From veniero at med.unibs.it Sun Apr 1 19:03:51 2012 From: veniero at med.unibs.it (veniero at med.unibs.it) Date: Sun, 1 Apr 2012 19:03:51 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: References: Message-ID: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> Dear FieldTrip users, I'm trying to run a cluster-based permutation tests on time-frequency data. I get the result: found 1 positive clusters in observed data found 0 negative clusters in observed data, but I'm not able to use clusterplot because if the following error: ??? Error using ==> ft_clusterplot at 171 no clusters present with a p-value lower than the specified alpha, nothing to plot Is this possible? Maybe it's just a trivial question. Many thanks, Mimma From Lilla.Magyari at mpi.nl Sun Apr 1 19:58:55 2012 From: Lilla.Magyari at mpi.nl (Magyari, Lilla) Date: Sun, 01 Apr 2012 19:58:55 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> Message-ID: <4F78975F.10607@mpi.nl> Dear Mimma, I am not exactly sure about what "found 1 positive clusters in observed data found 0 negative clusters in observed data" means but I would guess that it means only the number of clusters that you got after your test. This doesn't mean that these clusters are significant. Have you checked in the output of ft_freqstatistics if you have any significant clusters? (You can check it in the field stat.posclusters or stat.negclusters). Hope this helps Lilla veniero at med.unibs.it wrote: > Dear FieldTrip users, > I'm trying to run a cluster-based permutation tests on time-frequency > data. I get the result: > found 1 positive clusters in observed data found 0 negative clusters in > observed data, but I'm not able to use clusterplot because if the > following error: > ??? Error using ==> ft_clusterplot at 171 > no clusters present with a p-value lower than the specified alpha, nothing > to plot > > Is this possible? Maybe it's just a trivial question. > > Many thanks, > Mimma > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Mon Apr 2 09:24:35 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 02 Apr 2012 09:24:35 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> Message-ID: <4F795433.6000007@donders.ru.nl> Dear Mimma, Most likely, you specified a different alpha when calling ft_freqstatistics than when calling ft_clusterplot. Could you paste the cfg settings for both functions here, so that we can try to track down where exactly this error comes from? Best, Jörn On 4/1/2012 7:03 PM, veniero at med.unibs.it wrote: > Dear FieldTrip users, > I'm trying to run a cluster-based permutation tests on time-frequency > data. I get the result: > found 1 positive clusters in observed data found 0 negative clusters in > observed data, but I'm not able to use clusterplot because if the > following error: > ??? Error using ==> ft_clusterplot at 171 > no clusters present with a p-value lower than the specified alpha, nothing > to plot > > Is this possible? Maybe it's just a trivial question. > > Many thanks, > Mimma > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From veniero at med.unibs.it Mon Apr 2 11:11:30 2012 From: veniero at med.unibs.it (veniero at med.unibs.it) Date: Mon, 2 Apr 2012 11:11:30 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <4F795433.6000007@donders.ru.nl> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> <4F795433.6000007@donders.ru.nl> Message-ID: <3a64b4c61afcca813c6c64d8fed5a5b1.squirrel@mail.med.unibs.it> Dear Jörn, I'm copmparing two conditions gavgM1_post5 and gavgM1_pre5. Here the settings I'm using: cfg = []; cfg.channel = {'EEG'}; cfg.layout= 'biosemi64.lay'; cfg.latency = 'all'; cfg.frequency = [20 20]; cfg.avgeoverfreq = 'yes'; cfg.method = 'montecarlo'; cfg.statistic = '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; design = zeros(1,size(gavgM1_post5.powspctrm,1) + size(gavgM1_pre5.powspctrm,1)); design(1,1:size(gavgM1_post5.powspctrm,1)) = 1; design(1,(size(gavgM1_post5.powspctrm,1)+1):(size(gavgM1_post5.powspctrm,1)+... size(gavgM1_pre5.powspctrm,1))) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_freqstatistics(cfg, gavgM1_post5, gavgM1_pre5); For the clusterplot: stat.raweffect = gavgM1_post5.powspctrm - gavgM1_pre5.powspctrm; cfg = []; cfg.alpha = 0.025; cfg.zparam = 'raweffect'; cfg.zlim = [-1 1]; cfg.layout = 'biosemi64.lay'; ft_clusterplot(cfg, stat); Many thanks, Mimma > Dear Mimma, > > Most likely, you specified a different alpha when calling > ft_freqstatistics than when calling ft_clusterplot. Could you paste the > cfg settings for both functions here, so that we can try to track down > where exactly this error comes from? > > Best, > Jörn > > > On 4/1/2012 7:03 PM, veniero at med.unibs.it wrote: >> Dear FieldTrip users, >> I'm trying to run a cluster-based permutation tests on time-frequency >> data. I get the result: >> found 1 positive clusters in observed data found 0 negative clusters in >> observed data, but I'm not able to use clusterplot because if the >> following error: >> ??? Error using ==> ft_clusterplot at 171 >> no clusters present with a p-value lower than the specified alpha, >> nothing >> to plot >> >> Is this possible? Maybe it's just a trivial question. >> >> Many thanks, >> Mimma >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From jm.horschig at donders.ru.nl Mon Apr 2 16:34:16 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 02 Apr 2012 16:34:16 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <3a64b4c61afcca813c6c64d8fed5a5b1.squirrel@mail.med.unibs.it> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> <4F795433.6000007@donders.ru.nl> <3a64b4c61afcca813c6c64d8fed5a5b1.squirrel@mail.med.unibs.it> Message-ID: <4F79B8E8.3010807@donders.ru.nl> Dear Mimma, okay, I see. First of all, behaviour of ft_clusterplot is perfectly fine. The way ft_freqstatistics works is that it first computes a t-value for all datapoints, and then computes clusters in time, space and/or frequency, depending on whether you set cfg.avgovertime or cfg.avgoverfreq to 'yes'. All these t-values are uncorrected t-values, therefore the reliability of the statistics will suffer from multiple comparisons (as a side note, this might be an interesting read: http://www.danielbor.com/dilemma-weak-neuroimaging/ ). The test you specified will compute permutations of your data and then compare the actual observed t-value (as described above) with the distribution of the random permutations. Only if your observation lies in the significant head or tail of the permutation distribution (as defined by the first/last 2.5%, i.e. your alpha value), the found cluster will be considered to be significant. Thus, even if the t-value might be significant, it will be corrected thereafter by the cluster permutation. For a detailled description, I would advise you to read this paper on which the whole method is based on: http://www.sciencedirect.com/science/article/pii/S016502700700074X In your data, the observed cluster is not significant anymore after the cluster-based correction. You can also check it by typing stat.posclusters.prob, which will return a value > 0.025 Hope I described it somewhat comprehensible. Best, Jörn On 4/2/2012 11:11 AM, veniero at med.unibs.it wrote: > Dear Jörn, > I'm copmparing two conditions gavgM1_post5 and gavgM1_pre5. > Here the settings I'm using: > > cfg = []; > cfg.channel = {'EEG'}; > cfg.layout= 'biosemi64.lay'; > cfg.latency = 'all'; > cfg.frequency = [20 20]; > cfg.avgeoverfreq = 'yes'; > cfg.method = 'montecarlo'; > cfg.statistic = '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; > design = zeros(1,size(gavgM1_post5.powspctrm,1) + > size(gavgM1_pre5.powspctrm,1)); > design(1,1:size(gavgM1_post5.powspctrm,1)) = 1; > design(1,(size(gavgM1_post5.powspctrm,1)+1):(size(gavgM1_post5.powspctrm,1)+... > size(gavgM1_pre5.powspctrm,1))) = 2; > cfg.design = design; > cfg.ivar = 1; > > [stat] = ft_freqstatistics(cfg, gavgM1_post5, gavgM1_pre5); > > > For the clusterplot: > stat.raweffect = gavgM1_post5.powspctrm - gavgM1_pre5.powspctrm; > > cfg = []; > cfg.alpha = 0.025; > cfg.zparam = 'raweffect'; > cfg.zlim = [-1 1]; > cfg.layout = 'biosemi64.lay'; > ft_clusterplot(cfg, stat); > > Many thanks, > Mimma > > > >> Dear Mimma, >> >> Most likely, you specified a different alpha when calling >> ft_freqstatistics than when calling ft_clusterplot. Could you paste the >> cfg settings for both functions here, so that we can try to track down >> where exactly this error comes from? >> >> Best, >> Jörn >> >> >> On 4/1/2012 7:03 PM, veniero at med.unibs.it wrote: >>> Dear FieldTrip users, >>> I'm trying to run a cluster-based permutation tests on time-frequency >>> data. I get the result: >>> found 1 positive clusters in observed data found 0 negative clusters in >>> observed data, but I'm not able to use clusterplot because if the >>> following error: >>> ??? Error using ==> ft_clusterplot at 171 >>> no clusters present with a p-value lower than the specified alpha, >>> nothing >>> to plot >>> >>> Is this possible? Maybe it's just a trivial question. >>> >>> Many thanks, >>> Mimma >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> _______________________________________________ >> 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 -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From biomag.network.practical at gmail.com Mon Apr 2 17:12:03 2012 From: biomag.network.practical at gmail.com (Biomag Networks Satellite 25 Aug 2012) Date: Mon, 2 Apr 2012 17:12:03 +0200 Subject: [FieldTrip] Biomag Satellite Announcement: Open for Registration In-Reply-To: References: Message-ID: Dear Biomag community, We are pleased to announce that registration is now open for the Biomag 2012 Satellite Workshop on *"Studying the brain as a network using MEG: practical considerations." * * * *Date:* August 25, 2012 *Time:* 09:00-18:00 *Location:* ICM, the new Brain Institute at Hôpital Pitié-Salpêtrière; 47 Boulevard de l'Hôpital, 75013 Paris *Purpose of this Satellite:* It is becoming increasingly important to study the working brain as network both in cognitive and clinical neuroscience. MEG provides an excellent opportunity to study the functional interactions between various brain regions. There are now multiple approaches and tools available for doing this. The aim of the proposed workshop is to elucidate practical approaches for studying brain connectivity using MEG. This will be done by a set of presentations in which basics of connectivity and source space analysis are introduced. Then follows presentations by various toolbox developers. The toolbox presenters will be asked to 1) outline conceptually the types of connectivity approaches their toolboxes allow for and 2) describe how it practically can be done. Finally we will discuss how various connectivity measures can be tested using standardized data sets. Target audience: The workshop is targeted towards the advanced clinical or cognitive MEG user with an interest in embracing state-of-the-art methods for functional connectivity. Please see the satellite website for more details. You may register here. The registration deadline is June 30, 2012. Please note that there is a small (~10 euro) fee to cover costs, which you may pay at the door. For any further questions, you may send an email to the organizers at: biomag.network.practical at gmail.com We look forward to seeing you on August 25, 2012! Best regards, Ole Jensen, Sarang Dalal, and Johanna Zumer -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Mon Apr 2 21:18:19 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Mon, 2 Apr 2012 15:18:19 -0400 Subject: [FieldTrip] beamformer results smaller than brain In-Reply-To: References: Message-ID: Thanks, Arjen and Gio, I played around with cfg.inwardshift during ft_sourceanalysis, and adjusting it to somewhere between .25 and .5 gives decent results (it was originally set to 1), i.e. good coverage with no shrinkage. I'm actually a little confused about why one might need cfg.inwardshift parameter... Assuming the segmentation into different tissue types goes correctly, is it best to set the inwardshift parameters as close to 0 as possible (or not specify), since we'd want to put dipoles ranging the whole volume of the brain? Thanks! Akiko On Thu, Mar 29, 2012 at 5:13 AM, Gio Piantoni wrote: > Hi Akiko, > > Your headmodel looks pretty good and your beamformer plot seems to > cover most of the gray matter. > > However, it's good to check the location of your dipoles in respect to > your headmodel. For example, you can plot the .pos field of your > leadfield. Something like: > > ft_plot_mesh(bnd(3), 'facealpha', .5) > hold on > plot3(lead.pos(:,1), lead.pos(:,2), lead.pos(:,3), '.') > > It might well be that your grid is too coarse and some dipoles just > happen to be over the edge of the brain. Remember that your > "beamformer_result.png" is just an interpolation of the values of this > dipole grid. > > You can either try to make your grid more refined (but remember that > your computation time will significantly increase). Or you can > manipulate the way dipoles are considered inside or outside the brain > with "inwardshift" for ft_prepare_leadfield (although I'd advise > against using a negative value as some dipoles might really end up > outside of your brain mesh, with some numerical instabilities). > Another option (the easiest) is to nudge your grid by, say, a few > millimeters, so that the parietal dipoles will be just inside the > brain mesh. > > HTH, > > Gio > > -- > Giovanni Piantoni, MSc > Dept. Sleep & Cognition > Netherlands Institute for Neuroscience > Meibergdreef 47 > 1105 BA Amsterdam (NL) > > +31 20 5665492 > gio at gpiantoni.com > www.gpiantoni.com > > On Thu, Mar 29, 2012 at 00:22, Akiko Ikkai wrote: > > Hi Fieldtrip users, > > > > I'm hoping that someone could give me advice on segmentation and > beamformer > > on EEG data. I have EEG data set based on 128 channel cap. Thanks to the > > help I got in mid-Feb, I'm now able to create a decent > > segmentation (seg_results image attached) and volume conduction model. > > However, when I run beamformer based on these models, resulting > beamforming > > image is often smaller than the brain (beamformer_result attached). > > Particularly posterior parietal and occipital map is NaN. > > > > I have tried going back to segmentation and expanded brain by > using imdilate > > after ft_volumesegment such as: > > > > newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original > brain > > tissue from segmentation > > > > seg2.brain = newbrain; > > > > seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6; > > > > and run ft_prepare_mesh_new on seg2. Of course, I have to make sure > there is > > no intersect between different tissue types, so using imdilate has > > limitation. > > > > Could someone explain why this shrinkage might be happening, and how I > could > > fix it? > > > > Thanks in advance! Akiko > > > > -- > > Akiko Ikkai, Ph.D. > > Postdoctoral Fellow > > Department of Psychological and Brain Sciences > > Johns Hopkins University > > Ames Hall, 3400 N. Charles St. > > Baltimore, MD 21218 > > > > > > > > _______________________________________________ > > 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 > -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.vandenieuwenhuijzen at fcdonders.ru.nl Wed Apr 4 10:16:43 2012 From: m.vandenieuwenhuijzen at fcdonders.ru.nl (Marieke van de Nieuwenhuijzen) Date: Wed, 4 Apr 2012 10:16:43 +0200 (CEST) Subject: [FieldTrip] sudden errors in ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot In-Reply-To: <279226386.170300.1333525161466.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <1735698454.171384.1333527403632.JavaMail.root@draco.zimbra.ru.nl> Dear all, I have a problem with my beamforming script. The functions ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot all crash with the same main error, namely ??? Reference to non-existent field 'nChans'. Error in ==> ft_senstype at 188 elseif isheader && input.nChans==1 && ~isempty(regexp(input.label{1}, '^csc')) Error in ==> ft_convert_units at 56 if ft_senstype(obj, 'meg') Error in ==> ft_prepare_sourcemodel at 604 %(or of course ft_volumereslice, ft_volumesegment or ft_sourceplot, depending on the function) mri = ft_convert_units(mri); The only difference is that ft_volumereslice has the additional error layer Error in ==> ft_checkdata at 402 data = ft_convert_units(data); The code I am using is: cfg =[]; cfg.mri= subject.MRI; cfg.grid.warpmni = 'yes'; cfg.grid.resolution = 10; %resolution = 10 mm grid = ft_prepare_sourcemodel(cfg); mri = ft_read_mri(cfg.mri); mri.coordsys='ctf'; mri=ft_volumereslice([],mri); cfg = []; cfg.coordsys = 'ctf'; segmentedmri = ft_volumesegment(cfg, mri); mri.brainmask = segmentedmri.gray+segmentedmri.white+segmentedmri.csf; cfg = []; cfg.funparameter = 'brainmask'; figure; ft_sourceplot(cfg, mri); The curious thing is that this exact same code worked without any errors last week, but this week I am getting those errors. I am using the latest version of fieldtrip, and run ft_defaults before starting the script (although it also crashed when I didn't do that; I only started running ft_defaults when I got these errors). The fact that all errors seem to stem from the same error in ft_senstype, that this code has worked without any problems until last week, and that ft_senstype has been updated last Friday makes me suspect some bug during that update, but I am not sure about that. Does anyone have an idea as to what might be the problem here? Best, Marieke From r.oostenveld at donders.ru.nl Wed Apr 4 12:53:03 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 4 Apr 2012 12:53:03 +0200 Subject: [FieldTrip] sudden errors in ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot In-Reply-To: <1735698454.171384.1333527403632.JavaMail.root@draco.zimbra.ru.nl> References: <1735698454.171384.1333527403632.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <3B2F1399-1110-4339-A6EA-13DE99B083E6@donders.ru.nl> Dear Marieke The recently introduced bug has been tracked down and fixed. See http://bugzilla.fcdonders.nl/show_bug.cgi?id=1405 Sorry for the inconvenience. Robert On 4 Apr 2012, at 10:16, Marieke van de Nieuwenhuijzen wrote: > Dear all, > > I have a problem with my beamforming script. The functions ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot all crash with the same main error, namely > > ??? Reference to non-existent field 'nChans'. > > Error in ==> ft_senstype at 188 > elseif isheader && input.nChans==1 && ~isempty(regexp(input.label{1}, '^csc')) > > Error in ==> ft_convert_units at 56 > if ft_senstype(obj, 'meg') > > Error in ==> ft_prepare_sourcemodel at 604 %(or of course ft_volumereslice, ft_volumesegment or ft_sourceplot, depending on the function) > mri = ft_convert_units(mri); > > The only difference is that ft_volumereslice has the additional error layer > > Error in ==> ft_checkdata at 402 > data = ft_convert_units(data); > > The code I am using is: > > cfg =[]; > cfg.mri= subject.MRI; > cfg.grid.warpmni = 'yes'; > cfg.grid.resolution = 10; %resolution = 10 mm > grid = ft_prepare_sourcemodel(cfg); > > mri = ft_read_mri(cfg.mri); > mri.coordsys='ctf'; > mri=ft_volumereslice([],mri); > > cfg = []; > cfg.coordsys = 'ctf'; > segmentedmri = ft_volumesegment(cfg, mri); > > mri.brainmask = segmentedmri.gray+segmentedmri.white+segmentedmri.csf; > cfg = []; > cfg.funparameter = 'brainmask'; > figure; > ft_sourceplot(cfg, mri); > > The curious thing is that this exact same code worked without any errors last week, but this week I am getting those errors. > > I am using the latest version of fieldtrip, and run ft_defaults before starting the script (although it also crashed when I didn't do that; I only started running ft_defaults when I got these errors). > > The fact that all errors seem to stem from the same error in ft_senstype, that this code has worked without any problems until last week, and that ft_senstype has been updated last Friday makes me suspect some bug during that update, but I am not sure about that. > > Does anyone have an idea as to what might be the problem here? > > Best, > Marieke > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Wed Apr 4 12:56:09 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 4 Apr 2012 12:56:09 +0200 Subject: [FieldTrip] SPM-DCM course at the BIOMAG in Paris References: Message-ID: <60FE20C9-66C1-4682-B896-313A7E38E883@donders.ru.nl> Dear FieldTrip users Jean Daunizeau and Jeremie Mattout are organizing a DCM educational course at the BIOMAG conference in Paris in August. The registration for the course has just opened. Please see the attached flyer for further details best regards, Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Announcement_DCMcourse2012.pdf Type: application/pdf Size: 204397 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Fri Apr 6 20:05:56 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Fri, 6 Apr 2012 12:05:56 -0600 Subject: [FieldTrip] Removing channels from processed data Message-ID: Dear FieldTrippers, I'm using fieldtrip-20120405. I'm trying to remove a "bad" channel from a subject's processed data (output of ft_timelockanalysis and ft_freqanalysis). I've found the function ft_selectdata (which runs ft_selectdata_new), but when I define my cfg to remove the bad channel (cfg.channels={'all','-E59'}) and use the function, it also removes the dimord field which subsequent ft_* functions need (e.g., ft_multiplotER, ft_timelockgrandaverage). I could manually remove the channel, but I was hoping for a ft_* function that would modify the label field automatically. Manually replacing the channel with NaNs does not seem to be a solution because when I use ft_singleplotER to plot data from a ROI (i.e., multiple channels in a region) that includes this now-all-NaNs channel, nothing gets plotted (meaning a mean, and not a nanmean, function gets used to average over the ROI), so I fear the same thing will happen with other functions (e.g., ft_timelockstatistics). I also know I can use ft_rejectvisual early on in my processing, but I don't want to re-process my data (and I'm not currently using FT for artifact detection). So my question is: what's the best FieldTrip function-based way to remove a channel? Thanks, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Apr 6 20:50:11 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 6 Apr 2012 20:50:11 +0200 Subject: [FieldTrip] Removing channels from processed data In-Reply-To: References: Message-ID: <87CFA1EE-23A1-40B4-AF30-F96F63838BE7@donders.ru.nl> Dear Matt, It seems you have stumbled on some code that is still a bit under development, and apparently not really stable. ft_selectdata should be able to do the trick for you, but I suspect a bug in ft_selectdata_new, so I'd try ft_selectdata_old instead. To achieve this, you need to do something like this: selchan = ft_channelselection({'all' '-E59'}, data.label); data = ft_selectdata(data, 'channel', selchan); % notice the function's input now with key-value pairs, rather than a cfg. We hope to find some time to improve the ft_selectdata_new soon. For the time being, could you file a bug on this issue on our bugzilla website? (www.bugzilla.fcdonders.nl) Cheers, JM On Apr 6, 2012, at 8:05 PM, Matt Mollison wrote: > Dear FieldTrippers, > > I'm using fieldtrip-20120405. I'm trying to remove a "bad" channel from a subject's processed data (output of ft_timelockanalysis and ft_freqanalysis). I've found the function ft_selectdata (which runs ft_selectdata_new), but when I define my cfg to remove the bad channel (cfg.channels={'all','-E59'}) and use the function, it also removes the dimord field which subsequent ft_* functions need (e.g., ft_multiplotER, ft_timelockgrandaverage). > > I could manually remove the channel, but I was hoping for a ft_* function that would modify the label field automatically. Manually replacing the channel with NaNs does not seem to be a solution because when I use ft_singleplotER to plot data from a ROI (i.e., multiple channels in a region) that includes this now-all-NaNs channel, nothing gets plotted (meaning a mean, and not a nanmean, function gets used to average over the ROI), so I fear the same thing will happen with other functions (e.g., ft_timelockstatistics). I also know I can use ft_rejectvisual early on in my processing, but I don't want to re-process my data (and I'm not currently using FT for artifact detection). > > So my question is: what's the best FieldTrip function-based way to remove a channel? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Fri Apr 6 21:34:56 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Fri, 6 Apr 2012 13:34:56 -0600 Subject: [FieldTrip] Removing channels from processed data In-Reply-To: <87CFA1EE-23A1-40B4-AF30-F96F63838BE7@donders.ru.nl> References: <87CFA1EE-23A1-40B4-AF30-F96F63838BE7@donders.ru.nl> Message-ID: Thanks, JM. That seems to solve it. Bug submitted: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1409 Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Fri, Apr 6, 2012 at 12:50 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Matt, > > It seems you have stumbled on some code that is still a bit under > development, and apparently not really stable. > > ft_selectdata should be able to do the trick for you, but I suspect a bug > in ft_selectdata_new, so I'd try ft_selectdata_old instead. > > To achieve this, you need to do something like this: > > selchan = ft_channelselection({'all' '-E59'}, data.label); > data = ft_selectdata(data, 'channel', selchan); % notice the function's > input now with key-value pairs, rather than a cfg. > > We hope to find some time to improve the ft_selectdata_new soon. For the > time being, could you file a bug on this issue on our bugzilla website? ( > www.bugzilla.fcdonders.nl) > > Cheers, > > JM > > > On Apr 6, 2012, at 8:05 PM, Matt Mollison wrote: > > Dear FieldTrippers, > > I'm using fieldtrip-20120405. I'm trying to remove a "bad" channel from a > subject's processed data (output of ft_timelockanalysis and > ft_freqanalysis). I've found the function ft_selectdata (which runs > ft_selectdata_new), but when I define my cfg to remove the bad channel > (cfg.channels={'all','-E59'}) and use the function, it also removes the > dimord field which subsequent ft_* functions need (e.g., ft_multiplotER, > ft_timelockgrandaverage). > > I could manually remove the channel, but I was hoping for a ft_* function > that would modify the label field automatically. Manually replacing the > channel with NaNs does not seem to be a solution because when I use > ft_singleplotER to plot data from a ROI (i.e., multiple channels in a > region) that includes this now-all-NaNs channel, nothing gets plotted > (meaning a mean, and not a nanmean, function gets used to average over the > ROI), so I fear the same thing will happen with other functions (e.g., > ft_timelockstatistics). I also know I can use ft_rejectvisual early on in > my processing, but I don't want to re-process my data (and I'm not > currently using FT for artifact detection). > > So my question is: what's the best FieldTrip function-based way to remove > a channel? