable contains > > mri_K0012.unit, 'm' > > mri_K0012.dim, [432, 512, 180] > > mri_K0012.anatomy, <432, 512, 180 int16> > > mri_K0012.hdr, (1*1 structure) > > mri_K0012.transform, (4*4 double) > > mri_K0012.coordsys 'neuromag'. > > > Than I used > > > mri = ft_volumereslice([], mri); > > > the output is > > > ?the input is volume data with dimensions [432 > 512 180] > > reslicing from [432 512 180] to [256 256 256] > > the input is volume data with dimensions [256 > 256 256] > > the input is volume data with dimensions [432 > 512 180] > > selecting subvolume of 0.0% > > reslicing and interpolating anatomy > > interpolating > > ??? Attempted to access sel(1); index out of > bounds because numel(sel)=0. > > > Error in ==> ft_sourceinterpolate>my_interpn > at 663 > > ft_progress(sel(1)/num, 'interpolating > %.1f%%\n', 100*sel(1)/num); > > > Error in ==> ft_sourceinterpolate at 583 > > av( sel) = my_interpn(fv, ax(sel), > ay(sel), az(sel), cfg.interpmethod, > > cfg.feedback); > > > Error in ==> ft_volumereslice at 176 > > resliced = ft_sourceinterpolate(tmpcfg, mri, > resliced);? > > > I'm using matlab 7.6.0 (R2008a) and recently > downloaded fieltrip (also in my previous version of 2013 the error > was the same). > > > I'd be thankful for the comments. > > > Best Regards, > > Olga. > > P.S.Actually, I can project my sources > meaningfully into not interpolated MRI, altoough the images are > plotted upside down. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 18 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jan 21 09:16:55 2016 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 21 Jan 2016 08:16:55 +0000 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 In-Reply-To: References: Message-ID: Saeed, are you using 0 or 1 indexing for your triangles? You probably want to use 1 indexing. Best, Jan-Mathijs On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: Dear Fieldtrip community, I define the volume conductor as: vol = []; vol.bnd(1).pnt=skinpnt vol.bnd(1).tri=skinf vol.bnd(2).pnt=uteruspnt vol.bnd(2).tri=uterusf vol.bnd(3).pnt=uterinecontentpnt vol.bnd(3).tri=uterinecontentf vol.cond = c; But it result with the below error: Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); Thank you very much in advance for your help! Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 18 > To: fieldtrip at science.ru.nl > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 3. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 4. Source Localisation (aishwarya selvaraj) > 5. Re: Source Localisation (Hom?lle) > 6. Re: plotting neighbours (victoria schroeder) > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Cristiano Micheli) > 8. Re: Source Localisation (Munsif Jatoi) > 9. problems with mri interpolation (Olga Sysoeva) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 19 Jan 2016 15:35:00 +0100 > From: Laith Hamid > > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear community, > > My name is Laith Hamid and I am working in the University Medical > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and seizures. Currently I am analysing an EEG data set that was > recorded using a 256-channel EGI system and I wanted to ask whether you > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); Error in ft_headmodel_bemcp (line 101) vol = triangle4pt(vol); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 91) vol = ft_prepare_headmodel(cfg, vol); model that extends enough downwards to > accomodate all 256 electrodes. The current standard BEM model in the > template folder of Fieldtrip isn't appropriate for source analysis of > 256-channel EGI data. > > Thank you very much in advance for your help! > > Best, > > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Tue, 19 Jan 2016 16:16:54 +0100 > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > thanks for your question. You could refer to a factory schematic layout > such as the one in figure 4 of this publication: > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > and subsequently use the function ft_prepare_layout to manually track the > points of the custom design on your own (if you dont want to wait for > somebody from the FT to do the same for you). > > cfg = []; > cfg.image = 'figure4_layout_256_Frontiers.png'; > lay = ft_prepare_layout(cfg); > > The following tutorial describes the procedure in more details: > http://www.fieldtriptoolbox.org/tutorial/layout > > Please do not hesitate to get in touch with me for this and other matters. > > All the best > Cris Micheli > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > wrote: > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical Complex > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > seizures. Currently I am analysing an EEG data set that was recorded using > > a 256-channel EGI system and I wanted to ask whether you have a standard > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > electrodes. The current standard BEM model in the template folder of > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Tue, 19 Jan 2016 17:41:48 +0100 > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear Cris, > > thank you very much for your answer. I am refering to an issue that was > discussed in this thread from April 2013: > > [FieldTrip] source analysis EEG data without MRI > > The thread however does not offer a segmentation or head model for > download. Some electrodes in the EGI 256-electrodes cap are placed on > the cheeks or on the back of the neck and these areas are not modeled by > the standard BEM skin compartment in the standard BEM model. My question > was about a standard segmentation that extends the skin (and skull) > compartment downwards to allow these electrodes to sit on the nodes of > the skin mesh. > > Best, > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Tue, 19 Jan 2016 16:52:55 +0000 > From: aishwarya selvaraj > > To: "fieldtrip, donders" > > Subject: [FieldTrip] Source Localisation > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 5 > Date: Tue, 19 Jan 2016 17:06:13 +0000 > From: Hom?lle, S. (Simon) > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Aishwarya, > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > My recommended start would be: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > Hopefully this provides you good start working with EEG source reconstruction > > Best regards, > > Simon Hom?lle > PhD Candidate > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Phone: +31-(0)24-36-65059 > ________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > Sent: Tuesday, January 19, 2016 5:52 PM > To: fieldtrip, donders > Subject: [FieldTrip] Source Localisation > > Hi guys, > I'm currently working on source localization of EEG signals . > Im very new to it . > > > Can Anyone provide any inputs ?? > It would be of great help . > > -- > Regards, > Aishwarya > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 6 > Date: Tue, 19 Jan 2016 17:49:21 +0000 > From: victoria schroeder > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] plotting neighbours > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Thank you very much Philipp and Tzvetan! > > Things have become much clearer now. > > I would like to follow up with a very related question. I am trying to > replicate the analysis for the cluster based permutation test using the > code and the data provided. However, i run into two problems here > > First, i get the following error if i use the original code: > Attempted to access cfg.frequency(2); index out of bounds because > numel(cfg.frequency)=1. > > Error in ft_freqstatistics (line 187) > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > However, then no significant clusters are found. Which becomes clear when > trying to plot the cluster or by looking at the output of > ft_freqstatistics. > > Does the change in the code , change the output? How can i avoid the error > mentioned above and still get the same output from ft_freqstatistics as the > one provided on the webpage? > > > The relevant section of the toturial is provided below. > Thank you! > > Victoria > > Permutation test > > Now, run *ft_freqstatistics > * to compare > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > the following configuration is identical to the configuration that was used > for comparing event-related averages in the cluster-based permutation tests > on event related fields tutorial > . > Also see this tutorial > for > a detailed explanation of all the configuration settings. You can read more > about the *ft_prepare_neighbours > * function > in the FAQ's > . > > To load the planar gradient TFRs (also available on the FieldTrip FTP > servers,freqFIC_planar_cmb.mat > > and freqFC_planar_cmb.mat > ), > use: > > load freqFIC_planar_cmb > load freqFC_planar_cmb > > cfg = []; > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > cfg.latency = 'all'; > cfg.frequency = 20; > cfg.method = 'montecarlo'; > cfg.statistic = 'ft_statfun_indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > % prepare_neighbours determines what sensors may form clusters > cfg_neighb.method = 'distance'; > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > size(freqFC_planar_cmb.powspctrm,1)); > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > cfg.design = design; > cfg.ivar = 1; > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > Hi Victoria, > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > right I was only scrolling up to the part where the mags were analyzed. As > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > threat them separately, as I was naively thinking as non-neuormag user, but > > indeed combination of both is recommended as I have now learned :-)(thanks > > Phillip). I ran the following steps and I guess this should work for you. > > best > > tzvetan > > > > %% > > cfg = []; > > ComCon = ft_combineplanar(cfg,FreqCon); > > %% > > cfg = [] > > cfg.method = 'triangulation'; > > cfg.layout = 'neuromag306cmb.lay'; > > cfg.senstype = 'MEG'; > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > %% > > % plot neighbours > > cfg=[]; > > cfg.neighbours = neighbours; > > cfg.layout = 'neuromag306cmb.lay'; > > ft_neighbourplot(cfg); > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 7 > Date: Tue, 19 Jan 2016 20:50:24 +0100 > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Laith, > > this might be possible if you have the subject-specific MRI by following > the tutorial here: > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > and using the function ft_prepare_mesh and the tutorial command: > > cfg=[]; > cfg.tissue={'brain','skull','scalp'}; > cfg.numvertices = [3000 2000 1000]; > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > contain your triangulated surface with 1000 vertices. Let me know if that > works. Of course you should see the skin and the neck in the original MRI. > > If you do not have an anatomical MRI that extends down to the chin you > could try with a template, such as this: > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > and the corresponding segmented version > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > This goes down to the chin. Then you take care of rearranging the position > of the EEG electrodes according to this: > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > I hope this helped > Cris > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > wrote: > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > cheeks or on the back of the neck and these areas are not modeled by the > > standard BEM skin compartment in the standard BEM model. My question was > > about a standard segmentation that extends the skin (and skull) compartment > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > Best, > > Laith > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 8 > Date: Wed, 20 Jan 2016 12:17:12 +0800 > From: Munsif Jatoi > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Aishwarya, > > Please refer to main help tutorials. > > Also, you can find out the survey papers written in this area. For more, > SPM website can provide good help. > > Best, > Munsif. > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > S.Homolle at donders.ru.nl> wrote: > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source > > reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ------------------------------ > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > *To:* fieldtrip, donders > > *Subject:* [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > Munsif Ali H.Jatoi, > > Ph D Scholar, > Centre for Intelligent Signals and Imaging Research, > Universiti Teknologi PETRONAS, > Malaysia. > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 9 > Date: Wed, 20 Jan 2016 13:36:16 +0300 > From: Olga Sysoeva > > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] problems with mri interpolation > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > > I'm encounter the problem with MRI interpolation and reslicing using > > FT_VOLUMERESLICE. > > I have read my MRI from fif.file and this mri variable contains > > mri_K0012.unit, 'm' > > mri_K0012.dim, [432, 512, 180] > > mri_K0012.anatomy, <432, 512, 180 int16> > > mri_K0012.hdr, (1*1 structure) > > mri_K0012.transform, (4*4 double) > > mri_K0012.coordsys 'neuromag'. > > > Than I used > > > mri = ft_volumereslice([], mri); > > > the output is > > > ?the input is volume data with dimensions [432 > 512 180] > > reslicing from [432 512 180] to [256 256 256] > > the input is volume data with dimensions [256 > 256 256] > > the input is volume data with dimensions [432 > 512 180] > > selecting subvolume of 0.0% > > reslicing and interpolating anatomy > > interpolating > > ??? Attempted to access sel(1); index out of > bounds because numel(sel)=0. > > > Error in ==> ft_sourceinterpolate>my_interpn > at 663 > > ft_progress(sel(1)/num, 'interpolating > %.1f%%\n', 100*sel(1)/num); > > > Error in ==> ft_sourceinterpolate at 583 > > av( sel) = my_interpn(fv, ax(sel), > ay(sel), az(sel), cfg.interpmethod, > > cfg.feedback); > > > Error in ==> ft_volumereslice at 176 > > resliced = ft_sourceinterpolate(tmpcfg, mri, > resliced);? > > > I'm using matlab 7.6.0 (R2008a) and recently > downloaded fieltrip (also in my previous version of 2013 the error > was the same). > > > I'd be thankful for the comments. > > > Best Regards, > > Olga. > > P.S.Actually, I can project my sources > meaningfully into not interpolated MRI, altoough the images are > plotted upside down. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 18 > ***************************************** _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Thu Jan 21 12:06:13 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Thu, 21 Jan 2016 12:06:13 +0100 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 In-Reply-To: References: Message-ID: Hi Saeed, if the content of your triangulation connectivity matrices *skinf, uterusf, **uterinecontentf* is not made of integers you probably get the error you mentioned. Could this be the case? Out of curiosity, are you doing fetal recordings? Cris On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran wrote: > Dear Fieldtrip community, > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > > > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > To: fieldtrip at science.ru.nl > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 4. Source Localisation (aishwarya selvaraj) > > 5. Re: Source Localisation (Hom?lle) > > 6. Re: plotting neighbours (victoria schroeder) > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 8. Re: Source Localisation (Munsif Jatoi) > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > From: Laith Hamid > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > spikes and seizures. Currently I am analysing an EEG data set that was > > recorded using a 256-channel EGI system and I wanted to ask whether you > > have a standard BEM or FEM head Subscript indices must either be real > positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > model that extends enough downwards to > > accomodate all 256 electrodes. The current standard BEM model in the > > template folder of Fieldtrip isn't appropriate for source analysis of > > 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > thanks for your question. You could refer to a factory schematic layout > > such as the one in figure 4 of this publication: > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > and subsequently use the function ft_prepare_layout to manually track the > > points of the custom design on your own (if you dont want to wait for > > somebody from the FT to do the same for you). > > > > cfg = []; > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > lay = ft_prepare_layout(cfg); > > > > The following tutorial describes the procedure in more details: > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > Please do not hesitate to get in touch with me for this and other > matters. > > > > All the best > > Cris Micheli > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > wrote: > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > Complex > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes > and > > > seizures. Currently I am analysing an EEG data set that was recorded > using > > > a 256-channel EGI system and I wanted to ask whether you have a > standard > > > BEM or FEM head model that extends enough downwards to accomodate all > 256 > > > electrodes. The current standard BEM model in the template folder of > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > [FieldTrip] source analysis EEG data without MRI > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the cheeks or on the back of the neck and these areas are not modeled by > > the standard BEM skin compartment in the standard BEM model. My question > > was about a standard segmentation that extends the skin (and skull) > > compartment downwards to allow these electrodes to sit on the nodes of > > the skin mesh. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 4 > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > From: aishwarya selvaraj > > To: "fieldtrip, donders" > > Subject: [FieldTrip] Source Localisation > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > From: Hom?lle, S. (Simon) > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source > reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ________________________________ > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > Sent: Tuesday, January 19, 2016 5:52 PM > > To: fieldtrip, donders > > Subject: [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 6 > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > From: victoria schroeder > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] plotting neighbours > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Thank you very much Philipp and Tzvetan! > > > > Things have become much clearer now. > > > > I would like to follow up with a very related question. I am trying to > > replicate the analysis for the cluster based permutation test using the > > code and the data provided. However, i run into two problems here > > > > First, i get the following error if i use the original code: > > Attempted to access cfg.frequency(2); index out of bounds because > > numel(cfg.frequency)=1. > > > > Error in ft_freqstatistics (line 187) > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > fmax)]; > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > However, then no significant clusters are found. Which becomes clear when > > trying to plot the cluster or by looking at the output of > > ft_freqstatistics. > > > > Does the change in the code , change the output? How can i avoid the > error > > mentioned above and still get the same output from ft_freqstatistics as > the > > one provided on the webpage? > > > > > > The relevant section of the toturial is provided below. > > Thank you! > > > > Victoria > > > > Permutation test > > > > Now, run *ft_freqstatistics > > * to > compare > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > cfg.latency, > > the following configuration is identical to the configuration that was > used > > for comparing event-related averages in the cluster-based permutation > tests > > on event related fields tutorial > > . > > Also see this tutorial > > > for > > a detailed explanation of all the configuration settings. You can read > more > > about the *ft_prepare_neighbours > > * > function > > in the FAQ's > > >. > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > servers,freqFIC_planar_cmb.mat > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > and freqFC_planar_cmb.mat > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > >), > > use: > > > > load freqFIC_planar_cmb > > load freqFC_planar_cmb > > > > cfg = []; > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > cfg.latency = 'all'; > > cfg.frequency = 20; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > cfg.correctm = 'cluster'; > > cfg.clusteralpha = 0.05; > > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.tail = 0; > > cfg.clustertail = 0; > > cfg.alpha = 0.025; > > cfg.numrandomization = 500; > > % prepare_neighbours determines what sensors may form clusters > > cfg_neighb.method = 'distance'; > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > size(freqFC_planar_cmb.powspctrm,1)); > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > cfg.design = design; > > cfg.ivar = 1; > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > > > > Hi Victoria, > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > right I was only scrolling up to the part where the mags were > analyzed. As > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you > can > > > threat them separately, as I was naively thinking as non-neuormag > user, but > > > indeed combination of both is recommended as I have now learned > :-)(thanks > > > Phillip). I ran the following steps and I guess this should work for > you. > > > best > > > tzvetan > > > > > > %% > > > cfg = []; > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > %% > > > cfg = [] > > > cfg.method = 'triangulation'; > > > cfg.layout = 'neuromag306cmb.lay'; > > > cfg.senstype = 'MEG'; > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > %% > > > % plot neighbours > > > cfg=[]; > > > cfg.neighbours = neighbours; > > > cfg.layout = 'neuromag306cmb.lay'; > > > ft_neighbourplot(cfg); > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 7 > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > this might be possible if you have the subject-specific MRI by following > > the tutorial here: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > cfg=[]; > > cfg.tissue={'brain','skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > contain your triangulated surface with 1000 vertices. Let me know if that > > works. Of course you should see the skin and the neck in the original > MRI. > > > > If you do not have an anatomical MRI that extends down to the chin you > > could try with a template, such as this: > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > and the corresponding segmented version > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > This goes down to the chin. Then you take care of rearranging the > position > > of the EEG electrodes according to this: > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > I hope this helped > > Cris > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > wrote: > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > the > > > cheeks or on the back of the neck and these areas are not modeled by > the > > > standard BEM skin compartment in the standard BEM model. My question > was > > > about a standard segmentation that extends the skin (and skull) > compartment > > > downwards to allow these electrodes to sit on the nodes of the skin > mesh. > > > > > > Best, > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 8 > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > From: Munsif Jatoi > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Aishwarya, > > > > Please refer to main help tutorials. > > > > Also, you can find out the survey papers written in this area. For more, > > SPM website can provide good help. > > > > Best, > > Munsif. > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > S.Homolle at donders.ru.nl> wrote: > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ------------------------------ > > > *From:* fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > *To:* fieldtrip, donders > > > *Subject:* [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > -- > > Munsif Ali H.Jatoi, > > > > Ph D Scholar, > > Centre for Intelligent Signals and Imaging Research, > > Universiti Teknologi PETRONAS, > > Malaysia. > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 9 > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > From: Olga Sysoeva > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] problems with mri interpolation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Fieldtrippers, > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > FT_VOLUMERESLICE. > > > > I have read my MRI from fif.file and this mri variable contains > > > > mri_K0012.unit, 'm' > > > > mri_K0012.dim, [432, 512, 180] > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > mri_K0012.hdr, (1*1 structure) > > > > mri_K0012.transform, (4*4 double) > > > > mri_K0012.coordsys 'neuromag'. > > > > > > Than I used > > > > > > mri = ft_volumereslice([], mri); > > > > > > the output is > > > > > > ?the input is volume data with dimensions [432 > > 512 180] > > > > reslicing from [432 512 180] to [256 256 256] > > > > the input is volume data with dimensions [256 > > 256 256] > > > > the input is volume data with dimensions [432 > > 512 180] > > > > selecting subvolume of 0.0% > > > > reslicing and interpolating anatomy > > > > interpolating > > > > ??? Attempted to access sel(1); index out of > > bounds because numel(sel)=0. > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > at 663 > > > > ft_progress(sel(1)/num, 'interpolating > > %.1f%%\n', 100*sel(1)/num); > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > av( sel) = my_interpn(fv, ax(sel), > > ay(sel), az(sel), cfg.interpmethod, > > > > cfg.feedback); > > > > > > Error in ==> ft_volumereslice at 176 > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > resliced);? > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > downloaded fieltrip (also in my previous version of 2013 the error > > was the same). > > > > > > I'd be thankful for the comments. > > > > > > Best Regards, > > > > Olga. > > > > P.S.Actually, I can project my sources > > meaningfully into not interpolated MRI, altoough the images are > > plotted upside down. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mniqureshi at gist.ac.kr Thu Jan 21 13:59:06 2016 From: mniqureshi at gist.ac.kr (Muhammad Naveed Iqbal Qureshi) Date: Thu, 21 Jan 2016 21:59:06 +0900 Subject: [FieldTrip] difficulty in loading BCI-IV-2a dataset into fieldtrip for preprocessing Message-ID: <000b01d1544b$8323d8e0$896b8aa0$@gist.ac.kr> Hi, I am using BCI competition IV dataset 2a for my experiment. I want to preprocess it with field trip. I have written the following code for this task. addpath(genpath('E:\bbci_data\fieldtrip-20160118\fieldtrip-20160118')); cd 'E:\bbci_data\BCICIV_2a_gdf\'; %% Field Trip preprocessing code for i=1:9 file=num2str(i); file=strcat('A0',file,'T.gdf'); cfg = []; cfg.dataset = file ; cfg.trialdef.eventtype = 'Stimulus'; cfg.trialdef.eventvalue = {'left', 'right', 'both feet', 'tongue'}; cfg.trialdef.triallength = 8; % duration in seconds cfg.trialdef.ntrials = inf; % number of trials, inf results in as many as possible cfg.trialdef.prestim = 3; cfg.trialdef.poststim = 6; cfg = ft_definetrial(cfg); cfg.bpfilter = 'yes'; cfg.bpfreq = [0.5 100]; cfg.bpfilttype = 'but'; cfg.bpfiltord = 5; cfg.demean = 'yes'; cfg.detrend = 'yes'; trialdata_EO{i} = ft_preprocessing(cfg); end However, this code does not import the event and trigger information from the header file of the data. I will be highly obliged if anyone can help me in this regard. Thank in advance. Best Regards, Muhammad Naveed Iqbal Qureshi -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Thu Jan 21 19:14:01 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Thu, 21 Jan 2016 20:14:01 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 62, Issue 19 In-Reply-To: References: Message-ID: Thank you Jan and Cristiano; I downloaded another version of Fieldtrip thus the below error disappear: Error in triangle4pt (line 57) sph_pnt = pnt([tri(jj,:) lv],:); But now I have another error: Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example (line 100) vol = ft_prepare_headmodel(cfg, vol); Thank you for any suggestion Cristiano, I record the contraction of the uterus; Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 19 > To: fieldtrip at science.ru.nl > Date: Thu, 21 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > data recorded with EGI caps (Laith Hamid) (RICHARDS, JOHN) > 3. Re: fieldtrip Digest, Vol 62, Issue 18 (saeed zahran) > 4. Re: fieldtrip Digest, Vol 62, Issue 18 > (Schoffelen, J.M. (Jan Mathijs)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Jan 2016 13:39:30 +0100 > From: Laith Hamid > To: Fieldtrip > Subject: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps > Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1 at mail.uni-kiel.de> > Content-Type: text/plain; charset="us-ascii" > > > > Dear Cris, > > thank you very much for your answers yesterday. The segmentedmri > contained 'white', 'grey' and 'csf' so I needed to repeat the > segmentation using 'brain', 'skull' and 'scalp' as described in the > tutorial "Creating a BEM volume conduction model of the head for > source-reconstruction of EEG data" and everything worked smoothly > afterwards. The problem is solved now. > > Best, > Laith > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Wed, 20 Jan 2016 14:39:13 +0000 > From: "RICHARDS, JOHN" > To: "fieldtrip at science.ru.nl" , > "lah at pedneuro.uni-kiel.de" > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > 256-electrode EEG data recorded with EGI caps (Laith Hamid) > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Laith: > > I have a ?neurodevelopmental MRI database? (Richards, Sanchez et al., 2015; see my www site) that has average MRI templates that could be used. Each average has the whole head down to about the top of the neck. I did these purposely since I use EEG recording and the MNI template did not even go down far enough for the EGI 128 channel net. > > The database has average MRI templates for head (T1, T2) and brain. I also have FEM segmented heads for the entire head that could be used for this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, scalp), but ironically, I cut these off about 10% below the EGI 128 channel electrodes. However, you could use the three inner compartments for this and just add the rest of the head below the compartment?or use the whole-head FEM as is for a FEM-model, or use the segmented area below the skull for a whole-head BEM model. I also have average 128-channel EGI electrodes for each template. > > Additionally, the ?developmental? part of the ?neurodevelopmental MRI database? is that I have these for a wide range of ages (all ages?). I have a average for young adults (20-24 yrs), and average templates and FEM/BEM models for groups from 3 months through adulthood, and into late adulthood. So if you have specific neuro-pediatric applications you might be interested in using an age appropriate MRI average template rather than an adult template. > > See my www site for journal article references re this, and http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > Finally? I have been using these head models for FT-based FEM and BEM models. Possibly some of the actually field trip models I have would be useful to you. Some of the parts of the model do not use the electrodes (e.g., grid-dipoles, head-model) whereas the final models (leadfield) requires the electrode locations. The database also includes ?virtual? electrodes for the 10-10 system, which might be used to generate the 256 channel locations by knowing the relation between the 10-10 system and the EGI system based on EGI ELP files for the 256 channels. > > John > > *********************************************** > John E. Richards Carolina Distinguished Professor > Department of Psychology > University of South Carolina > Columbia, SC 29208 > Dept Phone: 803 777 2079 > Fax: 803 777 9558 > Email: richards-john at sc.edu > HTTP: jerlab.psych.sc.edu > *********************************************** > > > > > >---------------------------------------------------------------------- > > > >Message: 1 > >Date: Tue, 19 Jan 2016 15:35:00 +0100 > >From: Laith Hamid > >To: fieldtrip at science.ru.nl > >Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > >Content-Type: text/plain; charset="us-ascii" > > > > > > > >Dear community, > > > >My name is Laith Hamid and I am working in the University Medical > >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > >spikes and seizures. Currently I am analysing an EEG data set that was > >recorded using a 256-channel EGI system and I wanted to ask whether you > >have a standard BEM or FEM head model that extends enough downwards to > >accomodate all 256 electrodes. The current standard BEM model in the > >template folder of Fieldtrip isn't appropriate for source analysis of > >256-channel EGI data. > > > >Thank you very much in advance for your help! > > > >Best, > > > >Laith > > > > ------------------------------ > > Message: 3 > Date: Wed, 20 Jan 2016 19:37:32 +0200 > From: saeed zahran > To: "fieldtrip at science.ru.nl" > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Dear Fieldtrip community, > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > > > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > To: fieldtrip at science.ru.nl > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 4. Source Localisation (aishwarya selvaraj) > > 5. Re: Source Localisation (Hom?lle) > > 6. Re: plotting neighbours (victoria schroeder) > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 8. Re: Source Localisation (Munsif Jatoi) > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > From: Laith Hamid > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > spikes and seizures. Currently I am analysing an EEG data set that was > > recorded using a 256-channel EGI system and I wanted to ask whether you > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > model that extends enough downwards to > > accomodate all 256 electrodes. The current standard BEM model in the > > template folder of Fieldtrip isn't appropriate for source analysis of > > 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > thanks for your question. You could refer to a factory schematic layout > > such as the one in figure 4 of this publication: > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > and subsequently use the function ft_prepare_layout to manually track the > > points of the custom design on your own (if you dont want to wait for > > somebody from the FT to do the same for you). > > > > cfg = []; > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > lay = ft_prepare_layout(cfg); > > > > The following tutorial describes the procedure in more details: > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > All the best > > Cris Micheli > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > wrote: > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > electrodes. The current standard BEM model in the template folder of > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > [FieldTrip] source analysis EEG data without MRI > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the cheeks or on the back of the neck and these areas are not modeled by > > the standard BEM skin compartment in the standard BEM model. My question > > was about a standard segmentation that extends the skin (and skull) > > compartment downwards to allow these electrodes to sit on the nodes of > > the skin mesh. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 4 > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > From: aishwarya selvaraj > > To: "fieldtrip, donders" > > Subject: [FieldTrip] Source Localisation > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > From: Hom?lle, S. (Simon) > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ________________________________ > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > Sent: Tuesday, January 19, 2016 5:52 PM > > To: fieldtrip, donders > > Subject: [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 6 > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > From: victoria schroeder > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] plotting neighbours > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Thank you very much Philipp and Tzvetan! > > > > Things have become much clearer now. > > > > I would like to follow up with a very related question. I am trying to > > replicate the analysis for the cluster based permutation test using the > > code and the data provided. However, i run into two problems here > > > > First, i get the following error if i use the original code: > > Attempted to access cfg.frequency(2); index out of bounds because > > numel(cfg.frequency)=1. > > > > Error in ft_freqstatistics (line 187) > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > However, then no significant clusters are found. Which becomes clear when > > trying to plot the cluster or by looking at the output of > > ft_freqstatistics. > > > > Does the change in the code , change the output? How can i avoid the error > > mentioned above and still get the same output from ft_freqstatistics as the > > one provided on the webpage? > > > > > > The relevant section of the toturial is provided below. > > Thank you! > > > > Victoria > > > > Permutation test > > > > Now, run *ft_freqstatistics > > * to compare > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > the following configuration is identical to the configuration that was used > > for comparing event-related averages in the cluster-based permutation tests > > on event related fields tutorial > > . > > Also see this tutorial > > for > > a detailed explanation of all the configuration settings. You can read more > > about the *ft_prepare_neighbours > > * function > > in the FAQ's > > . > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > servers,freqFIC_planar_cmb.mat > > > > and freqFC_planar_cmb.mat > > ), > > use: > > > > load freqFIC_planar_cmb > > load freqFC_planar_cmb > > > > cfg = []; > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > cfg.latency = 'all'; > > cfg.frequency = 20; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > cfg.correctm = 'cluster'; > > cfg.clusteralpha = 0.05; > > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.tail = 0; > > cfg.clustertail = 0; > > cfg.alpha = 0.025; > > cfg.numrandomization = 500; > > % prepare_neighbours determines what sensors may form clusters > > cfg_neighb.method = 'distance'; > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > size(freqFC_planar_cmb.powspctrm,1)); > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > cfg.design = design; > > cfg.ivar = 1; > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > > > > > > > Hi Victoria, > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > right I was only scrolling up to the part where the mags were analyzed. As > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > Phillip). I ran the following steps and I guess this should work for you. > > > best > > > tzvetan > > > > > > %% > > > cfg = []; > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > %% > > > cfg = [] > > > cfg.method = 'triangulation'; > > > cfg.layout = 'neuromag306cmb.lay'; > > > cfg.senstype = 'MEG'; > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > %% > > > % plot neighbours > > > cfg=[]; > > > cfg.neighbours = neighbours; > > > cfg.layout = 'neuromag306cmb.lay'; > > > ft_neighbourplot(cfg); > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 7 > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > this might be possible if you have the subject-specific MRI by following > > the tutorial here: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > cfg=[]; > > cfg.tissue={'brain','skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > contain your triangulated surface with 1000 vertices. Let me know if that > > works. Of course you should see the skin and the neck in the original MRI. > > > > If you do not have an anatomical MRI that extends down to the chin you > > could try with a template, such as this: > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > and the corresponding segmented version > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > This goes down to the chin. Then you take care of rearranging the position > > of the EEG electrodes according to this: > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > I hope this helped > > Cris > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > wrote: > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > cheeks or on the back of the neck and these areas are not modeled by the > > > standard BEM skin compartment in the standard BEM model. My question was > > > about a standard segmentation that extends the skin (and skull) compartment > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 8 > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > From: Munsif Jatoi > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Aishwarya, > > > > Please refer to main help tutorials. > > > > Also, you can find out the survey papers written in this area. For more, > > SPM website can provide good help. > > > > Best, > > Munsif. > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > S.Homolle at donders.ru.nl> wrote: > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ------------------------------ > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > *To:* fieldtrip, donders > > > *Subject:* [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > -- > > Munsif Ali H.Jatoi, > > > > Ph D Scholar, > > Centre for Intelligent Signals and Imaging Research, > > Universiti Teknologi PETRONAS, > > Malaysia. > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 9 > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > From: Olga Sysoeva > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] problems with mri interpolation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Fieldtrippers, > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > FT_VOLUMERESLICE. > > > > I have read my MRI from fif.file and this mri variable contains > > > > mri_K0012.unit, 'm' > > > > mri_K0012.dim, [432, 512, 180] > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > mri_K0012.hdr, (1*1 structure) > > > > mri_K0012.transform, (4*4 double) > > > > mri_K0012.coordsys 'neuromag'. > > > > > > Than I used > > > > > > mri = ft_volumereslice([], mri); > > > > > > the output is > > > > > > ?the input is volume data with dimensions [432 > > 512 180] > > > > reslicing from [432 512 180] to [256 256 256] > > > > the input is volume data with dimensions [256 > > 256 256] > > > > the input is volume data with dimensions [432 > > 512 180] > > > > selecting subvolume of 0.0% > > > > reslicing and interpolating anatomy > > > > interpolating > > > > ??? Attempted to access sel(1); index out of > > bounds because numel(sel)=0. > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > at 663 > > > > ft_progress(sel(1)/num, 'interpolating > > %.1f%%\n', 100*sel(1)/num); > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > av( sel) = my_interpn(fv, ax(sel), > > ay(sel), az(sel), cfg.interpmethod, > > > > cfg.feedback); > > > > > > Error in ==> ft_volumereslice at 176 > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > resliced);? > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > downloaded fieltrip (also in my previous version of 2013 the error > > was the same). > > > > > > I'd be thankful for the comments. > > > > > > Best Regards, > > > > Olga. > > > > P.S.Actually, I can project my sources > > meaningfully into not interpolated MRI, altoough the images are > > plotted upside down. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > ***************************************** > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 4 > Date: Thu, 21 Jan 2016 08:16:55 +0000 > From: "Schoffelen, J.M. (Jan Mathijs)" > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Saeed, > > are you using 0 or 1 indexing for your triangles? You probably want to use 1 indexing. > > Best, > Jan-Mathijs > > > On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: > > Dear Fieldtrip community, > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > > > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > To: fieldtrip at science.ru.nl > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 4. Source Localisation (aishwarya selvaraj) > > 5. Re: Source Localisation (Hom?lle) > > 6. Re: plotting neighbours (victoria schroeder) > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Cristiano Micheli) > > 8. Re: Source Localisation (Munsif Jatoi) > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > From: Laith Hamid > > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear community, > > > > My name is Laith Hamid and I am working in the University Medical > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > spikes and seizures. Currently I am analysing an EEG data set that was > > recorded using a 256-channel EGI system and I wanted to ask whether you > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > Error in ft_headmodel_bemcp (line 101) > vol = triangle4pt(vol); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example_me (line 91) > vol = ft_prepare_headmodel(cfg, vol); > model that extends enough downwards to > > accomodate all 256 electrodes. The current standard BEM model in the > > template folder of Fieldtrip isn't appropriate for source analysis of > > 256-channel EGI data. > > > > Thank you very much in advance for your help! > > > > Best, > > > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > thanks for your question. You could refer to a factory schematic layout > > such as the one in figure 4 of this publication: > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > and subsequently use the function ft_prepare_layout to manually track the > > points of the custom design on your own (if you dont want to wait for > > somebody from the FT to do the same for you). > > > > cfg = []; > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > lay = ft_prepare_layout(cfg); > > > > The following tutorial describes the procedure in more details: > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > All the best > > Cris Micheli > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > wrote: > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > electrodes. The current standard BEM model in the template folder of > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answer. I am refering to an issue that was > > discussed in this thread from April 2013: > > > > [FieldTrip] source analysis EEG data without MRI > > > > The thread however does not offer a segmentation or head model for > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the cheeks or on the back of the neck and these areas are not modeled by > > the standard BEM skin compartment in the standard BEM model. My question > > was about a standard segmentation that extends the skin (and skull) > > compartment downwards to allow these electrodes to sit on the nodes of > > the skin mesh. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 4 > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > From: aishwarya selvaraj > > > To: "fieldtrip, donders" > > > Subject: [FieldTrip] Source Localisation > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > From: Hom?lle, S. (Simon) > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Aishwarya, > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > My recommended start would be: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > Best regards, > > > > Simon Hom?lle > > PhD Candidate > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Radboud University Nijmegen > > Phone: +31-(0)24-36-65059 > > ________________________________ > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > Sent: Tuesday, January 19, 2016 5:52 PM > > To: fieldtrip, donders > > Subject: [FieldTrip] Source Localisation > > > > Hi guys, > > I'm currently working on source localization of EEG signals . > > Im very new to it . > > > > > > Can Anyone provide any inputs ?? > > It would be of great help . > > > > -- > > Regards, > > Aishwarya > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 6 > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > From: victoria schroeder > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] plotting neighbours > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Thank you very much Philipp and Tzvetan! > > > > Things have become much clearer now. > > > > I would like to follow up with a very related question. I am trying to > > replicate the analysis for the cluster based permutation test using the > > code and the data provided. However, i run into two problems here > > > > First, i get the following error if i use the original code: > > Attempted to access cfg.frequency(2); index out of bounds because > > numel(cfg.frequency)=1. > > > > Error in ft_freqstatistics (line 187) > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > However, then no significant clusters are found. Which becomes clear when > > trying to plot the cluster or by looking at the output of > > ft_freqstatistics. > > > > Does the change in the code , change the output? How can i avoid the error > > mentioned above and still get the same output from ft_freqstatistics as the > > one provided on the webpage? > > > > > > The relevant section of the toturial is provided below. > > Thank you! > > > > Victoria > > > > Permutation test > > > > Now, run *ft_freqstatistics > > * to compare > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > the following configuration is identical to the configuration that was used > > for comparing event-related averages in the cluster-based permutation tests > > on event related fields tutorial > > . > > Also see this tutorial > > for > > a detailed explanation of all the configuration settings. You can read more > > about the *ft_prepare_neighbours > > * function > > in the FAQ's > > . > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > servers,freqFIC_planar_cmb.mat > > > > and freqFC_planar_cmb.mat > > ), > > use: > > > > load freqFIC_planar_cmb > > load freqFC_planar_cmb > > > > cfg = []; > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > cfg.latency = 'all'; > > cfg.frequency = 20; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > cfg.correctm = 'cluster'; > > cfg.clusteralpha = 0.05; > > cfg.clusterstatistic = 'maxsum'; > > cfg.minnbchan = 2; > > cfg.tail = 0; > > cfg.clustertail = 0; > > cfg.alpha = 0.025; > > cfg.numrandomization = 500; > > % prepare_neighbours determines what sensors may form clusters > > cfg_neighb.method = 'distance'; > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > size(freqFC_planar_cmb.powspctrm,1)); > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > cfg.design = design; > > cfg.ivar = 1; > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > > > > Hi Victoria, > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > right I was only scrolling up to the part where the mags were analyzed. As > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > Phillip). I ran the following steps and I guess this should work for you. > > > best > > > tzvetan > > > > > > %% > > > cfg = []; > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > %% > > > cfg = [] > > > cfg.method = 'triangulation'; > > > cfg.layout = 'neuromag306cmb.lay'; > > > cfg.senstype = 'MEG'; > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > %% > > > % plot neighbours > > > cfg=[]; > > > cfg.neighbours = neighbours; > > > cfg.layout = 'neuromag306cmb.lay'; > > > ft_neighbourplot(cfg); > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 7 > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Laith, > > > > this might be possible if you have the subject-specific MRI by following > > the tutorial here: > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > cfg=[]; > > cfg.tissue={'brain','skull','scalp'}; > > cfg.numvertices = [3000 2000 1000]; > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > contain your triangulated surface with 1000 vertices. Let me know if that > > works. Of course you should see the skin and the neck in the original MRI. > > > > If you do not have an anatomical MRI that extends down to the chin you > > could try with a template, such as this: > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > and the corresponding segmented version > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > This goes down to the chin. Then you take care of rearranging the position > > of the EEG electrodes according to this: > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > I hope this helped > > Cris > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > wrote: > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > cheeks or on the back of the neck and these areas are not modeled by the > > > standard BEM skin compartment in the standard BEM model. My question was > > > about a standard segmentation that extends the skin (and skull) compartment > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 8 > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > From: Munsif Jatoi > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Aishwarya, > > > > Please refer to main help tutorials. > > > > Also, you can find out the survey papers written in this area. For more, > > SPM website can provide good help. > > > > Best, > > Munsif. > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > S.Homolle at donders.ru.nl> wrote: > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ------------------------------ > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > *To:* fieldtrip, donders > > > *Subject:* [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > -- > > Munsif Ali H.Jatoi, > > > > Ph D Scholar, > > Centre for Intelligent Signals and Imaging Research, > > Universiti Teknologi PETRONAS, > > Malaysia. > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 9 > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > From: Olga Sysoeva > > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] problems with mri interpolation > > Message-ID: > > > > > Content-Type: text/plain; charset="utf-8" > > > > Dear Fieldtrippers, > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > FT_VOLUMERESLICE. > > > > I have read my MRI from fif.file and this mri variable contains > > > > mri_K0012.unit, 'm' > > > > mri_K0012.dim, [432, 512, 180] > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > mri_K0012.hdr, (1*1 structure) > > > > mri_K0012.transform, (4*4 double) > > > > mri_K0012.coordsys 'neuromag'. > > > > > > Than I used > > > > > > mri = ft_volumereslice([], mri); > > > > > > the output is > > > > > > ?the input is volume data with dimensions [432 > > 512 180] > > > > reslicing from [432 512 180] to [256 256 256] > > > > the input is volume data with dimensions [256 > > 256 256] > > > > the input is volume data with dimensions [432 > > 512 180] > > > > selecting subvolume of 0.0% > > > > reslicing and interpolating anatomy > > > > interpolating > > > > ??? Attempted to access sel(1); index out of > > bounds because numel(sel)=0. > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > at 663 > > > > ft_progress(sel(1)/num, 'interpolating > > %.1f%%\n', 100*sel(1)/num); > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > av( sel) = my_interpn(fv, ax(sel), > > ay(sel), az(sel), cfg.interpmethod, > > > > cfg.feedback); > > > > > > Error in ==> ft_volumereslice at 176 > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > resliced);? > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > downloaded fieltrip (also in my previous version of 2013 the error > > was the same). > > > > > > I'd be thankful for the comments. > > > > > > Best Regards, > > > > Olga. > > > > P.S.Actually, I can project my sources > > meaningfully into not interpolated MRI, altoough the images are > > plotted upside down. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > ***************************************** > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 19 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Thu Jan 21 19:22:42 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Thu, 21 Jan 2016 20:22:42 +0200 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Dear Fieldtrip Community, Dear Fieldtrip community, What does the error of the surface nesting means; I define the volume conductor as: vol = []; vol.bnd(1).pnt=skinpnt vol.bnd(1).tri=skinf vol.bnd(2).pnt=uteruspnt vol.bnd(2).tri=uterusf vol.bnd(3).pnt=uterinecontentpnt vol.bnd(3).tri=uterinecontentf vol.cond = c; But it result with the below error: Error using surface_nesting (line 26) the compartment nesting cannot be determined Error in ft_headmodel_bemcp (line 66) order = surface_nesting(vol.bnd, 'insidefirst'); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example (line 100) vol = ft_prepare_headmodel(cfg, vol); Thank you very much in advance for your help! Best regards Saeed Zahran > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 20 > To: fieldtrip at science.ru.nl > Date: Thu, 21 Jan 2016 19:14:24 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: fieldtrip Digest, Vol 62, Issue 18 (Cristiano Micheli) > 2. difficulty in loading BCI-IV-2a dataset into fieldtrip for > preprocessing (Muhammad Naveed Iqbal Qureshi) > 3. Re: fieldtrip Digest, Vol 62, Issue 19 (saeed zahran) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Jan 2016 12:06:13 +0100 > From: Cristiano Micheli > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Saeed, > if the content of your triangulation connectivity matrices *skinf, > uterusf, **uterinecontentf* is not made of integers you probably get the > error you mentioned. Could this be the case? > Out of curiosity, are you doing fetal recordings? > > Cris > > > On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran > wrote: > > > Dear Fieldtrip community, > > > > I define the volume conductor as: > > > > vol = []; > > vol.bnd(1).pnt=skinpnt > > vol.bnd(1).tri=skinf > > > > vol.bnd(2).pnt=uteruspnt > > vol.bnd(2).tri=uterusf > > > > vol.bnd(3).pnt=uterinecontentpnt > > vol.bnd(3).tri=uterinecontentf > > > > vol.cond = c; > > > > > > But it result with the below error: > > > > Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > Thank you very much in advance for your help! > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > To: fieldtrip at science.ru.nl > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 4. Source Localisation (aishwarya selvaraj) > > > 5. Re: Source Localisation (Hom?lle) > > > 6. Re: plotting neighbours (victoria schroeder) > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 8. Re: Source Localisation (Munsif Jatoi) > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > From: Laith Hamid > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > spikes and seizures. Currently I am analysing an EEG data set that was > > > recorded using a 256-channel EGI system and I wanted to ask whether you > > > have a standard BEM or FEM head Subscript indices must either be real > > positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > model that extends enough downwards to > > > accomodate all 256 electrodes. The current standard BEM model in the > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > thanks for your question. You could refer to a factory schematic layout > > > such as the one in figure 4 of this publication: > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > and subsequently use the function ft_prepare_layout to manually track the > > > points of the custom design on your own (if you dont want to wait for > > > somebody from the FT to do the same for you). > > > > > > cfg = []; > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > lay = ft_prepare_layout(cfg); > > > > > > The following tutorial describes the procedure in more details: > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > Please do not hesitate to get in touch with me for this and other > > matters. > > > > > > All the best > > > Cris Micheli > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > wrote: > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > Complex > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes > > and > > > > seizures. Currently I am analysing an EEG data set that was recorded > > using > > > > a 256-channel EGI system and I wanted to ask whether you have a > > standard > > > > BEM or FEM head model that extends enough downwards to accomodate all > > 256 > > > > electrodes. The current standard BEM model in the template folder of > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > > data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > the cheeks or on the back of the neck and these areas are not modeled by > > > the standard BEM skin compartment in the standard BEM model. My question > > > was about a standard segmentation that extends the skin (and skull) > > > compartment downwards to allow these electrodes to sit on the nodes of > > > the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > From: aishwarya selvaraj > > > To: "fieldtrip, donders" > > > Subject: [FieldTrip] Source Localisation > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > From: Hom?lle, S. (Simon) > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source > > reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ________________________________ > > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > To: fieldtrip, donders > > > Subject: [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 6 > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > From: victoria schroeder > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] plotting neighbours > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > Things have become much clearer now. > > > > > > I would like to follow up with a very related question. I am trying to > > > replicate the analysis for the cluster based permutation test using the > > > code and the data provided. However, i run into two problems here > > > > > > First, i get the following error if i use the original code: > > > Attempted to access cfg.frequency(2); index out of bounds because > > > numel(cfg.frequency)=1. > > > > > > Error in ft_freqstatistics (line 187) > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > > fmax)]; > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > > However, then no significant clusters are found. Which becomes clear when > > > trying to plot the cluster or by looking at the output of > > > ft_freqstatistics. > > > > > > Does the change in the code , change the output? How can i avoid the > > error > > > mentioned above and still get the same output from ft_freqstatistics as > > the > > > one provided on the webpage? > > > > > > > > > The relevant section of the toturial is provided below. > > > Thank you! > > > > > > Victoria > > > > > > Permutation test > > > > > > Now, run *ft_freqstatistics > > > * to > > compare > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > > cfg.latency, > > > the following configuration is identical to the configuration that was > > used > > > for comparing event-related averages in the cluster-based permutation > > tests > > > on event related fields tutorial > > > . > > > Also see this tutorial > > > > > for > > > a detailed explanation of all the configuration settings. You can read > > more > > > about the *ft_prepare_neighbours > > > * > > function > > > in the FAQ's > > > > >. > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > servers,freqFIC_planar_cmb.mat > > > < > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > < > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > > >), > > > use: > > > > > > load freqFIC_planar_cmb > > > load freqFC_planar_cmb > > > > > > cfg = []; > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > cfg.latency = 'all'; > > > cfg.frequency = 20; > > > cfg.method = 'montecarlo'; > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > cfg.correctm = 'cluster'; > > > cfg.clusteralpha = 0.05; > > > cfg.clusterstatistic = 'maxsum'; > > > cfg.minnbchan = 2; > > > cfg.tail = 0; > > > cfg.clustertail = 0; > > > cfg.alpha = 0.025; > > > cfg.numrandomization = 500; > > > % prepare_neighbours determines what sensors may form clusters > > > cfg_neighb.method = 'distance'; > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > size(freqFC_planar_cmb.powspctrm,1)); > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > cfg.design = design; > > > cfg.ivar = 1; > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov > >: > > > > > > > > > > > Hi Victoria, > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > > right I was only scrolling up to the part where the mags were > > analyzed. As > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you > > can > > > > threat them separately, as I was naively thinking as non-neuormag > > user, but > > > > indeed combination of both is recommended as I have now learned > > :-)(thanks > > > > Phillip). I ran the following steps and I guess this should work for > > you. > > > > best > > > > tzvetan > > > > > > > > %% > > > > cfg = []; > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > %% > > > > cfg = [] > > > > cfg.method = 'triangulation'; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > cfg.senstype = 'MEG'; > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > %% > > > > % plot neighbours > > > > cfg=[]; > > > > cfg.neighbours = neighbours; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 7 > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > this might be possible if you have the subject-specific MRI by following > > > the tutorial here: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > cfg=[]; > > > cfg.tissue={'brain','skull','scalp'}; > > > cfg.numvertices = [3000 2000 1000]; > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > > contain your triangulated surface with 1000 vertices. Let me know if that > > > works. Of course you should see the skin and the neck in the original > > MRI. > > > > > > If you do not have an anatomical MRI that extends down to the chin you > > > could try with a template, such as this: > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > and the corresponding segmented version > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > This goes down to the chin. Then you take care of rearranging the > > position > > > of the EEG electrodes according to this: > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > I hope this helped > > > Cris > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > wrote: > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that was > > > > discussed in this thread from April 2013: > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > the > > > > cheeks or on the back of the neck and these areas are not modeled by > > the > > > > standard BEM skin compartment in the standard BEM model. My question > > was > > > > about a standard segmentation that extends the skin (and skull) > > compartment > > > > downwards to allow these electrodes to sit on the nodes of the skin > > mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 8 > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > From: Munsif Jatoi > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Aishwarya, > > > > > > Please refer to main help tutorials. > > > > > > Also, you can find out the survey papers written in this area. For more, > > > SPM website can provide good help. > > > > > > Best, > > > Munsif. > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ------------------------------ > > > > *From:* fieldtrip-bounces at science.ru.nl [ > > fieldtrip-bounces at science.ru.nl] > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > *To:* fieldtrip, donders > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > -- > > > Munsif Ali H.Jatoi, > > > > > > Ph D Scholar, > > > Centre for Intelligent Signals and Imaging Research, > > > Universiti Teknologi PETRONAS, > > > Malaysia. > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > Message: 9 > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > From: Olga Sysoeva > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] problems with mri interpolation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Fieldtrippers, > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > FT_VOLUMERESLICE. > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > mri_K0012.unit, 'm' > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > mri_K0012.transform, (4*4 double) > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > Than I used > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > the output is > > > > > > > > > ?the input is volume data with dimensions [432 > > > 512 180] > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > the input is volume data with dimensions [256 > > > 256 256] > > > > > > the input is volume data with dimensions [432 > > > 512 180] > > > > > > selecting subvolume of 0.0% > > > > > > reslicing and interpolating anatomy > > > > > > interpolating > > > > > > ??? Attempted to access sel(1); index out of > > > bounds because numel(sel)=0. > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > at 663 > > > > > > ft_progress(sel(1)/num, 'interpolating > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > cfg.feedback); > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > resliced);? > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > downloaded fieltrip (also in my previous version of 2013 the error > > > was the same). > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > Best Regards, > > > > > > Olga. > > > > > > P.S.Actually, I can project my sources > > > meaningfully into not interpolated MRI, altoough the images are > > > plotted upside down. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > ***************************************** > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Thu, 21 Jan 2016 21:59:06 +0900 > From: "Muhammad Naveed Iqbal Qureshi" > To: > Subject: [FieldTrip] difficulty in loading BCI-IV-2a dataset into > fieldtrip for preprocessing > Message-ID: <000b01d1544b$8323d8e0$896b8aa0$@gist.ac.kr> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > > > I am using BCI competition IV dataset 2a for my experiment. > > I want to preprocess it with field trip. > > > > I have written the following code for this task. > > > > addpath(genpath('E:\bbci_data\fieldtrip-20160118\fieldtrip-20160118')); > > cd 'E:\bbci_data\BCICIV_2a_gdf\'; > > > > %% Field Trip preprocessing code > > for i=1:9 > > file=num2str(i); > > file=strcat('A0',file,'T.gdf'); > > cfg = []; > > cfg.dataset = file ; > > cfg.trialdef.eventtype = 'Stimulus'; > > cfg.trialdef.eventvalue = {'left', 'right', 'both feet', 'tongue'}; > > cfg.trialdef.triallength = 8; % duration in seconds > > cfg.trialdef.ntrials = inf; % number of trials, inf > results in as many as possible > > cfg.trialdef.prestim = 3; > > cfg.trialdef.poststim = 6; > > cfg = ft_definetrial(cfg); > > > > cfg.bpfilter = 'yes'; > > cfg.bpfreq = [0.5 100]; > > cfg.bpfilttype = 'but'; > > cfg.bpfiltord = 5; > > cfg.demean = 'yes'; > > cfg.detrend = 'yes'; > > trialdata_EO{i} = ft_preprocessing(cfg); > > end > > > > However, this code does not import the event and trigger information from > the header file of the data. > > I will be highly obliged if anyone can help me in this regard. > > > > Thank in advance. > > > > Best Regards, > Muhammad Naveed Iqbal Qureshi > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Thu, 21 Jan 2016 20:14:01 +0200 > From: saeed zahran > To: "fieldtrip at science.ru.nl" > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 19 > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Thank you Jan and Cristiano; > > I downloaded another version of Fieldtrip thus the below error disappear: > Error in triangle4pt (line 57) > sph_pnt = pnt([tri(jj,:) lv],:); > > But now I have another error: > > Error using surface_nesting (line 26) > the compartment nesting cannot be determined > > Error in ft_headmodel_bemcp (line 66) > order = surface_nesting(vol.bnd, 'insidefirst'); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example (line 100) > vol = ft_prepare_headmodel(cfg, vol); > Thank you for any suggestion > > Cristiano, I record the contraction of the uterus; > > > Best regards > Saeed Zahran > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 19 > > To: fieldtrip at science.ru.nl > > Date: Thu, 21 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > data recorded with EGI caps (Laith Hamid) (RICHARDS, JOHN) > > 3. Re: fieldtrip Digest, Vol 62, Issue 18 (saeed zahran) > > 4. Re: fieldtrip Digest, Vol 62, Issue 18 > > (Schoffelen, J.M. (Jan Mathijs)) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 20 Jan 2016 13:39:30 +0100 > > From: Laith Hamid > > To: Fieldtrip > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps > > Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1 at mail.uni-kiel.de> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Dear Cris, > > > > thank you very much for your answers yesterday. The segmentedmri > > contained 'white', 'grey' and 'csf' so I needed to repeat the > > segmentation using 'brain', 'skull' and 'scalp' as described in the > > tutorial "Creating a BEM volume conduction model of the head for > > source-reconstruction of EEG data" and everything worked smoothly > > afterwards. The problem is solved now. > > > > Best, > > Laith > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 2 > > Date: Wed, 20 Jan 2016 14:39:13 +0000 > > From: "RICHARDS, JOHN" > > To: "fieldtrip at science.ru.nl" , > > "lah at pedneuro.uni-kiel.de" > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > 256-electrode EEG data recorded with EGI caps (Laith Hamid) > > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > > > Laith: > > > > I have a ?neurodevelopmental MRI database? (Richards, Sanchez et al., 2015; see my www site) that has average MRI templates that could be used. Each average has the whole head down to about the top of the neck. I did these purposely since I use EEG recording and the MNI template did not even go down far enough for the EGI 128 channel net. > > > > The database has average MRI templates for head (T1, T2) and brain. I also have FEM segmented heads for the entire head that could be used for this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, scalp), but ironically, I cut these off about 10% below the EGI 128 channel electrodes. However, you could use the three inner compartments for this and just add the rest of the head below the compartment?or use the whole-head FEM as is for a FEM-model, or use the segmented area below the skull for a whole-head BEM model. I also have average 128-channel EGI electrodes for each template. > > > > Additionally, the ?developmental? part of the ?neurodevelopmental MRI database? is that I have these for a wide range of ages (all ages?). I have a average for young adults (20-24 yrs), and average templates and FEM/BEM models for groups from 3 months through adulthood, and into late adulthood. So if you have specific neuro-pediatric applications you might be interested in using an age appropriate MRI average template rather than an adult template. > > > > See my www site for journal article references re this, and http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > > > Finally? I have been using these head models for FT-based FEM and BEM models. Possibly some of the actually field trip models I have would be useful to you. Some of the parts of the model do not use the electrodes (e.g., grid-dipoles, head-model) whereas the final models (leadfield) requires the electrode locations. The database also includes ?virtual? electrodes for the 10-10 system, which might be used to generate the 256 channel locations by knowing the relation between the 10-10 system and the EGI system based on EGI ELP files for the 256 channels. > > > > John > > > > *********************************************** > > John E. Richards Carolina Distinguished Professor > > Department of Psychology > > University of South Carolina > > Columbia, SC 29208 > > Dept Phone: 803 777 2079 > > Fax: 803 777 9558 > > Email: richards-john at sc.edu > > HTTP: jerlab.psych.sc.edu > > *********************************************** > > > > > > > > > > >---------------------------------------------------------------------- > > > > > >Message: 1 > > >Date: Tue, 19 Jan 2016 15:35:00 +0100 > > >From: Laith Hamid > > >To: fieldtrip at science.ru.nl > > >Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > >Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > >Dear community, > > > > > >My name is Laith Hamid and I am working in the University Medical > > >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > >spikes and seizures. Currently I am analysing an EEG data set that was > > >recorded using a 256-channel EGI system and I wanted to ask whether you > > >have a standard BEM or FEM head model that extends enough downwards to > > >accomodate all 256 electrodes. The current standard BEM model in the > > >template folder of Fieldtrip isn't appropriate for source analysis of > > >256-channel EGI data. > > > > > >Thank you very much in advance for your help! > > > > > >Best, > > > > > >Laith > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Wed, 20 Jan 2016 19:37:32 +0200 > > From: saeed zahran > > To: "fieldtrip at science.ru.nl" > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Fieldtrip community, > > > > I define the volume conductor as: > > > > vol = []; > > vol.bnd(1).pnt=skinpnt > > vol.bnd(1).tri=skinf > > > > vol.bnd(2).pnt=uteruspnt > > vol.bnd(2).tri=uterusf > > > > vol.bnd(3).pnt=uterinecontentpnt > > vol.bnd(3).tri=uterinecontentf > > > > vol.cond = c; > > > > > > But it result with the below error: > > > > Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > Thank you very much in advance for your help! > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > To: fieldtrip at science.ru.nl > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 4. Source Localisation (aishwarya selvaraj) > > > 5. Re: Source Localisation (Hom?lle) > > > 6. Re: plotting neighbours (victoria schroeder) > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 8. Re: Source Localisation (Munsif Jatoi) > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > From: Laith Hamid > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > spikes and seizures. Currently I am analysing an EEG data set that was > > > recorded using a 256-channel EGI system and I wanted to ask whether you > > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > model that extends enough downwards to > > > accomodate all 256 electrodes. The current standard BEM model in the > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > thanks for your question. You could refer to a factory schematic layout > > > such as the one in figure 4 of this publication: > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > and subsequently use the function ft_prepare_layout to manually track the > > > points of the custom design on your own (if you dont want to wait for > > > somebody from the FT to do the same for you). > > > > > > cfg = []; > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > lay = ft_prepare_layout(cfg); > > > > > > The following tutorial describes the procedure in more details: > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > > > All the best > > > Cris Micheli > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > wrote: > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > > electrodes. The current standard BEM model in the template folder of > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > the cheeks or on the back of the neck and these areas are not modeled by > > > the standard BEM skin compartment in the standard BEM model. My question > > > was about a standard segmentation that extends the skin (and skull) > > > compartment downwards to allow these electrodes to sit on the nodes of > > > the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > From: aishwarya selvaraj > > > To: "fieldtrip, donders" > > > Subject: [FieldTrip] Source Localisation > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > From: Hom?lle, S. (Simon) > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ________________________________ > > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > To: fieldtrip, donders > > > Subject: [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 6 > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > From: victoria schroeder > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] plotting neighbours > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > Things have become much clearer now. > > > > > > I would like to follow up with a very related question. I am trying to > > > replicate the analysis for the cluster based permutation test using the > > > code and the data provided. However, i run into two problems here > > > > > > First, i get the following error if i use the original code: > > > Attempted to access cfg.frequency(2); index out of bounds because > > > numel(cfg.frequency)=1. > > > > > > Error in ft_freqstatistics (line 187) > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > > However, then no significant clusters are found. Which becomes clear when > > > trying to plot the cluster or by looking at the output of > > > ft_freqstatistics. > > > > > > Does the change in the code , change the output? How can i avoid the error > > > mentioned above and still get the same output from ft_freqstatistics as the > > > one provided on the webpage? > > > > > > > > > The relevant section of the toturial is provided below. > > > Thank you! > > > > > > Victoria > > > > > > Permutation test > > > > > > Now, run *ft_freqstatistics > > > * to compare > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > > the following configuration is identical to the configuration that was used > > > for comparing event-related averages in the cluster-based permutation tests > > > on event related fields tutorial > > > . > > > Also see this tutorial > > > for > > > a detailed explanation of all the configuration settings. You can read more > > > about the *ft_prepare_neighbours > > > * function > > > in the FAQ's > > > . > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > servers,freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > ), > > > use: > > > > > > load freqFIC_planar_cmb > > > load freqFC_planar_cmb > > > > > > cfg = []; > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > cfg.latency = 'all'; > > > cfg.frequency = 20; > > > cfg.method = 