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > 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 dashiel.munding at gmail.com Sun Apr 8 20:52:40 2012 From: dashiel.munding at gmail.com (Dashiel Munding) Date: Sun, 8 Apr 2012 20:52:40 +0200 Subject: [FieldTrip] Problem reading trials into ft_rejectvisual Message-ID: Hello all, I'm trying to figure out a way of reading only selected trials into analysis without running through ft_rejectvisual every time. I have a list of trials that I have already rejected, and the documentation (http://fieldtrip.fcdonders.nl/reference/ft_rejectvisual) says that I should be able to use cfg.trials as a 1xN vector to put in a list of those trials that I want to use : cfg.trials = 'all' or a selection given as a 1xN vector (default = 'all') I've tried various formats for this vector (I'm new to both MATLAB and fieldtrip, so this might be a simple solve) but I can't get a positive result. I know I can save out the variable and read it in again at a later date, but this seems like a very inefficient way of doing it if all I need is a list of numbers, instead of a 1.5gb .m file... Has anyone come across/solved this problem? Can anyone provide me with an example of the syntax fieldtrip is expecting? I've tried: cfg.trials = {'all' '-56', '-151', '-232', '-53'}; cfg.trials = {'1','2','3','4','5','6','7','8','9','10','46'}; cfg.trials = {1,2,3,4,5,6,7,8,9,10,46}; and some other efforts to no avail! Thanks in advance, and sorry for naivety! Dashiel From dashiel.munding at gmail.com Sun Apr 8 20:56:22 2012 From: dashiel.munding at gmail.com (Dashiel Munding) Date: Sun, 8 Apr 2012 20:56:22 +0200 Subject: [FieldTrip] Problem reading trials into ft_rejectvisual In-Reply-To: References: Message-ID: Thought an example of the error message I'm getting might be useful in diagnosing the problem. I would delve further but I'm not an experienced MATLAB user, so I don't think my investigation would be very fruitful! --- Error using subsindex Function 'subsindex' is not defined for values of class 'cell'. Error in selfromraw (line 11) data.trial = data.trial(selrpt); Error in ft_selectdata_old (line 544) data = selfromraw(data, 'rpt', selrpt); Error in ft_selectdata (line 45) [varargout{1:nargout}] = ft_selectdata_old(varargin{:}); Error in ft_rejectvisual (line 196) data = ft_selectdata(data, 'rpt', cfg.trials); On 8 April 2012 20:52, Dashiel Munding wrote: > Hello all, > > I'm trying to figure out a way of reading only selected trials into > analysis without running through ft_rejectvisual every time. I have a > list of trials that I have already rejected, and the documentation > (http://fieldtrip.fcdonders.nl/reference/ft_rejectvisual) says that I > should be able to use cfg.trials as a 1xN vector to put in a list of > those trials that I want to use : > > cfg.trials      = 'all' or a selection given as a 1xN vector (default = 'all') > > I've tried various formats for this vector (I'm new to both MATLAB and > fieldtrip, so this might be a simple solve) but I can't get a positive > result. I know I can save out the variable and read it in again at a > later date, but this seems like a very inefficient way of doing it if > all I need is a list of numbers, instead of a 1.5gb .m file... > > Has anyone come across/solved this problem? Can anyone provide me with > an example of the syntax fieldtrip is expecting? > > I've tried: > > cfg.trials = {'all' '-56', '-151', '-232', '-53'}; > > cfg.trials = {'1','2','3','4','5','6','7','8','9','10','46'}; > > cfg.trials = {1,2,3,4,5,6,7,8,9,10,46}; > > and some other efforts to no avail! > > Thanks in advance, and sorry for naivety! > > Dashiel From matt.mollison at gmail.com Sun Apr 8 21:17:31 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Sun, 8 Apr 2012 13:17:31 -0600 Subject: [FieldTrip] Problem reading trials into ft_rejectvisual In-Reply-To: References: Message-ID: Dashiel, You're using curly braces {} for trial indexing; this creates a cell array, which you don't want. Try using brackets [] to form a vector: cfg.trials = [1,2,3,4,5,6,7,8,9,10,46]; Check out http://www.mathworks.com/help/techdoc/ref/specialcharacters.htmlfor more matlab character syntax. Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Sun, Apr 8, 2012 at 12:56 PM, Dashiel Munding wrote: > Thought an example of the error message I'm getting might be useful in > diagnosing the problem. I would delve further but I'm not an > experienced MATLAB user, so I don't think my investigation would be > very fruitful! > > --- > > Error using subsindex > Function 'subsindex' is not defined for values of class 'cell'. > > Error in selfromraw (line 11) > data.trial = data.trial(selrpt); > > Error in ft_selectdata_old (line 544) > data = selfromraw(data, 'rpt', selrpt); > > Error in ft_selectdata (line 45) > [varargout{1:nargout}] = ft_selectdata_old(varargin{:}); > > Error in ft_rejectvisual (line 196) > data = ft_selectdata(data, 'rpt', cfg.trials); > > On 8 April 2012 20:52, Dashiel Munding wrote: > > Hello all, > > > > I'm trying to figure out a way of reading only selected trials into > > analysis without running through ft_rejectvisual every time. I have a > > list of trials that I have already rejected, and the documentation > > (http://fieldtrip.fcdonders.nl/reference/ft_rejectvisual) says that I > > should be able to use cfg.trials as a 1xN vector to put in a list of > > those trials that I want to use : > > > > cfg.trials = 'all' or a selection given as a 1xN vector (default = > 'all') > > > > I've tried various formats for this vector (I'm new to both MATLAB and > > fieldtrip, so this might be a simple solve) but I can't get a positive > > result. I know I can save out the variable and read it in again at a > > later date, but this seems like a very inefficient way of doing it if > > all I need is a list of numbers, instead of a 1.5gb .m file... > > > > Has anyone come across/solved this problem? Can anyone provide me with > > an example of the syntax fieldtrip is expecting? > > > > I've tried: > > > > cfg.trials = {'all' '-56', '-151', '-232', '-53'}; > > > > cfg.trials = {'1','2','3','4','5','6','7','8','9','10','46'}; > > > > cfg.trials = {1,2,3,4,5,6,7,8,9,10,46}; > > > > and some other efforts to no avail! > > > > Thanks in advance, and sorry for naivety! > > > > Dashiel > > _______________________________________________ > 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 jarang.hahm at gmail.com Tue Apr 10 11:40:03 2012 From: jarang.hahm at gmail.com (Jarang Hahm) Date: Tue, 10 Apr 2012 18:40:03 +0900 Subject: [FieldTrip] =?utf-8?q?=5BFieldTrip=E2=80=8B=5D_Data_handling_afte?= =?utf-8?q?r_excluding_single_sensors_=28Neuromag=29?= Message-ID: Hi all, We are using Neuromag 306 sensors VectorView system. And only gradiometer sensors (204 sensors) are used for analysis. In the artifact rejection, I excluded four bad sensors, not as a pair, among 204 sensors. After time-frequency analysis, I got lost when combine the sensors. How can I deal with the data with a single sensor in part? Should I reject the sensor as a pair? Or, combine the signals only for the paired sensors? I want you to suggest the proper way to handle the data of one sensor in a pair. Thank you in advance, Jarang Hahm -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Tue Apr 10 13:16:47 2012 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Tue, 10 Apr 2012 13:16:47 +0200 Subject: [FieldTrip] =?utf-8?q?=5BFieldTrip=E2=80=8B=5D_Data_handling_afte?= =?utf-8?q?r_excluding_single_sensors_=28Neuromag=29?= In-Reply-To: References: Message-ID: Dear Jarang, I think there are two options: 1.) You exclude as a pair, as combining the two orthogonal sensors you want to capture the different directions of the magnetic field. 2.) Or you look at the horizontal and vertical gradiometers separately. The following script should allow you to extract the two different sensor types channel = ft_channelselection('MEG*2',data.label); index = match_str(data.label,channel); gradH_F = data; gradH_F.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); gradH_S = data; gradH_S.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); channel = ft_channelselection('MEG*3',data.label); index = match_str(data.label,channel); gradV_F = data; gradV_F.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); gradV_S = data; gradV_S.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); data is a grand mean time frequency matrix with keep individuals = yes. I hope that helps. Best, Stephan El 10/04/2012, a las 11:40, Jarang Hahm escribió: > Hi all, > > > We are using Neuromag 306 sensors VectorView system. > And only gradiometer sensors (204 sensors) are used for analysis. > > > > In the artifact rejection, I excluded four bad sensors, not as a pair, among 204 sensors. > > After time-frequency analysis, I got lost when combine the sensors. > > > > How can I deal with the data with a single sensor in part? > > Should I reject the sensor as a pair? Or, combine the signals only for the paired sensors? > > > I want you to suggest the proper way to handle the data of one sensor in a pair. > > > > > Thank you in advance, > > > > Jarang Hahm > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Tue Apr 10 21:58:18 2012 From: lihqih at gmail.com (qi li) Date: Tue, 10 Apr 2012 15:58:18 -0400 Subject: [FieldTrip] ft_multiplotER Message-ID: Hi there, I tried to plot with the instruction in the tutorial. cfg=[];cfg.layout='ctf275'; ft_multiplotER(cfg,data) and get the following message 'reading layout from file ctf275.lay Error using ft_prepare_layout>readlay (line 668) could not open layout file: ctf275.lay' Any hints to solve the issue would be highly appreciated! From eelke.spaak at donders.ru.nl Wed Apr 11 08:02:11 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 11 Apr 2012 08:02:11 +0200 Subject: [FieldTrip] ft_multiplotER In-Reply-To: References: Message-ID: Hi qi, Could you try: cfg.layout = 'CTF275.lay'; so, uppercase letters 'CTF' and include the extension. That should work (at least, if the data you are trying to plot is from a CTF 275 system, which I assume it is). Best, Eelke On 10 April 2012 21:58, qi li wrote: > Hi there, > > I tried to plot with the instruction in the tutorial. > > cfg=[];cfg.layout='ctf275'; > ft_multiplotER(cfg,data) > and get the following message > > 'reading layout from file ctf275.lay > Error using ft_prepare_layout>readlay (line 668) > could not open layout file: ctf275.lay' > > Any hints to solve the issue would be highly appreciated! > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lihqih at gmail.com Wed Apr 11 22:13:23 2012 From: lihqih at gmail.com (qi li) Date: Wed, 11 Apr 2012 16:13:23 -0400 Subject: [FieldTrip] question on the coordinate Message-ID: Hi there, Our MRI data was already alined to Talariach coordinate. Let me call it mri. I aligned the MRI coordinate to MEG by ft_volumerealign and produce a variable called mri_other. mri_other=ft_volumerealign(cfg,mri); Now I reslice by mrirs=ft_volumereslice(cfg,mri_other) and do segmentation by cfg.coordsys='ctf; seg=ft_volumesegment(cfg,mrirs); I found mrirs.transform is not equal to mri_other.transform. Is this correct? I think re-slicing and segmentation should not change the transformation matrix. The last question is since our mri data was already aligned to Talariach, do we need to realign segmented? Thank you all! Qi From explena at gmail.com Thu Apr 12 10:57:44 2012 From: explena at gmail.com (Shen-Mou Hsu) Date: Thu, 12 Apr 2012 16:57:44 +0800 Subject: [FieldTrip] [problem] zero plv Message-ID: Dear Users, I try to calculate the phase locking values following the tutorial and encounter a problem. First, I ran freqanalysis as follows: cfg = []; cfg.channel = 'EEG'; cfg.method = 'mtmfft'; cfg.foi = 8:1:120; cfg.keeptrials = 'yes'; cfg.ouput = 'fourier'; cfg.tapsmofrq = 2; Phase= ft_freqanalysis(cfg, data); I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) Then, I ran connectivity analysis as follows cfg = []; cfg.method = 'plv'; PLV = ft_connectivityanalysis(cfg, Phase); Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: [0x113 double] I wondered if there is anything wrong with the previous steps. Many thanks! Shen-Mou Hsu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 12 11:37:04 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 12 Apr 2012 11:37:04 +0200 Subject: [FieldTrip] [problem] zero plv In-Reply-To: References: Message-ID: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> Hi Shen-Mou, There's a typo in the cfg that you supply to ft_freqanalysis -> cfg.ouput should read cfg.output BW, JM On Apr 12, 2012, at 10:57 AM, Shen-Mou Hsu wrote: > Dear Users, > > I try to calculate the phase locking values following the tutorial and encounter a problem. > > First, I ran freqanalysis as follows: > cfg = []; > cfg.channel = 'EEG'; > cfg.method = 'mtmfft'; > cfg.foi = 8:1:120; > cfg.keeptrials = 'yes'; > cfg.ouput = 'fourier'; > cfg.tapsmofrq = 2; > Phase= ft_freqanalysis(cfg, data); > > I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) > > Then, I ran connectivity analysis as follows > cfg = []; > cfg.method = 'plv'; > PLV = ft_connectivityanalysis(cfg, Phase); > > Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: [0x113 double] > > I wondered if there is anything wrong with the previous steps. Many thanks! > > Shen-Mou Hsu > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From explena at gmail.com Thu Apr 12 12:15:40 2012 From: explena at gmail.com (Shen-Mou Hsu) Date: Thu, 12 Apr 2012 18:15:40 +0800 Subject: [FieldTrip] [problem] zero plv In-Reply-To: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> References: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> Message-ID: Hi JM, Apologize for such a stupid mistake. However, I have amended the typo and the results are the same. Both cumsumcnt and cumtapcnt returned constant values, 1101 (timepoints) and 3, respectively. I am indebted to your kindness in this matter. Shen-Mou On Thu, Apr 12, 2012 at 5:37 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Shen-Mou, > > There's a typo in the cfg that you supply to ft_freqanalysis -> cfg.ouput > should read cfg.output > > BW, > > JM > > On Apr 12, 2012, at 10:57 AM, Shen-Mou Hsu wrote: > > Dear Users, > > I try to calculate the phase locking values following the tutorial and > encounter a problem. > > First, I ran freqanalysis as follows: > cfg = []; > cfg.channel = 'EEG'; > cfg.method = 'mtmfft'; > cfg.foi = 8:1:120; > cfg.keeptrials = 'yes'; > cfg.ouput = 'fourier'; > cfg.tapsmofrq = 2; > Phase= ft_freqanalysis(cfg, data); > > I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are > constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) > > Then, I ran connectivity analysis as follows > cfg = []; > cfg.method = 'plv'; > PLV = ft_connectivityanalysis(cfg, Phase); > > Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: > [0x113 double] > > I wondered if there is anything wrong with the previous steps. Many thanks! > > Shen-Mou Hsu > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > 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 explena at gmail.com Thu Apr 12 12:57:18 2012 From: explena at gmail.com (Shen-Mou Hsu) Date: Thu, 12 Apr 2012 18:57:18 +0800 Subject: [FieldTrip] [problem] zero plv In-Reply-To: References: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> Message-ID: Dear JM, After correcting the typo you pointed out, I do get the plv. Many thanks indeed! Shen-Mou On Thu, Apr 12, 2012 at 6:15 PM, Shen-Mou Hsu wrote: > Hi JM, > > Apologize for such a stupid mistake. However, I have amended the typo and > the results are the same. Both cumsumcnt and cumtapcnt returned constant > values, 1101 (timepoints) and 3, respectively. I am indebted to your > kindness in this matter. > > Shen-Mou > > > On Thu, Apr 12, 2012 at 5:37 PM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Shen-Mou, >> >> There's a typo in the cfg that you supply to ft_freqanalysis -> cfg.ouput >> should read cfg.output >> >> BW, >> >> JM >> >> On Apr 12, 2012, at 10:57 AM, Shen-Mou Hsu wrote: >> >> Dear Users, >> >> I try to calculate the phase locking values following the tutorial and >> encounter a problem. >> >> First, I ran freqanalysis as follows: >> cfg = []; >> cfg.channel = 'EEG'; >> cfg.method = 'mtmfft'; >> cfg.foi = 8:1:120; >> cfg.keeptrials = 'yes'; >> cfg.ouput = 'fourier'; >> cfg.tapsmofrq = 2; >> Phase= ft_freqanalysis(cfg, data); >> >> I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are >> constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) >> >> Then, I ran connectivity analysis as follows >> cfg = []; >> cfg.method = 'plv'; >> PLV = ft_connectivityanalysis(cfg, Phase); >> >> Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: >> [0x113 double] >> >> I wondered if there is anything wrong with the previous steps. Many >> thanks! >> >> Shen-Mou Hsu >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> 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 fredericroux at hotmail.de Thu Apr 12 19:01:49 2012 From: fredericroux at hotmail.de (Frederic Roux) Date: Thu, 12 Apr 2012 19:01:49 +0200 Subject: [FieldTrip] randomization vs permutation using ft_sourceanalysis Message-ID: Dear all, I would like to compute first level statistics of resting state source activity during eyes open and eyes closed to be able to compare this contrast across a group of subjects with different ages. I noticed that ft_sourceanalysis offers the possibility to contrast two conditions using cfg.randomization or cfg.permutation. The help documentation mentions that these options are required if one wants to contrast two conditions and apparently they do something different since they are mutually exclusive (one can not call ft_sourcenalysis with both). However, it is not clear to me how both options differ and how the data structure that is being returned can be used with ft_sourcestatistics. Any help would be as always highly appreciated. Best, Fred -- Frédéric Roux, PhD student Department of Neurophysiology Max Planck Institute for Brain Research D-60529 Frankfurt am Main Frederic.Roux at brain.mpg.de +49(0)69630183225 -------------- next part -------------- An HTML attachment was scrubbed... URL: From candida at nmr.mgh.harvard.edu Thu Apr 12 19:21:38 2012 From: candida at nmr.mgh.harvard.edu (Candida Jane Maria Ustine) Date: Thu, 12 Apr 2012 13:21:38 -0400 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data Message-ID: Hello All, I have just started reading about fieldtrip and I am learning a lot of exciting things. I have MEG data using the neuromag system and I wanted to run the Independent Component Analysis on the .fif files to remove the EOG and ECG artifact from them. I see that the documentation provided in the website( http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts) has resources to handle CTF datasets, and I was wondering if anyone has looked into the option of using the .fif files directly. Or is there a way to convert the *.fif files to the CTF format as there is an MNE utility to do the reverse mne_ctf2fif? Thanks much for your time and help! Best, Candida -- Candida Jane Maria Ustine Martinos Center for Biomedical Imaging MGH Kuperberg Lab The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Thu Apr 12 20:34:54 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Thu, 12 Apr 2012 13:34:54 -0500 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact Message-ID: Hi Candida, Welcome to FieldTrip. It seems you can import Neuromag data directly into FieldTrip: see http://fieldtrip.fcdonders.nl/getting_started/neuromag . Once the data are read into FieldTrip you can just save them as MATLAB files and you should be able to treat them the same as data from any other source once they're in FieldTrip's format. Best, Steve Politzer-Ahles On Thu, Apr 12, 2012 at 12:22 PM, wrote: > > Message: 4 > Date: Thu, 12 Apr 2012 13:21:38 -0400 > From: Candida Jane Maria Ustine > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact > on Neuromag(*.fif) data > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello All, > > I have just started reading about fieldtrip and I am learning a lot of > exciting things. > > I have MEG data using the neuromag system and I wanted to run the > Independent Component Analysis on the .fif files to remove the EOG and ECG > artifact from them. I see that the documentation provided in the website( > > http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts > ) > has resources to handle CTF datasets, and I was wondering if anyone has > looked into the option of using the .fif files directly. > Or is there a way to convert the *.fif files to the CTF format as there is > an MNE utility to do the reverse mne_ctf2fif? > > Thanks much for your time and help! > > Best, > Candida > > > > -- > Candida Jane Maria Ustine > Martinos Center for Biomedical Imaging > MGH > Kuperberg Lab > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Partners Compliance > HelpLine at http://www.partners.org/complianceline . If the e-mail was > sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120412/f79ae1c8/attachment.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 17, Issue 11 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rapela at ucsd.edu Thu Apr 12 21:41:54 2012 From: rapela at ucsd.edu (Joaquin Rapela) Date: Thu, 12 Apr 2012 12:41:54 -0700 Subject: [FieldTrip] Postdoctoral position in motor control Message-ID: <20120412194154.GA17424@dreaming.ucsd.edu> Please contact Prof. Della-Maggiore (vdellamaggiore at fmed.uba.ar) if you are interested in the following postdoctoral position in the lively city of Buenos Aires, Argentina. Cordially, Joaquin The Physiology of Action Lab (www.physiologyofactionlab.info) is looking for a candidate to fill a postdoctoral position in the Department of Physiology of the University of Buenos Aires, Argentina. The Labortory focuses on Human Behavioral Neuroscience, particularly in the area of motor control. We use Transcranial Magnetic Stimulation, Magnetic Resonance Imaging, EEG and psychophysics to study the neural mechanisms at the basis of different aspects of motor control. These include motor resonance and action understanding during action observation, online motor control and motor learning. Plastic changes induced by learning and stroke are also main interests of the lab. We are looking for a Ph.D. with a background in Neuroscience and, preferably, with experience in one ore more of the techniques used in the lab, and data analysis. Candidates with knowledge of Matlab would have priority. The postdoc is funded by a fellowship from the National Agency for the Promotion of Science and Technology (Argentina). Interested candidates could contact Dr. Valeria Della Maggiore at vdellamaggiore at fmed.uba.ar with a CV, a letter of interest and one or two references (email). Many thanks -- Valeria Della-Maggiore, Ph. D Department of Physiology, School of Medicine University of Buenos Aires Paraguay 2155, Capital Federal Buenos Aires, C1121ABG Argentina phone 54 11 5 950 9500 (2132) http://www.physiologyofactionlab.info ------------------------------------------------------------ being wild and disciplined at the same time.... -- Joaquin Rapela, PhD Swartz Center for Computational Neuroscience University of California San Diego 9500 Gilman Drive, San Diego, CA 92093-0559 tel: (858) 822-7536 fax: (858) 822-7556 http://sccn.ucsd.edu/~rapela ---------------------------------- the gods do not grant men all their gifts at once Nestor in The Iliad From alexandre.gramfort at inria.fr Fri Apr 13 08:50:39 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 13 Apr 2012 08:50:39 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: Message-ID: hi Candida, you should be able to import your fif files into fieldtrip but be careful when applying ICA on neuromag data as channels have different types and you have signals with 2 orders of magnitude difference between gradiometers and magnetometers. I am curious to know if fieldtrip handles this properly? and if so how. Also can Fieldtrip write data back into fif files keeping intact all the measurement info? thanks Alex -- Alexandre Gramfort, PhD alexandre.gramfort at inria.fr INRIA Parietal Project Team, NeuroSpin CEA Saclay Bat. 145, PC 156 91191 Gif-sur-Yvette, France http://alexandre.gramfort.net On Thu, Apr 12, 2012 at 7:21 PM, Candida Jane Maria Ustine wrote: > Hello All, > > I have just started reading about fieldtrip and I am learning a lot of > exciting things. > > I have MEG data using the neuromag system and I wanted to run the > Independent Component Analysis on the .fif files to remove the EOG and ECG > artifact from them. I see that the documentation provided in the > website(http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts) > has resources to handle CTF datasets, and I was wondering if anyone has > looked into the option of using the .fif files directly. > Or is there a way to convert the *.fif files to the CTF format as there is > an MNE utility to do the reverse mne_ctf2fif? > > Thanks much for your time and help! > > Best, > Candida > > > > -- > Candida Jane Maria Ustine > Martinos Center for Biomedical Imaging > MGH > Kuperberg Lab > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Partners Compliance > HelpLine at http://www.partners.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact the > sender and properly dispose of the e-mail. > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From jan.schoffelen at donders.ru.nl Fri Apr 13 09:01:40 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 Apr 2012 09:01:40 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: Message-ID: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> Hi Alex, > I am curious to know if fieldtrip handles this properly? and if so how. It depends a bit on the exact algorithm that is used, but for example the runica implementation (we use the EEGlab code for this) performs a whitening of the data prior to the decomposition. This would address the difference in magnitude issue, wouldn't it? > Also can Fieldtrip write data back into fif files keeping intact > all the measurement info? Not really; I have some code of Lauri's (which is not yet in FT), which can write epoched data to a fif-file. However, most of the measurement info is lost along the way. Also, since we're not fif-experts, it's not trivial for us to find out how the measurement info should be formatted. Of course it is possible to reverse engineer this from the mne-code, but this is heavily geared towards elekta hardware. Yet, I could imagine that this functionality could be valuable, because it would enable two-way traffic of data between FT and MNE-suite. Do you happen to have any code that writes meaningful measurement info? Best, Jan-Mathijs > > thanks > > Alex > -- > Alexandre Gramfort, PhD > alexandre.gramfort at inria.fr > INRIA Parietal Project Team, NeuroSpin CEA Saclay > Bat. 145, PC 156 > 91191 Gif-sur-Yvette, France > http://alexandre.gramfort.net > > On Thu, Apr 12, 2012 at 7:21 PM, Candida Jane Maria Ustine > wrote: >> Hello All, >> >> I have just started reading about fieldtrip and I am learning a lot of >> exciting things. >> >> I have MEG data using the neuromag system and I wanted to run the >> Independent Component Analysis on the .fif files to remove the EOG and ECG >> artifact from them. I see that the documentation provided in the >> website(http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts) >> has resources to handle CTF datasets, and I was wondering if anyone has >> looked into the option of using the .fif files directly. >> Or is there a way to convert the *.fif files to the CTF format as there is >> an MNE utility to do the reverse mne_ctf2fif? >> >> Thanks much for your time and help! >> >> Best, >> Candida >> >> >> >> -- >> Candida Jane Maria Ustine >> Martinos Center for Biomedical Imaging >> MGH >> Kuperberg Lab >> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Partners Compliance >> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent >> to you in error but does not contain patient information, please contact the >> sender and properly dispose of the e-mail. >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Fri Apr 13 09:22:53 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 13 Apr 2012 09:22:53 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> References: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> Message-ID: hi Jan-Mathijs, thanks for the quick answer. > It depends a bit on the exact algorithm that is used, but for example the > runica implementation (we use the EEGlab code for this) performs a whitening > of the data prior to the decomposition. This would address the difference in > magnitude issue, wouldn't it? it does yes. My question is then how do you compute the withering matrix? > Also can Fieldtrip write data back into fif files keeping intact > all the measurement info? > > Not really; I have some code of Lauri's (which is not yet in FT), which can > write epoched data to a fif-file. However, most of the measurement info is > lost along the way. that's what I feared. > Also, since we're not fif-experts, it's not trivial for > us to find out how the measurement info should be formatted. Of course it is > possible to reverse engineer this from the mne-code, but this is heavily > geared towards elekta hardware. Yet, I could imagine that this functionality > could be valuable, because it would enable two-way traffic of data between > FT and MNE-suite. that would be very valuable indeed. > Do you happen to have any code that writes meaningful > measurement info? not in one function or at least not in matlab. one should have a fiff_write_meas_info.m that does the opposite to: https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_read_meas_info.m part of the answer is in: https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_write_evoked.m a python example is in : https://github.com/mne-tools/mne-python/blob/master/mne/fiff/meas_info.py#L235 but I agree you need a fairly good understanding of the fif format… we might have to sit down together to do this. Alex From Andrew.Dykstra at med.uni-heidelberg.de Fri Apr 13 09:51:01 2012 From: Andrew.Dykstra at med.uni-heidelberg.de (Andrew R. Dykstra) Date: Fri, 13 Apr 2012 09:51:01 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data Message-ID: Hi Candida, An alternative to using fieldtrip would be EEGLAB (I believe Fieldtrip using the code there anyway). I was able to run ICA on my combined EEG/Neuromag-122 data using a combination of the MNE MATLAB toolbox (specifically, fiff_setup_read_raw & fiff_read_raw_segment) and EEGLAB's import from MATLAB matrix functionality. More work would be required to retain the sensor locations and resulting component topographies. Then, along the lines of Alex's concerns, you could run the decomposition separately for each sensor type (Mags/Grads/EEG). This may be unnecessary if the runica algorithm handles this properly (assuming you have imported the sensor types along with the time series data into EEGLAB). After subtracting out the artifact components, you could then replace the appropriate entires of your original data matrix and use fiff_write_raw_segment (from the nightly build of the MNE suite). Hope this helps, Andy -- Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov -------------- next part -------------- An HTML attachment was scrubbed... URL: From grion at sissa.it Fri Apr 13 11:14:08 2012 From: grion at sissa.it (Natalia Grion) Date: Fri, 13 Apr 2012 11:14:08 +0200 Subject: [FieldTrip] PLV definition and implementation Message-ID: <20120413111408.Horde.eLHMRh8V4mxPh_5gqW4WfWA@webmail.sissa.it> Dear Fieldtripers, I would like to know how you define and implement 'plv' (phase locking value) in the fieldtrip. I do not see any documentation on this issue of reference paper and I'm confused by the fact that this definition was used by Lachaux (1999) and fieldtrip is taking the cross-spectrum and doing some treatment (difficult to follow in the series of functions involved) to ignore amplitude consistency (I guess a different treatment from coherence 'coh' function). Could you clarify this to me or give me a reference paper? Thanks! Natalia From jan.schoffelen at donders.ru.nl Fri Apr 13 11:57:56 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 Apr 2012 11:57:56 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> Message-ID: <5DB5ADAB-2E6A-4B90-B8AD-69D7CF315BB4@donders.ru.nl> Hi Alex, > it does yes. My question is then how do you compute the withering matrix? That's the magic of EEGlab ;-). I did not look into the code but I would assume based on the estimate of the precision matrix. Do you think the magnitude problem will lead to numerical issues upon inversion of the covariance matrix? >> Also can Fieldtrip write data back into fif files keeping intact >> all the measurement info? >> >> Not really; I have some code of Lauri's (which is not yet in FT), which can >> write epoched data to a fif-file. However, most of the measurement info is >> lost along the way. > > that's what I feared. > >> Also, since we're not fif-experts, it's not trivial for >> us to find out how the measurement info should be formatted. Of course it is >> possible to reverse engineer this from the mne-code, but this is heavily >> geared towards elekta hardware. Yet, I could imagine that this functionality >> could be valuable, because it would enable two-way traffic of data between >> FT and MNE-suite. > > that would be very valuable indeed. > >> Do you happen to have any code that writes meaningful >> measurement info? > > not in one function or at least not in matlab. > > one should have a fiff_write_meas_info.m that does the opposite to: > > https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_read_meas_info.m > > part of the answer is in: > > https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_write_evoked.m > > a python example is in : > > https://github.com/mne-tools/mne-python/blob/master/mne/fiff/meas_info.py#L235 > > but I agree you need a fairly good understanding of the fif format… > > we might have to sit down together to do this. I am afraid so. Well, I would certainly be up for it, because it would further strengthen both packages. Shall I come to you, or will you come to me ;-)? JM > Alex > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Fri Apr 13 12:08:10 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 13 Apr 2012 12:08:10 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: <5DB5ADAB-2E6A-4B90-B8AD-69D7CF315BB4@donders.ru.nl> References: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> <5DB5ADAB-2E6A-4B90-B8AD-69D7CF315BB4@donders.ru.nl> Message-ID: hi JM, > That's the magic of EEGlab ;-). I did not look into the code but I would > assume based on the estimate of the precision matrix. Do you think the > magnitude problem will lead to numerical issues upon inversion of the > covariance matrix? probably not. > I am afraid so. Well, I would certainly be up for it, because it would > further strengthen both packages. Shall I come to you, or will you come to > me ;-)? Unless I come to you first, you'll come to me for Biomag in august I guess. Alex From Panagiotis.Tsiatsis at Tuebingen.MPG.de Fri Apr 13 19:00:14 2012 From: Panagiotis.Tsiatsis at Tuebingen.MPG.de (Panagiotis Tsiatsis) Date: Fri, 13 Apr 2012 19:00:14 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: Message-ID: <4F885B9E.6000307@Tuebingen.MPG.de> On 4/13/2012 8:50 AM, Alexandre Gramfort wrote: > but be careful when applying ICA on neuromag data as > channels have different types and you have signals > with 2 orders of magnitude difference between gradiometers > and magnetometers. > > I am curious to know if fieldtrip handles this properly? and if so how. Hi all, I am also working with CTF MEG data. What I ve been basically doing up to now was to split the datasets in two subsets: one containing only the MEGGRAD sensors (let s call it A) and another containing all the rest (let it be B). Then I would apply ICA only on the set containing the main MEG sensors, subtract the EOG-related components and re-construct the data without them (A'). Finally, I would merge A' with B. This works fine and the results that I am getting are convincing, the only problem is that of course the reference channels are still contaminated. I don t know if this would be a problem in subsequent analysis, ie source localization, maybe somebody who has more experience further down this road could comment on that. Best, Panagiotis -- Panagiotis S. Tsiatsis Max Planck Institute for Biological Cybernetics Cognitive NeuroImaging Group Tuebingen, Germany From cas243 at georgetown.edu Fri Apr 13 19:52:47 2012 From: cas243 at georgetown.edu (Clara A. Scholl) Date: Fri, 13 Apr 2012 13:52:47 -0400 Subject: [FieldTrip] dimensions for coherence Message-ID: Dear Fieldtrip users, I'm encountering a problem with calculating coherence between two time courses. I suspect I'm misunderstanding something very basic. When I calculate the coherence using data with multiple trials -- with dimensions rpttap_chan_freq, everything works fine (I get a coherence spectrum calculation that is averaged over the rpt dimension). However if I want to limit the calculation to data with dimensions chan_freq (i.e. find the coherence between the fourier spectra (containing both amplitude and phase info) of a single timecourse on two different channels (where those channels are specified using cfg.channelcmb)), I get an error. I've tried to do this two different ways. If I still use the rpttap_chan_freq data, I tried specifying cfg.trials=1 in the connectivity analysis input, and the error given is: ??? Index exceeds matrix dimensions. Error in ==> ft_connectivity_corr at 131 p1 = reshape(input(j,powindx(:,1),:,:,:), siz(2:end)); Error in ==> ft_connectivityanalysis at 471 [datout, varout, nrpt] = ft_connectivity_corr(data.(inparam), optarg{:}); ->>If I input frequency data with dimensions chan_freq into ft_connectivityanalysis (still only specifying cfg.method='coh' and the channel combinations I'm interested in with cfg.channelcmb) the output is: ??? Index exceeds matrix dimensions. Error in ==> ft_checkdata>fixcsd at 843 tmpdat1 = data.fourierspctrm(indx,cmbindx(:,1),:,:); Error in ==> ft_checkdata at 629 data = fixcsd(data, cmbrepresentation, channelcmb); Error in ==> univariate2bivariate at 37 data = ft_checkdata(data, 'cmbrepresentation', 'sparse', 'channelcmb', cmb); Error in ==> ft_connectivityanalysis at 320 [data, powindx, hasrpt] = univariate2bivariate(data, 'fourierspctrm', 'crsspctrm', dtype, 'cmb', cfg.channelcmb, 'keeprpt', normrpt); ->>Does the coherence calculation appear to require more than one (complex) value at each channel & frequency band of interest? Am I confused about what the rpttap dimension contains? My time window is narrow and my fft calculation only has 1 taper, is that a problem? Because the fourier calculation at each channel_frequency point contains both amplitude and phase information, wouldn't data with chan_freq dimensions be sufficient to calculate the cross spectral densities between the fourier transforms of two channels? Thanks for any guidance, Clara From jan.schoffelen at donders.ru.nl Fri Apr 13 20:28:31 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 Apr 2012 20:28:31 +0200 Subject: [FieldTrip] dimensions for coherence In-Reply-To: References: Message-ID: Hi Clara, Did you check the tutorial on the website? http://fieldtrip.fcdonders.nl/tutorial/connectivity The input data to ft_connectivityanalysis has some requirements. For coherence, you either need a freq-structure containing a 'fourierspctrm' field, or a 'crsspctrm' (+ 'powspctrm') field. The 'fourierspctrm' by definition should have a dimord of 'rpttap_chan_freq(_time', and the 'crsspctrm' may have lost the 'rpt' or 'rpttap' dimension. If your freq data looks different, you will not be able to compute coherence. Admittedly, the error messages you get are quite unspecific, but given the scarce information you are providing with respect to what exactly you have been doing, I can only give some general advice and point you to the documentation. Best, Jan-Mathijs On Apr 13, 2012, at 7:52 PM, Clara A. Scholl wrote: > Dear Fieldtrip users, > > I'm encountering a problem with calculating coherence between two time > courses. I suspect I'm misunderstanding something very basic. > > When I calculate the coherence using data with multiple trials -- with > dimensions rpttap_chan_freq, everything works fine (I get a coherence > spectrum calculation that is averaged over the rpt dimension). > However if I want to limit the calculation to data with dimensions > chan_freq (i.e. find the coherence between the fourier spectra > (containing both amplitude and phase info) of a single timecourse on > two different channels (where those channels are specified using > cfg.channelcmb)), I get an error. I've tried to do this two different > ways. If I still use the rpttap_chan_freq data, I tried specifying > cfg.trials=1 in the connectivity analysis input, and the error given > is: > ??? Index exceeds matrix dimensions. > > Error in ==> ft_connectivity_corr at 131 > p1 = reshape(input(j,powindx(:,1),:,:,:), siz(2:end)); > > Error in ==> ft_connectivityanalysis at 471 > [datout, varout, nrpt] = ft_connectivity_corr(data.(inparam), optarg{:}); > > > ->>If I input frequency data with dimensions chan_freq into > ft_connectivityanalysis (still only specifying cfg.method='coh' and > the channel combinations I'm interested in with cfg.channelcmb) the > output is: > > ??? Index exceeds matrix dimensions. > > Error in ==> ft_checkdata>fixcsd at 843 > tmpdat1 = data.fourierspctrm(indx,cmbindx(:,1),:,:); > > Error in ==> ft_checkdata at 629 > data = fixcsd(data, cmbrepresentation, channelcmb); > > Error in ==> univariate2bivariate at 37 > data = ft_checkdata(data, 'cmbrepresentation', 'sparse', > 'channelcmb', cmb); > > Error in ==> ft_connectivityanalysis at 320 > [data, powindx, hasrpt] = univariate2bivariate(data, > 'fourierspctrm', 'crsspctrm', dtype, 'cmb', cfg.channelcmb, 'keeprpt', > normrpt); > > > ->>Does the coherence calculation appear to require more than one > (complex) value at each channel & frequency band of interest? Am I > confused about what the rpttap dimension contains? My time window is > narrow and my fft calculation only has 1 taper, is that a problem? > Because the fourier calculation at each channel_frequency point > contains both amplitude and phase information, wouldn't data with > chan_freq dimensions be sufficient to calculate the cross spectral > densities between the fourier transforms of two channels? > > Thanks for any guidance, > Clara > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cas243 at georgetown.edu Fri Apr 13 21:01:34 2012 From: cas243 at georgetown.edu (Clara A. Scholl) Date: Fri, 13 Apr 2012 15:01:34 -0400 Subject: [FieldTrip] dimensions for coherence In-Reply-To: References: Message-ID: Thank you Jan-Mathijs! I was using the the coherence tutorial (http://fieldtrip.fcdonders.nl/tutorial/coherence) but after reading the connectivity tutorial I'm still confused. A more parsimonious way to phrase my question would be: Why do I get an error when my fourierspctrm with dimord rpttap_chan_freq has dimensions of 1 x 128 x 10 (the key being, just 1 rpttap value for each channel x frequency combination)? At each channel & frequency, fourierspctrum contains a complex value so the data structure contains the phase and amplitude information at each channel and frequency, which I think -- perhaps incorrectly -- should be sufficient to calculate the coherence. I'll paste below an example of the error I'm getting, beginning with the initial data structure through the ft_connectivityanalysis error. IF the initial data structure (called tmp in this example) has rpt size > 1, then I don't get the error. Thanks, Clara tmp = label: {128x1 cell} time: [0.3380 0.3400 0.3420 0.3440 0.3460 0.3480 0.3500 0.3520 0.3540 0.3560 0.3580 0.3600 0.3620 0.3640 0.3660 0.3680 0.3700 0.3720] cfg: [1x1 struct] trial: [1x128x18 double] sampleinfo: [1 18] dimord: 'rpt_chan_time' >> cfg=[]; cfg.output='fourier'; cfg.method='mtmfft'; cfg.tapsmofrq=28; cfg.channel={'all'}; freqm0=ft_freqanalysis(cfg, tmp) the input is timelock data with 128 channels and 18 timebins processing trials Warning: using only one taper for specified smoothing > In specest/private/warning_once at 75 In ft_specest_mtmfft at 96 In ft_freqanalysis at 519 processing trial 1/1 nfft: 18 samples, datalength: 18 samples, 1 tapers the call to "ft_freqanalysis" took 0 seconds and an estimated 0 MB freqm0 = label: {128x1 cell} dimord: 'rpttap_chan_freq' freq: [0 27.7778 55.5556 83.3333 111.1111 138.8889 166.6667 194.4444 222.2222 250.0000] fourierspctrm: [1x128x10 double] cumsumcnt: 18 cumtapcnt: 1 cfg: [1x1 struct] >> cfg=[]; cfg.method='coh'; cfg.channelcmb={'E34', 'E98'}; fdm0=ft_connectivityanalysis(cfg, freqm0) selection fourierspctrm along dimension 2 ??? Index exceeds matrix dimensions. Error in ==> ft_connectivity_corr at 131 p1 = reshape(input(j,powindx(:,1),:,:,:), siz(2:end)); Error in ==> ft_connectivityanalysis at 471 [datout, varout, nrpt] = ft_connectivity_corr(data.(inparam), optarg{:}); From alexandre.gramfort at inria.fr Sun Apr 15 14:34:44 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Sun, 15 Apr 2012 14:34:44 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: <4F885B9E.6000307@Tuebingen.MPG.de> References: <4F885B9E.6000307@Tuebingen.MPG.de> Message-ID: Dear Panagiotis, the only potential caveat I see for the inverse problem is that you reduce the rank of your data but using ICA. To take care of this you make sure that your inverse solver takes it into account via the whitening noise covariance matrix that should also be applied to the gain/leadfield matrix. Alex On Fri, Apr 13, 2012 at 7:00 PM, Panagiotis Tsiatsis wrote: > On 4/13/2012 8:50 AM, Alexandre Gramfort wrote: >> >> but be careful when applying ICA on neuromag data as >> channels have different types and you have signals >> with 2 orders of magnitude difference between gradiometers >> and magnetometers. >> >> I am curious to know if fieldtrip handles this properly? and if so how. > > Hi all, > > I am also working with CTF MEG data. What I ve been basically doing up to > now was to split the datasets in two subsets: one containing only the > MEGGRAD sensors (let s call it A)  and another containing all the rest (let > it be B). Then I would apply ICA only on the set containing the main MEG > sensors, subtract the EOG-related components and re-construct the data > without them (A'). Finally, I would merge A' with B. This works fine and the > results that I am getting are convincing, the only problem is that of course > the reference channels are still contaminated. I don t know if this would be > a problem in subsequent analysis, ie source localization, maybe somebody who > has more experience further down this road could comment on that. > > > Best, > Panagiotis > > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From B.Haendel at gmx.net Mon Apr 16 15:56:13 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Mon, 16 Apr 2012 15:56:13 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad Message-ID: <20120416135613.3220@gmx.net> Dear fieldtrip users, has anyone experience in using ft_denoise_synthetic? If I try to calculate 3rd order grads in the below specified way the data does not change with respect to the input data (which has no synthetic gradiometer applied). Is there some obvious misunderstanding on my side of how to use this function or is our environment truly noiseless :) Cheers, Barbara cfg=[]; cfg.gradient ='G3BR'; cfg.trials = 'all'; data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); >> data_3rdorder.grad.balance ans = G1BR: [1x1 struct] G2BR: [1x1 struct] G3BR: [1x1 struct] current: 'G3BR' previous: {'none'} >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) ans = 0 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From michael.wibral at web.de Mon Apr 16 16:46:27 2012 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 16 Apr 2012 16:46:27 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <20120416135613.3220@gmx.net> References: <20120416135613.3220@gmx.net> Message-ID: An HTML attachment was scrubbed... URL: From stan.vanpelt at fcdonders.ru.nl Mon Apr 16 16:59:25 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Mon, 16 Apr 2012 16:59:25 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: Message-ID: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> Hi Barbara, I can replicate your finding, but am unsure what is causing it. Maybe the difference/correction is lower than the Matlab or CTF precision? In any case, i f the 3rd order gradients were on, ft_denoise_synthetic would undo the G3BR-balancing, ergo it toggles. Best, Stan ----- Oorspronkelijk bericht ----- > Van: "Michael Wibral" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Maandag 16 april 2012 16:46:27 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hi Barbara, > are you certain that the original data do not have 3rd gradients > enabled? - looking at them once in dataEditor, switching to 3rd grads > and accidentally forgetting to unclick 'save parameters with dataset' > will make them have 3rd grads... > When I last used ft_denoise_synthetic it worked pretty much as > described (??). > Michael > Gesendet: Montag, 16. April 2012 um 15:56 Uhr > Von: "Barbara Haendel" > An: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] ft_denoise_synthetic 3rd order grad > Dear fieldtrip users, > has anyone experience in using ft_denoise_synthetic? If I try to > calculate 3rd order grads in the below specified way the data does not > change with respect to the input data (which has no synthetic > gradiometer applied). Is there some obvious misunderstanding on my > side of how to use this function or is our environment truly noiseless > :) > Cheers, > Barbara > cfg=[]; > cfg.gradient ='G3BR'; > cfg.trials = 'all'; > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > >> data_3rdorder.grad.balance > ans = > G1BR: [1x1 struct] > G2BR: [1x1 struct] > G3BR: [1x1 struct] > current: 'G3BR' > previous: {'none'} > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > ans = 0 > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 -- Stan van Pelt Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 10981 Fax: (+31) (0)24 36 10989 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Panagiotis.Tsiatsis at Tuebingen.MPG.de Mon Apr 16 17:53:56 2012 From: Panagiotis.Tsiatsis at Tuebingen.MPG.de (Panagiotis Tsiatsis) Date: Mon, 16 Apr 2012 17:53:56 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <4F8C4094.2020707@Tuebingen.MPG.de> Hello girls and guys, It is working for my CTF MEG data - the version that I have is v4692 2011-11-07. The other thing that might cause a problem could be ommiting the reference channels definition before the ft_ preprocessing command that gave you your "dataprepro" i.e maybe you might need something like this cfg = []; ... //various preprocessing parameters ... cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; dataprepro = ft_preprocessing(cfg); Hope you are lucky :) Best, Panagiotis On 4/16/2012 4:59 PM, Stan van Pelt wrote: > Hi Barbara, > > I can replicate your finding, but am unsure what is causing it. Maybe > the difference/correction is lower than the Matlab or CTF precision? > In any case, if the 3rd order gradients were on, ft_denoise_synthetic > would undo the G3BR-balancing, ergo it toggles. > > Best, > Stan > > > ------------------------------------------------------------------------ > > *Van: *"Michael Wibral" > *Aan: *"Email discussion list for the FieldTrip project" > > *Verzonden: *Maandag 16 april 2012 16:46:27 > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > Hi Barbara, > > are you certain that the original data do not have 3rd gradients > enabled? - looking at them once in dataEditor, switching to 3rd > grads and accidentally forgetting to unclick 'save parameters with > dataset' will make them have 3rd grads... > > When I last used ft_denoise_synthetic it worked pretty much as > described (??). > > Michael > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > *Von:* "Barbara Haendel" > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > Dear fieldtrip users, > > has anyone experience in using ft_denoise_synthetic? If I try to > calculate 3rd order grads in the below specified way the data does > not change with respect to the input data (which has no synthetic > gradiometer applied). Is there some obvious misunderstanding on my > side of how to use this function or is our environment truly > noiseless :) > > Cheers, > Barbara > > cfg=[]; > cfg.gradient ='G3BR'; > cfg.trials = 'all'; > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > >> data_3rdorder.grad.balance > > ans = > > G1BR: [1x1 struct] > G2BR: [1x1 struct] > G3BR: [1x1 struct] > current: 'G3BR' > previous: {'none'} > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > ans = 0 > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 > > > > > -- > Stan van Pelt > > Donders Institute for Brain, Cognition and Behaviour, Radboud > University Nijmegen > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > E-mail: stan.vanpelt at donders.ru.nl > Website: www.ru.nl/donders/ > Phone: (+31) (0)24 36 10981 > Fax: (+31) (0)24 36 10989 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Panagiotis S. Tsiatsis Max Planck Institute for Biological Cybernetics Cognitive NeuroImaging Group Tuebingen, Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue Apr 17 00:07:45 2012 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 17 Apr 2012 00:07:45 +0200 Subject: [FieldTrip] NeuroScan QuikCap64 Message-ID: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> Hi, I have recently started using a NeuroScan 64 Channel SynAmps2 System with a QuikCap. Does anyone know how to prepare a layout for this cap? From the Scan4.2. software, I only get x and y coordinates, but no z coordinates, and on the setup CD I can only find PDF files with the layout. Any suggestions are welcome. Thanks a lot, Julian ******************************************** Julian Keil International Laboratory for Brain Music and Sound Research (BRAMS) Pavillon 1430 Mont-Royal Université de Montréal Montréal, Québec Canada, H2V 4P3 julian.keil at uni-konstanz.de +1-514-343-6111-29653 www.brams.