'montecarlo'; > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > cfg.correctm = 'cluster'; > > > cfg.clusteralpha = 0.05; > > > cfg.clusterstatistic = 'maxsum'; > > > cfg.minnbchan = 2; > > > cfg.tail = 0; > > > cfg.clustertail = 0; > > > cfg.alpha = 0.025; > > > cfg.numrandomization = 500; > > > % prepare_neighbours determines what sensors may form clusters > > > cfg_neighb.method = 'distance'; > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > size(freqFC_planar_cmb.powspctrm,1)); > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > cfg.design = design; > > > cfg.ivar = 1; > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov : > > > > > > > > > > > Hi Victoria, > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > > right I was only scrolling up to the part where the mags were analyzed. As > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > > Phillip). I ran the following steps and I guess this should work for you. > > > > best > > > > tzvetan > > > > > > > > %% > > > > cfg = []; > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > %% > > > > cfg = [] > > > > cfg.method = 'triangulation'; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > cfg.senstype = 'MEG'; > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > %% > > > > % plot neighbours > > > > cfg=[]; > > > > cfg.neighbours = neighbours; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 7 > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > From: Cristiano Micheli > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > this might be possible if you have the subject-specific MRI by following > > > the tutorial here: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > cfg=[]; > > > cfg.tissue={'brain','skull','scalp'}; > > > cfg.numvertices = [3000 2000 1000]; > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > > contain your triangulated surface with 1000 vertices. Let me know if that > > > works. Of course you should see the skin and the neck in the original MRI. > > > > > > If you do not have an anatomical MRI that extends down to the chin you > > > could try with a template, such as this: > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > and the corresponding segmented version > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > This goes down to the chin. Then you take care of rearranging the position > > > of the EEG electrodes according to this: > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > I hope this helped > > > Cris > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > wrote: > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that was > > > > discussed in this thread from April 2013: > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > > cheeks or on the back of the neck and these areas are not modeled by the > > > > standard BEM skin compartment in the standard BEM model. My question was > > > > about a standard segmentation that extends the skin (and skull) compartment > > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 8 > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > From: Munsif Jatoi > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Aishwarya, > > > > > > Please refer to main help tutorials. > > > > > > Also, you can find out the survey papers written in this area. For more, > > > SPM website can provide good help. > > > > > > Best, > > > Munsif. > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ------------------------------ > > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > *To:* fieldtrip, donders > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > -- > > > Munsif Ali H.Jatoi, > > > > > > Ph D Scholar, > > > Centre for Intelligent Signals and Imaging Research, > > > Universiti Teknologi PETRONAS, > > > Malaysia. > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 9 > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > From: Olga Sysoeva > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] problems with mri interpolation > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Fieldtrippers, > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > FT_VOLUMERESLICE. > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > mri_K0012.unit, 'm' > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > mri_K0012.transform, (4*4 double) > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > Than I used > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > the output is > > > > > > > > > ?the input is volume data with dimensions [432 > > > 512 180] > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > the input is volume data with dimensions [256 > > > 256 256] > > > > > > the input is volume data with dimensions [432 > > > 512 180] > > > > > > selecting subvolume of 0.0% > > > > > > reslicing and interpolating anatomy > > > > > > interpolating > > > > > > ??? Attempted to access sel(1); index out of > > > bounds because numel(sel)=0. > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > at 663 > > > > > > ft_progress(sel(1)/num, 'interpolating > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > cfg.feedback); > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > resliced);? > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > downloaded fieltrip (also in my previous version of 2013 the error > > > was the same). > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > Best Regards, > > > > > > Olga. > > > > > > P.S.Actually, I can project my sources > > > meaningfully into not interpolated MRI, altoough the images are > > > plotted upside down. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > ***************************************** > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 4 > > Date: Thu, 21 Jan 2016 08:16:55 +0000 > > From: "Schoffelen, J.M. (Jan Mathijs)" > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Saeed, > > > > are you using 0 or 1 indexing for your triangles? You probably want to use 1 indexing. > > > > Best, > > Jan-Mathijs > > > > > > On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: > > > > Dear Fieldtrip community, > > > > I define the volume conductor as: > > > > vol = []; > > vol.bnd(1).pnt=skinpnt > > vol.bnd(1).tri=skinf > > > > vol.bnd(2).pnt=uteruspnt > > vol.bnd(2).tri=uterusf > > > > vol.bnd(3).pnt=uterinecontentpnt > > vol.bnd(3).tri=uterinecontentf > > > > vol.cond = c; > > > > > > But it result with the below error: > > > > Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > Thank you very much in advance for your help! > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > To: fieldtrip at science.ru.nl > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 4. Source Localisation (aishwarya selvaraj) > > > 5. Re: Source Localisation (Hom?lle) > > > 6. Re: plotting neighbours (victoria schroeder) > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Cristiano Micheli) > > > 8. Re: Source Localisation (Munsif Jatoi) > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > From: Laith Hamid > > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear community, > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > spikes and seizures. Currently I am analysing an EEG data set that was > > > recorded using a 256-channel EGI system and I wanted to ask whether you > > > have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals. > > > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > Error in ft_headmodel_bemcp (line 101) > > vol = triangle4pt(vol); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > vol = ft_prepare_headmodel(cfg, vol); > > model that extends enough downwards to > > > accomodate all 256 electrodes. The current standard BEM model in the > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > 256-channel EGI data. > > > > > > Thank you very much in advance for your help! > > > > > > Best, > > > > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > thanks for your question. You could refer to a factory schematic layout > > > such as the one in figure 4 of this publication: > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > and subsequently use the function ft_prepare_layout to manually track the > > > points of the custom design on your own (if you dont want to wait for > > > somebody from the FT to do the same for you). > > > > > > cfg = []; > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > lay = ft_prepare_layout(cfg); > > > > > > The following tutorial describes the procedure in more details: > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > Please do not hesitate to get in touch with me for this and other matters. > > > > > > All the best > > > Cris Micheli > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid > > > > wrote: > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical Complex > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and > > > > seizures. Currently I am analysing an EEG data set that was recorded using > > > > a 256-channel EGI system and I wanted to ask whether you have a standard > > > > BEM or FEM head model that extends enough downwards to accomodate all 256 > > > > electrodes. The current standard BEM model in the template folder of > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > From: Laith Hamid > > > > To: Fieldtrip > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answer. I am refering to an issue that was > > > discussed in this thread from April 2013: > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > The thread however does not offer a segmentation or head model for > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > the cheeks or on the back of the neck and these areas are not modeled by > > > the standard BEM skin compartment in the standard BEM model. My question > > > was about a standard segmentation that extends the skin (and skull) > > > compartment downwards to allow these electrodes to sit on the nodes of > > > the skin mesh. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > From: aishwarya selvaraj > > > > To: "fieldtrip, donders" > > > > Subject: [FieldTrip] Source Localisation > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > From: Hom?lle, S. (Simon) > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Aishwarya, > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several tutorials about source reconstruction. > > > > > > My recommended start would be: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > Hopefully this provides you good start working with EEG source reconstruction > > > > > > Best regards, > > > > > > Simon Hom?lle > > > PhD Candidate > > > Donders Institute for Brain, Cognition and Behaviour > > > Centre for Cognitive Neuroimaging > > > Radboud University Nijmegen > > > Phone: +31-(0)24-36-65059 > > > ________________________________ > > > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > To: fieldtrip, donders > > > Subject: [FieldTrip] Source Localisation > > > > > > Hi guys, > > > I'm currently working on source localization of EEG signals . > > > Im very new to it . > > > > > > > > > Can Anyone provide any inputs ?? > > > It would be of great help . > > > > > > -- > > > Regards, > > > Aishwarya > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 6 > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > From: victoria schroeder > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] plotting neighbours > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > Things have become much clearer now. > > > > > > I would like to follow up with a very related question. I am trying to > > > replicate the analysis for the cluster based permutation test using the > > > code and the data provided. However, i run into two problems here > > > > > > First, i get the following error if i use the original code: > > > Attempted to access cfg.frequency(2); index out of bounds because > > > numel(cfg.frequency)=1. > > > > > > Error in ft_freqstatistics (line 187) > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)]; > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20]. > > > However, then no significant clusters are found. Which becomes clear when > > > trying to plot the cluster or by looking at the output of > > > ft_freqstatistics. > > > > > > Does the change in the code , change the output? How can i avoid the error > > > mentioned above and still get the same output from ft_freqstatistics as the > > > one provided on the webpage? > > > > > > > > > The relevant section of the toturial is provided below. > > > Thank you! > > > > > > Victoria > > > > > > Permutation test > > > > > > Now, run *ft_freqstatistics > > > * to compare > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency, > > > the following configuration is identical to the configuration that was used > > > for comparing event-related averages in the cluster-based permutation tests > > > on event related fields tutorial > > > . > > > Also see this tutorial > > > for > > > a detailed explanation of all the configuration settings. You can read more > > > about the *ft_prepare_neighbours > > > * function > > > in the FAQ's > > > . > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > servers,freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > ), > > > use: > > > > > > load freqFIC_planar_cmb > > > load freqFC_planar_cmb > > > > > > cfg = []; > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > cfg.latency = 'all'; > > > cfg.frequency = 20; > > > cfg.method = 'montecarlo'; > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > cfg.correctm = 'cluster'; > > > cfg.clusteralpha = 0.05; > > > cfg.clusterstatistic = 'maxsum'; > > > cfg.minnbchan = 2; > > > cfg.tail = 0; > > > cfg.clustertail = 0; > > > cfg.alpha = 0.025; > > > cfg.numrandomization = 500; > > > % prepare_neighbours determines what sensors may form clusters > > > cfg_neighb.method = 'distance'; > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > size(freqFC_planar_cmb.powspctrm,1)); > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > cfg.design = design; > > > cfg.ivar = 1; > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb); > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov >: > > > > > > > > > > > Hi Victoria, > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. You are > > > > right I was only scrolling up to the part where the mags were analyzed. As > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can > > > > threat them separately, as I was naively thinking as non-neuormag user, but > > > > indeed combination of both is recommended as I have now learned :-)(thanks > > > > Phillip). I ran the following steps and I guess this should work for you. > > > > best > > > > tzvetan > > > > > > > > %% > > > > cfg = []; > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > %% > > > > cfg = [] > > > > cfg.method = 'triangulation'; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > cfg.senstype = 'MEG'; > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > %% > > > > % plot neighbours > > > > cfg=[]; > > > > cfg.neighbours = neighbours; > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 7 > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Laith, > > > > > > this might be possible if you have the subject-specific MRI by following > > > the tutorial here: > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > cfg=[]; > > > cfg.tissue={'brain','skull','scalp'}; > > > cfg.numvertices = [3000 2000 1000]; > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable should > > > contain your triangulated surface with 1000 vertices. Let me know if that > > > works. Of course you should see the skin and the neck in the original MRI. > > > > > > If you do not have an anatomical MRI that extends down to the chin you > > > could try with a template, such as this: > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > and the corresponding segmented version > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > This goes down to the chin. Then you take care of rearranging the position > > > of the EEG electrodes according to this: > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > I hope this helped > > > Cris > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid > > > > wrote: > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that was > > > > discussed in this thread from April 2013: > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on the > > > > cheeks or on the back of the neck and these areas are not modeled by the > > > > standard BEM skin compartment in the standard BEM model. My question was > > > > about a standard segmentation that extends the skin (and skull) compartment > > > > downwards to allow these electrodes to sit on the nodes of the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 8 > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > From: Munsif Jatoi > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Aishwarya, > > > > > > Please refer to main help tutorials. > > > > > > Also, you can find out the survey papers written in this area. For more, > > > SPM website can provide good help. > > > > > > Best, > > > Munsif. > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ------------------------------ > > > > *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > *To:* fieldtrip, donders > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > -- > > > Munsif Ali H.Jatoi, > > > > > > Ph D Scholar, > > > Centre for Intelligent Signals and Imaging Research, > > > Universiti Teknologi PETRONAS, > > > Malaysia. > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > Message: 9 > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > From: Olga Sysoeva > > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] problems with mri interpolation > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Dear Fieldtrippers, > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > FT_VOLUMERESLICE. > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > mri_K0012.unit, 'm' > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > mri_K0012.transform, (4*4 double) > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > Than I used > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > the output is > > > > > > > > > ?the input is volume data with dimensions [432 > > > 512 180] > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > the input is volume data with dimensions [256 > > > 256 256] > > > > > > the input is volume data with dimensions [432 > > > 512 180] > > > > > > selecting subvolume of 0.0% > > > > > > reslicing and interpolating anatomy > > > > > > interpolating > > > > > > ??? Attempted to access sel(1); index out of > > > bounds because numel(sel)=0. > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > at 663 > > > > > > ft_progress(sel(1)/num, 'interpolating > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > cfg.feedback); > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > resliced);? > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > downloaded fieltrip (also in my previous version of 2013 the error > > > was the same). > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > Best Regards, > > > > > > Olga. > > > > > > P.S.Actually, I can project my sources > > > meaningfully into not interpolated MRI, altoough the images are > > > plotted upside down. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > ***************************************** > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 19 > > ***************************************** > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 20 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.thomas at nin.knaw.nl Fri Jan 22 12:16:59 2016 From: r.thomas at nin.knaw.nl (Rajat Thomas) Date: Fri, 22 Jan 2016 11:16:59 +0000 Subject: [FieldTrip] ROI based analysis Message-ID: <1453461419134.82627@nin.knaw.nl> ?Dear Fieldtrippers, Has anyone fixed with problem with ROI based analysis in Fieldtrip. I see that it says ROI analysis needs to be fixed for new implementation. Are there newer functions that do this? Any help would be highly appreciated. Thanks Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam -------------- next part -------------- An HTML attachment was scrubbed... URL: From mortaheb.sepehr at yahoo.com Sat Jan 23 13:39:07 2016 From: mortaheb.sepehr at yahoo.com (Sepehr Mortaheb) Date: Sat, 23 Jan 2016 12:39:07 +0000 (UTC) Subject: [FieldTrip] Synthetic EEG References: <814709100.138411.1453552747072.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <814709100.138411.1453552747072.JavaMail.yahoo@mail.yahoo.com> Hi, How can I generate a synthetic EEG signal using forward models of FieldTrip?  -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Sat Jan 23 17:14:06 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Sat, 23 Jan 2016 17:14:06 +0100 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Dear Saeed, it might depend on the boundaries. If they are not nested (one is inside another, which is inside another, etc... like chinese boxes) then you have a fundamental problem. This is a constraint of the BEM algorithm in order for it to work properly. Have you tried plotting the triangulated meshes? Do they look nested? I hope this helps for now, Cris On Thu, Jan 21, 2016 at 7:22 PM, saeed zahran wrote: > Dear Fieldtrip Community, > > Dear Fieldtrip community, > > > What does the error of the surface nesting means; > > I define the volume conductor as: > > vol = []; > vol.bnd(1).pnt=skinpnt > vol.bnd(1).tri=skinf > > vol.bnd(2).pnt=uteruspnt > vol.bnd(2).tri=uterusf > > vol.bnd(3).pnt=uterinecontentpnt > vol.bnd(3).tri=uterinecontentf > > vol.cond = c; > > > But it result with the below error: > > Error using surface_nesting (line 26) > the compartment nesting cannot be determined > > Error in ft_headmodel_bemcp (line 66) > order = surface_nesting(vol.bnd, 'insidefirst'); > > Error in ft_prepare_headmodel (line 253) > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > Error in openmeeg_eeg_leadfield_example (line 100) > vol = ft_prepare_headmodel(cfg, vol); > Thank you very much in advance for your help! > > Best regards > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 20 > > To: fieldtrip at science.ru.nl > > Date: Thu, 21 Jan 2016 19:14:24 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. Re: fieldtrip Digest, Vol 62, Issue 18 (Cristiano Micheli) > > 2. difficulty in loading BCI-IV-2a dataset into fieldtrip for > > preprocessing (Muhammad Naveed Iqbal Qureshi) > > 3. Re: fieldtrip Digest, Vol 62, Issue 19 (saeed zahran) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 21 Jan 2016 12:06:13 +0100 > > From: Cristiano Micheli > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Hi Saeed, > > if the content of your triangulation connectivity matrices *skinf, > > uterusf, **uterinecontentf* is not made of integers you probably get the > > error you mentioned. Could this be the case? > > Out of curiosity, are you doing fetal recordings? > > > > Cris > > > > > > On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran > > wrote: > > > > > Dear Fieldtrip community, > > > > > > I define the volume conductor as: > > > > > > vol = []; > > > vol.bnd(1).pnt=skinpnt > > > vol.bnd(1).tri=skinf > > > > > > vol.bnd(2).pnt=uteruspnt > > > vol.bnd(2).tri=uterusf > > > > > > vol.bnd(3).pnt=uterinecontentpnt > > > vol.bnd(3).tri=uterinecontentf > > > > > > vol.cond = c; > > > > > > > > > But it result with the below error: > > > > > > Subscript indices must either be real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > > > > Thank you very much in advance for your help! > > > > > > Best regards > > > Saeed Zahran > > > > > > > From: fieldtrip-request at science.ru.nl > > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > > To: fieldtrip at science.ru.nl > > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > > > Send fieldtrip mailing list submissions to > > > > fieldtrip at science.ru.nl > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > or, via email, send a message with subject or body 'help' to > > > > fieldtrip-request at science.ru.nl > > > > > > > > You can reach the person managing the list at > > > > fieldtrip-owner at science.ru.nl > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 4. Source Localisation (aishwarya selvaraj) > > > > 5. Re: Source Localisation (Hom?lle) > > > > 6. Re: plotting neighbours (victoria schroeder) > > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 8. Re: Source Localisation (Munsif Jatoi) > > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > > From: Laith Hamid > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > > spikes and seizures. Currently I am analysing an EEG data set that > was > > > > recorded using a 256-channel EGI system and I wanted to ask whether > you > > > > have a standard BEM or FEM head Subscript indices must either be real > > > positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > model that extends enough downwards to > > > > accomodate all 256 electrodes. The current standard BEM model in the > > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > > 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > thanks for your question. You could refer to a factory schematic > layout > > > > such as the one in figure 4 of this publication: > > > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > > > and subsequently use the function ft_prepare_layout to manually > track the > > > > points of the custom design on your own (if you dont want to wait for > > > > somebody from the FT to do the same for you). > > > > > > > > cfg = []; > > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > > lay = ft_prepare_layout(cfg); > > > > > > > > The following tutorial describes the procedure in more details: > > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > > > Please do not hesitate to get in touch with me for this and other > > > matters. > > > > > > > > All the best > > > > Cris Micheli > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear community, > > > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > Complex > > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes > > > and > > > > > seizures. Currently I am analysing an EEG data set that was > recorded > > > using > > > > > a 256-channel EGI system and I wanted to ask whether you have a > > > standard > > > > > BEM or FEM head model that extends enough downwards to accomodate > all > > > 256 > > > > > electrodes. The current standard BEM model in the template folder > of > > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > > > data. > > > > > > > > > > Thank you very much in advance for your help! > > > > > > > > > > Best, > > > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > > From: Laith Hamid > > > > To: Fieldtrip > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that > was > > > > discussed in this thread from April 2013: > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > > the cheeks or on the back of the neck and these areas are not > modeled by > > > > the standard BEM skin compartment in the standard BEM model. My > question > > > > was about a standard segmentation that extends the skin (and skull) > > > > compartment downwards to allow these electrodes to sit on the nodes > of > > > > the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 4 > > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > > From: aishwarya selvaraj > > > > To: "fieldtrip, donders" > > > > Subject: [FieldTrip] Source Localisation > > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 5 > > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > > From: Hom?lle, S. (Simon) > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ________________________________ > > > > From: fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > > To: fieldtrip, donders > > > > Subject: [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 6 > > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > > From: victoria schroeder > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] plotting neighbours > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > > > Things have become much clearer now. > > > > > > > > I would like to follow up with a very related question. I am trying > to > > > > replicate the analysis for the cluster based permutation test using > the > > > > code and the data provided. However, i run into two problems here > > > > > > > > First, i get the following error if i use the original code: > > > > Attempted to access cfg.frequency(2); index out of bounds because > > > > numel(cfg.frequency)=1. > > > > > > > > Error in ft_freqstatistics (line 187) > > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > > > fmax)]; > > > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 > 20]. > > > > However, then no significant clusters are found. Which becomes clear > when > > > > trying to plot the cluster or by looking at the output of > > > > ft_freqstatistics. > > > > > > > > Does the change in the code , change the output? How can i avoid the > > > error > > > > mentioned above and still get the same output from ft_freqstatistics > as > > > the > > > > one provided on the webpage? > > > > > > > > > > > > The relevant section of the toturial is provided below. > > > > Thank you! > > > > > > > > Victoria > > > > > > > > Permutation test > > > > > > > > Now, run *ft_freqstatistics > > > > * to > > > compare > > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > > > cfg.latency, > > > > the following configuration is identical to the configuration that > was > > > used > > > > for comparing event-related averages in the cluster-based permutation > > > tests > > > > on event related fields tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>. > > > > Also see this tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> > > > for > > > > a detailed explanation of all the configuration settings. You can > read > > > more > > > > about the *ft_prepare_neighbours > > > > * > > > function > > > > in the FAQ's > > > > < > http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work > > > >. > > > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > > servers,freqFIC_planar_cmb.mat > > > > < > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > > > and freqFC_planar_cmb.mat > > > > < > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > > > >), > > > > use: > > > > > > > > load freqFIC_planar_cmb > > > > load freqFC_planar_cmb > > > > > > > > cfg = []; > > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > > cfg.latency = 'all'; > > > > cfg.frequency = 20; > > > > cfg.method = 'montecarlo'; > > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > > cfg.correctm = 'cluster'; > > > > cfg.clusteralpha = 0.05; > > > > cfg.clusterstatistic = 'maxsum'; > > > > cfg.minnbchan = 2; > > > > cfg.tail = 0; > > > > cfg.clustertail = 0; > > > > cfg.alpha = 0.025; > > > > cfg.numrandomization = 500; > > > > % prepare_neighbours determines what sensors may form clusters > > > > cfg_neighb.method = 'distance'; > > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > > size(freqFC_planar_cmb.powspctrm,1)); > > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > > > cfg.design = design; > > > > cfg.ivar = 1; > > > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, > freqFC_planar_cmb); > > > > > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov < > tzvetan.popov at uni-konstanz.de > > > >: > > > > > > > > > > > > > > Hi Victoria, > > > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. > You are > > > > > right I was only scrolling up to the part where the mags were > > > analyzed. As > > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course > you > > > can > > > > > threat them separately, as I was naively thinking as non-neuormag > > > user, but > > > > > indeed combination of both is recommended as I have now learned > > > :-)(thanks > > > > > Phillip). I ran the following steps and I guess this should work > for > > > you. > > > > > best > > > > > tzvetan > > > > > > > > > > %% > > > > > cfg = []; > > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > > %% > > > > > cfg = [] > > > > > cfg.method = 'triangulation'; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > cfg.senstype = 'MEG'; > > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > > %% > > > > > % plot neighbours > > > > > cfg=[]; > > > > > cfg.neighbours = neighbours; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 7 > > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > this might be possible if you have the subject-specific MRI by > following > > > > the tutorial here: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > > > cfg=[]; > > > > cfg.tissue={'brain','skull','scalp'}; > > > > cfg.numvertices = [3000 2000 1000]; > > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable > should > > > > contain your triangulated surface with 1000 vertices. Let me know if > that > > > > works. Of course you should see the skin and the neck in the original > > > MRI. > > > > > > > > If you do not have an anatomical MRI that extends down to the chin > you > > > > could try with a template, such as this: > > > > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > > and the corresponding segmented version > > > > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > > > This goes down to the chin. Then you take care of rearranging the > > > position > > > > of the EEG electrodes according to this: > > > > > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > > > I hope this helped > > > > Cris > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear Cris, > > > > > > > > > > thank you very much for your answer. I am refering to an issue > that was > > > > > discussed in this thread from April 2013: > > > > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > > download. Some electrodes in the EGI 256-electrodes cap are placed > on > > > the > > > > > cheeks or on the back of the neck and these areas are not modeled > by > > > the > > > > > standard BEM skin compartment in the standard BEM model. My > question > > > was > > > > > about a standard segmentation that extends the skin (and skull) > > > compartment > > > > > downwards to allow these electrodes to sit on the nodes of the skin > > > mesh. > > > > > > > > > > Best, > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 8 > > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > > From: Munsif Jatoi > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Aishwarya, > > > > > > > > Please refer to main help tutorials. > > > > > > > > Also, you can find out the survey papers written in this area. For > more, > > > > SPM website can provide good help. > > > > > > > > Best, > > > > Munsif. > > > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > > > Dear Aishwarya, > > > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > > tutorials about source reconstruction. > > > > > > > > > > My recommended start would be: > > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > > reconstruction > > > > > > > > > > Best regards, > > > > > > > > > > Simon Hom?lle > > > > > PhD Candidate > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > Centre for Cognitive Neuroimaging > > > > > Radboud University Nijmegen > > > > > Phone: +31-(0)24-36-65059 > > > > > ------------------------------ > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > > > fieldtrip-bounces at science.ru.nl] > > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > > *To:* fieldtrip, donders > > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > > > Hi guys, > > > > > I'm currently working on source localization of EEG signals . > > > > > Im very new to it . > > > > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > > It would be of great help . > > > > > > > > > > -- > > > > > Regards, > > > > > Aishwarya > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > > > > > > -- > > > > Munsif Ali H.Jatoi, > > > > > > > > Ph D Scholar, > > > > Centre for Intelligent Signals and Imaging Research, > > > > Universiti Teknologi PETRONAS, > > > > Malaysia. > > > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > Message: 9 > > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > > From: Olga Sysoeva > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] problems with mri interpolation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Fieldtrippers, > > > > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > > > FT_VOLUMERESLICE. > > > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > > > mri_K0012.unit, 'm' > > > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > > > mri_K0012.transform, (4*4 double) > > > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > > > > Than I used > > > > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > > > > the output is > > > > > > > > > > > > ?the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > > > the input is volume data with dimensions [256 > > > > 256 256] > > > > > > > > the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > selecting subvolume of 0.0% > > > > > > > > reslicing and interpolating anatomy > > > > > > > > interpolating > > > > > > > > ??? Attempted to access sel(1); index out of > > > > bounds because numel(sel)=0. > > > > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > > at 663 > > > > > > > > ft_progress(sel(1)/num, 'interpolating > > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > > > cfg.feedback); > > > > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > > resliced);? > > > > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > > downloaded fieltrip (also in my previous version of 2013 the error > > > > was the same). > > > > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > > > > Best Regards, > > > > > > > > Olga. > > > > > > > > P.S.Actually, I can project my sources > > > > meaningfully into not interpolated MRI, altoough the images are > > > > plotted upside down. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > > ***************************************** > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/5f4a716a/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 2 > > Date: Thu, 21 Jan 2016 21:59:06 +0900 > > From: "Muhammad Naveed Iqbal Qureshi" > > To: > > Subject: [FieldTrip] difficulty in loading BCI-IV-2a dataset into > > fieldtrip for preprocessing > > Message-ID: <000b01d1544b$8323d8e0$896b8aa0$@gist.ac.kr> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi, > > > > > > > > I am using BCI competition IV dataset 2a for my experiment. > > > > I want to preprocess it with field trip. > > > > > > > > I have written the following code for this task. > > > > > > > > addpath(genpath('E:\bbci_data\fieldtrip-20160118\fieldtrip-20160118')); > > > > cd 'E:\bbci_data\BCICIV_2a_gdf\'; > > > > > > > > %% Field Trip preprocessing code > > > > for i=1:9 > > > > file=num2str(i); > > > > file=strcat('A0',file,'T.gdf'); > > > > cfg = []; > > > > cfg.dataset = file ; > > > > cfg.trialdef.eventtype = 'Stimulus'; > > > > cfg.trialdef.eventvalue = {'left', 'right', 'both feet', 'tongue'}; > > > > cfg.trialdef.triallength = 8; % duration in seconds > > > > cfg.trialdef.ntrials = inf; % number of trials, inf > > results in as many as possible > > > > cfg.trialdef.prestim = 3; > > > > cfg.trialdef.poststim = 6; > > > > cfg = ft_definetrial(cfg); > > > > > > > > cfg.bpfilter = 'yes'; > > > > cfg.bpfreq = [0.5 100]; > > > > cfg.bpfilttype = 'but'; > > > > cfg.bpfiltord = 5; > > > > cfg.demean = 'yes'; > > > > cfg.detrend = 'yes'; > > > > trialdata_EO{i} = ft_preprocessing(cfg); > > > > end > > > > > > > > However, this code does not import the event and trigger information from > > the header file of the data. > > > > I will be highly obliged if anyone can help me in this regard. > > > > > > > > Thank in advance. > > > > > > > > Best Regards, > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/1dbb2d2d/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 21 Jan 2016 20:14:01 +0200 > > From: saeed zahran > > To: "fieldtrip at science.ru.nl" > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 19 > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Thank you Jan and Cristiano; > > > > I downloaded another version of Fieldtrip thus the below error disappear: > > Error in triangle4pt (line 57) > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > But now I have another error: > > > > Error using surface_nesting (line 26) > > the compartment nesting cannot be determined > > > > Error in ft_headmodel_bemcp (line 66) > > order = surface_nesting(vol.bnd, 'insidefirst'); > > > > Error in ft_prepare_headmodel (line 253) > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > Error in openmeeg_eeg_leadfield_example (line 100) > > vol = ft_prepare_headmodel(cfg, vol); > > Thank you for any suggestion > > > > Cristiano, I record the contraction of the uterus; > > > > > > Best regards > > Saeed Zahran > > > > > From: fieldtrip-request at science.ru.nl > > > Subject: fieldtrip Digest, Vol 62, Issue 19 > > > To: fieldtrip at science.ru.nl > > > Date: Thu, 21 Jan 2016 12:00:02 +0100 > > > > > > Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > > You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > data recorded with EGI caps (Laith Hamid) (RICHARDS, JOHN) > > > 3. Re: fieldtrip Digest, Vol 62, Issue 18 (saeed zahran) > > > 4. Re: fieldtrip Digest, Vol 62, Issue 18 > > > (Schoffelen, J.M. (Jan Mathijs)) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Wed, 20 Jan 2016 13:39:30 +0100 > > > From: Laith Hamid > > > To: Fieldtrip > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps > > > Message-ID: <5ee6eeedb5d8a3a42f96840711d87ef1 at mail.uni-kiel.de> > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > Dear Cris, > > > > > > thank you very much for your answers yesterday. The segmentedmri > > > contained 'white', 'grey' and 'csf' so I needed to repeat the > > > segmentation using 'brain', 'skull' and 'scalp' as described in the > > > tutorial "Creating a BEM volume conduction model of the head for > > > source-reconstruction of EEG data" and everything worked smoothly > > > afterwards. The problem is solved now. > > > > > > Best, > > > Laith > > > > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/e700c8d6/attachment-0001.html > > > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Wed, 20 Jan 2016 14:39:13 +0000 > > > From: "RICHARDS, JOHN" > > > To: "fieldtrip at science.ru.nl" , > > > "lah at pedneuro.uni-kiel.de" > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > 256-electrode EEG data recorded with EGI caps (Laith Hamid) > > > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > > > > > Laith: > > > > > > I have a ?neurodevelopmental MRI database? (Richards, Sanchez et al., > 2015; see my www site) that has average MRI templates that could be used. > Each average has the whole head down to about the top of the neck. I did > these purposely since I use EEG recording and the MNI template did not even > go down far enough for the EGI 128 channel net. > > > > > > The database has average MRI templates for head (T1, T2) and brain. I > also have FEM segmented heads for the entire head that could be used for > this. Additionally, I have BEM segmented heads (e.g., brain, csf, skull, > scalp), but ironically, I cut these off about 10% below the EGI 128 channel > electrodes. However, you could use the three inner compartments for this > and just add the rest of the head below the compartment?or use the > whole-head FEM as is for a FEM-model, or use the segmented area below the > skull for a whole-head BEM model. I also have average 128-channel EGI > electrodes for each template. > > > > > > Additionally, the ?developmental? part of the ?neurodevelopmental MRI > database? is that I have these for a wide range of ages (all ages?). I have > a average for young adults (20-24 yrs), and average templates and FEM/BEM > models for groups from 3 months through adulthood, and into late adulthood. > So if you have specific neuro-pediatric applications you might be > interested in using an age appropriate MRI average template rather than an > adult template. > > > > > > See my www site for journal article references re this, and > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > > > > > Finally? I have been using these head models for FT-based FEM and BEM > models. Possibly some of the actually field trip models I have would be > useful to you. Some of the parts of the model do not use the electrodes > (e.g., grid-dipoles, head-model) whereas the final models (leadfield) > requires the electrode locations. The database also includes ?virtual? > electrodes for the 10-10 system, which might be used to generate the 256 > channel locations by knowing the relation between the 10-10 system and the > EGI system based on EGI ELP files for the 256 channels. > > > > > > John > > > > > > *********************************************** > > > John E. Richards Carolina Distinguished Professor > > > Department of Psychology > > > University of South Carolina > > > Columbia, SC 29208 > > > Dept Phone: 803 777 2079 > > > Fax: 803 777 9558 > > > Email: richards-john at sc.edu > > > HTTP: jerlab.psych.sc.edu > > > *********************************************** > > > > > > > > > > > > > > > >---------------------------------------------------------------------- > > > > > > > >Message: 1 > > > >Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > >From: Laith Hamid > > > >To: fieldtrip at science.ru.nl > > > >Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > >Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > >Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > >Dear community, > > > > > > > >My name is Laith Hamid and I am working in the University Medical > > > >Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > >spikes and seizures. Currently I am analysing an EEG data set that was > > > >recorded using a 256-channel EGI system and I wanted to ask whether > you > > > >have a standard BEM or FEM head model that extends enough downwards to > > > >accomodate all 256 electrodes. The current standard BEM model in the > > > >template folder of Fieldtrip isn't appropriate for source analysis of > > > >256-channel EGI data. > > > > > > > >Thank you very much in advance for your help! > > > > > > > >Best, > > > > > > > >Laith > > > > > > > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Wed, 20 Jan 2016 19:37:32 +0200 > > > From: saeed zahran > > > To: "fieldtrip at science.ru.nl" > > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear Fieldtrip community, > > > > > > I define the volume conductor as: > > > > > > vol = []; > > > vol.bnd(1).pnt=skinpnt > > > vol.bnd(1).tri=skinf > > > > > > vol.bnd(2).pnt=uteruspnt > > > vol.bnd(2).tri=uterusf > > > > > > vol.bnd(3).pnt=uterinecontentpnt > > > vol.bnd(3).tri=uterinecontentf > > > > > > vol.cond = c; > > > > > > > > > But it result with the below error: > > > > > > Subscript indices must either be real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > > > > Thank you very much in advance for your help! > > > > > > Best regards > > > Saeed Zahran > > > > > > > From: fieldtrip-request at science.ru.nl > > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > > To: fieldtrip at science.ru.nl > > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > > > Send fieldtrip mailing list submissions to > > > > fieldtrip at science.ru.nl > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > or, via email, send a message with subject or body 'help' to > > > > fieldtrip-request at science.ru.nl > > > > > > > > You can reach the person managing the list at > > > > fieldtrip-owner at science.ru.nl > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 4. Source Localisation (aishwarya selvaraj) > > > > 5. Re: Source Localisation (Hom?lle) > > > > 6. Re: plotting neighbours (victoria schroeder) > > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 8. Re: Source Localisation (Munsif Jatoi) > > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > > From: Laith Hamid > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > > spikes and seizures. Currently I am analysing an EEG data set that > was > > > > recorded using a 256-channel EGI system and I wanted to ask whether > you > > > > have a standard BEM or FEM head Subscript indices must either be > real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > model that extends enough downwards to > > > > accomodate all 256 electrodes. The current standard BEM model in the > > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > > 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > thanks for your question. You could refer to a factory schematic > layout > > > > such as the one in figure 4 of this publication: > > > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > > > and subsequently use the function ft_prepare_layout to manually > track the > > > > points of the custom design on your own (if you dont want to wait for > > > > somebody from the FT to do the same for you). > > > > > > > > cfg = []; > > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > > lay = ft_prepare_layout(cfg); > > > > > > > > The following tutorial describes the procedure in more details: > > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > > > Please do not hesitate to get in touch with me for this and other > matters. > > > > > > > > All the best > > > > Cris Micheli > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear community, > > > > > > > > > > My name is Laith Hamid and I am working in the University Medical > Complex > > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and > > > > > seizures. Currently I am analysing an EEG data set that was > recorded using > > > > > a 256-channel EGI system and I wanted to ask whether you have a > standard > > > > > BEM or FEM head model that extends enough downwards to accomodate > all 256 > > > > > electrodes. The current standard BEM model in the template folder > of > > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > data. > > > > > > > > > > Thank you very much in advance for your help! > > > > > > > > > > Best, > > > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > > From: Laith Hamid > > > > To: Fieldtrip > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that > was > > > > discussed in this thread from April 2013: > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > > the cheeks or on the back of the neck and these areas are not > modeled by > > > > the standard BEM skin compartment in the standard BEM model. My > question > > > > was about a standard segmentation that extends the skin (and skull) > > > > compartment downwards to allow these electrodes to sit on the nodes > of > > > > the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 4 > > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > > From: aishwarya selvaraj > > > > To: "fieldtrip, donders" > > > > Subject: [FieldTrip] Source Localisation > > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 5 > > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > > From: Hom?lle, S. (Simon) > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ________________________________ > > > > From: fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] on behalf of aishwarya selvaraj [ > aishwaryaselvaraj1708 at gmail.com] > > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > > To: fieldtrip, donders > > > > Subject: [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 6 > > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > > From: victoria schroeder > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] plotting neighbours > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > > > Things have become much clearer now. > > > > > > > > I would like to follow up with a very related question. I am trying > to > > > > replicate the analysis for the cluster based permutation test using > the > > > > code and the data provided. However, i run into two problems here > > > > > > > > First, i get the following error if i use the original code: > > > > Attempted to access cfg.frequency(2); index out of bounds because > > > > numel(cfg.frequency)=1. > > > > > > > > Error in ft_freqstatistics (line 187) > > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > fmax)]; > > > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 > 20]. > > > > However, then no significant clusters are found. Which becomes clear > when > > > > trying to plot the cluster or by looking at the output of > > > > ft_freqstatistics. > > > > > > > > Does the change in the code , change the output? How can i avoid the > error > > > > mentioned above and still get the same output from ft_freqstatistics > as the > > > > one provided on the webpage? > > > > > > > > > > > > The relevant section of the toturial is provided below. > > > > Thank you! > > > > > > > > Victoria > > > > > > > > Permutation test > > > > > > > > Now, run *ft_freqstatistics > > > > * to > compare > > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > cfg.latency, > > > > the following configuration is identical to the configuration that > was used > > > > for comparing event-related averages in the cluster-based > permutation tests > > > > on event related fields tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>. > > > > Also see this tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> for > > > > a detailed explanation of all the configuration settings. You can > read more > > > > about the *ft_prepare_neighbours > > > > * > function > > > > in the FAQ's > > > > < > http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work>. > > > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > > servers,freqFIC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > >), > > > > use: > > > > > > > > load freqFIC_planar_cmb > > > > load freqFC_planar_cmb > > > > > > > > cfg = []; > > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > > cfg.latency = 'all'; > > > > cfg.frequency = 20; > > > > cfg.method = 'montecarlo'; > > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > > cfg.correctm = 'cluster'; > > > > cfg.clusteralpha = 0.05; > > > > cfg.clusterstatistic = 'maxsum'; > > > > cfg.minnbchan = 2; > > > > cfg.tail = 0; > > > > cfg.clustertail = 0; > > > > cfg.alpha = 0.025; > > > > cfg.numrandomization = 500; > > > > % prepare_neighbours determines what sensors may form clusters > > > > cfg_neighb.method = 'distance'; > > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > > size(freqFC_planar_cmb.powspctrm,1)); > > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > > > cfg.design = design; > > > > cfg.ivar = 1; > > > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, > freqFC_planar_cmb); > > > > > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov < > tzvetan.popov at uni-konstanz.de>: > > > > > > > > > > > > > > Hi Victoria, > > > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. > You are > > > > > right I was only scrolling up to the part where the mags were > analyzed. As > > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course > you can > > > > > threat them separately, as I was naively thinking as non-neuormag > user, but > > > > > indeed combination of both is recommended as I have now learned > :-)(thanks > > > > > Phillip). I ran the following steps and I guess this should work > for you. > > > > > best > > > > > tzvetan > > > > > > > > > > %% > > > > > cfg = []; > > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > > %% > > > > > cfg = [] > > > > > cfg.method = 'triangulation'; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > cfg.senstype = 'MEG'; > > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > > %% > > > > > % plot neighbours > > > > > cfg=[]; > > > > > cfg.neighbours = neighbours; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 7 > > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > > From: Cristiano Micheli > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > this might be possible if you have the subject-specific MRI by > following > > > > the tutorial here: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > > > cfg=[]; > > > > cfg.tissue={'brain','skull','scalp'}; > > > > cfg.numvertices = [3000 2000 1000]; > > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable > should > > > > contain your triangulated surface with 1000 vertices. Let me know if > that > > > > works. Of course you should see the skin and the neck in the > original MRI. > > > > > > > > If you do not have an anatomical MRI that extends down to the chin > you > > > > could try with a template, such as this: > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > > and the corresponding segmented version > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > > > This goes down to the chin. Then you take care of rearranging the > position > > > > of the EEG electrodes according to this: > > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > > > I hope this helped > > > > Cris > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear Cris, > > > > > > > > > > thank you very much for your answer. I am refering to an issue > that was > > > > > discussed in this thread from April 2013: > > > > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > > download. Some electrodes in the EGI 256-electrodes cap are placed > on the > > > > > cheeks or on the back of the neck and these areas are not modeled > by the > > > > > standard BEM skin compartment in the standard BEM model. My > question was > > > > > about a standard segmentation that extends the skin (and skull) > compartment > > > > > downwards to allow these electrodes to sit on the nodes of the > skin mesh. > > > > > > > > > > Best, > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 8 > > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > > From: Munsif Jatoi > > > > To: FieldTrip discussion list > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Aishwarya, > > > > > > > > Please refer to main help tutorials. > > > > > > > > Also, you can find out the survey papers written in this area. For > more, > > > > SPM website can provide good help. > > > > > > > > Best, > > > > Munsif. > > > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > > > Dear Aishwarya, > > > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > > tutorials about source reconstruction. > > > > > > > > > > My recommended start would be: > > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > > reconstruction > > > > > > > > > > Best regards, > > > > > > > > > > Simon Hom?lle > > > > > PhD Candidate > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > Centre for Cognitive Neuroimaging > > > > > Radboud University Nijmegen > > > > > Phone: +31-(0)24-36-65059 > > > > > ------------------------------ > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > fieldtrip-bounces at science.ru.nl] > > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com] > > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > > *To:* fieldtrip, donders > > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > > > Hi guys, > > > > > I'm currently working on source localization of EEG signals . > > > > > Im very new to it . > > > > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > > It would be of great help . > > > > > > > > > > -- > > > > > Regards, > > > > > Aishwarya > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > > > > > > -- > > > > Munsif Ali H.Jatoi, > > > > > > > > Ph D Scholar, > > > > Centre for Intelligent Signals and Imaging Research, > > > > Universiti Teknologi PETRONAS, > > > > Malaysia. > > > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 9 > > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > > From: Olga Sysoeva > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] problems with mri interpolation > > > > Message-ID: > > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Fieldtrippers, > > > > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > > > FT_VOLUMERESLICE. > > > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > > > mri_K0012.unit, 'm' > > > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > > > mri_K0012.transform, (4*4 double) > > > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > > > > Than I used > > > > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > > > > the output is > > > > > > > > > > > > ?the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > > > the input is volume data with dimensions [256 > > > > 256 256] > > > > > > > > the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > selecting subvolume of 0.0% > > > > > > > > reslicing and interpolating anatomy > > > > > > > > interpolating > > > > > > > > ??? Attempted to access sel(1); index out of > > > > bounds because numel(sel)=0. > > > > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > > at 663 > > > > > > > > ft_progress(sel(1)/num, 'interpolating > > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > > > cfg.feedback); > > > > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > > resliced);? > > > > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > > downloaded fieltrip (also in my previous version of 2013 the error > > > > was the same). > > > > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > > > > Best Regards, > > > > > > > > Olga. > > > > > > > > P.S.Actually, I can project my sources > > > > meaningfully into not interpolated MRI, altoough the images are > > > > plotted upside down. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > > ***************************************** > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/0d8cf652/attachment-0001.html > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Thu, 21 Jan 2016 08:16:55 +0000 > > > From: "Schoffelen, J.M. (Jan Mathijs)" > > > To: FieldTrip discussion list > > > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 62, Issue 18 > > > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Saeed, > > > > > > are you using 0 or 1 indexing for your triangles? You probably want to > use 1 indexing. > > > > > > Best, > > > Jan-Mathijs > > > > > > > > > On Jan 20, 2016, at 6:37 PM, saeed zahran > wrote: > > > > > > Dear Fieldtrip community, > > > > > > I define the volume conductor as: > > > > > > vol = []; > > > vol.bnd(1).pnt=skinpnt > > > vol.bnd(1).tri=skinf > > > > > > vol.bnd(2).pnt=uteruspnt > > > vol.bnd(2).tri=uterusf > > > > > > vol.bnd(3).pnt=uterinecontentpnt > > > vol.bnd(3).tri=uterinecontentf > > > > > > vol.cond = c; > > > > > > > > > But it result with the below error: > > > > > > Subscript indices must either be real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > > > > > > > Thank you very much in advance for your help! > > > > > > Best regards > > > Saeed Zahran > > > > > > > From: fieldtrip-request at science.ru.nl fieldtrip-request at science.ru.nl> > > > > Subject: fieldtrip Digest, Vol 62, Issue 18 > > > > To: fieldtrip at science.ru.nl > > > > Date: Wed, 20 Jan 2016 12:00:02 +0100 > > > > > > > > Send fieldtrip mailing list submissions to > > > > fieldtrip at science.ru.nl > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > or, via email, send a message with subject or body 'help' to > > > > fieldtrip-request at science.ru.nl fieldtrip-request at science.ru.nl> > > > > > > > > You can reach the person managing the list at > > > > fieldtrip-owner at science.ru.nl > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > than "Re: Contents of fieldtrip digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 2. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 3. Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Laith Hamid) > > > > 4. Source Localisation (aishwarya selvaraj) > > > > 5. Re: Source Localisation (Hom?lle) > > > > 6. Re: plotting neighbours (victoria schroeder) > > > > 7. Re: Standard BEM or FEM models for use with 256-electrode EEG > > > > data recorded with EGI caps (Cristiano Micheli) > > > > 8. Re: Source Localisation (Munsif Jatoi) > > > > 9. problems with mri interpolation (Olga Sysoeva) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Tue, 19 Jan 2016 15:35:00 +0100 > > > > From: Laith Hamid lah at pedneuro.uni-kiel.de>> > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <0c2e8c0fa08db25ba3bb87c130fe0d7f at mail.uni-kiel.de > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear community, > > > > > > > > My name is Laith Hamid and I am working in the University Medical > > > > Complex of Schleswig-Holstein in Kiel on source analysis of epileptic > > > > spikes and seizures. Currently I am analysing an EEG data set that > was > > > > recorded using a 256-channel EGI system and I wanted to ask whether > you > > > > have a standard BEM or FEM head Subscript indices must either be > real positive integers or logicals. > > > > > > Error in triangle4pt (line 57) > > > sph_pnt = pnt([tri(jj,:) lv],:); > > > > > > Error in ft_headmodel_bemcp (line 101) > > > vol = triangle4pt(vol); > > > > > > Error in ft_prepare_headmodel (line 253) > > > vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); > > > > > > Error in openmeeg_eeg_leadfield_example_me (line 91) > > > vol = ft_prepare_headmodel(cfg, vol); > > > model that extends enough downwards to > > > > accomodate all 256 electrodes. The current standard BEM model in the > > > > template folder of Fieldtrip isn't appropriate for source analysis of > > > > 256-channel EGI data. > > > > > > > > Thank you very much in advance for your help! > > > > > > > > Best, > > > > > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Tue, 19 Jan 2016 16:16:54 +0100 > > > > From: Cristiano Micheli michelic72 at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > thanks for your question. You could refer to a factory schematic > layout > > > > such as the one in figure 4 of this publication: > > > > > http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract > > > > > > > > and subsequently use the function ft_prepare_layout to manually > track the > > > > points of the custom design on your own (if you dont want to wait for > > > > somebody from the FT to do the same for you). > > > > > > > > cfg = []; > > > > cfg.image = 'figure4_layout_256_Frontiers.png'; > > > > lay = ft_prepare_layout(cfg); > > > > > > > > The following tutorial describes the procedure in more details: > > > > http://www.fieldtriptoolbox.org/tutorial/layout > > > > > > > > Please do not hesitate to get in touch with me for this and other > matters. > > > > > > > > All the best > > > > Cris Micheli > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear community, > > > > > > > > > > My name is Laith Hamid and I am working in the University Medical > Complex > > > > > of Schleswig-Holstein in Kiel on source analysis of epileptic > spikes and > > > > > seizures. Currently I am analysing an EEG data set that was > recorded using > > > > > a 256-channel EGI system and I wanted to ask whether you have a > standard > > > > > BEM or FEM head model that extends enough downwards to accomodate > all 256 > > > > > electrodes. The current standard BEM model in the template folder > of > > > > > Fieldtrip isn't appropriate for source analysis of 256-channel EGI > data. > > > > > > > > > > Thank you very much in advance for your help! > > > > > > > > > > Best, > > > > > > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Tue, 19 Jan 2016 17:41:48 +0100 > > > > From: Laith Hamid lah at pedneuro.uni-kiel.de>> > > > > To: Fieldtrip fieldtrip at science.ru.nl>> > > > > Subject: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: <61e8cefadba890a26ecd0b9adf0bca9b at mail.uni-kiel.de > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > > > > > > > Dear Cris, > > > > > > > > thank you very much for your answer. I am refering to an issue that > was > > > > discussed in this thread from April 2013: > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > The thread however does not offer a segmentation or head model for > > > > download. Some electrodes in the EGI 256-electrodes cap are placed on > > > > the cheeks or on the back of the neck and these areas are not > modeled by > > > > the standard BEM skin compartment in the standard BEM model. My > question > > > > was about a standard segmentation that extends the skin (and skull) > > > > compartment downwards to allow these electrodes to sit on the nodes > of > > > > the skin mesh. > > > > > > > > Best, > > > > Laith > > > > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 4 > > > > Date: Tue, 19 Jan 2016 16:52:55 +0000 > > > > From: aishwarya selvaraj aishwaryaselvaraj1708 at gmail.com>> > > > > To: "fieldtrip, donders" fieldtrip at donders.ru.nl>> > > > > Subject: [FieldTrip] Source Localisation > > > > Message-ID: <3ff5de7a69704e8d9e873e3f94120ad7 at EXPRD01.hosting.ru.nl > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 5 > > > > Date: Tue, 19 Jan 2016 17:06:13 +0000 > > > > From: Hom?lle, S. (Simon) S.Homolle at donders.ru.nl>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > <2247A6E8AF3DB04AAB11BDDD86B72F830335254E at exprd01.hosting.ru.nl > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear Aishwarya, > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > tutorials about source reconstruction. > > > > > > > > My recommended start would be: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > reconstruction > > > > > > > > Best regards, > > > > > > > > Simon Hom?lle > > > > PhD Candidate > > > > Donders Institute for Brain, Cognition and Behaviour > > > > Centre for Cognitive Neuroimaging > > > > Radboud University Nijmegen > > > > Phone: +31-(0)24-36-65059 > > > > ________________________________ > > > > From: fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl>] on behalf of aishwarya selvaraj [ > aishwaryaselvaraj1708 at gmail.com] > > > > Sent: Tuesday, January 19, 2016 5:52 PM > > > > To: fieldtrip, donders > > > > Subject: [FieldTrip] Source Localisation > > > > > > > > Hi guys, > > > > I'm currently working on source localization of EEG signals . > > > > Im very new to it . > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > It would be of great help . > > > > > > > > -- > > > > Regards, > > > > Aishwarya > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 6 > > > > Date: Tue, 19 Jan 2016 17:49:21 +0000 > > > > From: victoria schroeder vic.schroeder2 at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] plotting neighbours > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Thank you very much Philipp and Tzvetan! > > > > > > > > Things have become much clearer now. > > > > > > > > I would like to follow up with a very related question. I am trying > to > > > > replicate the analysis for the cluster based permutation test using > the > > > > code and the data provided. However, i run into two problems here > > > > > > > > First, i get the following error if i use the original code: > > > > Attempted to access cfg.frequency(2); index out of bounds because > > > > numel(cfg.frequency)=1. > > > > > > > > Error in ft_freqstatistics (line 187) > > > > cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), > fmax)]; > > > > > > > > Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 > 20]. > > > > However, then no significant clusters are found. Which becomes clear > when > > > > trying to plot the cluster or by looking at the output of > > > > ft_freqstatistics. > > > > > > > > Does the change in the code , change the output? How can i avoid the > error > > > > mentioned above and still get the same output from ft_freqstatistics > as the > > > > one provided on the webpage? > > > > > > > > > > > > The relevant section of the toturial is provided below. > > > > Thank you! > > > > > > > > Victoria > > > > > > > > Permutation test > > > > > > > > Now, run *ft_freqstatistics > > > > * to > compare > > > > freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field > cfg.latency, > > > > the following configuration is identical to the configuration that > was used > > > > for comparing event-related averages in the cluster-based > permutation tests > > > > on event related fields tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock>. > > > > Also see this tutorial > > > > < > http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock> for > > > > a detailed explanation of all the configuration settings. You can > read more > > > > about the *ft_prepare_neighbours > > > > * > function > > > > in the FAQ's > > > > < > http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work>. > > > > > > > > To load the planar gradient TFRs (also available on the FieldTrip FTP > > > > servers,freqFIC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat > > > > > > and freqFC_planar_cmb.mat > > > > < > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat > >), > > > > use: > > > > > > > > load freqFIC_planar_cmb > > > > load freqFC_planar_cmb > > > > > > > > cfg = []; > > > > cfg.channel = {'MEG', '-MLP31', '-MLO12'}; > > > > cfg.latency = 'all'; > > > > cfg.frequency = 20; > > > > cfg.method = 'montecarlo'; > > > > cfg.statistic = 'ft_statfun_indepsamplesT'; > > > > cfg.correctm = 'cluster'; > > > > cfg.clusteralpha = 0.05; > > > > cfg.clusterstatistic = 'maxsum'; > > > > cfg.minnbchan = 2; > > > > cfg.tail = 0; > > > > cfg.clustertail = 0; > > > > cfg.alpha = 0.025; > > > > cfg.numrandomization = 500; > > > > % prepare_neighbours determines what sensors may form clusters > > > > cfg_neighb.method = 'distance'; > > > > cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC); > > > > > > > > design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) + > > > > size(freqFC_planar_cmb.powspctrm,1)); > > > > design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1; > > > > > design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+... > > > > size(freqFC_planar_cmb.powspctrm,1))) = 2; > > > > > > > > cfg.design = design; > > > > cfg.ivar = 1; > > > > > > > > [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, > freqFC_planar_cmb); > > > > > > > > > > > > > > > > 2016-01-18 17:57 GMT+00:00 Tzvetan Popov < > tzvetan.popov at uni-konstanz.de>: > > > > > > > > > > > > > > Hi Victoria, > > > > > > > > > > oopsy, I think I confused you dramatically. I?m sorry for this. > You are > > > > > right I was only scrolling up to the part where the mags were > analyzed. As > > > > > for combining the MEG*2 and MEG*3 I was wrong there too. Of course > you can > > > > > threat them separately, as I was naively thinking as non-neuormag > user, but > > > > > indeed combination of both is recommended as I have now learned > :-)(thanks > > > > > Phillip). I ran the following steps and I guess this should work > for you. > > > > > best > > > > > tzvetan > > > > > > > > > > %% > > > > > cfg = []; > > > > > ComCon = ft_combineplanar(cfg,FreqCon); > > > > > %% > > > > > cfg = [] > > > > > cfg.method = 'triangulation'; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > cfg.senstype = 'MEG'; > > > > > neighbours = ft_prepare_neighbours(cfg, ComCon) > > > > > %% > > > > > % plot neighbours > > > > > cfg=[]; > > > > > cfg.neighbours = neighbours; > > > > > cfg.layout = 'neuromag306cmb.lay'; > > > > > ft_neighbourplot(cfg); > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 7 > > > > Date: Tue, 19 Jan 2016 20:50:24 +0100 > > > > From: Cristiano Micheli michelic72 at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Standard BEM or FEM models for use with > > > > 256-electrode EEG data recorded with EGI caps > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Laith, > > > > > > > > this might be possible if you have the subject-specific MRI by > following > > > > the tutorial here: > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > > > > and using the function ft_prepare_mesh and the tutorial command: > > > > > > > > cfg=[]; > > > > cfg.tissue={'brain','skull','scalp'}; > > > > cfg.numvertices = [3000 2000 1000]; > > > > bnd=ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > > > > > which uses the segmented MRI (see tutorial). The bnd(3) variable > should > > > > contain your triangulated surface with 1000 vertices. Let me know if > that > > > > works. Of course you should see the skin and the neck in the > original MRI. > > > > > > > > If you do not have an anatomical MRI that extends down to the chin > you > > > > could try with a template, such as this: > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri > > > > and the corresponding segmented version > > > > > ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat > > > > > > > > This goes down to the chin. Then you take care of rearranging the > position > > > > of the EEG electrodes according to this: > > > > > > > > > http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel > > > > > > > > I hope this helped > > > > Cris > > > > > > > > > > > > > > > > > > > > On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid < > lah at pedneuro.uni-kiel.de> > > > > wrote: > > > > > > > > > Dear Cris, > > > > > > > > > > thank you very much for your answer. I am refering to an issue > that was > > > > > discussed in this thread from April 2013: > > > > > > > > > > > > > > > [FieldTrip] source analysis EEG data without MRI > > > > > > > > > > > > > > > The thread however does not offer a segmentation or head model for > > > > > download. Some electrodes in the EGI 256-electrodes cap are placed > on the > > > > > cheeks or on the back of the neck and these areas are not modeled > by the > > > > > standard BEM skin compartment in the standard BEM model. My > question was > > > > > about a standard segmentation that extends the skin (and skull) > compartment > > > > > downwards to allow these electrodes to sit on the nodes of the > skin mesh. > > > > > > > > > > Best, > > > > > Laith > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 8 > > > > Date: Wed, 20 Jan 2016 12:17:12 +0800 > > > > From: Munsif Jatoi munsif.jatoi at gmail.com>> > > > > To: FieldTrip discussion list fieldtrip at science.ru.nl>> > > > > Subject: Re: [FieldTrip] Source Localisation > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Aishwarya, > > > > > > > > Please refer to main help tutorials. > > > > > > > > Also, you can find out the survey papers written in this area. For > more, > > > > SPM website can provide good help. > > > > > > > > Best, > > > > Munsif. > > > > > > > > On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) < > > > > S.Homolle at donders.ru.nl> wrote: > > > > > > > > > Dear Aishwarya, > > > > > > > > > > Under http://www.fieldtriptoolbox.org/tutorial there are several > > > > > tutorials about source reconstruction. > > > > > > > > > > My recommended start would be: > > > > > http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem > > > > > http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate > > > > > > > > > > > > > > > Hopefully this provides you good start working with EEG source > > > > > reconstruction > > > > > > > > > > Best regards, > > > > > > > > > > Simon Hom?lle > > > > > PhD Candidate > > > > > Donders Institute for Brain, Cognition and Behaviour > > > > > Centre for Cognitive Neuroimaging > > > > > Radboud University Nijmegen > > > > > Phone: +31-(0)24-36-65059 > > > > > ------------------------------ > > > > > *From:* fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl>] > > > > > on behalf of aishwarya selvaraj [aishwaryaselvaraj1708 at gmail.com > ] > > > > > *Sent:* Tuesday, January 19, 2016 5:52 PM > > > > > *To:* fieldtrip, donders > > > > > *Subject:* [FieldTrip] Source Localisation > > > > > > > > > > Hi guys, > > > > > I'm currently working on source localization of EEG signals . > > > > > Im very new to it . > > > > > > > > > > > > > > > Can Anyone provide any inputs ?? > > > > > It would be of great help . > > > > > > > > > > -- > > > > > Regards, > > > > > Aishwarya > > > > > > > > > > _______________________________________________ > > > > > fieldtrip mailing list > > > > > fieldtrip at donders.ru.nl > > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > > > > > > > > > > > > -- > > > > Munsif Ali H.Jatoi, > > > > > > > > Ph D Scholar, > > > > Centre for Intelligent Signals and Imaging Research, > > > > Universiti Teknologi PETRONAS, > > > > Malaysia. > > > > > > > > http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > Message: 9 > > > > Date: Wed, 20 Jan 2016 13:36:16 +0300 > > > > From: Olga Sysoeva olga.v.sysoeva at gmail.com>> > > > > To: fieldtrip at science.ru.nl > > > > Subject: [FieldTrip] problems with mri interpolation > > > > Message-ID: > > > > >> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > Dear Fieldtrippers, > > > > > > > > > > > > I'm encounter the problem with MRI interpolation and reslicing using > > > > > > > > FT_VOLUMERESLICE. > > > > > > > > I have read my MRI from fif.file and this mri variable contains > > > > > > > > mri_K0012.unit, 'm' > > > > > > > > mri_K0012.dim, [432, 512, 180] > > > > > > > > mri_K0012.anatomy, <432, 512, 180 int16> > > > > > > > > mri_K0012.hdr, (1*1 structure) > > > > > > > > mri_K0012.transform, (4*4 double) > > > > > > > > mri_K0012.coordsys 'neuromag'. > > > > > > > > > > > > Than I used > > > > > > > > > > > > mri = ft_volumereslice([], mri); > > > > > > > > > > > > the output is > > > > > > > > > > > > ?the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > reslicing from [432 512 180] to [256 256 256] > > > > > > > > the input is volume data with dimensions [256 > > > > 256 256] > > > > > > > > the input is volume data with dimensions [432 > > > > 512 180] > > > > > > > > selecting subvolume of 0.0% > > > > > > > > reslicing and interpolating anatomy > > > > > > > > interpolating > > > > > > > > ??? Attempted to access sel(1); index out of > > > > bounds because numel(sel)=0. > > > > > > > > > > > > Error in ==> ft_sourceinterpolate>my_interpn > > > > at 663 > > > > > > > > ft_progress(sel(1)/num, 'interpolating > > > > %.1f%%\n', 100*sel(1)/num); > > > > > > > > > > > > Error in ==> ft_sourceinterpolate at 583 > > > > > > > > av( sel) = my_interpn(fv, ax(sel), > > > > ay(sel), az(sel), cfg.interpmethod, > > > > > > > > cfg.feedback); > > > > > > > > > > > > Error in ==> ft_volumereslice at 176 > > > > > > > > resliced = ft_sourceinterpolate(tmpcfg, mri, > > > > resliced);? > > > > > > > > > > > > I'm using matlab 7.6.0 (R2008a) and recently > > > > downloaded fieltrip (also in my previous version of 2013 the error > > > > was the same). > > > > > > > > > > > > I'd be thankful for the comments. > > > > > > > > > > > > Best Regards, > > > > > > > > Olga. > > > > > > > > P.S.Actually, I can project my sources > > > > meaningfully into not interpolated MRI, altoough the images are > > > > plotted upside down. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > fieldtrip mailing list > > > > fieldtrip at donders.ru.nl > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > End of fieldtrip Digest, Vol 62, Issue 18 > > > > ***************************************** > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/d9124654/attachment-0001.html > > > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > End of fieldtrip Digest, Vol 62, Issue 19 > > > ***************************************** > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160121/043a7628/attachment.html > > > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 20 > > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.roux at bcbl.eu Mon Jan 25 11:55:27 2016 From: f.roux at bcbl.eu (=?utf-8?B?RnLDqWTDqXJpYw==?