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Tue Apr 17 08:41:01 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Tue, 17 Apr 2012 09:41:01 +0300 Subject: [FieldTrip] Signal viewer + Biosemi Message-ID: Hello, I looked I the Signal viewer example in the following page: http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer I just want to know how could I view a signal coming directly from the biosemi device? (I think the following line should be changed: cfg.dataset = 'buffer://localhost:1972'; but I don't know what to put) Thanks for your help -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From diana.ibanescu at gmail.com Tue Apr 17 10:33:11 2012 From: diana.ibanescu at gmail.com (Diana Ibanescu) Date: Tue, 17 Apr 2012 10:33:11 +0200 Subject: [FieldTrip] Function ft_prepare_bemmodel deprecated... Message-ID: Hello, I am interested in an example how to compute an EEG leadfield with OpenMEEG in the Fieldtrip toolbox. I found a demo script here: http://fieldtrip.fcdonders.nl/example/testing_bem_created_leadfields When I call the function ft_prepare_bemmodel(cfg, vol) I receive the following warning: "Warning: FT_PREPARE_BEMMODEL is deprecated, please use FT_HEADMODEL_BEM_... with cfg.method = 'bem_bladeebla' instead." The function ft_headmodel_bem_openmeeg receive as parameter "geom" while ft_prepare_bemmodel receive other parameters: vol = ft_headmodel_openmeeg(geom, ...) Optional input arguments should be specified in key-value pairs and can include isolatedsource = string, 'yes' or 'no' hdmfile = string, filename with BEM headmodel conductivity = vector, conductivity of each compartment Are the 2 functions similar? Is there any demo updated after the function ft_prepare_bemmodel became deprecated? What function can I use instead? Thank you, Diana. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue Apr 17 11:35:17 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 17 Apr 2012 11:35:17 +0200 Subject: [FieldTrip] NeuroScan QuikCap64 In-Reply-To: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> References: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> Message-ID: Hi Julian, Have a look at our layout tutorial: http://fieldtrip.fcdonders.nl/tutorial/layout Starting from the PDF files (or bitmap (jpg/png) files based on them) you should be able to easily create a layout using ft_prepare_layout. Best, Eelke On 17 April 2012 00:07, Julian Keil wrote: > Hi, > > I have recently started using a NeuroScan 64 Channel SynAmps2 System with a > QuikCap. > Does anyone know how to prepare a layout for this cap? > From the Scan4.2. software, I only get x and y coordinates, but no z > coordinates, and on the setup CD I can only find PDF files with the layout. > > Any suggestions are welcome. > > Thanks a lot, > > Julian > > > > ******************************************** > Julian Keil > > International Laboratory for Brain > Music and Sound Research (BRAMS) > > Pavillon 1430 Mont-Royal > Université de Montréal > Montréal, Québec > Canada,  H2V 4P3 > > julian.keil at uni-konstanz.de > +1-514-343-6111-29653 > www.brams.org > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Tue Apr 17 12:57:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 17 Apr 2012 12:57:37 +0200 Subject: [FieldTrip] NeuroScan QuikCap64 In-Reply-To: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> References: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> Message-ID: <4F8D4CA1.2050108@donders.ru.nl> Hi Julian, layout-files are in 2D, thus there is no need for a third dimenstion. You can use the x- and y-coordinates from your software package. If you got a third coordinate, you can try to build an elect-structure, see: http://fieldtrip.fcdonders.nl/faq/how_are_electrodes_magnetometers_or_gradiometers_described In case you got no third dimension, you can just set the z-coordinates to 0 for the elect-structure. It won't be 100% correct though, but the best you can do when only having a 2D layout at hand. You can also try one of the other layouts that we have that look similar, i.e. any layout that obeys the 1020-system (I am using easycapM11.lay, just try ft_prepare_layout while setting cfg.feedback='yes') Best, Jörn On 4/17/2012 12:07 AM, Julian Keil wrote: > Hi, > > I have recently started using a NeuroScan 64 Channel SynAmps2 System > with a QuikCap. > Does anyone know how to prepare a layout for this cap? > From the Scan4.2. software, I only get x and y coordinates, but no z > coordinates, and on the setup CD I can only find PDF files with the > layout. > > Any suggestions are welcome. > > Thanks a lot, > > Julian > > > > ********************************************** > *Julian Keil* > * > * > /International Laboratory for Brain/ > /Music and Sound Research (BRAMS)/ > > Pavillon 1430 Mont-Royal > Université de Montréal > Montréal, Québec > Canada, H2V 4P3 > > julian.keil at uni-konstanz.de > +1-514-343-6111-29653 > www.brams.org > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.severens at maartenskliniek.nl Tue Apr 17 14:51:41 2012 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Tue, 17 Apr 2012 14:51:41 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Hi Hamza You first need to start a buffer to read the data from de biosemi device, so start the biosemi2ft, see here http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. Then if you do not change the defaults you do not need to change the cfg.dataset field for the signal viewer. There is also a signal viewer based on c code (so no extra matlab session is necessary). You can find it here: fieldtrip/realtime/utilities/viewer Best, Marianne ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] Sent: Tuesday, April 17, 2012 8:41 AM To: Email discussion list for the FieldTrip project Subject: [FieldTrip] Signal viewer + Biosemi Hello, I looked I the Signal viewer example in the following page: http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer I just want to know how could I view a signal coming directly from the biosemi device? (I think the following line should be changed: cfg.dataset = 'buffer://localhost:1972'; but I don't know what to put) Thanks for your help -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From giulia.rizza at tiscali.it Tue Apr 17 15:04:23 2012 From: giulia.rizza at tiscali.it (Giulia Rizza) Date: Tue, 17 Apr 2012 15:04:23 +0200 (CEST) Subject: [FieldTrip] R: NeuroScan QuikCap64 Message-ID: <29197848.94691334667863183.JavaMail.defaultUser@defaultHost> Hi Julian I had the same problem some time ago and I found a list of the coordinates for all the channels in the download session of this link (then I followed the instructions in the FT tutorial): http://robertoostenveld. ruhosting.nl/index.php/electrode/#aes1994 Hope this helps Giulia >---- Messaggio originale---- >Da: julian.keil at gmail.com >Data: 17/04/2012 0.07 >A: "Email discussion list for the FieldTrip project" >Ogg: [FieldTrip] NeuroScan QuikCap64 > >Hi, > >I have recently started using a NeuroScan 64 Channel SynAmps2 System with a QuikCap. >Does anyone know how to prepare a layout for this cap? >From the Scan4.2. software, I only get x and y coordinates, but no z coordinates, and on the setup CD I can only find PDF files with the layout. > >Any suggestions are welcome. > >Thanks a lot, > >Julian > > > >******************************************** >Julian Keil > >International Laboratory for Brain >Music and Sound Research (BRAMS) > >Pavillon 1430 Mont-Royal >Université de Montréal >Montréal, Québec >Canada, H2V 4P3 > >julian.keil at uni-konstanz.de >+1-514-343-6111-29653 >www.brams.org > > > > > > >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru. nl/mailman/listinfo/fieldtrip Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più di uno spot in TV.Per ogni nuovo abbonato 30 € di premio per te e per lui! Un amico al mese e parli e navighisempre gratis: http://freelosophy.tiscali.it/ From julian.keil at gmail.com Tue Apr 17 15:21:16 2012 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 17 Apr 2012 15:21:16 +0200 Subject: [FieldTrip] R: NeuroScan QuikCap64 In-Reply-To: <29197848.94691334667863183.JavaMail.defaultUser@defaultHost> References: <29197848.94691334667863183.JavaMail.defaultUser@defaultHost> Message-ID: <4A1B2E1E-A2CE-4381-AF8F-20EE9A83A7E7@gmail.com> Hi, thanks a lot you all! Out of laziness, I wanted to avoid doing the layout by hand from the image file :-) And thanks to Catarina, who sent me the 3D-Positions, I didn't have to. So if anyone ever runs into the same problem, here's a .mat-file with labels, positions (as provided by NeuroScan) and the created layout. Best, Julian ******************************************** Julian Keil International Laboratory for Brain Music and Sound Research (BRAMS) Pavillon 1430 Mont-Royal Université de Montréal Montréal, Québec Canada, H2V 4P3 julian.keil at uni-konstanz.de +1-514-343-6111-29653 www.brams.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NeuroScan64.mat Type: application/x-matlab-workspace Size: 4265 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at fcdonders.ru.nl Tue Apr 17 16:13:46 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Tue, 17 Apr 2012 16:13:46 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <4F8C4094.2020707@Tuebingen.MPG.de> Message-ID: <2082724711.41482.1334672026438.JavaMail.root@sculptor.zimbra.ru.nl> Hi Panagiotis, Good point, thanks. It works for me now. Best, Stan ----- Oorspronkelijk bericht ----- > Van: "Panagiotis Tsiatsis" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Maandag 16 april 2012 17:53:56 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hello girls and guys, > It is working for my CTF MEG data - the version that I have is v4692 > 2011-11-07. > The other thing that might cause a problem could be ommiting the > reference channels definition before the ft_ preprocessing command > that gave you your "dataprepro" > i.e maybe you might need something like this > cfg = []; > ... > //various preprocessing parameters > ... > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > dataprepro = ft_preprocessing(cfg); > Hope you are lucky :) > Best, > Panagiotis > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > Hi Barbara, > > I can replicate your finding, but am unsure what is causing it. > > Maybe > > the difference/correction is lower than the Matlab or CTF precision? > > In any case, if the 3rd order gradients were on, > > ft_denoise_synthetic > > would undo the G3BR-balancing, ergo it toggles. > > Best, > > Stan > > ----- Oorspronkelijk bericht ----- > > > Van: "Michael Wibral" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > > Verzonden: Maandag 16 april 2012 16:46:27 > > > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Hi Barbara, > > > are you certain that the original data do not have 3rd gradients > > > enabled? - looking at them once in dataEditor, switching to 3rd > > > grads > > > and accidentally forgetting to unclick 'save parameters with > > > dataset' > > > will make them have 3rd grads... > > > When I last used ft_denoise_synthetic it worked pretty much as > > > described (??). > > > Michael > > > Gesendet: Montag, 16. April 2012 um 15:56 Uhr > > > Von: "Barbara Haendel" > > > An: fieldtrip at donders.ru.nl > > > Betreff: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Dear fieldtrip users, > > > has anyone experience in using ft_denoise_synthetic? If I try to > > > calculate 3rd order grads in the below specified way the data does > > > not > > > change with respect to the input data (which has no synthetic > > > gradiometer applied). Is there some obvious misunderstanding on my > > > side of how to use this function or is our environment truly > > > noiseless > > > :) > > > Cheers, > > > Barbara > > > cfg=[]; > > > cfg.gradient ='G3BR'; > > > cfg.trials = 'all'; > > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > >> data_3rdorder.grad.balance > > > ans = > > > G1BR: [1x1 struct] > > > G2BR: [1x1 struct] > > > G3BR: [1x1 struct] > > > current: 'G3BR' > > > previous: {'none'} > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > ans = 0 > > > -- > > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > > Jetzt informieren: > > > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > > _______________________________________________ > > > 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 > > -- > > Stan van Pelt > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > University Nijmegen > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > E-mail: stan.vanpelt at donders.ru.nl > > Website: www.ru.nl/donders/ > > Phone: (+31) (0)24 36 10981 > > Fax: (+31) (0)24 36 10989 > > _______________________________________________ > > fieldtrip mailing list fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Stan van Pelt Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 10981 Fax: (+31) (0)24 36 10989 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at mac.com Tue Apr 17 22:39:48 2012 From: nathanweisz at mac.com (Nathan Weisz) Date: Tue, 17 Apr 2012 22:39:48 +0200 Subject: [FieldTrip] postdoc positions @ CIMeC Message-ID: Dear all, not directly fieldtrip related ... I will be soon posting calls for postdoc positions at my new institution: http://www.unitn.it/cimec The postdoc positions will be within a new ERC-funded project (http://cordis.europa.eu/projects/rcn/103253_en.html), which will investigate the role of ongoing oscillatory activity patterns on perception. The studies conducted within this project will mainly use MEG and combined EEG / TMS. Apart from offline studies, relevant brain activity patterns will be used to control experiments in "realtime". I would be interested in getting in touch with postdocs or soon-to-be-postdocs who may be interested in working in such a project. The CIMeC offers access to state-of-the-art neuroimaging / -stimulation facilities along with an international and academically stimulating flair. Needless to say that it is located in a beautiful surrounding for the out-of-the-lab times (especially for mountain and water-sport lovers) and wine + food are not too bad as well. The salary is internationally competetive. Please pass this on to anyone you think might be interested. Best, Nathan -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Wed Apr 18 09:18:04 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 18 Apr 2012 10:18:04 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: Thank you Marianne I did not ask for just viewing the signal only, but to do realtime processing in general. Thanks again Hamza On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne < m.severens at maartenskliniek.nl> wrote: > Hi Hamza > > You first need to start a buffer to read the data from de biosemi device, > so start the biosemi2ft, see here > http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. > Then if you do not change the defaults you do not need to change the > cfg.dataset field for the signal viewer. > > There is also a signal viewer based on c code (so no extra matlab session > is necessary). You can find it here: fieldtrip/realtime/utilities/viewer > > Best, Marianne > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] > Sent: Tuesday, April 17, 2012 8:41 AM > To: Email discussion list for the FieldTrip project > Subject: [FieldTrip] Signal viewer + Biosemi > > Hello, > > I looked I the Signal viewer example in the following page: > http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer > > I just want to know how could I view a signal coming directly from the > biosemi device? > (I think the following line should be changed: > cfg.dataset = 'buffer://localhost:1972'; > but I don't know what to put) > > Thanks for your help > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is > geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking > van deze informatie is conform het Privacy reglement van de Sint > Maartenskliniek. De informatie is uitsluitend bestemd voor de > geadresseerde. Gebruik van deze informatie door anderen dan de > geadresseerde is, zonder voorafgaande schriftelijke toestemming van de > rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de > juiste en volledige overbrenging van de inhoud van een gezonden e-mail, > noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.vandenbroek at donders.ru.nl Wed Apr 18 10:04:34 2012 From: p.vandenbroek at donders.ru.nl (Philip van den Broek) Date: Wed, 18 Apr 2012 10:04:34 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> Hi Hamza, In that case you might be interested in BrainStream (for documentation, see website www.brainstream.nu), which also contains a section about how we connect to all fieldtrip supported devices. Might you be interested in BrainStream, the code can be downloaded from (http://code.google.com/p/brainstream/). Kind Regards Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > Thank you Marianne > > I did not ask for just viewing the signal only, but to do realtime processing in general. > > Thanks again > > Hamza > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne wrote: > Hi Hamza > > You first need to start a buffer to read the data from de biosemi device, so start the biosemi2ft, see here http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. Then if you do not change the defaults you do not need to change the cfg.dataset field for the signal viewer. > > There is also a signal viewer based on c code (so no extra matlab session is necessary). You can find it here: fieldtrip/realtime/utilities/viewer > > Best, Marianne > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] > Sent: Tuesday, April 17, 2012 8:41 AM > To: Email discussion list for the FieldTrip project > Subject: [FieldTrip] Signal viewer + Biosemi > > Hello, > > I looked I the Signal viewer example in the following page: > http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer > > I just want to know how could I view a signal coming directly from the biosemi device? > (I think the following line should be changed: > cfg.dataset = 'buffer://localhost:1972'; > but I don't know what to put) > > Thanks for your help > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 hamzaf at sabanciuniv.edu Wed Apr 18 10:52:16 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 18 Apr 2012 11:52:16 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> Message-ID: Thanks Philip I downloaded the BrainStream code but I did not work with it yet. But when you recommend me to use BrainStream is it because it contains things that fieldtrip functions cannot do or because it is just another alternative for making online experiments? I did not looked carefully at BrainStream webpage, but I feel that fieldtrip is more flexible regarding help and mailing. Regards Hamza On Wed, Apr 18, 2012 at 11:04 AM, Philip van den Broek < p.vandenbroek at donders.ru.nl> wrote: > Hi Hamza, > > In that case you might be interested in BrainStream (for documentation, > see website www.brainstream.nu), which also contains a section about how > we connect to all fieldtrip supported devices. Might you be interested in > BrainStream, the code can be downloaded from ( > http://code.google.com/p/brainstream/). > > Kind Regards > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > > Thank you Marianne > > I did not ask for just viewing the signal only, but to do realtime > processing in general. > > Thanks again > > Hamza > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne < > m.severens at maartenskliniek.nl> wrote: > >> Hi Hamza >> >> You first need to start a buffer to read the data from de biosemi device, >> so start the biosemi2ft, see here >> http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. >> Then if you do not change the defaults you do not need to change the >> cfg.dataset field for the signal viewer. >> >> There is also a signal viewer based on c code (so no extra matlab session >> is necessary). You can find it here: fieldtrip/realtime/utilities/viewer >> >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] >> On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >> Sent: Tuesday, April 17, 2012 8:41 AM >> To: Email discussion list for the FieldTrip project >> Subject: [FieldTrip] Signal viewer + Biosemi >> >> Hello, >> >> I looked I the Signal viewer example in the following page: >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >> >> I just want to know how could I view a signal coming directly from the >> biosemi device? >> (I think the following line should be changed: >> cfg.dataset = 'buffer://localhost:1972'; >> but I don't know what to put) >> >> Thanks for your help >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking >> van deze informatie is conform het Privacy reglement van de Sint >> Maartenskliniek. De informatie is uitsluitend bestemd voor de >> geadresseerde. Gebruik van deze informatie door anderen dan de >> geadresseerde is, zonder voorafgaande schriftelijke toestemming van de >> rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de >> juiste en volledige overbrenging van de inhoud van een gezonden e-mail, >> noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.vandenbroek at donders.ru.nl Wed Apr 18 12:10:54 2012 From: p.vandenbroek at donders.ru.nl (Philip van den Broek) Date: Wed, 18 Apr 2012 12:10:54 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> Message-ID: <2ADC0647-2CD2-4F84-8A1D-BAB78AB57E68@donders.ru.nl> Hi Hamza, > But when you recommend me to use BrainStream is it because it contains things that fieldtrip functions cannot do or because it is just another alternative for making online experiments? No, you should be able to do everything with fieldtrip. It is indeed another alternative for making online experiments with a different approach, which I thought might be of interest to you (or in general to anyone else involved in conducting real-time (BCI) experiments), but in the end off course that's something you can only decide. BrainStream is designed specifically for defining and executing real-time experiments and uses fieldtrips realtime buffer and hardware interfacing solutions (i.e., biosemi2ft, tmsi2ft etc.). It has all kind of built-in solutions for starting extra Matlab clients, automatic parallel execution, easy access to and switching between devices, information exchange, simulating from file or random data. In the design, you can use any Matlab code, including fieldtrip functions. However, you need to learn its specific way of defining experiments. Kind regards Philip > > Regards > > Hamza > > On Wed, Apr 18, 2012 at 11:04 AM, Philip van den Broek wrote: > Hi Hamza, > > In that case you might be interested in BrainStream (for documentation, see website www.brainstream.nu), which also contains a section about how we connect to all fieldtrip supported devices. Might you be interested in BrainStream, the code can be downloaded from (http://code.google.com/p/brainstream/). > > Kind Regards > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > >> Thank you Marianne >> >> I did not ask for just viewing the signal only, but to do realtime processing in general. >> >> Thanks again >> >> Hamza >> >> On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne wrote: >> Hi Hamza >> >> You first need to start a buffer to read the data from de biosemi device, so start the biosemi2ft, see here http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. Then if you do not change the defaults you do not need to change the cfg.dataset field for the signal viewer. >> >> There is also a signal viewer based on c code (so no extra matlab session is necessary). You can find it here: fieldtrip/realtime/utilities/viewer >> >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >> Sent: Tuesday, April 17, 2012 8:41 AM >> To: Email discussion list for the FieldTrip project >> Subject: [FieldTrip] Signal viewer + Biosemi >> >> Hello, >> >> I looked I the Signal viewer example in the following page: >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >> >> I just want to know how could I view a signal coming directly from the biosemi device? >> (I think the following line should be changed: >> cfg.dataset = 'buffer://localhost:1972'; >> but I don't know what to put) >> >> Thanks for your help >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> _______________________________________________ >> 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 > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 hamzaf at sabanciuniv.edu Wed Apr 18 16:30:55 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 18 Apr 2012 17:30:55 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: <2ADC0647-2CD2-4F84-8A1D-BAB78AB57E68@donders.ru.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> <2ADC0647-2CD2-4F84-8A1D-BAB78AB57E68@donders.ru.nl> Message-ID: Thanks a lot Philip for the information. Regards Hamza On Wed, Apr 18, 2012 at 1:10 PM, Philip van den Broek < p.vandenbroek at donders.ru.nl> wrote: > Hi Hamza, > > But when you recommend me to use BrainStream is it because it contains > things that fieldtrip functions cannot do or because it is just another > alternative for making online experiments? > > No, you should be able to do everything with fieldtrip. It is indeed > another alternative for making online experiments with a different > approach, which I thought might be of interest to you (or in general to > anyone else involved in conducting real-time (BCI) experiments), but in the > end off course that's something you can only decide. > BrainStream is designed specifically for defining and executing real-time > experiments and uses fieldtrips realtime buffer and hardware interfacing > solutions (i.e., biosemi2ft, tmsi2ft etc.). It has all kind of built-in > solutions for starting extra Matlab clients, automatic parallel execution, > easy access to and switching between devices, information exchange, > simulating from file or random data. In the design, you can use any Matlab > code, including fieldtrip functions. However, you need to learn its > specific way of defining experiments. > > Kind regards > Philip > > > > Regards > > Hamza > > On Wed, Apr 18, 2012 at 11:04 AM, Philip van den Broek < > p.vandenbroek at donders.ru.nl> wrote: > >> Hi Hamza, >> >> In that case you might be interested in BrainStream (for documentation, >> see website www.brainstream.nu), which also contains a section about how >> we connect to all fieldtrip supported devices. Might you be interested in >> BrainStream, the code can be downloaded from ( >> http://code.google.com/p/brainstream/). >> >> Kind Regards >> >> Philip van den Broek >> Radboud University Nijmegen >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> >> On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: >> >> Thank you Marianne >> >> I did not ask for just viewing the signal only, but to do realtime >> processing in general. >> >> Thanks again >> >> Hamza >> >> On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne < >> m.severens at maartenskliniek.nl> wrote: >> >>> Hi Hamza >>> >>> You first need to start a buffer to read the data from de biosemi >>> device, so start the biosemi2ft, see here >>> http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. >>> Then if you do not change the defaults you do not need to change the >>> cfg.dataset field for the signal viewer. >>> >>> There is also a signal viewer based on c code (so no extra matlab >>> session is necessary). You can find it here: >>> fieldtrip/realtime/utilities/viewer >>> >>> Best, Marianne >>> ________________________________________ >>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] >>> On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >>> Sent: Tuesday, April 17, 2012 8:41 AM >>> To: Email discussion list for the FieldTrip project >>> Subject: [FieldTrip] Signal viewer + Biosemi >>> >>> Hello, >>> >>> I looked I the Signal viewer example in the following page: >>> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >>> >>> I just want to know how could I view a signal coming directly from the >>> biosemi device? >>> (I think the following line should be changed: >>> cfg.dataset = 'buffer://localhost:1972'; >>> but I don't know what to put) >>> >>> Thanks for your help >>> >>> >>> -- >>> Hamza Fawzi Altakroury >>> Graduate student - MA >>> Faculty of Engineering and Natural Sciences >>> Sabancı University >>> >>> Disclaimer >>> Vrijgave van de informatie verzonden met dit e-mail bericht is >>> geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking >>> van deze informatie is conform het Privacy reglement van de Sint >>> Maartenskliniek. De informatie is uitsluitend bestemd voor de >>> geadresseerde. Gebruik van deze informatie door anderen dan de >>> geadresseerde is, zonder voorafgaande schriftelijke toestemming van de >>> rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de >>> juiste en volledige overbrenging van de inhoud van een gezonden e-mail, >>> noch voor de ontvangst daarvan. >>> >>> Sint Maartenskliniek >>> Hengstdal 3, >>> 6574 NA Ubbergen (bij Nijmegen) >>> Telefoon 024-3659 911 >>> Telefax 024-3659 204 >>> KvK nummer 41055111 >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> _______________________________________________ >> 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 >> > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Wed Apr 18 23:02:49 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Wed, 18 Apr 2012 23:02:49 +0200 Subject: [FieldTrip] Function ft_prepare_bemmodel deprecated... In-Reply-To: References: Message-ID: Hello diana, thanks for reporting the API change. I'll see if I can update the scripts: openmeeg_eeg_leadfield_example.m openmeeg_meg_leadfield_example.m feel free to give it a try if I am not too reactive... Alex On Tue, Apr 17, 2012 at 10:33 AM, Diana Ibanescu wrote: > Hello, > > I am interested in an example how to compute an EEG leadfield with OpenMEEG > in the Fieldtrip toolbox. I found a demo script here: > http://fieldtrip.fcdonders.nl/example/testing_bem_created_leadfields > When I call the function ft_prepare_bemmodel(cfg, vol) I receive the > following warning: > "Warning: FT_PREPARE_BEMMODEL is deprecated, please use FT_HEADMODEL_BEM_... > with cfg.method = 'bem_bladeebla' > instead." > The function ft_headmodel_bem_openmeeg receive as parameter "geom" while > ft_prepare_bemmodel receive other parameters: >  vol = ft_headmodel_openmeeg(geom, ...) > >   Optional input arguments should be specified in key-value pairs and can >   include >     isolatedsource   = string, 'yes' or 'no' >     hdmfile          = string, filename with BEM headmodel >     conductivity     = vector, conductivity of each compartment > > Are the 2 functions similar? Is there any demo updated after the function > ft_prepare_bemmodel became deprecated? What function can I use instead? > > Thank you, > Diana. > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From B.Haendel at gmx.net Thu Apr 19 08:59:39 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Thu, 19 Apr 2012 08:59:39 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <4F8C4094.2020707@Tuebingen.MPG.de> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de> Message-ID: <20120419065939.195940@gmx.net> Hey there, thanks a lot for the replies! Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. Thanks again, Barbara -------- Original-Nachricht -------- > Datum: Mon, 16 Apr 2012 17:53:56 +0200 > Von: Panagiotis Tsiatsis > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hello girls and guys, > > It is working for my CTF MEG data - the version that I have is v4692 > 2011-11-07. > > The other thing that might cause a problem could be ommiting the > reference channels definition before the ft_ preprocessing command that > gave you your "dataprepro" > > i.e maybe you might need something like this > > cfg = []; > > ... > //various preprocessing parameters > ... > > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > > dataprepro = ft_preprocessing(cfg); > > > Hope you are lucky :) > > Best, > Panagiotis > > > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > Hi Barbara, > > > > I can replicate your finding, but am unsure what is causing it. Maybe > > the difference/correction is lower than the Matlab or CTF precision? > > In any case, if the 3rd order gradients were on, ft_denoise_synthetic > > would undo the G3BR-balancing, ergo it toggles. > > > > Best, > > Stan > > > > > > ------------------------------------------------------------------------ > > > > *Van: *"Michael Wibral" > > *Aan: *"Email discussion list for the FieldTrip project" > > > > *Verzonden: *Maandag 16 april 2012 16:46:27 > > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Hi Barbara, > > > > are you certain that the original data do not have 3rd gradients > > enabled? - looking at them once in dataEditor, switching to 3rd > > grads and accidentally forgetting to unclick 'save parameters with > > dataset' will make them have 3rd grads... > > > > When I last used ft_denoise_synthetic it worked pretty much as > > described (??). > > > > Michael > > > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > > *Von:* "Barbara Haendel" > > *An:* fieldtrip at donders.ru.nl > > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Dear fieldtrip users, > > > > has anyone experience in using ft_denoise_synthetic? If I try to > > calculate 3rd order grads in the below specified way the data does > > not change with respect to the input data (which has no synthetic > > gradiometer applied). Is there some obvious misunderstanding on my > > side of how to use this function or is our environment truly > > noiseless :) > > > > Cheers, > > Barbara > > > > cfg=[]; > > cfg.gradient ='G3BR'; > > cfg.trials = 'all'; > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > > > > >> data_3rdorder.grad.balance > > > > ans = > > > > G1BR: [1x1 struct] > > G2BR: [1x1 struct] > > G3BR: [1x1 struct] > > current: 'G3BR' > > previous: {'none'} > > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > > ans = 0 > > > > -- > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > Jetzt informieren: > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > _______________________________________________ > > 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 > > > > > > > > > > -- > > Stan van Pelt > > > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > University Nijmegen > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > E-mail: stan.vanpelt at donders.ru.nl > > Website: www.ru.nl/donders/ > > Phone: (+31) (0)24 36 10981 > > Fax: (+31) (0)24 36 10989 > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From B.Haendel at gmx.net Thu Apr 19 08:59:39 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Thu, 19 Apr 2012 08:59:39 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <4F8C4094.2020707@Tuebingen.MPG.de> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de> Message-ID: <20120419065939.195940@gmx.net> Hey there, thanks a lot for the replies! Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. Thanks again, Barbara -------- Original-Nachricht -------- > Datum: Mon, 16 Apr 2012 17:53:56 +0200 > Von: Panagiotis Tsiatsis > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hello girls and guys, > > It is working for my CTF MEG data - the version that I have is v4692 > 2011-11-07. > > The other thing that might cause a problem could be ommiting the > reference channels definition before the ft_ preprocessing command that > gave you your "dataprepro" > > i.e maybe you might need something like this > > cfg = []; > > ... > //various preprocessing parameters > ... > > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > > dataprepro = ft_preprocessing(cfg); > > > Hope you are lucky :) > > Best, > Panagiotis > > > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > Hi Barbara, > > > > I can replicate your finding, but am unsure what is causing it. Maybe > > the difference/correction is lower than the Matlab or CTF precision? > > In any case, if the 3rd order gradients were on, ft_denoise_synthetic > > would undo the G3BR-balancing, ergo it toggles. > > > > Best, > > Stan > > > > > > ------------------------------------------------------------------------ > > > > *Van: *"Michael Wibral" > > *Aan: *"Email discussion list for the FieldTrip project" > > > > *Verzonden: *Maandag 16 april 2012 16:46:27 > > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Hi Barbara, > > > > are you certain that the original data do not have 3rd gradients > > enabled? - looking at them once in dataEditor, switching to 3rd > > grads and accidentally forgetting to unclick 'save parameters with > > dataset' will make them have 3rd grads... > > > > When I last used ft_denoise_synthetic it worked pretty much as > > described (??). > > > > Michael > > > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > > *Von:* "Barbara Haendel" > > *An:* fieldtrip at donders.ru.nl > > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Dear fieldtrip users, > > > > has anyone experience in using ft_denoise_synthetic? If I try to > > calculate 3rd order grads in the below specified way the data does > > not change with respect to the input data (which has no synthetic > > gradiometer applied). Is there some obvious misunderstanding on my > > side of how to use this function or is our environment truly > > noiseless :) > > > > Cheers, > > Barbara > > > > cfg=[]; > > cfg.gradient ='G3BR'; > > cfg.trials = 'all'; > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > > > > >> data_3rdorder.grad.balance > > > > ans = > > > > G1BR: [1x1 struct] > > G2BR: [1x1 struct] > > G3BR: [1x1 struct] > > current: 'G3BR' > > previous: {'none'} > > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > > ans = 0 > > > > -- > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > Jetzt informieren: > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > _______________________________________________ > > 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 > > > > > > > > > > -- > > Stan van Pelt > > > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > University Nijmegen > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > E-mail: stan.vanpelt at donders.ru.nl > > Website: www.ru.nl/donders/ > > Phone: (+31) (0)24 36 10981 > > Fax: (+31) (0)24 36 10989 > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From jan.schoffelen at donders.ru.nl Thu Apr 19 10:02:43 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 19 Apr 2012 10:02:43 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <20120419065939.195940@gmx.net> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de> <20120419065939.195940@gmx.net> Message-ID: Hi Barbara, Good plan to adjust the code a bit in this respect. Could you please file a bug about this on our bugzilla list: bugzilla.fcdonders.nl Best wishes, Jan-Mathijs On Apr 19, 2012, at 8:59 AM, Barbara Haendel wrote: > > > Hey there, thanks a lot for the replies! > > Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. > > Thanks again, > Barbara > > > > > -------- Original-Nachricht -------- >> Datum: Mon, 16 Apr 2012 17:53:56 +0200 >> Von: Panagiotis Tsiatsis >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > >> Hello girls and guys, >> >> It is working for my CTF MEG data - the version that I have is v4692 >> 2011-11-07. >> >> The other thing that might cause a problem could be ommiting the >> reference channels definition before the ft_ preprocessing command that >> gave you your "dataprepro" >> >> i.e maybe you might need something like this >> >> cfg = []; >> >> ... >> //various preprocessing parameters >> ... >> >> cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; >> >> dataprepro = ft_preprocessing(cfg); >> >> >> Hope you are lucky :) >> >> Best, >> Panagiotis >> >> >> On 4/16/2012 4:59 PM, Stan van Pelt wrote: >>> Hi Barbara, >>> >>> I can replicate your finding, but am unsure what is causing it. Maybe >>> the difference/correction is lower than the Matlab or CTF precision? >>> In any case, if the 3rd order gradients were on, ft_denoise_synthetic >>> would undo the G3BR-balancing, ergo it toggles. >>> >>> Best, >>> Stan >>> >>> >>> ------------------------------------------------------------------------ >>> >>> *Van: *"Michael Wibral" >>> *Aan: *"Email discussion list for the FieldTrip project" >>> >>> *Verzonden: *Maandag 16 april 2012 16:46:27 >>> *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad >>> >>> Hi Barbara, >>> >>> are you certain that the original data do not have 3rd gradients >>> enabled? - looking at them once in dataEditor, switching to 3rd >>> grads and accidentally forgetting to unclick 'save parameters with >>> dataset' will make them have 3rd grads... >>> >>> When I last used ft_denoise_synthetic it worked pretty much as >>> described (??). >>> >>> Michael >>> >>> *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr >>> *Von:* "Barbara Haendel" >>> *An:* fieldtrip at donders.ru.nl >>> *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad >>> >>> Dear fieldtrip users, >>> >>> has anyone experience in using ft_denoise_synthetic? If I try to >>> calculate 3rd order grads in the below specified way the data does >>> not change with respect to the input data (which has no synthetic >>> gradiometer applied). Is there some obvious misunderstanding on my >>> side of how to use this function or is our environment truly >>> noiseless :) >>> >>> Cheers, >>> Barbara >>> >>> cfg=[]; >>> cfg.gradient ='G3BR'; >>> cfg.trials = 'all'; >>> data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); >>> >>> >>>>> data_3rdorder.grad.balance >>> >>> ans = >>> >>> G1BR: [1x1 struct] >>> G2BR: [1x1 struct] >>> G3BR: [1x1 struct] >>> current: 'G3BR' >>> previous: {'none'} >>> >>>>> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) >>> >>> ans = 0 >>> >>> -- >>> NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! >>> Jetzt informieren: >> http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a >>> _______________________________________________ >>> 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 >>> >>> >>> >>> >>> -- >>> Stan van Pelt >>> >>> Donders Institute for Brain, Cognition and Behaviour, Radboud >>> University Nijmegen >>> Kapittelweg 29, 6525 EN Nijmegen, Netherlands >>> E-mail: stan.vanpelt at donders.ru.nl >>> Website: www.ru.nl/donders/ >>> Phone: (+31) (0)24 36 10981 >>> Fax: (+31) (0)24 36 10989 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Panagiotis S. Tsiatsis >> Max Planck Institute for Biological Cybernetics >> Cognitive NeuroImaging Group >> Tuebingen, Germany >> > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Thu Apr 19 10:24:57 2012 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 19 Apr 2012 10:24:57 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <20120419065939.195940@gmx.net> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de>, <20120419065939.195940@gmx.net> Message-ID: An HTML attachment was scrubbed... URL: From B.Haendel at gmx.net Thu Apr 19 11:01:59 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Thu, 19 Apr 2012 11:01:59 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de>, <20120419065939.195940@gmx.net> Message-ID: <20120419090159.195980@gmx.net> Hey Michael, I completely agree that there should be a warning especially because the specification in data.grad.balance.current is consequently wrong. As Jan-Mathijs suggested I filed a bug report to fieldtrip. Best, Barbara -------- Original-Nachricht -------- > Datum: Thu, 19 Apr 2012 10:24:57 +0200 (CEST) > Von: "Michael Wibral" > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de From b.reuderink at donders.ru.nl Thu Apr 19 12:48:03 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 19 Apr 2012 12:48:03 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: Dear Hamza, Could you perhaps elaborate on your question? I was also under the impression that you asked how to view the (real time) Biosemi signals --- which Marianne explained. What are you trying to achieve, what is your approach, and on what aspect are you asking for help? Best, Boris On Wed, Apr 18, 2012 at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > Thank you Marianne > > I did not ask for just viewing the signal only, but to do realtime > processing in general. > > Thanks again > > Hamza > > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne > wrote: >> >> Hi Hamza >> >> You first need to start a buffer to read the data from de biosemi device, >> so start the biosemi2ft, see here >> http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. >> Then if you do not change the defaults you do not need to change the >> cfg.dataset field for the signal viewer. >> >> There is also a signal viewer based on c code (so no extra matlab session >> is necessary). You can find it here: fieldtrip/realtime/utilities/viewer >> >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On >> Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >> Sent: Tuesday, April 17, 2012 8:41 AM >> To: Email discussion list for the FieldTrip project >> Subject: [FieldTrip] Signal viewer + Biosemi >> >> Hello, >> >> I looked I the Signal viewer example in the following page: >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >> >> I just want to know how could I view a signal coming directly from the >> biosemi device? >> (I think the following line should be changed: >>  cfg.dataset        = 'buffer://localhost:1972'; >> but I don't know what to put) >> >> Thanks for your help >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van >> deze informatie is conform het Privacy reglement van de Sint >> Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. >> Gebruik van deze informatie door anderen dan de geadresseerde is, zonder >> voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De >> Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging >> van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From alexandre.gramfort at inria.fr Fri Apr 20 09:13:33 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 20 Apr 2012 09:13:33 +0200 Subject: [FieldTrip] Function ft_prepare_bemmodel deprecated... In-Reply-To: References: Message-ID: Hello Diana, I've just fixed on the svn the OpenMEEG demo scripts which had accidentally been broken. Once you update your version, you should now be able to run: openmeeg_eeg_leadfield_example.m  openmeeg_meg_leadfield_example.m which will confirm that OpenMEEG works as expected. Best, Alex On Wed, Apr 18, 2012 at 11:02 PM, Alexandre Gramfort wrote: > Hello diana, > > thanks for reporting the API change. > > I'll see if I can update the scripts: > > openmeeg_eeg_leadfield_example.m  openmeeg_meg_leadfield_example.m > > feel free to give it a try if I am not too reactive... > > Alex > > On Tue, Apr 17, 2012 at 10:33 AM, Diana Ibanescu > wrote: >> Hello, >> >> I am interested in an example how to compute an EEG leadfield with OpenMEEG >> in the Fieldtrip toolbox. I found a demo script here: >> http://fieldtrip.fcdonders.nl/example/testing_bem_created_leadfields >> When I call the function ft_prepare_bemmodel(cfg, vol) I receive the >> following warning: >> "Warning: FT_PREPARE_BEMMODEL is deprecated, please use FT_HEADMODEL_BEM_... >> with cfg.method = 'bem_bladeebla' >> instead." >> The function ft_headmodel_bem_openmeeg receive as parameter "geom" while >> ft_prepare_bemmodel receive other parameters: >>  vol = ft_headmodel_openmeeg(geom, ...) >> >>   Optional input arguments should be specified in key-value pairs and can >>   include >>     isolatedsource   = string, 'yes' or 'no' >>     hdmfile          = string, filename with BEM headmodel >>     conductivity     = vector, conductivity of each compartment >> >> Are the 2 functions similar? Is there any demo updated after the function >> ft_prepare_bemmodel became deprecated? What function can I use instead? >> >> Thank you, >> Diana. >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> From hamzaf at sabanciuniv.edu Sat Apr 21 09:28:57 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 21 Apr 2012 10:28:57 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: Dear Boris Due to my misunderstanding I thought the realtime processing is done by reading the data from a gdf file that is created by the biosemi2ft function. Reading the signal viewer discription on your site made me understand the realtime processing and reading from a buffter. To read the data from the biosemi I thought I should change the address (cfg.dataset = 'buffer://localhost:1972';), but, thanks to Marianne, I could view the signals easily from biosemi by keeping the line as it is. The command lines that I typed are: In cmd: *biosemi2ft example.config.txt out - *In MatLab: *cfg = []; * *cfg.blocksize = 1; % seconds * *cfg.dataset = 'buffer://localhost:1972'; % where to read the data* Best, Hamza On Thu, Apr 19, 2012 at 1:48 PM, Boris Reuderink wrote: > Dear Hamza, > > Could you perhaps elaborate on your question? I was also under the > impression that you asked how to view the (real time) Biosemi signals > --- which Marianne explained. What are you trying to achieve, what is > your approach, and on what aspect are you asking for help? > > Best, > > Boris > > On Wed, Apr 18, 2012 at 9:18 AM, Hamza Fawzi Altakroury (Student) > wrote: > > Thank you Marianne > > > > I did not ask for just viewing the signal only, but to do realtime > > processing in general. > > > > Thanks again > > > > Hamza > > > > > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne > > wrote: > >> > >> Hi Hamza > >> > >> You first need to start a buffer to read the data from de biosemi > device, > >> so start the biosemi2ft, see here > >> > http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. > >> Then if you do not change the defaults you do not need to change the > >> cfg.dataset field for the signal viewer. > >> > >> There is also a signal viewer based on c code (so no extra matlab > session > >> is necessary). You can find it here: fieldtrip/realtime/utilities/viewer > >> > >> Best, Marianne > >> ________________________________________ > >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > On > >> Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] > >> Sent: Tuesday, April 17, 2012 8:41 AM > >> To: Email discussion list for the FieldTrip project > >> Subject: [FieldTrip] Signal viewer + Biosemi > >> > >> Hello, > >> > >> I looked I the Signal viewer example in the following page: > >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer > >> > >> I just want to know how could I view a signal coming directly from the > >> biosemi device? > >> (I think the following line should be changed: > >> cfg.dataset = 'buffer://localhost:1972'; > >> but I don't know what to put) > >> > >> Thanks for your help > >> > >> > >> -- > >> Hamza Fawzi Altakroury > >> Graduate student - MA > >> Faculty of Engineering and Natural Sciences > >> Sabancı University > >> > >> Disclaimer > >> Vrijgave van de informatie verzonden met dit e-mail bericht is > >> geaccordeerd door de ontvanger en/of zijn behandelend arts. > Verstrekking van > >> deze informatie is conform het Privacy reglement van de Sint > >> Maartenskliniek. De informatie is uitsluitend bestemd voor de > geadresseerde. > >> Gebruik van deze informatie door anderen dan de geadresseerde is, zonder > >> voorafgaande schriftelijke toestemming van de rechthebbende , verboden. > De > >> Sint Maartenskliniek staat niet in voor de juiste en volledige > overbrenging > >> van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > >> > >> Sint Maartenskliniek > >> Hengstdal 3, > >> 6574 NA Ubbergen (bij Nijmegen) > >> Telefoon 024-3659 911 > >> Telefax 024-3659 204 > >> KvK nummer 41055111 > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > twitter.com/#!/breuderink | > github.com/breuderink | borisreuderink.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at gmx.de Sun Apr 22 09:07:06 2012 From: paul_c at gmx.de (Paul Czienskowski) Date: Sun, 22 Apr 2012 09:07:06 +0200 Subject: [FieldTrip] Question concerning ft_headmodel_bem_openmeeg Message-ID: <4F93AE1A.50405@gmx.de> Dear all, I want to create headmodels with the ft_headmodel_bem_openmeeg function, and - for I formerly used the ft_prepare_bemmodel function - decided to delve into the new function first, to see how it works. Anyway, I stumbled upon something that puzzled me a bit. In line 96 to 106, the boundaries are rearranged to be inside first, which to my understanding means, that the first boundary in the array of boundaries will be the innermost one (i.e. the brain in my case) and the last boundary will be the outermost one (i.e. skin). Everything's fine hitherto. But from line 108 on, things become quite odd. Line 108 and 109 define the first compartment to be the skin and the last to be the source compartment. This is cross-checked again in line 127 to 129. To my understanding this is a contradiction and I would appreciate, if anybody could tell me if I got something completely wrong, or if the function does odd things. If the function is correct, there should at least be a comment explaining why this contradiction makes sense anyway. Best regards, Paul From matt.mollison at gmail.com Mon Apr 23 05:54:33 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Sun, 22 Apr 2012 21:54:33 -0600 Subject: [FieldTrip] Oscillatory power normalization Message-ID: Hi FieldTrippers, In almost all the papers I've read involving oscillatory power, some kind of transformation is done to the data due to the 1/f power spectrum effect (power decreases as frequency increases). I'm mostly looking at within-subjects experiments (every subject behaved in all conditions) comparing conditions across subjects, but it seems like normalizing the power spectrum should apply in any case (especially if any kind of parametric stats are done—right?). Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis to make these transformations (e.g., log10 normalization, dB normalization [EEGLab does this], vector length normalization, etc.; the only thing I see is in ft_sourcedescriptives, but I'm not doing source analyses), and it confuses me why this is the case. I can't find much discussion regarding the 1/f issue on the FT wiki or the mailing list. This seems like an important step that is missing from any frequency analysis workflow. Am I missing something (meaning I just don't see the option), am I misunderstanding something (meaning I'm incorrect in this assumption), or is this an issue that needs to be fixed? Thanks, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon Apr 23 08:49:00 2012 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Mon, 23 Apr 2012 08:49:00 +0200 Subject: [FieldTrip] Oscillatory power normalization In-Reply-To: References: Message-ID: <6CC16DD9-C72B-4CA4-A7C9-D504BBCF9447@psi.ucm.es> Hi Matt, I think Fieltrip does not do these transformations. However you could do cfg.baselinetype = 'relative' (power post/power pre) and take the log10 and multiply by 10 (TF.powerspctrm). Then you should have dB. best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 23/04/2012, a las 05:54, Matt Mollison escribió: > Hi FieldTrippers, > > In almost all the papers I've read involving oscillatory power, some kind of transformation is done to the data due to the 1/f power spectrum effect (power decreases as frequency increases). I'm mostly looking at within-subjects experiments (every subject behaved in all conditions) comparing conditions across subjects, but it seems like normalizing the power spectrum should apply in any case (especially if any kind of parametric stats are done—right?). > > Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis to make these transformations (e.g., log10 normalization, dB normalization [EEGLab does this], vector length normalization, etc.; the only thing I see is in ft_sourcedescriptives, but I'm not doing source analyses), and it confuses me why this is the case. I can't find much discussion regarding the 1/f issue on the FT wiki or the mailing list. This seems like an important step that is missing from any frequency analysis workflow. Am I missing something (meaning I just don't see the option), am I misunderstanding something (meaning I'm incorrect in this assumption), or is this an issue that needs to be fixed? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > _______________________________________________ > 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 eelke.spaak at donders.ru.nl Mon Apr 23 11:54:42 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 23 Apr 2012 11:54:42 +0200 Subject: [FieldTrip] Oscillatory power normalization In-Reply-To: References: Message-ID: Hi Matt, When you are comparing power across conditions, it is not really necessary to apply an explicit correction for the dominant 1/f component of the raw spectrum. Since this 1/f component is present in both conditions, when you subtract power in one condition from power in another condition (or compute the ratio, or log-ratio, or relative change, or whatever), the 1/f will cancel out and you will only be left with whatever is due to your experimental manipulation. This is true because the contrast is done per frequency. (Note that comparing activity versus baseline is just a special case of looking at a contrast between conditions, so the same argument holds there.) The only time when an explicit correction for 1/f is useful, is when you want to look at raw power. The most dominant oscillatory features (visual alpha, visual contrast induced gamma...) will usually be evident in raw spectra without such a correction, by the way. Correcting for 1/f can be done in many ways, the most simple one is simply taking the logarithm of power, something like: freqCorrected = freqUncorrected; freqCorrected.powspctrm = log10(freqCorrected.powspctrm); Or you could take the first derivative in the time domain (equivalent to multiplying the spectrum with f, search for post by Robert on this on the FT list). Or you could take the log of both the frequency- and power axes, then fit a line, and subtract it, then transform back (10^corrected data). But, the main point is: in the vast majority of typical cognitive experiments, correcting for 1/f is not needed. Best, Eelke On 23 April 2012 05:54, Matt Mollison wrote: > Hi FieldTrippers, > > In almost all the papers I've read involving oscillatory power, some kind of > transformation is done to the data due to the 1/f power spectrum effect > (power decreases as frequency increases). I'm mostly looking at > within-subjects experiments (every subject behaved in all conditions) > comparing conditions across subjects, but it seems like normalizing the > power spectrum should apply in any case (especially if any kind of > parametric stats are done—right?). > > Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis > to make these transformations (e.g., log10 normalization, dB normalization > [EEGLab does this], vector length normalization, etc.; the only thing I see > is in ft_sourcedescriptives, but I'm not doing source analyses), and it > confuses me why this is the case. I can't find much discussion regarding the > 1/f issue on the FT wiki or the mailing list. This seems like an important > step that is missing from any frequency analysis workflow. Am I missing > something (meaning I just don't see the option), am I misunderstanding > something (meaning I'm incorrect in this assumption), or is this an issue > that needs to be fixed? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jdien07 at mac.com Tue Apr 24 08:41:20 2012 From: jdien07 at mac.com (Joseph Dien) Date: Tue, 24 Apr 2012 02:41:20 -0400 Subject: [FieldTrip] Oscillatory power normalization In-Reply-To: References: Message-ID: <454AC917-60FD-4CF6-BF21-242DF4B5B4D0@mac.com> I'm new to spectral analysis so take anything I say with a grain of salt: 1) If one intends on taking the average of a band (like 8-12Hz for alpha), seems like maybe helpful to correct for 1/f so the lower bands don't dominate? 2) Another issue is spectral density (correcting for frequency bin width for discrete Fourier). As far as I can tell, FieldTrip isn't doing this. Seems like it should be standard. Or at least it should say in the documentation whether it is being done. Am I wrong? Cheers! Joe On Apr 23, 2012, at 5:54 AM, Eelke Spaak wrote: > Hi Matt, > > When you are comparing power across conditions, it is not really > necessary to apply an explicit correction for the dominant 1/f > component of the raw spectrum. Since this 1/f component is present in > both conditions, when you subtract power in one condition from power > in another condition (or compute the ratio, or log-ratio, or relative > change, or whatever), the 1/f will cancel out and you will only be > left with whatever is due to your experimental manipulation. This is > true because the contrast is done per frequency. (Note that comparing > activity versus baseline is just a special case of looking at a > contrast between conditions, so the same argument holds there.) > > The only time when an explicit correction for 1/f is useful, is when > you want to look at raw power. The most dominant oscillatory features > (visual alpha, visual contrast induced gamma...) will usually be > evident in raw spectra without such a correction, by the way. > Correcting for 1/f can be done in many ways, the most simple one is > simply taking the logarithm of power, something like: > > freqCorrected = freqUncorrected; > freqCorrected.powspctrm = log10(freqCorrected.powspctrm); > > Or you could take the first derivative in the time domain (equivalent > to multiplying the spectrum with f, search for post by Robert on this > on the FT list). Or you could take the log of both the frequency- and > power axes, then fit a line, and subtract it, then transform back > (10^corrected data). > > But, the main point is: in the vast majority of typical cognitive > experiments, correcting for 1/f is not needed. > > Best, > Eelke > > On 23 April 2012 05:54, Matt Mollison wrote: >> Hi FieldTrippers, >> >> In almost all the papers I've read involving oscillatory power, some kind of >> transformation is done to the data due to the 1/f power spectrum effect >> (power decreases as frequency increases). I'm mostly looking at >> within-subjects experiments (every subject behaved in all conditions) >> comparing conditions across subjects, but it seems like normalizing the >> power spectrum should apply in any case (especially if any kind of >> parametric stats are done—right?). >> >> Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis >> to make these transformations (e.g., log10 normalization, dB normalization >> [EEGLab does this], vector length normalization, etc.; the only thing I see >> is in ft_sourcedescriptives, but I'm not doing source analyses), and it >> confuses me why this is the case. I can't find much discussion regarding the >> 1/f issue on the FT wiki or the mailing list. This seems like an important >> step that is missing from any frequency analysis workflow. Am I missing >> something (meaning I just don't see the option), am I misunderstanding >> something (meaning I'm incorrect in this assumption), or is this an issue >> that needs to be fixed? >> >> Thanks, >> Matt >> >> -- >> Univ. of Colorado at Boulder >> Dept. of Psychology and Neuroscience >> matthew.mollison at colorado.edu >> http://psych.colorado.edu/~mollison/ >> >> _______________________________________________ >> 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 -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ From stan.vanpelt at fcdonders.ru.nl Tue Apr 24 10:14:54 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Tue, 24 Apr 2012 10:14:54 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: Message-ID: <506536226.7942.1335255294672.JavaMail.root@sculptor.zimbra.ru.nl> Hi all, A follow-up question on the implementation of 3rd-order gradiometer correction in FT: I am puzzling how one can do both 3-order grad. correction and dft-filtering properly using FT. the logical sequency would be to do ft_denoise_synthetic first, and subsequently dft-filtering using ft_preprocessing. However, in that case it is no longer possible to pad the data when calling ft_preprocessing, because it now processes trial-data (output from ft_denoise_synthetic), and doesn't read in the original dataset anymore. or am I mistaken here? I could see 3 alternatives, which seem to be more like (computationally) suboptimal workarounds: - Apply ft_denoise_synthetic on the entire dataset, then dft-filter the entire dataset, and then run ft_redefinetrial to cut the data into actual trials - Adjust the trial definition such that longer data segments are read in, equivalent to your padding size. Then apply ft_denoise_synthetic on these trials, then dft-filter them, and then run ft_redefinetrial to cut the data into actual trials - Doing the 3-rd order grad. correction first using the DataEditor, and then process it further using FT. Any thoughts? Best, Stan ----- Oorspronkelijk bericht ----- > Van: "Michael Wibral" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Donderdag 19 april 2012 10:24:57 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hey there, > sorry for not thinking about it any earlier, indeed I can confirm that > ft_denoise.. needs the reference channels to function properly. I > remember having to preprocess in a funny order in old ft versions, to > do artefcat rejection without the refs and denoising with the refs. > Personally, I think the code should check whether the refs are there > and otherwise throw an error. Since ft_denoise.. only concerns CTF > (and bti??) systems, where the refs have fixed names this could be > easily implemented, or am I mistaken? > Best, > Michael > Gesendet: Donnerstag, 19. April 2012 um 08:59 Uhr > Von: "Barbara Haendel" > An: "Email discussion list for the FieldTrip project" > , fieldtrip at donders.ru.nl > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hey there, thanks a lot for the replies! > Panagiotis hit the mark. Indeed the reference channels were excluded > in the first round of preprocessing. May be one could include a short > note on that in the ft_denoise m-file description since only including > relevant channels is the normal way to treat data in preprocessing. > Thanks again, > Barbara > -------- Original-Nachricht -------- > > Datum: Mon, 16 Apr 2012 17:53:56 +0200 > > Von: Panagiotis Tsiatsis > > An: Email discussion list for the FieldTrip project > > > > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > Hello girls and guys, > > > > It is working for my CTF MEG data - the version that I have is v4692 > > 2011-11-07. > > > > The other thing that might cause a problem could be ommiting the > > reference channels definition before the ft_ preprocessing command > > that > > gave you your "dataprepro" > > > > i.e maybe you might need something like this > > > > cfg = []; > > > > ... > > //various preprocessing parameters > > ... > > > > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > > > > dataprepro = ft_preprocessing(cfg); > > > > > > Hope you are lucky :) > > > > Best, > > Panagiotis > > > > > > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > > Hi Barbara, > > > > > > I can replicate your finding, but am unsure what is causing it. > > > Maybe > > > the difference/correction is lower than the Matlab or CTF > > > precision? > > > In any case, if the 3rd order gradients were on, > > > ft_denoise_synthetic > > > would undo the G3BR-balancing, ergo it toggles. > > > > > > Best, > > > Stan > > > > > > > > > ------------------------------------------------------------------------ > > > > > > *Van: *"Michael Wibral" > > > *Aan: *"Email discussion list for the FieldTrip project" > > > > > > *Verzonden: *Maandag 16 april 2012 16:46:27 > > > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > > > Hi Barbara, > > > > > > are you certain that the original data do not have 3rd gradients > > > enabled? - looking at them once in dataEditor, switching to 3rd > > > grads and accidentally forgetting to unclick 'save parameters with > > > dataset' will make them have 3rd grads... > > > > > > When I last used ft_denoise_synthetic it worked pretty much as > > > described (??). > > > > > > Michael > > > > > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > > > *Von:* "Barbara Haendel" > > > *An:* fieldtrip at donders.ru.nl > > > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > > > Dear fieldtrip users, > > > > > > has anyone experience in using ft_denoise_synthetic? If I try to > > > calculate 3rd order grads in the below specified way the data does > > > not change with respect to the input data (which has no synthetic > > > gradiometer applied). Is there some obvious misunderstanding on my > > > side of how to use this function or is our environment truly > > > noiseless :) > > > > > > Cheers, > > > Barbara > > > > > > cfg=[]; > > > cfg.gradient ='G3BR'; > > > cfg.trials = 'all'; > > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > > > > > > > >> data_3rdorder.grad.balance > > > > > > ans = > > > > > > G1BR: [1x1 struct] > > > G2BR: [1x1 struct] > > > G3BR: [1x1 struct] > > > current: 'G3BR' > > > previous: {'none'} > > > > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > > > > ans = 0 > > > > > > -- > > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > > Jetzt informieren: > > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > > _______________________________________________ > > > 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 > > > > > > > > > > > > > > > -- > > > Stan van Pelt > > > > > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > > University Nijmegen > > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > > E-mail: stan.vanpelt at donders.ru.nl > > > Website: www.ru.nl/donders/ > > > Phone: (+31) (0)24 36 10981 > > > Fax: (+31) (0)24 36 10989 > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > > Panagiotis S. Tsiatsis > > Max Planck Institute for Biological Cybernetics > > Cognitive NeuroImaging Group > > Tuebingen, Germany > > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 -- Stan van Pelt Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 10981 Fax: (+31) (0)24 36 10989 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue Apr 24 10:26:18 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 24 Apr 2012 10:26:18 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <506536226.7942.1335255294672.JavaMail.root@sculptor.zimbra.ru.nl> References: <506536226.7942.1335255294672.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Hi Stan, To me, it seems all three options would be fine, and I actually don't think they are computationally suboptimal. I would probably go for option 2, and have done so with a similar problem in the past. This worked well for me. Best, Eelke On 24 April 2012 10:14, Stan van Pelt wrote: > Hi all, > > A follow-up question on the implementation of 3rd-order gradiometer > correction in FT: > > I am puzzling how one can do both 3-order grad. correction and dft-filtering > properly using FT. the logical sequency would be to do ft_denoise_synthetic > first, and subsequently dft-filtering using ft_preprocessing. However, in > that case it is no longer possible to pad the data when calling > ft_preprocessing, because it now processes trial-data (output from > ft_denoise_synthetic), and doesn't read in the original dataset anymore. or > am I mistaken here? > > I could see 3 alternatives, which seem to be more > like (computationally) suboptimal workarounds: > - Apply ft_denoise_synthetic on the entire dataset, then dft-filter the > entire dataset, and then run ft_redefinetrial to cut the data into actual > trials > - Adjust the trial definition such that longer data segments are read in, > equivalent to your padding size. Then apply ft_denoise_synthetic on these > trials, then dft-filter them, and then run ft_redefinetrial to cut the data > into actual trials > - Doing the 3-rd order grad. correction first using the DataEditor, and then > process it further using FT. > > Any thoughts? > > Best, Stan > > > ________________________________ > > Van: "Michael Wibral" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Donderdag 19 april 2012 10:24:57 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Hey there, > > sorry for not thinking about it any earlier, indeed I can confirm that > ft_denoise.. needs the reference channels to function properly. I remember > having to preprocess in a funny order in old ft versions, to do artefcat > rejection without the refs and denoising with the refs. > > Personally, I think the code should check whether the refs are there and > otherwise throw an error. Since ft_denoise.. only concerns CTF (and bti??) > systems, where the refs have fixed names this could be easily implemented, > or am I mistaken? > > Best, > Michael > Gesendet: Donnerstag, 19. April 2012 um 08:59 Uhr > Von: "Barbara Haendel" > An: "Email discussion list for the FieldTrip project" > , fieldtrip at donders.ru.nl > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Hey there, thanks a lot for the replies! > > Panagiotis hit the mark. Indeed the reference channels were excluded in the > first round of preprocessing. May be one could include a short note on that > in the ft_denoise m-file description since only including relevant channels > is the normal way to treat data in preprocessing. > > Thanks again, > Barbara > > > > > -------- Original-Nachricht -------- >> Datum: Mon, 16 Apr 2012 17:53:56 +0200 >> Von: Panagiotis Tsiatsis >> An: Email discussion list for the FieldTrip project >> >> Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > >> Hello girls and guys, >> >> It is working for my CTF MEG data - the version that I have is v4692 >> 2011-11-07. >> >> The other thing that might cause a problem could be ommiting the >> reference channels definition before the ft_ preprocessing command that >> gave you your "dataprepro" >> >> i.e maybe you might need something like this >> >> cfg = []; >> >> ... >> //various preprocessing parameters >> ... >> >> cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; >> >> dataprepro = ft_preprocessing(cfg); >> >> >> Hope you are lucky :) >> >> Best, >> Panagiotis >> >> >> On 4/16/2012 4:59 PM, Stan van Pelt wrote: >> > Hi Barbara, >> > >> > I can replicate your finding, but am unsure what is causing it. Maybe >> > the difference/correction is lower than the Matlab or CTF precision? >> > In any case, if the 3rd order gradients were on, ft_denoise_synthetic >> > would undo the G3BR-balancing, ergo it toggles. >> > >> > Best, >> > Stan >> > >> > >> > ------------------------------------------------------------------------ >> > >> > *Van: *"Michael Wibral" >> > *Aan: *"Email discussion list for the FieldTrip project" >> > >> > *Verzonden: *Maandag 16 april 2012 16:46:27 >> > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad >> > >> > Hi Barbara, >> > >> > are you certain that the original data do not have 3rd gradients >> > enabled? - looking at them once in dataEditor, switching to 3rd >> > grads and accidentally forgetting to unclick 'save parameters with >> > dataset' will make them have 3rd grads... >> > >> > When I last used ft_denoise_synthetic it worked pretty much as >> > described (??). >> > >> > Michael >> > >> > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr >> > *Von:* "Barbara Haendel" >> > *An:* fieldtrip at donders.ru.nl >> > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad >> > >> > Dear fieldtrip users, >> > >> > has anyone experience in using ft_denoise_synthetic? If I try to >> > calculate 3rd order grads in the below specified way the data does >> > not change with respect to the input data (which has no synthetic >> > gradiometer applied). Is there some obvious misunderstanding on my >> > side of how to use this function or is our environment truly >> > noiseless :) >> > >> > Cheers, >> > Barbara >> > >> > cfg=[]; >> > cfg.gradient ='G3BR'; >> > cfg.trials = 'all'; >> > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); >> > >> > >> > >> data_3rdorder.grad.balance >> > >> > ans = >> > >> > G1BR: [1x1 struct] >> > G2BR: [1x1 struct] >> > G3BR: [1x1 struct] >> > current: 'G3BR' >> > previous: {'none'} >> > >> > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) >> > >> > ans = 0 >> > >> > -- >> > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! >> > Jetzt informieren: >> http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a >> > _______________________________________________ >> > 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 >> > >> > >> > >> > >> > -- >> > Stan van Pelt >> > >> > Donders Institute for Brain, Cognition and Behaviour, Radboud >> > University Nijmegen >> > Kapittelweg 29, 6525 EN Nijmegen, Netherlands >> > E-mail: stan.vanpelt at donders.ru.nl >> > Website: www.ru.nl/donders/ >> > Phone: (+31) (0)24 36 10981 >> > Fax: (+31) (0)24 36 10989 >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Panagiotis S. Tsiatsis >> Max Planck Institute for Biological Cybernetics >> Cognitive NeuroImaging Group >> Tuebingen, Germany >> > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 > > > > > -- > Stan van Pelt > > Donders Institute for Brain, Cognition and Behaviour, Radboud University > Nijmegen > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > E-mail:  stan.vanpelt at donders.ru.nl > Website: www.ru.nl/donders/ > Phone:  (+31) (0)24 36 10981 > Fax:    (+31) (0)24 36 10989 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From alexandre.gramfort at inria.fr Wed Apr 25 09:07:07 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Wed, 25 Apr 2012 09:07:07 +0200 Subject: [FieldTrip] Question concerning ft_headmodel_bem_openmeeg In-Reply-To: <4F93AE1A.50405@gmx.de> References: <4F93AE1A.50405@gmx.de> Message-ID: Hi Paul, I've not looked into the new functions yet and I am not sure it has been ever tested for openmeeg (robert, cristiano?). I'd stick to the old functions for urgent matters. Feel free to send me a patch if you end up fixing problems with the new ones. I'll review the changes ASAP. Best, Alex On Sun, Apr 22, 2012 at 9:07 AM, Paul Czienskowski wrote: > Dear all, > > I want to create headmodels with the ft_headmodel_bem_openmeeg function, and > - for I formerly used the ft_prepare_bemmodel function - decided to delve > into the new function first, to see how it works. Anyway, I stumbled upon > something that puzzled me a bit. In line 96 to 106, the boundaries are > rearranged to be inside first, which to my understanding means, that the > first boundary in the array of boundaries will be the innermost one (i.e. > the brain in my case) and the last boundary will be the outermost one (i.e. > skin). Everything's fine hitherto. But from line 108 on, things become quite > odd. Line 108 and 109 define the first compartment to be the skin and the > last to be the source compartment. This is cross-checked again in line 127 > to 129. To my understanding this is a contradiction and I would appreciate, > if anybody could tell me if I got something completely wrong, or if the > function does odd things. If the function is correct, there should at least > be a comment explaining why this contradiction makes sense anyway. > > Best regards, > Paul > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From v.poghosyan at humanbraindynamics.com Wed Apr 25 13:29:25 2012 From: v.poghosyan at humanbraindynamics.com (Vahe Poghosyan) Date: Wed, 25 Apr 2012 14:29:25 +0300 Subject: [FieldTrip] General questions In-Reply-To: References: <4F93AE1A.50405@gmx.de> Message-ID: <00ec01cd22d6$ad53fa00$07fbee00$@poghosyan@humanbraindynamics.com> Dear fieldtrip users and developer, I am new to fieldtrip. I think it's an excellent toolbox (thanks to the developers), but have few general questions: 1. I understand that fieldtrip is a data analysis toolbox, however the results of the analysis need to be visualized. I find the fieldtrip visualization functions, especially of the source analysis results (e.g. ft_sourceplot, ft_sourceinterpolate, ft_sourcemovie) inadequate. My question is how do you usually visualize the results of the source analysis? Do you write your own matlab functions, including font-ends to fieldtrip plotting functions or you use other freely/commercially available tools that can import fieldtrip structures or you are satisfied with what is provided in the fieldtrip toolbox? 2. It seems that the documentation provided on the fieldtrip website is not very up-to-date and the descriptions of many configuration options in the *.m files are not documented. At the moment to understand all the available configuration options, and what different functions are doing and how they are implemented, I am debugging them step-by-step. Short of debugging or every time asking questions in this list, is there another way of getting information about all the available configuration options for different fieldtrip functions and their implementation details? 3. I found some functions in the fieldtrip's SVN (trunc) version (on googlecode), which are not available in the daily releases on the ftp server (e.g. ft_surfacecheck). Is it safe to use those functions (I understand that the toolbox is released under GPL)? 4. Are the measurement units used throughout fieldtrip functions basic SI (International System of Units) units? More specifically, what are the units of the inputs to ft_dipolesimulation (cfg.dip.signal, cfg.dip.amplitude)? Are they A*m or nA*m or something else? What are the units of the output from the minimumnormestimate? A/m? Thanks in advance Vahe Poghosyan, Ph.D. Senior Scientist Lab. for Human Brain Dynamics AAI Scientific Cultural Services Ltd. http://aaiscs.com/LHBD/ From jpnv2006 at gmail.com Wed Apr 25 16:39:05 2012 From: jpnv2006 at gmail.com (Juan Pablo Neira) Date: Wed, 25 Apr 2012 16:39:05 +0200 Subject: [FieldTrip] Individual MRI - Atlas Message-ID: Hello, I would like to know if it is possible to use the ft_sourceplot function with an individual MRI (coordsys: ctf) and an Atlas A tried to use one atlas from the Faq "aal_MNI_V4.img". After ft_prepare_atlas the coordinate system was coord:mni. When I used the ft_sourceplot function (ortho method), there were some warnings about labels not found and points outside the atlas, but I always clicked in inside my MRI. Should I have my MRI and the atlas in the same coordinate system (mni)? Regards, Juan Pablo Neira Vesga From yuvharpaz at gmail.com Wed Apr 25 20:13:10 2012 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Wed, 25 Apr 2012 21:13:10 +0300 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: References: Message-ID: Hi there I had left to right error with this atlas in sourceplot. download the newer .nii version. http://fmri.wfubmc.edu/software/PickAtlas yuval On 25 April 2012 17:39, Juan Pablo Neira wrote: > Hello, > > I would like to know if it is possible to use the ft_sourceplot > function with an individual MRI (coordsys: ctf) and an Atlas > > A tried to use one atlas from the Faq "aal_MNI_V4.img". After > ft_prepare_atlas the coordinate system was coord:mni. > > When I used the ft_sourceplot function (ortho method), there were some > warnings about labels not found and points outside the atlas, but I > always clicked in inside my MRI. Should I have my MRI and the atlas > in the same coordinate system (mni)? > > Regards, > > Juan Pablo Neira Vesga > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Apr 26 00:04:12 2012 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Wed, 25 Apr 2012 22:04:12 +0000 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <7270aa3bcbfd9.4f574cba@mail.uh.edu> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>, <7270aa3bcbfd9.4f574cba@mail.uh.edu> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> Hi I encounted the same problem with ft_databrowser: ************* fetching artifacts... Error using ft_fetch_data (line 57) data does not contain a consistent trial definition, fetching data is not possible Error in ft_databrowser>redraw_cb (line 1159) art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); Error in ft_databrowser (line 535) redraw_cb(h); **************** The same data works OK with [data] = ft_rejectvisual(cfg, data) I have: MacOS 10.6.8 MATLAB 7.13.0.564 (R2011b) Matlab re-installation did not help in my case. I would be grateful for any tips. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] Sent: Wednesday, March 07, 2012 6:55 PM To: Email discussion list for the FieldTrip project Cc: fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] Error -> ft_databrowser Hi Michael, I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution. But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution. Mehmet ----- Original Message ----- From: "Epstein, Michael" Date: Wednesday, March 7, 2012 11:29 am Subject: Re: [FieldTrip] Error -> ft_databrowser To: fieldtrip at donders.ru.nl > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list. > > -Michael > > > ________________________________ > Dear Fieldtrippers, > > > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? > > > fieldtrip version 20120130, matlab version R2010a, operating system windows 7. > > > Thanks in advance for any suggestions. > > > > ??? Error using ==> ft_fetch_data at 57 > data does not contain a consistent trial definition, fetching data is not > possible > > > Error in ==> ft_databrowser>redraw_cb at 1159 > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); > > > Error in ==> ft_databrowser at 535 > redraw_cb(h); > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > _______________________________________________ > 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 r.vandermeij at donders.ru.nl Thu Apr 26 10:13:18 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Thu, 26 Apr 2012 10:13:18 +0200 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org> <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> Message-ID: Hi Elena, >From the looks of it you are using an old version of FieldTrip. Could you download the latest version and see if the problem persists? Best, Roemer On Thu, Apr 26, 2012 at 12:04 AM, Elena Orekhova wrote: > Hi > I encounted the same problem with ft_databrowser: > > ************* > fetching artifacts... Error using ft_fetch_data (line 57) > > data does not contain a consistent trial definition, fetching data is not > possible > > Error in ft_databrowser>redraw_cb (line 1159) > > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > Error in ft_databrowser (line 535) > redraw_cb(h); > **************** > > The same data works OK with > [data] = ft_rejectvisual(cfg, data) > > I have: > MacOS 10.6.8 > MATLAB 7.13.0.564 (R2011b) > > Matlab re-installation did not help in my case. > I would be grateful for any tips. > > Elena > ------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] > *Sent:* Wednesday, March 07, 2012 6:55 PM > > *To:* Email discussion list for the FieldTrip project > *Cc:* fieldtrip at donders.ru.nl > *Subject:* Re: [FieldTrip] Error -> ft_databrowser > > Hi Michael, > > > I have posted the question actually but I didn't hear any suggestions > about it. The same error was posted yesterday by someone else. > > > just to repeat what i have replied in the other post, i tried many things > to solve it (changed the code, run the databrowser code line by line, > updated fieldtrip version at etc.), but none of them solved the problem. I > started getting the error after I tried using parallel processing scripts > in matlab. But as i said, i have no basis to say that this caused the > problem. So basically, i do not know any scientific solution. > > > But an old school method solved the problem in my case. Simply i > uninstalled and re-installed matlab. Never got the error again. You may > want to try this. I have no other solution. > > > Mehmet > > > > > > ----- Original Message ----- > From: "Epstein, Michael" > Date: Wednesday, March 7, 2012 11:29 am > Subject: Re: [FieldTrip] Error -> ft_databrowser > To: fieldtrip at donders.ru.nl > > > Hi - I am actually encountering the same error with databrowser, > and was wondering if you ever came up with a solution to this problem - or > if anyone else has a solution - I didn't find a response on the mailing > list. > > > > > > -Michael > > > > > > > > > > ------------------------------ > > > Dear Fieldtrippers, > > > > > > > > > I am encountering a strange error while i try to use ft_databrowser. > The error code is as below. I have never seen this error earlier. I used > ft_databrowser many times and its only last 2 days that i am getting the > error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and > used the newer version but still the same error. Strangely, i dont get this > error when i tried with other computers (same matlab version (R2010a), same > operating system (windows 7) on both computers. Has anyone got this error > before? what may cause this error? > > > > > > > > > fieldtrip version 20120130, matlab version R2010a, operating system > windows 7. > > > > > > > > > Thanks in advance for any suggestions. > > > > > > > > > > > > ??? Error using ==> ft_fetch_data at 57 > > > data does not contain a consistent trial definition, fetching data is > not > > > possible > > > > > > > > > Error in ==> ft_databrowser>redraw_cb at 1159 > > > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > > > > > > > > Error in ==> ft_databrowser at 535 > > > redraw_cb(h); > > > > > ------------------------------ > > Conserve Resources. Print only when necessary. > > > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended > recipient. It may contain confidential information which is legally > privilegedor otherwise protected by law. If you received this e-mail in > error or from someone who is not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or > copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your > cooperation. > > > _______________________________________________ > > 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 > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Apr 26 10:19:56 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 26 Apr 2012 10:19:56 +0200 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>, <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> Message-ID: <4F99052C.1010508@donders.ru.nl> Hi Elena, most likely your data has trials with overlapping sample points. Unfortunately, the databrowser does not support this, or to be more specific ft_fetch_data does not support this. The reason for this is that a specific segment in time is defined twice in your data, and it is not clear what segment it is you would like to look at (due to filter artifacts and other preprocessing steps, the data will most likely have different values for the same sample points). For non-continuous data (already preprocessed data), it should be able to implement this nonetheless, but that's on our todo list. The best way for now is to call ft_redefinetrial and cut out the overlapping segments. You could also hack your way around this by removing data.sampleinfo. FieldTrip will then make up arbitrary, meaningless sample numbers. Keep in mind that we do not recommend this though. There is no way that the reconstructed sample numbers can be traced back to your original data! (well... if your programming skills are reasonable enough, it is possible, but that requires some further hacking, and a lot of effort). Best, Jörn On 4/26/2012 12:04 AM, Elena Orekhova wrote: > Hi > I encounted the same problem with ft_databrowser: > > ************* > fetching artifacts... Error using ft_fetch_data (line 57) > data does not contain a consistent trial definition, fetching data is not > possible > > Error in ft_databrowser>redraw_cb (line 1159) > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > Error in ft_databrowser (line 535) > redraw_cb(h); > **************** > > The same data works OK with > [data] = ft_rejectvisual(cfg, data) > > I have: > MacOS 10.6.8 > MATLAB 7.13.0.564 (R2011b) > > Matlab re-installation did not help in my case. > I would be grateful for any tips. > > Elena > ------------------------------------------------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun > [mcoskun at mail.uh.edu] > *Sent:* Wednesday, March 07, 2012 6:55 PM > *To:* Email discussion list for the FieldTrip project > *Cc:* fieldtrip at donders.ru.nl > *Subject:* Re: [FieldTrip] Error -> ft_databrowser > > Hi Michael, > > > I have posted the question actually but I didn't hear any suggestions > about it. The same error was posted yesterday by someone else. > > > just to repeat what i have replied in the other post, i tried many > things to solve it (changed the code, run the databrowser code line by > line, updated fieldtrip version at etc.), but none of them solved the > problem. I started getting the error after I tried using parallel > processing scripts in matlab. But as i said, i have no basis to say > that this caused the problem. So basically, i do not know any > scientific solution. > > > But an old school method solved the problem in my case. Simply i > uninstalled and re-installed matlab. Never got the error again. You > may want to try this. I have no other solution. > > > Mehmet > > > > > > ----- Original Message ----- > From: "Epstein, Michael" > Date: Wednesday, March 7, 2012 11:29 am > Subject: Re: [FieldTrip] Error -> ft_databrowser > To: fieldtrip at donders.ru.nl > > > Hi - I am actually encountering the same error with databrowser, and > was wondering if you ever came up with a solution to this problem - or > if anyone else has a solution - I didn't find a response on the > mailing list. > > > > > > -Michael > > > > > > > > > > > ------------------------------------------------------------------------ > > > Dear Fieldtrippers, > > > > > > > > > I am encountering a strange error while i try to use ft_databrowser. > The error code is as below. I have never seen this error earlier. I > used ft_databrowser many times and its only last 2 days that i am > getting the error. I downloaded a newer version of fieldtrip > (fieldtrip-20120130) and used the newer version but still the same > error. Strangely, i dont get this error when i tried with other > computers (same matlab version (R2010a), same operating system > (windows 7) on both computers. Has anyone got this error before? what > may cause this error? > > > > > > > > > fieldtrip version 20120130, matlab version R2010a, operating system > windows 7. > > > > > > > > > Thanks in advance for any suggestions. > > > > > > > > > > > > ??? Error using ==> ft_fetch_data at 57 > > > data does not contain a consistent trial definition, fetching data is not > > > possible > > > > > > > > > Error in ==> ft_databrowser>redraw_cb at 1159 > > > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > > > > > > > > Error in ==> ft_databrowser at 535 > > > redraw_cb(h); > > > > > > ------------------------------------------------------------------------ > > Conserve Resources. Print only when necessary. > > > > IMPORTANT NOTICE: This e-mail is meant only for the use of the > intended recipient. It may contain confidential information which is > legally privilegedor otherwise protected by law. If you received this > e-mail in error or from someone who is not authorized to send it to > you, you are strictly prohibited from reviewing, using, disseminating, > distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF > THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. > Thank you for your cooperation. > > > _______________________________________________ > > 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 -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Apr 26 10:47:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 26 Apr 2012 10:47:37 +0200 Subject: [FieldTrip] General questions In-Reply-To: <00ec01cd22d6$ad53fa00$07fbee00$@poghosyan@humanbraindynamics.com> References: <4F93AE1A.50405@gmx.de> <00ec01cd22d6$ad53fa00$07fbee00$@poghosyan@humanbraindynamics.com> Message-ID: <4F990BA9.5030709@donders.ru.nl> Dear Vahe, thanks for your elaborate feedback. Of course, we are working hard to make FieldTrip more intuitive and user-friendly. We are quite aware that there are lot of things which are suboptimal, some of them that you also pointed out. Here's my comments on your points: > 1. I understand that fieldtrip is a data analysis toolbox, however the > results of the analysis need to be visualized. I find the fieldtrip > visualization functions, especially of the source analysis results (e.g. > ft_sourceplot, ft_sourceinterpolate, ft_sourcemovie) inadequate. > My question is how do you usually visualize the results of the source > analysis? Do you write your own matlab functions, including font-ends to > fieldtrip plotting functions or you use other freely/commercially available > tools that can import fieldtrip structures or you are satisfied with what is > provided in the fieldtrip toolbox? What exactly do you find inadequate? The way the plots look like or the way you need to call the functions? I have to admit that plotting results in sourcespace is more complex than plotting in sensor space. This is simply because there are so many more options and parameters. The intention of FT is not to provide the user with an easy-to-click GUI which hides important options, but to require the user to think him-/herself about important options like downsampling, interpolation options, normalization, etc. (to answer your question on my behalf: I am satisfied, once I found out how to plot - which took some time). > 2. It seems that the documentation provided on the fieldtrip website is not > very up-to-date and the descriptions of many configuration options in the > *.m files are not documented. At the moment to understand all the available > configuration options, and what different functions are doing and how they > are implemented, I am debugging them step-by-step. > Short of debugging or every time asking questions in this list, is there > another way of getting information about all the available configuration > options for different fieldtrip functions and their implementation details? Yes, there is an overview other than what the help is showing: http://fieldtrip.fcdonders.nl/reference/index For a function overview: http://fieldtrip.fcdonders.nl/reference The function and configuration reference of the FieldTrip wiki is literally a collection of all the helps. Note that for some functions, there are undocumented functions (which has a reason), they are mostly hidden and explained in the comments below the help. We (will) try to make the naming consistent throughout FieldTrip, so that, once acquainted with the naming scheme, the cfg options should be self-explanatory. Can you point to a particular example where the cfg-options are not documented adequately? This is for us sometimes a bit hard to figure out, because we know FT already quite well and thus need to rely on feedback of new users. But if you have any questions how a certain function works, or about the algorithm behind, feel free to just write a mail to this list - that's what it is there for ;) > 3. I found some functions in the fieldtrip's SVN (trunc) version (on > googlecode), which are not available in the daily releases on the ftp server > (e.g. ft_surfacecheck). > Is it safe to use those functions (I understand that the toolbox is released > under GPL)? Sorry, I don't know as I have neither written nor used these functions. > 4. Are the measurement units used throughout fieldtrip functions basic SI > (International System of Units) units? More specifically, what are the units > of the inputs to ft_dipolesimulation (cfg.dip.signal, cfg.dip.amplitude)? > Are they A*m or nA*m or something else? What are the units of the output > from the minimumnormestimate? A/m? I also cannot be of much help here, but as far as I know unit declaration are a consistent problem throughout FieldTrip, and currently we are working on restructuring the code and making this clearer. I would be tempted to say that the unit is a 'what-you-put-in-comes-out', i.e. if your data is measured in nA and the distance measured in cm, then the unit will be nA*cm. But, I don't know exactly. You can try to search the FieldTrip wiki for 'units' or any related search term, but I am afraid that most pages will be rather a collection of To-Dos for/from one of us. Maybe mire helpful might be this to search in the mailinglist for old posts on units (I couldn't find any, sorry)" http://fieldtrip.fcdonders.nl/discussion_list I hope Robert or Jan-Mathijs (currently on vacation) can give you more elaborate feedback on the last two question of yours. Best, Jörn > > > Thanks in advance > > Vahe Poghosyan, Ph.D. > Senior Scientist > Lab. for Human Brain Dynamics > AAI Scientific Cultural Services Ltd. > http://aaiscs.com/LHBD/ > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From Elena.Orekhova at neuro.gu.se Thu Apr 26 11:20:05 2012 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 26 Apr 2012 09:20:05 +0000 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org> <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se>, Message-ID: <32CC77C0C8A7AD4B9410934642608E1F25391E36@exchccr1.neuro.gu.se> Indeed it works OK for the latest version. Thank you! Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Roemer van der Meij [r.vandermeij at donders.ru.nl] Sent: Thursday, April 26, 2012 10:13 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] Error -> ft_databrowser Hi Elena, >From the looks of it you are using an old version of FieldTrip. Could you download the latest version and see if the problem persists? Best, Roemer On Thu, Apr 26, 2012 at 12:04 AM, Elena Orekhova > wrote: Hi I encounted the same problem with ft_databrowser: ************* fetching artifacts... Error using ft_fetch_data (line 57) data does not contain a consistent trial definition, fetching data is not possible Error in ft_databrowser>redraw_cb (line 1159) art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); Error in ft_databrowser (line 535) redraw_cb(h); **************** The same data works OK with [data] = ft_rejectvisual(cfg, data) I have: MacOS 10.6.8 MATLAB 7.13.0.564 (R2011b) Matlab re-installation did not help in my case. I would be grateful for any tips. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] Sent: Wednesday, March 07, 2012 6:55 PM To: Email discussion list for the FieldTrip project Cc: fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] Error -> ft_databrowser Hi Michael, I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution. But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution. Mehmet ----- Original Message ----- From: "Epstein, Michael" > Date: Wednesday, March 7, 2012 11:29 am Subject: Re: [FieldTrip] Error -> ft_databrowser To: fieldtrip at donders.ru.nl > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list. > > -Michael > > > ________________________________ > Dear Fieldtrippers, > > > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? > > > fieldtrip version 20120130, matlab version R2010a, operating system windows 7. > > > Thanks in advance for any suggestions. > > > > ??? Error using ==> ft_fetch_data at 57 > data does not contain a consistent trial definition, fetching data is not > possible > > > Error in ==> ft_databrowser>redraw_cb at 1159 > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); > > > Error in ==> ft_databrowser at 535 > redraw_cb(h); > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > _______________________________________________ > 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 -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From bibi.raquel at gmail.com Thu Apr 26 14:30:14 2012 From: bibi.raquel at gmail.com (Raquel Bibi) Date: Thu, 26 Apr 2012 08:30:14 -0400 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <4F99052C.1010508@donders.ru.nl> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org> <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> <4F99052C.1010508@donders.ru.nl> Message-ID: <6FA6AC40-1549-475F-93C3-80681B6BDAF5@gmail.com> Another way of knowing sample information is to include it again in the trl definition of your trial function so that the 4th ( any column after the first three) column reads event(i).sample. The information will always be available in the trialinfo field of the data. Regards, Raquel Sent from my iPhone On Apr 26, 2012, at 4:19 AM, "Jörn M. Horschig" wrote: > Hi Elena, > > most likely your data has trials with overlapping sample points. Unfortunately, the databrowser does not support this, or to be more specific ft_fetch_data does not support this. The reason for this is that a specific segment in time is defined twice in your data, and it is not clear what segment it is you would like to look at (due to filter artifacts and other preprocessing steps, the data will most likely have different values for the same sample points). For non-continuous data (already preprocessed data), it should be able to implement this nonetheless, but that's on our todo list. The best way for now is to call ft_redefinetrial and cut out the overlapping segments. > > You could also hack your way around this by removing data.sampleinfo. FieldTrip will then make up arbitrary, meaningless sample numbers. Keep in mind that we do not recommend this though. There is no way that the reconstructed sample numbers can be traced back to your original data! (well... if your programming skills are reasonable enough, it is possible, but that requires some further hacking, and a lot of effort). > > Best, > Jörn > > On 4/26/2012 12:04 AM, Elena Orekhova wrote: >> >> Hi >> I encounted the same problem with ft_databrowser: >> >> ************* >> fetching artifacts... Error using ft_fetch_data (line 57) >> data does not contain a consistent trial definition, fetching data is not >> possible >> >> Error in ft_databrowser>redraw_cb (line 1159) >> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', >> endsample); >> >> Error in ft_databrowser (line 535) >> redraw_cb(h); >> **************** >> >> The same data works OK with >> [data] = ft_rejectvisual(cfg, data) >> >> I have: >> MacOS 10.6.8 >> MATLAB 7.13.0.564 (R2011b) >> >> Matlab re-installation did not help in my case. >> I would be grateful for any tips. >> >> Elena >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] >> Sent: Wednesday, March 07, 2012 6:55 PM >> To: Email discussion list for the FieldTrip project >> Cc: fieldtrip at donders.ru.nl >> Subject: Re: [FieldTrip] Error -> ft_databrowser >> >> Hi Michael, >> >> >> I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. >> >> >> just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution. >> >> >> But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution. >> >> >> Mehmet >> >> >> >> >> >> ----- Original Message ----- >> From: "Epstein, Michael" >> Date: Wednesday, March 7, 2012 11:29 am >> Subject: Re: [FieldTrip] Error -> ft_databrowser >> To: fieldtrip at donders.ru.nl >> >> > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list. >> > >> > -Michael >> > >> > >> > >> > Dear Fieldtrippers, >> > >> > >> > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? >> > >> > >> > fieldtrip version 20120130, matlab version R2010a, operating system windows 7. >> > > > _______________________________________________ > 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 r.oostenveld at donders.ru.nl Thu Apr 26 23:35:31 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 26 Apr 2012 23:35:31 +0200 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: References: Message-ID: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> Hi Juan You should indeed have the data and the atlas in the same coordinate system (e.g. MNI). They don't need to have the same resolution. best Robert On 25 Apr 2012, at 16:39, Juan Pablo Neira wrote: > Hello, > > I would like to know if it is possible to use the ft_sourceplot > function with an individual MRI (coordsys: ctf) and an Atlas > > A tried to use one atlas from the Faq "aal_MNI_V4.img". After > ft_prepare_atlas the coordinate system was coord:mni. > > When I used the ft_sourceplot function (ortho method), there were some > warnings about labels not found and points outside the atlas, but I > always clicked in inside my MRI. Should I have my MRI and the atlas > in the same coordinate system (mni)? > > Regards, > > Juan Pablo Neira Vesga > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From anokhina at psychiatry.wustl.edu Thu Apr 26 23:38:05 2012 From: anokhina at psychiatry.wustl.edu (Anokhin, Andrey) Date: Thu, 26 Apr 2012 21:38:05 +0000 Subject: [FieldTrip] POSTDOC POSITION Message-ID: A postdoctoral training position is available in the Department of Psychiatry at Washington University School of Medicine. The successful candidate will participate in an interdisciplinary research program linking genetics, brain function, and behavior in order to understand the etiology of addiction and related characteristics such as impulsivity and reward dysregulation. We are seeking a psychophysiologist/neuroscientist/biomedical engineer with a strong background in the analysis of EEG, ERP, and/or fMRI data. This position is available within National Institute on Drug Abuse funded Institutional National Research Service Award to support multi-disciplinary training in drug abuse (including nicotine and tobacco dependence) research. The primary focus of this position will be on advanced analysis of brain electrophysiology and fMRI data obtained in large genetically informative samples (twins, genotyping data). The overall goal of his research is to investigate brain mechanisms mediating genetic influences on individual differences in self-regulation of behavior, including inhibitory control, performance monitoring, decision making, and reinforcement learning. The candidate will have opportunity to interact with multi-disciplinary faculty and obtain research training in different areas including statistical/quantitative, molecular and genetic epidemiologic, clinical and neuroscience aspects of research on substance use disorders. The position is available immediately, and applications will be accepted until the position is filled. Washington University in St. Louis is an Affirmative Action/Equal Opportunity Employer. To apply, please contact Andrey Anokhin (Andrey at wustl.edu). ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jpnv2006 at gmail.com Fri Apr 27 09:53:03 2012 From: jpnv2006 at gmail.com (Juan Pablo Neira) Date: Fri, 27 Apr 2012 09:53:03 +0200 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> References: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> Message-ID: Thank you for your help, But is there any possibility of not using an MNI (average) brain and take advantage of the atlas.? We are working with individual MRIs and we do not want to visualize results in the MNI brain. We could build an atlas, based on our MRI, with other toolbox. But now we would like to use this atlas in the ft_sourceplot and ft_volumelookup functions. Thanks in advance, Juan Pablo Neira On Thu, Apr 26, 2012 at 11:35 PM, Robert Oostenveld wrote: > Hi Juan > > You should indeed have the data and the atlas in the same coordinate system (e.g. MNI). They don't need to have the same resolution. > > best > Robert > > > On 25 Apr 2012, at 16:39, Juan Pablo Neira wrote: > >> Hello, >> >> I would like to know if it is possible to use the ft_sourceplot >> function with an individual MRI (coordsys: ctf) and an Atlas >> >> A tried to use one atlas from the Faq "aal_MNI_V4.img".  After >> ft_prepare_atlas the coordinate system was coord:mni. >> >> When I used the ft_sourceplot function (ortho method), there were some >> warnings about labels not found and points outside the atlas, but I >> always clicked in inside my MRI.  Should I have my MRI and the atlas >> in the same coordinate system (mni)? >> >> Regards, >> >> Juan Pablo Neira Vesga >> _______________________________________________ >> 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 Elena.Orekhova at neuro.gu.se Fri Apr 27 11:07:18 2012 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 27 Apr 2012 09:07:18 +0000 Subject: [FieldTrip] ft_volumereslice problem Message-ID: <32CC77C0C8A7AD4B9410934642608E1F25391F48@exchccr1.neuro.gu.se> Hi, I try to reslice MRI from [157 204 203] to [256 256 256] I do: cfg = []; cfg.dim = [256 256 256]; mri_resl = ft_volumereslice(cfg, mri); but I get the error (see below) I use latest FT version with Mac OS 10.6.8 and Matlab 7.13.0.564 (R2011b) Thanks in advance Elena ********************* the input is volume data with dimensions [157 204 203] reslicing from [157 204 203] to [256 256 256] the input is volume data with dimensions [157 204 203] the input is volume data with dimensions [256 256 256] 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 (line 467) ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ft_sourceinterpolate (line 376) av( sel) = my_interpn(fv, ax(sel), ay(sel), az(sel), cfg.interpmethod, cfg.feedback); Error in ft_volumereslice (line 147) reslice = ft_sourceinterpolate(tmpcfg, mri, reslice); -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuvharpaz at gmail.com Fri Apr 27 18:02:35 2012 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Fri, 27 Apr 2012 19:02:35 +0300 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: References: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> Message-ID: Dear Juan Pablo Neira I think what has to be done in this case is first to transfer the MRI to MNI space following steps described here. http://fieldtrip.fcdonders.nl/development/minimum_norm_estimate_new?s[]=mri&s[]=mni then you use the transformation in reverse on the atlas so you end up with an MNI atlas reshaped according to the individual MRI. then you can set sourceplot to use the atlas and give you names of regions when using the plot (ortho mode) interactively. you can also generate masks to color regions etc. I haven't done it but it should be possible. Yuval On 27 April 2012 10:53, Juan Pablo Neira wrote: > Thank you for your help, > > But is there any possibility of not using an MNI (average) brain and > take advantage of the atlas.? We are working with individual MRIs and > we do not want to visualize results in the MNI brain. > > We could build an atlas, based on our MRI, with other toolbox. But > now we would like to use this atlas in the ft_sourceplot and > ft_volumelookup functions. > > Thanks in advance, > > Juan Pablo Neira > > On Thu, Apr 26, 2012 at 11:35 PM, Robert Oostenveld > wrote: > > Hi Juan > > > > You should indeed have the data and the atlas in the same coordinate > system (e.g. MNI). They don't need to have the same resolution. > > > > best > > Robert > > > > > > On 25 Apr 2012, at 16:39, Juan Pablo Neira wrote: > > > >> Hello, > >> > >> I would like to know if it is possible to use the ft_sourceplot > >> function with an individual MRI (coordsys: ctf) and an Atlas > >> > >> A tried to use one atlas from the Faq "aal_MNI_V4.img". After > >> ft_prepare_atlas the coordinate system was coord:mni. > >> > >> When I used the ft_sourceplot function (ortho method), there were some > >> warnings about labels not found and points outside the atlas, but I > >> always clicked in inside my MRI. Should I have my MRI and the atlas > >> in the same coordinate system (mni)? > >> > >> Regards, > >> > >> Juan Pablo Neira Vesga > >> _______________________________________________ > >> 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 > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.N.Maijers at student.ru.nl Sat Apr 28 16:01:25 2012 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Sat, 28 Apr 2012 16:01:25 +0200 Subject: [FieldTrip] Problem in ft_timelockstatistics() phase Message-ID: <20120428160125.521cf366@sander-H57M-USB3> Hi, I am trying to rework a small FieldTrip experiment I did last year (reproduction of larger experiment done by Irina Simanova). Calling ft_timelockstatistics() on two ERP data partitions results in an error: "Undefined function 'fieldnames' for input arguments of type 'cell'." I'm running FieldTrip under MATLAB R2011b 64-bit on Linux. I see a possible cause of the problem, in that these data we pre-analysed with ft_timelockanalysis() a year ago, or longer. I read them from parts of the data set I was supplied with. Maybe there have been breaking changes to this function in the meantime? The cfg struct that I pass as parameter seems in line with the current documentation, though. LOG: >> main() data_set_location = /media/SAMSUNG/0,data_set/EEG/0 MATLAB output_dir = /tmp/EEG Data set part file: timelock10_lp Data set part file: timelock11_lp CONTRAST [class 1, size = 220]: participant timelock10_lp on condition avg_anm_aud_lp [class 2, size = 224]: participant timelock10_lp on condition avg_tls_aud_lp cfg method: 'crossvalidate' latency: [0 0.7000] channel: {1x60 cell} nfolds: 5 mva: {2x1 cell} design: [444x1 double] class_1_data__struct avg: [62x501 double] var: [62x501 double] fsample: 500 time: [1x501 double] dof: [62x501 double] label: {62x1 cell} trial: [220x62x501 double] dimord: 'rpt_chan_time' cfg: [1x1 struct] class_2_data__struct avg: [62x501 double] var: [62x501 double] fsample: 500 time: [1x501 double] dof: [62x501 double] label: {62x1 cell} trial: [224x62x501 double] dimord: 'rpt_chan_time' cfg: [1x1 struct] selected 60 channels selected 351 time bins selected 1 frequency bins using "ft_statistics_crossvalidate" for the statistical testing fixing random number generator for reproducibility creating sample indices using 5-fold cross-validation validating fold 1 of 5 for 1 datasets validating fold 2 of 5 for 1 datasets validating fold 3 of 5 for 1 datasets validating fold 4 of 5 for 1 datasets validating fold 5 of 5 for 1 datasets Undefined function 'fieldnames' for input arguments of type 'cell'. Error in ft_statistics_crossvalidate (line 84) fn = fieldnames(stat.model{1}); Error in statistics_wrapper (line 298) [stat] = statmethod(cfg, dat, design); Error in ft_timelockstatistics (line 110) [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Error in main/modeling (line 203) stat = ft_timelockstatistics(cfg, class_1_datastruct, class_2_datastruct); Error in main/statistics (line 225) stat = modeling(data_set, method, obj_class_1_and_2); Error in main/ERP_experiment (line 374) stats = statistics(data_set, contrasts, method); Error in main (line 401) stats_x = ERP_experiment(data_set_location, 'RR', output_dir) Any suggestions would be welcom! Kind regards, Sander Maijers From hamzaf at sabanciuniv.edu Sat Apr 28 18:08:16 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 28 Apr 2012 19:08:16 +0300 Subject: [FieldTrip] Error in a given example Message-ID: Hello, While trying to understand the ft_deinetrial I tried the following example from the page ( http://fieldtrip.fcdonders.nl/tutorial/preprocessing) cfg = []; cfg.dataset = 'Subject01.ds'; cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for fully incongruent (FIC). cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 2; % in seconds cfg = ft_definetrial(cfg); I get the following error readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) reading the events from 'Subject01.ds\Subject01.res4' readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) ??? Error using ==> ft_definetrial at 185 no trials were defined, see FT_DEFINETRIAL for help I wonder why? Best -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sat Apr 28 18:12:20 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 28 Apr 2012 19:12:20 +0300 Subject: [FieldTrip] cfg.trialdef.eventtype Message-ID: Hello, I wonder what should be written after in this variable (cfg.trialdef.eventtype) ? and what is meant by '?' ? Best -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Apr 29 07:01:00 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 29 Apr 2012 08:01:00 +0300 Subject: [FieldTrip] Error in a given example In-Reply-To: References: Message-ID: Hello, I discovered the solution, I should but the full path of 'Subject01.ds'. I did not saw that in the tutorial but I found that in the previous messages. Best On Sat, Apr 28, 2012 at 7:08 PM, Hamza Fawzi Altakroury (Student) < hamzaf at sabanciuniv.edu> wrote: > Hello, > > While trying to understand the ft_deinetrial > > I tried the following example from the page ( > http://fieldtrip.fcdonders.nl/tutorial/preprocessing) > > cfg = []; > cfg.dataset = 'Subject01.ds'; > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for > fully incongruent (FIC). > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 2; % in seconds > cfg = ft_definetrial(cfg); > > I get the following error > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > reading the events from 'Subject01.ds\Subject01.res4' > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > ??? Error using ==> ft_definetrial at 185 > no trials were defined, see FT_DEFINETRIAL for help > > > I wonder why? > > Best > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Apr 29 07:07:55 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 29 Apr 2012 08:07:55 +0300 Subject: [FieldTrip] cfg.trialdef.eventtype In-Reply-To: References: Message-ID: Sorry in being rush in asking questions, I found the solution By typing '?' we get info about the file, one of them the eventtype. Hamza On Sat, Apr 28, 2012 at 7:12 PM, Hamza Fawzi Altakroury (Student) < hamzaf at sabanciuniv.edu> wrote: > Hello, > > I wonder what should be written after in this variable > (cfg.trialdef.eventtype) ? > and what is meant by '?' ? > > Best > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From vitoria.piai at gmail.com Sun Apr 29 15:19:16 2012 From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=) Date: Sun, 29 Apr 2012 15:19:16 +0200 Subject: [FieldTrip] error in ft_databrowser Message-ID: <4F9D3FD4.2050301@gmail.com> Hi there, I'm getting the following error when trying ft_databrowser on the output of ft_componentanalysis (ft_topoplotIC on the same dataset works fine): ??? Error using ==> keyvalcheck at 77 the input argument 'tag' is forbidden Error in ==> ft_plot_text at 44 keyvalcheck(varargin, 'optional', {'hpos', 'vpos', 'width', 'height', 'hlim', 'vlim', 'Color', .... Error in ==> ft_databrowser>redraw_cb at 1346 ft_plot_text(labelx(laysel), labely(laysel), opt.hdr.label(chanindx(i)), 'tag', 'timecourse', 'HorizontalAlignment', 'right'); Error in ==> ft_databrowser at 548 redraw_cb(h); I'm using the ft_databrowser version updated on the 25th of April. Is this a bug? Thank you, Vitória -- ** Please consider the environment - do you really need to print? ** From veniero at med.unibs.it Sun Apr 1 19:03:51 2012 From: veniero at med.unibs.it (veniero at med.unibs.it) Date: Sun, 1 Apr 2012 19:03:51 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: References: Message-ID: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> Dear FieldTrip users, I'm trying to run a cluster-based permutation tests on time-frequency data. I get the result: found 1 positive clusters in observed data found 0 negative clusters in observed data, but I'm not able to use clusterplot because if the following error: ??? Error using ==> ft_clusterplot at 171 no clusters present with a p-value lower than the specified alpha, nothing to plot Is this possible? Maybe it's just a trivial question. Many thanks, Mimma From Lilla.Magyari at mpi.nl Sun Apr 1 19:58:55 2012 From: Lilla.Magyari at mpi.nl (Magyari, Lilla) Date: Sun, 01 Apr 2012 19:58:55 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> Message-ID: <4F78975F.10607@mpi.nl> Dear Mimma, I am not exactly sure about what "found 1 positive clusters in observed data found 0 negative clusters in observed data" means but I would guess that it means only the number of clusters that you got after your test. This doesn't mean that these clusters are significant. Have you checked in the output of ft_freqstatistics if you have any significant clusters? (You can check it in the field stat.posclusters or stat.negclusters). Hope this helps Lilla veniero at med.unibs.it wrote: > Dear FieldTrip users, > I'm trying to run a cluster-based permutation tests on time-frequency > data. I get the result: > found 1 positive clusters in observed data found 0 negative clusters in > observed data, but I'm not able to use clusterplot because if the > following error: > ??? Error using ==> ft_clusterplot at 171 > no clusters present with a p-value lower than the specified alpha, nothing > to plot > > Is this possible? Maybe it's just a trivial question. > > Many thanks, > Mimma > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Mon Apr 2 09:24:35 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 02 Apr 2012 09:24:35 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> Message-ID: <4F795433.6000007@donders.ru.nl> Dear Mimma, Most likely, you specified a different alpha when calling ft_freqstatistics than when calling ft_clusterplot. Could you paste the cfg settings for both functions here, so that we can try to track down where exactly this error comes from? Best, Jörn On 4/1/2012 7:03 PM, veniero at med.unibs.it wrote: > Dear FieldTrip users, > I'm trying to run a cluster-based permutation tests on time-frequency > data. I get the result: > found 1 positive clusters in observed data found 0 negative clusters in > observed data, but I'm not able to use clusterplot because if the > following error: > ??? Error using ==> ft_clusterplot at 171 > no clusters present with a p-value lower than the specified alpha, nothing > to plot > > Is this possible? Maybe it's just a trivial question. > > Many thanks, > Mimma > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From veniero at med.unibs.it Mon Apr 2 11:11:30 2012 From: veniero at med.unibs.it (veniero at med.unibs.it) Date: Mon, 2 Apr 2012 11:11:30 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <4F795433.6000007@donders.ru.nl> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> <4F795433.6000007@donders.ru.nl> Message-ID: <3a64b4c61afcca813c6c64d8fed5a5b1.squirrel@mail.med.unibs.it> Dear Jörn, I'm copmparing two conditions gavgM1_post5 and gavgM1_pre5. Here the settings I'm using: cfg = []; cfg.channel = {'EEG'}; cfg.layout= 'biosemi64.lay'; cfg.latency = 'all'; cfg.frequency = [20 20]; cfg.avgeoverfreq = 'yes'; cfg.method = 'montecarlo'; cfg.statistic = '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; design = zeros(1,size(gavgM1_post5.powspctrm,1) + size(gavgM1_pre5.powspctrm,1)); design(1,1:size(gavgM1_post5.powspctrm,1)) = 1; design(1,(size(gavgM1_post5.powspctrm,1)+1):(size(gavgM1_post5.powspctrm,1)+... size(gavgM1_pre5.powspctrm,1))) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_freqstatistics(cfg, gavgM1_post5, gavgM1_pre5); For the clusterplot: stat.raweffect = gavgM1_post5.powspctrm - gavgM1_pre5.powspctrm; cfg = []; cfg.alpha = 0.025; cfg.zparam = 'raweffect'; cfg.zlim = [-1 1]; cfg.layout = 'biosemi64.lay'; ft_clusterplot(cfg, stat); Many thanks, Mimma > Dear Mimma, > > Most likely, you specified a different alpha when calling > ft_freqstatistics than when calling ft_clusterplot. Could you paste the > cfg settings for both functions here, so that we can try to track down > where exactly this error comes from? > > Best, > Jörn > > > On 4/1/2012 7:03 PM, veniero at med.unibs.it wrote: >> Dear FieldTrip users, >> I'm trying to run a cluster-based permutation tests on time-frequency >> data. I get the result: >> found 1 positive clusters in observed data found 0 negative clusters in >> observed data, but I'm not able to use clusterplot because if the >> following error: >> ??? Error using ==> ft_clusterplot at 171 >> no clusters present with a p-value lower than the specified alpha, >> nothing >> to plot >> >> Is this possible? Maybe it's just a trivial question. >> >> Many thanks, >> Mimma >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From jm.horschig at donders.ru.nl Mon Apr 2 16:34:16 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 02 Apr 2012 16:34:16 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <3a64b4c61afcca813c6c64d8fed5a5b1.squirrel@mail.med.unibs.it> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> <4F795433.6000007@donders.ru.nl> <3a64b4c61afcca813c6c64d8fed5a5b1.squirrel@mail.med.unibs.it> Message-ID: <4F79B8E8.3010807@donders.ru.nl> Dear Mimma, okay, I see. First of all, behaviour of ft_clusterplot is perfectly fine. The way ft_freqstatistics works is that it first computes a t-value for all datapoints, and then computes clusters in time, space and/or frequency, depending on whether you set cfg.avgovertime or cfg.avgoverfreq to 'yes'. All these t-values are uncorrected t-values, therefore the reliability of the statistics will suffer from multiple comparisons (as a side note, this might be an interesting read: http://www.danielbor.com/dilemma-weak-neuroimaging/ ). The test you specified will compute permutations of your data and then compare the actual observed t-value (as described above) with the distribution of the random permutations. Only if your observation lies in the significant head or tail of the permutation distribution (as defined by the first/last 2.5%, i.e. your alpha value), the found cluster will be considered to be significant. Thus, even if the t-value might be significant, it will be corrected thereafter by the cluster permutation. For a detailled description, I would advise you to read this paper on which the whole method is based on: http://www.sciencedirect.com/science/article/pii/S016502700700074X In your data, the observed cluster is not significant anymore after the cluster-based correction. You can also check it by typing stat.posclusters.prob, which will return a value > 0.025 Hope I described it somewhat comprehensible. Best, Jörn On 4/2/2012 11:11 AM, veniero at med.unibs.it wrote: > Dear Jörn, > I'm copmparing two conditions gavgM1_post5 and gavgM1_pre5. > Here the settings I'm using: > > cfg = []; > cfg.channel = {'EEG'}; > cfg.layout= 'biosemi64.lay'; > cfg.latency = 'all'; > cfg.frequency = [20 20]; > cfg.avgeoverfreq = 'yes'; > cfg.method = 'montecarlo'; > cfg.statistic = '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; > design = zeros(1,size(gavgM1_post5.powspctrm,1) + > size(gavgM1_pre5.powspctrm,1)); > design(1,1:size(gavgM1_