= Roux) Date: Mon, 25 Jan 2016 11:55:27 +0100 (CET) Subject: [FieldTrip] cross-frequency coupling between MEG planar channel twins? Message-ID: <1957967079.822957.1453719327381.JavaMail.zimbra@bcbl.eu> Dear all, in my MEG-data (Elekta Vectorview System) I am observing that the amplitude of higher frequencies over one planar gradient channel is coupled to the phase of lower frequencies on its corresponding twin-channel . I am attaching a figure to illustrate this. The upper row shows a low-frequency oscillation for one planar-channel and the bottom row shows the amplitude of a higher-frequency oscillation on its corresponding twin channel. Note that this separation is fairly consistent across other channels as well. My question relates to what could explain such a coupling of low and high freq activity over channel-pairs with different gradient orientations (ie vertical vs. horizontal)? Could this be an indicator of two separate sources which are being picked up by the different spatial sensitivity of the planar gradients and where the phase of one source modulates the amplitude of the other source? Any comments or suggestions on this would be highly appreciated. Fred -- Frédéric Roux Postdoctoral Scientist, Marie-Curie fellow BCBL. Basque Center on Cognition, Brain & Language. f.roux at bcbl.eu Tel: +34 943 309 300 Ext 211 Fax: +34 943 309 052 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer --------------------------------------------------------------------------- “The probability of success is difficult to estimate; but if we never search the chance of success is zero.” -------------- next part -------------- A non-text attachment was scrubbed... Name: low_high_coupling_planar_grads_TFR.png Type: image/png Size: 26838 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: low_high_coupling_planar_grads.png Type: image/png Size: 11179 bytes Desc: not available URL: From saeedzahran at hotmail.com Mon Jan 25 18:08:07 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Mon, 25 Jan 2016 19:08:07 +0200 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Thank you Cris, but I am sure that the meshes is nested, does it require to calculate the normal for each vertices? Best regards Saeed. > From: fieldtrip-request at science.ru.nl > Subject: fieldtrip Digest, Vol 62, Issue 24 > To: fieldtrip at science.ru.nl > Date: Mon, 25 Jan 2016 12:00:02 +0100 > > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. cross-frequency coupling between MEG planar channel twins? > (Fr?d?ric Roux) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 25 Jan 2016 11:55:27 +0100 (CET) > From: Fr?d?ric Roux > To: FieldTrip discussion list > Subject: [FieldTrip] cross-frequency coupling between MEG planar > channel twins? > Message-ID: <1957967079.822957.1453719327381.JavaMail.zimbra at bcbl.eu> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > in my MEG-data (Elekta Vectorview System) I am observing that the amplitude of higher frequencies over one planar gradient channel is coupled to the > phase of lower frequencies on its corresponding twin-channel . I am attaching a figure to illustrate this. The upper row shows a low-frequency oscillation for one planar-channel and the bottom row shows the amplitude of a higher-frequency oscillation on its corresponding twin channel. Note that this separation is fairly consistent across other channels as well. > > My question relates to what could explain such a coupling of low and high freq activity over channel-pairs with different gradient orientations (ie vertical vs. horizontal)? > > Could this be an indicator of two separate sources which are being picked up by the different spatial sensitivity of the planar gradients and where the phase of one source modulates the amplitude of the other source? > > Any comments or suggestions on this would be highly appreciated. > > Fred > > > > > > > > -- > Fr?d?ric Roux > Postdoctoral Scientist, Marie-Curie fellow > BCBL. Basque Center on Cognition, Brain & Language. > > f.roux at bcbl.eu > Tel: +34 943 309 300 Ext 211 > Fax: +34 943 309 052 > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > --------------------------------------------------------------------------- > > ?The probability of success is difficult to estimate; but if we never search the chance of success is zero.? > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: low_high_coupling_planar_grads_TFR.png > Type: image/png > Size: 26838 bytes > Desc: not available > URL: > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: low_high_coupling_planar_grads.png > Type: image/png > Size: 11179 bytes > Desc: not available > URL: > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 62, Issue 24 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From toni.rbaena at gmail.com Mon Jan 25 18:15:55 2016 From: toni.rbaena at gmail.com (Antonio Rodriguez) Date: Mon, 25 Jan 2016 18:15:55 +0100 Subject: [FieldTrip] =?utf-8?q?Can=C2=B4t_read_CFS_files=2E?= Message-ID: Dear Fieldtrippers, My name is Antonio Rodriguez, i´m very new with fieldtrip., We´re trying to open a file with CFS extension (Cambridge Electronic Design), which is the format that Signal Software returns, but i can´t read the file. I´m trying to load the file "dataset.cfs"; no error is prompted but nothing is loaded in the Workspace, I found in the tutorial that fieldtrip is able to open this kind of files. Am i doing anything wrong? Thank you. Antonio Rodriguez, University of Seville. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Mon Jan 25 18:57:04 2016 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Mon, 25 Jan 2016 09:57:04 -0800 Subject: [FieldTrip] =?utf-8?q?Can=C2=B4t_read_CFS_files=2E?= In-Reply-To: References: Message-ID: Hi Antonio, How are you trying to load the file? To see whether your format is supported, try: hdr = ft_read_header('dataset.cfs') Hope that gets you started, Arjen 2016-01-25 9:15 GMT-08:00 Antonio Rodriguez : > Dear Fieldtrippers, > > My name is Antonio Rodriguez, i´m very new with fieldtrip., We´re trying > to open a file with CFS extension (Cambridge Electronic Design), which is > the format that Signal Software returns, but i can´t read the file. > > I´m trying to load the file "dataset.cfs"; no error is prompted but > nothing is loaded in the Workspace, I found in the tutorial that fieldtrip > is able to open this kind of files. > > Am i doing anything wrong? > > Thank you. > > > Antonio Rodriguez, University of Seville. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Mon Jan 25 19:41:53 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Mon, 25 Jan 2016 19:41:53 +0100 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: Message-ID: Hi Saeed, could you be more specific by attaching the nesting matrix? You find it by typing: dbstop if error in the matlab workspace. and then by running your script again. The script will stop at the line where it fails and at that point you will be able to look inside the local variables of the subfunction that is returning the error (in your case it is the private function surface_nesting.m). Please copy the content of the variables *nesting* and * numboundaries* in the next email. At that point I will have enough information to help you. I don't think the normals are a problem here. Best regards, Cris On Mon, Jan 25, 2016 at 6:08 PM, saeed zahran wrote: > Thank you Cris, but I am sure that the meshes is nested, > does it require to calculate the normal for each vertices? > > Best regards > Saeed. > > > > From: fieldtrip-request at science.ru.nl > > Subject: fieldtrip Digest, Vol 62, Issue 24 > > To: fieldtrip at science.ru.nl > > Date: Mon, 25 Jan 2016 12:00:02 +0100 > > > > Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > > You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of fieldtrip digest..." > > > > > > Today's Topics: > > > > 1. cross-frequency coupling between MEG planar channel twins? > > (Fr?d?ric Roux) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 25 Jan 2016 11:55:27 +0100 (CET) > > From: Fr?d?ric Roux > > To: FieldTrip discussion list > > Subject: [FieldTrip] cross-frequency coupling between MEG planar > > channel twins? > > Message-ID: <1957967079.822957.1453719327381.JavaMail.zimbra at bcbl.eu> > > Content-Type: text/plain; charset="utf-8" > > > > Dear all, > > > > in my MEG-data (Elekta Vectorview System) I am observing that the > amplitude of higher frequencies over one planar gradient channel is coupled > to the > > phase of lower frequencies on its corresponding twin-channel . I am > attaching a figure to illustrate this. The upper row shows a low-frequency > oscillation for one planar-channel and the bottom row shows the amplitude > of a higher-frequency oscillation on its corresponding twin channel. Note > that this separation is fairly consistent across other channels as well. > > > > My question relates to what could explain such a coupling of low and > high freq activity over channel-pairs with different gradient orientations > (ie vertical vs. horizontal)? > > > > Could this be an indicator of two separate sources which are being > picked up by the different spatial sensitivity of the planar gradients and > where the phase of one source modulates the amplitude of the other source? > > > > Any comments or suggestions on this would be highly appreciated. > > > > Fred > > > > > > > > > > > > > > > > -- > > Fr?d?ric Roux > > Postdoctoral Scientist, Marie-Curie fellow > > BCBL. Basque Center on Cognition, Brain & Language. > > > > f.roux at bcbl.eu > > Tel: +34 943 309 300 Ext 211 > > Fax: +34 943 309 052 > > > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > --------------------------------------------------------------------------- > > > > ?The probability of success is difficult to estimate; but if we never > search the chance of success is zero.? > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: low_high_coupling_planar_grads_TFR.png > > Type: image/png > > Size: 26838 bytes > > Desc: not available > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160125/c41f609c/attachment-0002.png > > > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: low_high_coupling_planar_grads.png > > Type: image/png > > Size: 11179 bytes > > Desc: not available > > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160125/c41f609c/attachment-0003.png > > > > > > ------------------------------ > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > End of fieldtrip Digest, Vol 62, Issue 24 > > ***************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Tue Jan 26 00:25:13 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Tue, 26 Jan 2016 00:25:13 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: Message-ID: Dear FieldTrip users, I'm looking for the best method to analyse the relationship between ERP and behavioural data but all I've been able to find so far are methods to compare ERPs (or more generally time-series). Consider the following example: 20 participants performed a memory-related task in which they had to respond based on the difference between the target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 samples at 200 Hz) and responses were recorded; ERPs were then created based on epochs in which the responses were correct. Similarly, response accuracy was averaged over all successful epochs per each subject. The resulting data are therefore: 20 participants x 50 channels x 1000 samples (ERP) and 20 averages of accuracy (one value per participant). My objective is to identify which portion of the ERP data best explains (or predicts) the changes in accuracy. In other words, in which time interval is the most significant difference between people who do well in the task and those who don't. So far I've been doing correlations between ERP at each time point and overall accuracy, which is unreliable due to multiple comparisons (correction methods are reportedly too conservative). Nevertheless, certain channels show quite strong correlations in multiple time intervals. How would you approach this problem, please? Many thanks! Best regards, Harold -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue Jan 26 06:35:58 2016 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 26 Jan 2016 06:35:58 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: Message-ID: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Dear Harold, have you checked out ft_statfun_correlationT? This sounds like the function you're looking for. Use cfg.statistic = 'ft_statfun_correlationT' in your call to ft_timelockstatistics. Plus you can use all the correction methods available in FT. See the FAQ for more info: http://www.fieldtriptoolbox.org/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables Good luck, Julian ******************** Dr. Julian Keil AG Multisensorische Integration Psychiatrische Universitätsklinik der Charité im St. Hedwig-Krankenhaus Große Hamburger Straße 5-11, Raum A007 10115 Berlin Telefon: +49-30-2311-1879 Fax: +49-30-2311-2209 http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration Am 26.01.2016 um 00:25 schrieb Harold Cavendish: > Dear FieldTrip users, > > I'm looking for the best method to analyse the relationship between ERP and behavioural data but all I've been able to find so far are methods to compare ERPs (or more generally time-series). > > Consider the following example: 20 participants performed a memory-related task in which they had to respond based on the difference between the target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 samples at 200 Hz) and responses were recorded; ERPs were then created based on epochs in which the responses were correct. Similarly, response accuracy was averaged over all successful epochs per each subject. > > The resulting data are therefore: 20 participants x 50 channels x 1000 samples (ERP) and 20 averages of accuracy (one value per participant). > > My objective is to identify which portion of the ERP data best explains (or predicts) the changes in accuracy. In other words, in which time interval is the most significant difference between people who do well in the task and those who don't. > > So far I've been doing correlations between ERP at each time point and overall accuracy, which is unreliable due to multiple comparisons (correction methods are reportedly too conservative). Nevertheless, certain channels show quite strong correlations in multiple time intervals. > > How would you approach this problem, please? > > Many thanks! > > Best regards, > Harold > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From stephen.politzer-ahles at ling-phil.ox.ac.uk Tue Jan 26 12:08:32 2016 From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles) Date: Tue, 26 Jan 2016 11:08:32 +0000 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data Message-ID: Hi Harold, If you're only interested in identifying which timepoints have the best correlation, multiple comparisons aren't really an issue; if you're not worried about testing for significance, then the place where you see the highest estimate is the highest. See e.g., Hauk et al. 2006 in NeuroImage, and Smith & Kutas 2015 in Psychophysiology, for similar analyses. If you're interested in finding a part of the waveform where the correlation is significantly different from zero while also dealing with multiple comparisons, you could use [spatio]temporal clustering (Maris & Oostenveld 2007). Just make an event-related regression coefficient (as described in Hauk et al.; just do a regression at each timepoint, and then rather than plotting the ERP amplitude at each timepoint, plot the regression estimate (*b*) at each timepoint, to derive a similar waveform) and then test that waveform against 0 using temporal clustering. Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/ > Message: 5 > Date: Tue, 26 Jan 2016 00:25:13 +0100 > From: Harold Cavendish > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Fwd: Identify a window of best correlation > between ERP and behavioural data > Message-ID: > < > CALOTjvZXPNWHLefXrG6uss7uF3kkXie7qjiWqEcesOUqWay6qA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear FieldTrip users, > > I'm looking for the best method to analyse the relationship between ERP and > behavioural data but all I've been able to find so far are methods to > compare ERPs (or more generally time-series). > > Consider the following example: 20 participants performed a memory-related > task in which they had to respond based on the difference between the > target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 > samples at 200 Hz) and responses were recorded; ERPs were then created > based on epochs in which the responses were correct. Similarly, response > accuracy was averaged over all successful epochs per each subject. > > The resulting data are therefore: 20 participants x 50 channels x 1000 > samples (ERP) and 20 averages of accuracy (one value per participant). > > My objective is to identify which portion of the ERP data best explains (or > predicts) the changes in accuracy. In other words, in which time interval > is the most significant difference between people who do well in the task > and those who don't. > > So far I've been doing correlations between ERP at each time point and > overall accuracy, which is unreliable due to multiple comparisons > (correction methods are reportedly too conservative). Nevertheless, certain > channels show quite strong correlations in multiple time intervals. > > How would you approach this problem, please? > > Many thanks! > > Best regards, > Harold > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160126/b5769634/attachment-0001.html > > > > ------------------------------ > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lah at pedneuro.uni-kiel.de Wed Jan 27 10:51:13 2016 From: lah at pedneuro.uni-kiel.de (Laith Hamid) Date: Wed, 27 Jan 2016 10:51:13 +0100 Subject: [FieldTrip] Two questions regarding source analysis in Fieldtrip Message-ID: <4fcc207813cc3640c68f3d637e011a79@mail.uni-kiel.de> Dear Community, I have two questions regarding source analysis in Fieldtrip. 1- Is it possible to estimate the regularization parameter (lambda) in ft_timelockanalysis or ft_sourceanalysis? How is it automatically determined if it is not specified by the user? 2- The source analysis results of ft_sourceanalysis contain information aobut time series of the sources. How can I show a specific point in time (e.g. the epileptic spike's peak) in ft_sourceplot? or is this information lost in ft_sourceinterpolate? Thank you very much for your help. Best, Laith Hamid -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Wed Jan 27 14:04:21 2016 From: michelic72 at gmail.com (Cristiano Micheli) Date: Wed, 27 Jan 2016 14:04:21 +0100 Subject: [FieldTrip] Two questions regarding source analysis in Fieldtrip In-Reply-To: <4fcc207813cc3640c68f3d637e011a79@mail.uni-kiel.de> References: <4fcc207813cc3640c68f3d637e011a79@mail.uni-kiel.de> Message-ID: Hi Laith On Wed, Jan 27, 2016 at 10:51 AM, Laith Hamid wrote: > > Dear Community, > > I have two questions regarding source analysis in Fieldtrip. > > 1- Is it possible to estimate the regularization parameter (lambda) in > ft_timelockanalysis or ft_sourceanalysis? How is it automatically > determined if it is not specified by the user? > > I am reporting a mail by M Wibral (2-3-2009) from the FieldTrip mailing list here below: *Hi Marco,in a nutshell the effect of the lambda parameter is to smoothe your solution in space, it also makes it more stable in the presence of noise. You might know that the estimation of the covariance matrix for beamforming requires quite a lot of data. CTF/VSM (a MEG manufacturer) used to suggest to have your data satisfy the following relationship:3000 < BW[Hz] * #trials *EffectLength[s]Where BW[Hz] is the bandwidth of your effect of interest in Hz, #trials is the number of trials that contain that effect, and EffectLength[s] is the length of your effect in seconds (NOT ms!).Here's an example: You have an effect between 30 and 60Hz, so the bandwidth of that effect is 30Hz. The effect is visible (say at the electrode level) for 400ms=0.4s in each trial. Now you calculate the number of trials to be:#trials > 3000 / ( BW[Hz] * EffectLength[s]) = 3000/(0.4*30)= 250. This means that you would need 250 artifact free, valid trials. Choosing a larger lambda can help to reduce the amount of data necessary, but you get a more smeared out solution.A good introduction and simulation results for various values of lambda can be found in:Neuroimage. 2008 Feb 15;39(4):1788-802. Epub 2007 Oct 10Optimising experimental design for MEG beamformer imaging.Brookes MJ, Vrba J, Robinson SE, Stevenson CM, Peters AM, Barnes GR, Hillebrand A, Morris PG.Hope this helps,* *Michael* In short, if you have enough trials you do not need to smoothe your solution. If not, then apply the rule of thumb described above. I believe you have an option to declare lambda in percentages as well (e.g. lambda = '5%'; ) You can refer to this tutorial too: http://www.fieldtriptoolbox.org/tutorial/beamformer 2- The source analysis results of ft_sourceanalysis contain information > aobut time series of the sources. How can I show a specific point in time > (e.g. the epileptic spike's peak) in ft_sourceplot? or is this information > lost in ft_sourceinterpolate? > Can you add your scripts/code? This will add context to the conversation and allow users to help you further. If I understand your question, you can try to use the ft_sourcemovie function, for example like in this tutorial: http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate Here it is applied to minimum norm solutions, but the same concept holds for LCMV beamformer (which you are using right?) I hope this helps Cris > Thank you very much for your help. > > Best, > > Laith Hamid > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From adamaron at ucsd.edu Wed Jan 27 22:22:39 2016 From: adamaron at ucsd.edu (Adam Aron) Date: Wed, 27 Jan 2016 13:22:39 -0800 Subject: [FieldTrip] Postdoc position in simultaneous electrophysiology of frontal cortex and basal ganglia during action control in humans Message-ID: A funded postdoctoral position is available in the lab of Adam Aron (PhD) at University of California San Diego (www.aronlab.org ) to work collaboratively with Nader Pouratian (MD, PhD) at University of California Los Angeles (http://tinyurl.com/gwuvbja ). The studies will be done in the operating room in patients with Parkinson’s disease who are having electrodes implanted in global pallidus or subthalamic nucleus. The project is to design behavioral tasks, acquire simultaneous local field potential data from basal ganglia and frontal cortex (ECoG) while patients perform the tasks, and to analyze the data using time frequency methods and measures of connectivity and causal flow. The candidate will be based in San Diego with occasional travel to Los Angeles for data collection. This is a substantial postdoctoral training opportunity either for candidates with signal processing expertise (engineering/computer science/neuroscience) who want to branch out into cognition (especially as it pertains to action control); or for cognitive neuroscience candidates who already have cognitive (and frontal-basal-ganglia) expertise and want to learn human electrophysiological analysis methods. Candidates must have a PhD, or be about to be awarded one. Applications (and enquiries) should be sent to adamaron at ucsd.edu and should consist in: - a subject line “electrophysiology of frontal cortex and basal ganglia” - a cover letter describing research interests and how those are a match for the lab - a CV - contact info for references Salary is commensurate with NIH-rates. Non US Citizens are welcome. Full University of California benefits are provided. Applications for the position are open until March 15th 2016. The position is available immediately and for ~3 years. A delayed start time is also possible. --------------------------------------- Adam R. Aron Professor, Department of Psychology Neuroscience Graduate Program University of California, San Diego www.aronlab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From hayes.brenner at gmail.com Thu Jan 28 03:57:20 2016 From: hayes.brenner at gmail.com (Hayes Brenner) Date: Wed, 27 Jan 2016 20:57:20 -0600 Subject: [FieldTrip] How to select trials based on their timing Message-ID: Hello everyone! I'm fairly new to Fieldtrip, so I apologize if this question seems trivial, but I've been stuck for a while and I would greatly appreciate everyone's help. I have a set of data that I'm working on to get a better sense of how to process EEG data. I'm having trouble with this part when given these instructions: "let's only grab trials in which a '30' also appeared along side the '20'. [These labels are a part of cfg.trialdef.eventtype]. This '30' event code denotes a certain kind of trial in the experiment in which only the colored square was presented. The '30' event code should onset at the same time or within just a few milliseconds of the onset of the '20'. Third, let's also only grab trials in which subjects correctly responded with a button press to the stimulus (i.e., the colored square). To do this, you'll need to make sure there is a '90' following the '20'. The button press (or event code '90') should appear within 1000 ms of the onset of the '20'. My question is: how can I designate my code so that I can have a data set that meets the following conditions? I know I should use an 'if' or 'for' but I'm not sure how to write it exactly. Any advice? I've included my code as is without including the file upload. As of now, I created 3 data sets, each one with the required markers (20, 30, and 90). ft_defaults; cfg = []; cfg.trialdef.eventtype = '?'; ft_definetrial(cfg); cfg.trialdef.eventtype = 'Stim'; cfg.trialdef.prestim = 0.2; cfg.trialdef.poststim = .8; cfg.trialdef.eventvalue = '20'; cfg1=ft_definetrial(cfg); cfg.trialdef.eventvalue = '30'; cfg2=ft_definetrial(cfg); cfg.trialdef.eventvalue = '90'; cfg3=ft_definetrial(cfg); cfg.lpfilter='yes'; cfg.lpfreq = 30; cfg.reref = 'yes'; cfg.implicitref = 'REF'; cfg.refchannel = {'LM' 'REF'}; trialdata1 = ft_preprocessing(cfg1); trialdata2 = ft_preprocessing(cfg2); trialdata3 = ft_preprocessing(cfg3); Thank you all so much! Hayes Brenner -------------- next part -------------- An HTML attachment was scrubbed... URL: From saeedzahran at hotmail.com Thu Jan 28 12:06:34 2016 From: saeedzahran at hotmail.com (saeed zahran) Date: Thu, 28 Jan 2016 13:06:34 +0200 Subject: [FieldTrip] The compartment nesting cannot be determined In-Reply-To: References: , Message-ID: Dear Cris, Thank you for your time and consideration. I have solved the problem, after I add 1 to all the faces, since there was zeros in the faces, Faces=load('Faces.mat'); Faces=Faces.Faces; Points=load('Points.mat'); Points=Points.Points; Rfaces=load('Rfaces.mat'); Rfaces=Rfaces.Rfaces; Rpoints=load('Rpoints.mat'); Rpoints=Rpoints.Rpoints; RRfaces=load('RRfaces.mat'); RRfaces=RRfaces.RRfaces; RRpoints=load('RRpoints.mat'); RRpoints=RRpoints.RRpoints; Faces=Faces+1; Rfaces=Rfaces+1; RRfaces=RRfaces+1; vol = []; vol.bnd(1).pnt=Points; vol.bnd(1).tri=Faces; vol.bnd(2).pnt=Rpoints; vol.bnd(2).tri=Rfaces; vol.bnd(3).pnt=RRpoints; vol.bnd(3).tri=RRfaces; vol.cond = c; but I have the below error:Attempted to access vol.cond(4); index out of bounds because numel(vol.cond)=3. Error in ft_headmodel_bemcp (line 154) weight = (vol.cond(2)-vol.cond(3))/((vol.cond(3)+vol.cond(4)));%*2*pi); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 167) vol = ft_prepare_headmodel(cfg, vol); With two boundaries I have the below error: Attempted to access vol.cond(3); index out of bounds because numel(vol.cond)=2. Error in ft_headmodel_bemcp (line 129) weight = (vol.cond(1)-vol.cond(2))/((vol.cond(2)+vol.cond(3)));%*2*pi); Error in ft_prepare_headmodel (line 253) vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity); Error in openmeeg_eeg_leadfield_example_me (line 167) vol = ft_prepare_headmodel(cfg, vol); Best regards Saeed. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.politzer-ahles at ling-phil.ox.ac.uk Thu Jan 28 12:10:16 2016 From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles) Date: Thu, 28 Jan 2016 11:10:16 +0000 Subject: [FieldTrip] How to select trials based on their timing Message-ID: Hi Hayes, This isn't really about Fieldtrip specifically, but is a MATLAB programming issue; that is to say, the solution isn't a special Fieldtrip function or anything like that, just basic MATLAB coding. (There might be a Fieldtrip-internal solution, like there is in ERPLAB for relatively complex trial selection, but I'm not aware of it.) All you really need to do is rewrite the trigger numbers so they distinguish the kinds of triggers you actually need. For example, rather than all trials of a given condition being coded as 30, you might want correct trials in that condition to be 31 and incorrect trials 32; the same logic also goes for recoding the trials based on whether or not there was a 20 nearby. All this information about trial timing is available in the 'cfg.trl' matrix that is created after you run ft_definetrial (see http://www.fieldtriptoolbox.org/reference/definetrial for details about how this matrix is organized). So all you need to do is write a FOR loop that iterates through each row of the trl matrix, and for each row checks (using an IF statement) whether that row meets the various conditions you outlined, and rewrites that row's trigger code if it meets those conditions. Then you can pull out a list of which trials you want (this is doable with basic MATLAB code, e.g., find(cfg.trl(:,3)==31) gives you a list of the row numbers of every trial with a code of 31) and use that list with ft_preprocessing to process just the trials you want. Best, Steve --- Stephen Politzer-Ahles University of Oxford Language and Brain Lab Faculty of Linguistics, Phonetics & Philology http://users.ox.ac.uk/~cpgl0080/ > Message: 3 > Date: Wed, 27 Jan 2016 20:57:20 -0600 > From: Hayes Brenner > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] How to select trials based on their timing > Message-ID: > < > CAB--YMYoCGP7KKCW-a7DwP2iZgyCVO-D_SJh1dmjUP79NtcLow at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello everyone! I'm fairly new to Fieldtrip, so I apologize if this > question seems trivial, but I've been stuck for a while and I would greatly > appreciate everyone's help. > > I have a set of data that I'm working on to get a better sense of how to > process EEG data. I'm having trouble with this part when given these > instructions: > > "let's only grab trials in which a '30' also appeared along side the '20'. > [These labels are a part of cfg.trialdef.eventtype]. This '30' event code > denotes a certain kind of trial in the experiment in which only the colored > square was presented. The '30' event code should onset at the same time or > within just a few milliseconds of the onset of the '20'. Third, let's also > only grab trials in which subjects correctly responded with a button press > to the stimulus (i.e., the colored square). To do this, you'll need to make > sure there is a '90' following the '20'. The button press (or event code > '90') should appear within 1000 ms of the onset of the '20'. > > My question is: how can I designate my code so that I can have a data set > that meets the following conditions? I know I should use an 'if' or 'for' > but I'm not sure how to write it exactly. Any advice? I've included my code > as is without including the file upload. As of now, I created 3 data sets, > each one with the required markers (20, 30, and 90). > > ft_defaults; > cfg = []; > cfg.trialdef.eventtype = '?'; > ft_definetrial(cfg); > cfg.trialdef.eventtype = 'Stim'; > cfg.trialdef.prestim = 0.2; > cfg.trialdef.poststim = .8; > cfg.trialdef.eventvalue = '20'; > cfg1=ft_definetrial(cfg); > cfg.trialdef.eventvalue = '30'; > cfg2=ft_definetrial(cfg); > cfg.trialdef.eventvalue = '90'; > cfg3=ft_definetrial(cfg); > cfg.lpfilter='yes'; > cfg.lpfreq = 30; > cfg.reref = 'yes'; > cfg.implicitref = 'REF'; > cfg.refchannel = {'LM' 'REF'}; > trialdata1 = ft_preprocessing(cfg1); > trialdata2 = ft_preprocessing(cfg2); > trialdata3 = ft_preprocessing(cfg3); > > Thank you all so much! > > Hayes Brenner > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160127/b0726da2/attachment-0001.html > > > > ------------------------------ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Thu Jan 28 13:31:37 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Thu, 28 Jan 2016 13:31:37 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> References: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Message-ID: Dear Julian, thank you for your help, I believe I read the same page but I didn't realise it could be used with ft_timelockstatistics – the way certain ft_ functions fit others is still a bit unclear to me (it's practically my first contact with FT). Now, it appears to be exactly what I'm looking for. I took me some time to figure out how to import my already processed data (ERPs averaged per subject) into FieldTrip and run the test but it seems I've succeeded. However, ft_timelockstatistics(cfg, data) gave me the following warnings: *1. Warning: the data does not contain a trial definition* *2. Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous* *recording* *3. Warning: doing a two-sided test without correcting p-values or alpha-level, p-values and alpha-level* *will reflect one-sided tests per tail* Should I be worried about these? (Here's the full output: https://gist.github.com/anonymous/1866a2b1a424dd9f0ac9) Finally, the resulting *stat* structure contains 10 fields but I'm not sure what *mask*, *stat* and *ref* represent. Is there any guidance on how to report the results like in the case of comparisons between conditions ( http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test )? Many thanks! Harold 2016-01-26 6:35 GMT+01:00 Julian Keil : > Dear Harold, > > have you checked out ft_statfun_correlationT? > This sounds like the function you're looking for. Use cfg.statistic = > 'ft_statfun_correlationT' in your call to ft_timelockstatistics. > Plus you can use all the correction methods available in FT. > See the FAQ for more info: > http://www.fieldtriptoolbox.org/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables > > Good luck, > > Julian > > ******************** > *Dr. Julian Keil* > > AG Multisensorische Integration > Psychiatrische Universitätsklinik > der Charité im St. Hedwig-Krankenhaus > Große Hamburger Straße 5-11, Raum A007 > 10115 Berlin > > Telefon: +49-30-2311-1879 > Fax: +49-30-2311-2209 > > http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration > > Am 26.01.2016 um 00:25 schrieb Harold Cavendish: > > Dear FieldTrip users, > > I'm looking for the best method to analyse the relationship between ERP > and behavioural data but all I've been able to find so far are methods to > compare ERPs (or more generally time-series). > > Consider the following example: 20 participants performed a memory-related > task in which they had to respond based on the difference between the > target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 > samples at 200 Hz) and responses were recorded; ERPs were then created > based on epochs in which the responses were correct. Similarly, response > accuracy was averaged over all successful epochs per each subject. > > The resulting data are therefore: 20 participants x 50 channels x 1000 > samples (ERP) and 20 averages of accuracy (one value per participant). > > My objective is to identify which portion of the ERP data best explains > (or predicts) the changes in accuracy. In other words, in which time > interval is the most significant difference between people who do well in > the task and those who don't. > > So far I've been doing correlations between ERP at each time point and > overall accuracy, which is unreliable due to multiple comparisons > (correction methods are reportedly too conservative). Nevertheless, certain > channels show quite strong correlations in multiple time intervals. > > How would you approach this problem, please? > > Many thanks! > > Best regards, > Harold > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Thu Jan 28 13:37:38 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Thu, 28 Jan 2016 13:37:38 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: Message-ID: Dear Steve, thank you for your help, the references are greatly appreciated! Indeed, I'd like to extend the analysis to identifying parts where the correlation is significantly different; I am going to try this approach. Best regards, Harold 2016-01-26 12:08 GMT+01:00 Stephen Politzer-Ahles < stephen.politzer-ahles at ling-phil.ox.ac.uk>: > Hi Harold, > > If you're only interested in identifying which timepoints have the best > correlation, multiple comparisons aren't really an issue; if you're not > worried about testing for significance, then the place where you see the > highest estimate is the highest. See e.g., Hauk et al. 2006 in NeuroImage, > and Smith & Kutas 2015 in Psychophysiology, for similar analyses. > > If you're interested in finding a part of the waveform where the > correlation is significantly different from zero while also dealing with > multiple comparisons, you could use [spatio]temporal clustering (Maris & > Oostenveld 2007). Just make an event-related regression coefficient (as > described in Hauk et al.; just do a regression at each timepoint, and then > rather than plotting the ERP amplitude at each timepoint, plot the > regression estimate (*b*) at each timepoint, to derive a similar > waveform) and then test that waveform against 0 using temporal clustering. > > Best, > Steve > > > > > --- > Stephen Politzer-Ahles > University of Oxford > Language and Brain Lab > Faculty of Linguistics, Phonetics & Philology > http://users.ox.ac.uk/~cpgl0080/ > > > >> Message: 5 >> Date: Tue, 26 Jan 2016 00:25:13 +0100 >> From: Harold Cavendish >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] Fwd: Identify a window of best correlation >> between ERP and behavioural data >> Message-ID: >> < >> CALOTjvZXPNWHLefXrG6uss7uF3kkXie7qjiWqEcesOUqWay6qA at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Dear FieldTrip users, >> >> I'm looking for the best method to analyse the relationship between ERP >> and >> behavioural data but all I've been able to find so far are methods to >> compare ERPs (or more generally time-series). >> >> Consider the following example: 20 participants performed a memory-related >> task in which they had to respond based on the difference between the >> target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 >> samples at 200 Hz) and responses were recorded; ERPs were then created >> based on epochs in which the responses were correct. Similarly, response >> accuracy was averaged over all successful epochs per each subject. >> >> The resulting data are therefore: 20 participants x 50 channels x 1000 >> samples (ERP) and 20 averages of accuracy (one value per participant). >> >> My objective is to identify which portion of the ERP data best explains >> (or >> predicts) the changes in accuracy. In other words, in which time interval >> is the most significant difference between people who do well in the task >> and those who don't. >> >> So far I've been doing correlations between ERP at each time point and >> overall accuracy, which is unreliable due to multiple comparisons >> (correction methods are reportedly too conservative). Nevertheless, >> certain >> channels show quite strong correlations in multiple time intervals. >> >> How would you approach this problem, please? >> >> Many thanks! >> >> Best regards, >> Harold >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160126/b5769634/attachment-0001.html >> > >> >> ------------------------------ >> >> >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Thu Jan 28 14:25:42 2016 From: julian.keil at gmail.com (Julian Keil) Date: Thu, 28 Jan 2016 14:25:42 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Message-ID: Dear Harold, as far as the warnings go, maybe someone closer to the development team can chime in here. I think you can safely ignore warnings 1 and 2. With respect to warning 3, you actually need to set cfg.correcttail = 'alpha'; to set the alpha from e.g. .05 to 0.025 for a two sided test. As for your output, mask is a binary mask corrected for multiple comparisons, i.e. values of 1 designate the significant elements. stat contains the actual t-values. Depending on the method you used, the output will vary. If you also paste your code and the output, it's a bit easier to explain. I suggest to look at some papers in which fieldtrip-stats have been reported to get an idea what is appropriate. I'll blatantly advertise my own work here: Keil, J., Müller, N., Hartmann, T., & Weisz, N. (2014). Prestimulus beta power and phase synchrony influence the sound-induced flash illusion. Cerebral Cortex, 24(5), 1278–1288. http://doi.org/10.1093/cercor/bhs409 Keil, J., Müller, N., Ihssen, N., & Weisz, N. (2012). On the variability of the McGurk effect: audiovisual integration depends on prestimulus brain states. Cerebral Cortex, 22(1), 221–231. http://doi.org/10.1093/cercor/bhr125 And an excellent tutorial by Joachim Gross et al.: Gross, J., Baillet, S., Barnes, G. R., Henson, R. N., Hillebrand, A., Jensen, O., et al. (2012). Good practice for conducting and reporting MEG research. NeuroImage, 1–15. http://doi.org/10.1016/j.neuroimage.2012.10.001 Good luck, Julian Am 28.01.2016 um 13:31 schrieb Harold Cavendish: > Dear Julian, > > thank you for your help, I believe I read the same page but I didn't realise it could be used with ft_timelockstatistics – the way certain ft_ functions fit others is still a bit unclear to me (it's practically my first contact with FT). Now, it appears to be exactly what I'm looking for. > > I took me some time to figure out how to import my already processed data (ERPs averaged per subject) into FieldTrip and run the test but it seems I've succeeded. However, ft_timelockstatistics(cfg, data) gave me the following warnings: > > 1. Warning: the data does not contain a trial definition > 2. Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous > recording > 3. Warning: doing a two-sided test without correcting p-values or alpha-level, p-values and alpha-level > will reflect one-sided tests per tail > > Should I be worried about these? (Here's the full output: https://gist.github.com/anonymous/1866a2b1a424dd9f0ac9) > > Finally, the resulting stat structure contains 10 fields but I'm not sure what mask, stat and ref represent. Is there any guidance on how to report the results like in the case of comparisons between conditions (http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test)? > > Many thanks! > Harold > > > 2016-01-26 6:35 GMT+01:00 Julian Keil : > Dear Harold, > > have you checked out ft_statfun_correlationT? > This sounds like the function you're looking for. Use cfg.statistic = 'ft_statfun_correlationT' in your call to ft_timelockstatistics. > Plus you can use all the correction methods available in FT. > See the FAQ for more info: http://www.fieldtriptoolbox.org/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables > > Good luck, > > Julian > > ******************** > Dr. Julian Keil > > AG Multisensorische Integration > Psychiatrische Universitätsklinik > der Charité im St. Hedwig-Krankenhaus > Große Hamburger Straße 5-11, Raum A007 > 10115 Berlin > > Telefon: +49-30-2311-1879 > Fax: +49-30-2311-2209 > http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration > > Am 26.01.2016 um 00:25 schrieb Harold Cavendish: > >> Dear FieldTrip users, >> >> I'm looking for the best method to analyse the relationship between ERP and behavioural data but all I've been able to find so far are methods to compare ERPs (or more generally time-series). >> >> Consider the following example: 20 participants performed a memory-related task in which they had to respond based on the difference between the target stimulus and the probe stimulus. EEG (50 electrodes, about 1000 samples at 200 Hz) and responses were recorded; ERPs were then created based on epochs in which the responses were correct. Similarly, response accuracy was averaged over all successful epochs per each subject. >> >> The resulting data are therefore: 20 participants x 50 channels x 1000 samples (ERP) and 20 averages of accuracy (one value per participant). >> >> My objective is to identify which portion of the ERP data best explains (or predicts) the changes in accuracy. In other words, in which time interval is the most significant difference between people who do well in the task and those who don't. >> >> So far I've been doing correlations between ERP at each time point and overall accuracy, which is unreliable due to multiple comparisons (correction methods are reportedly too conservative). Nevertheless, certain channels show quite strong correlations in multiple time intervals. >> >> How would you approach this problem, please? >> >> Many thanks! >> >> Best regards, >> Harold >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 495 bytes Desc: Message signed with OpenPGP using GPGMail URL: From changa5 at mcmaster.ca Fri Jan 29 04:25:47 2016 From: changa5 at mcmaster.ca (Andrew Chang) Date: Thu, 28 Jan 2016 22:25:47 -0500 Subject: [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. Fieldtrip) In-Reply-To: References: <1f8be01d14f99$8f379470$ada6bd50$@besa.de> Message-ID: Hi Harald, I did the ICA based on the continuos recorded block (~7 minutes), including 100 trials, with PCA option on. The attached file is the ICA topography and waveform (ICA 22). The spectrum showed that the peak power was at ~11Hz. I suspected it is a neck movement artifact, because the generator seems to be in the front of the neck. Also, I got another similar ICA component from another subject, and the topography seems to be centered at the back of the neck, would it be considered as neck movement too. Thank you very much once again! Best, Andrew On Mon, Jan 18, 2016 at 7:49 AM, Harald Bornfleth wrote: > Dear Andrew, > > > > A couple of questions popped up. > > 1) The neck movement artifact, is this something with low frequency, > or is it a muscle artifact? > > 2) Did you calculate the ICA on one data screen (e.g. 10 seconds or > 20 seconds), or over the whole data set? > > > > If you could send us screen shots showing the ICA wave forms and the > accompanying topographies, then we could comment on the classification. (In > BESA, you right-click on the label of a component and select “Map > topography” to show the topography map of that component.) > > I include my colleague and ICA expert Nicole Ille on CC. > > > > Best regards, > > Harald > > > > > > *From:* c.andrew123 at gmail.com [mailto:c.andrew123 at gmail.com] *On Behalf > Of *Andrew Chang > *Sent:* 17 January 2016 19:57 > *To:* Harald.Bornfleth at besa.de; FieldTrip discussion list < > fieldtrip at science.ru.nl> > *Subject:* Re: [FieldTrip] Comparing ICA methods between toolboxes (BESA > vs. Fieldtrip) > > > > Hi Dr. Bornfleth, > > > > Thanks for your reply very much. > > I would like to use ICA to remove eye blinks and eye movements, neck > movements, as well as cardiac and powerline artifacts. The segment I have > is a continuous EEG recording for 10 minutes, which is one block of my > experiment including many trials. > > Before ICA, the segment have been high-pass (0.3 Hz) and low-pass (100 > Hz). The components showing activities around the eyes, the back of the > neck, and 60 Hz were removed. As for the cardiac artifact, I it is based on > visual inspection on the waveform to see whether it looks like an EKG. > > Any further comments are appreciated! > > > > Best, > > Andrew > > > > On Fri, Jan 15, 2016 at 8:35 AM, Harald Bornfleth < > Harald.Bornfleth at besa.de> wrote: > > Dear Andrew, > > > > Thanks for bringing this up. I can try to shed some light on the ICA > method used in BESA Research; however, I can not comment on the > implementation in FieldTrip. > > > > The method behind ICA analysis in BESA Research is the extended infomax > ICA algorithm (Lee TW et al.: Independent component analysis using an > extended infomax algorithm for mixed sub-Gaussian and super-Gaussian > sources. Neural Computation 11(2), 1999, 409-433). This algorithm is very > well suited to remove cardiac and powerline artifacts. Depending on the > data, it may also be used to remove ocular (blink) and electrode artifacts. > To assess whether your artifact removal is trustworthy more information > about your processing steps are needed. What types of artifacts are you > trying to correct? What segments are you using to determine the artifact > topographies and what segments are you finally correcting? > > > > Best regards, > > Harald > > > > > > *Dr. Harald Bornfleth* > > Product Manager BESA Research > > > > *BESA GmbH* > > Freihamer Strasse 18 > > 82166 Graefelfing/Germany > > http://www.besa.de > > > > E: Harald.Bornfleth at besa.de > > T: +49 89 8980 9968 > > > > > > HRB Munich 109956 > > CEO: Dr. Tobias Scherg, CFO: Theodor Scherg > > Director of Research: Dr. Michael Scherg > > > > > > > > > > > > > > *From:* fieldtrip-bounces at science.ru.nl [ > mailto:fieldtrip-bounces at science.ru.nl ] *On > Behalf Of *Andrew Chang > *Sent:* Sonntag, 10. Januar 2016 21:18 > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Comparing ICA methods between toolboxes (BESA vs. > Fieldtrip) > > > > Dear Fieldtrip users, > > > > I am wondering whether anyone has compared the performances of the ICA > methods among M/EEG toolboxes. Especially, how is the performance of ICA in > BESA Research 6.0, compared to Fieldtrip? > > I have an EEG data set which has been processed in BESA, including > removing artifact using ICA. I am wondering whether I can trust it, or > I should reprocess it in Fieldtrip. Any comments will be appreciated! > > > > Happy new year! > > > > Best, > > Andrew > > > > -- > > Andrew Chang > Ph.D. Candidate > Auditory Development Lab > > Department of Psychology, Neuroscience & Behaviour > McMaster University > > http://changa5.wordpress.com/ > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > > Andrew Chang > Ph.D. Candidate > Auditory Development Lab > > Department of Psychology, Neuroscience & Behaviour > McMaster University > > http://changa5.wordpress.com/ > -- Andrew Chang Ph.D. Candidate Auditory Development Lab Department of Psychology, Neuroscience & Behaviour McMaster University http://changa5.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 螢幕快照 2016-01-28 下午10.14.20.png Type: image/png Size: 694915 bytes Desc: not available URL: From labdipsco at unitn.it Fri Jan 29 12:28:02 2016 From: labdipsco at unitn.it (Laboratori_Didattici Rovereto) Date: Fri, 29 Jan 2016 12:28:02 +0100 Subject: [FieldTrip] Problem importing cfg structure from eeg lab Message-ID: Dear FieldTripers, we are new in the field of Frequency Analysis. We have some problem in importing data from eeglab into ft (we are using the eeglab2fieldtrip function). data=eeglab2fieldtrip(EEG,'preprocessing','none'); data.label=data.label'; data.trialinfo=repmat(condition,1,length(data.trial))'; After the import, we checked the data with ft_databroswer([],data) and we see all the trials and the channels. However our cfg contains only "version" and then when we run ft_freqanalysis the function works but is applied only to 1 trial. Do we make a mistake in the importing phase or in applying ft_freqanalysis?? Thanks a lot, Paolo and Simone -------------- next part -------------- An HTML attachment was scrubbed... URL: From Darren.Kadis at cchmc.org Fri Jan 29 18:46:34 2016 From: Darren.Kadis at cchmc.org (Kadis, Darren) Date: Fri, 29 Jan 2016 17:46:34 +0000 Subject: [FieldTrip] Post-doctoral research position in language MEG (Cincinnati OH) Message-ID: <927408BECA23304AA310FCEDD94A02651110E1C8@MCEXMB1.chmccorp.cchmc.org> Post Doc, Cincinnati, USA Post-doctoral research position in language MEG We invite applications for a post-doctoral research position in Neurology at Cincinnati Children's Hospital Medical Center (CCHMC). The successful applicant will contribute to ongoing MEG studies of pediatric language and epilepsy. This is a two-year position focused in one or more of the following areas: * Methods for multimodal neuroimaging, with a focus on integration of fMRI and MEG data * Source-space connectivity techniques, designed to overcome challenges related to leakage, impact of inverse solution, etc. * Validation of integrated imaging and analysis protocols for mapping language in children undergoing epilepsy surgery (MEG, fMRI, EEG, ECoG, stimulation mapping, pathology, and outcome data available) The post-doctoral fellow will regularly interact with clinical and research faculty, other post-docs, graduate students, and research staff in the Divisions of Neurology and Radiology, the Pediatric Neuroimaging Research Consortium (PNRC) and the Imaging Research Center (IRC). He/she is expected to contribute to our regular research discussions, and to present at research meetings within CCHMC and at major conferences (e.g., BIOMAG, OHBM). The successful candidate will have completed their PhD in biomedical or electrical engineering, physics, computer science, psychology, neuroscience, or a related discipline. He/she will have experience in collection and analysis of electrophysiological data, expertise in signal processing, with strong programming skills (MATLAB or a similar environment). The ideal candidate would also have prior experience in neuroimaging and a solid background in neuroanatomy, and familiarity with M/EEG analysis software (e.g., FieldTrip/SPM, Brainstorm, Brainwave, BESA, MNE). All qualified recent graduates, or those nearing completion of their PhD, are encouraged to apply. CCHMC is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, age, genetic information, physical or mental disability, military or veteran status, sexual orientation, or other protected status in accordance with applicable federal, state, and local laws and regulations. Applicants should submit a cover letter and current CV (including a list of scholarly publications), along with the names and contact information for three referees to: Darren S. Kadis, PhD Assistant Professor, Division of Neurology Pediatric Neuroimaging Research Consortium Cincinnati Children's Hospital Medical Center c/o Kimra Smith Kimra.Smith at cchmc.org Review of applications will begin immediately. We anticipate a start date in the spring, 2016. -------------- next part -------------- An HTML attachment was scrubbed... URL: From harold.cav89 at gmail.com Sat Jan 30 22:24:22 2016 From: harold.cav89 at gmail.com (Harold Cavendish) Date: Sat, 30 Jan 2016 22:24:22 +0100 Subject: [FieldTrip] Fwd: Identify a window of best correlation between ERP and behavioural data In-Reply-To: References: <7B6FE7F8-76E7-4EB8-8D62-520CA7ABEB49@gmail.com> Message-ID: Dear Julian, thank you for your help so far! I've read the papers and I'm starting to piece it all together. I've ran into some issues with FieldTrip (hence my delay) which are still persistent but I don't want to come here with every problem I encounter so I'm going to give it a couple more days on my own. My original question has been fully answered and the rest is another matter. Best wishes, Harold -------------- next part -------------- An HTML attachment was scrubbed... URL: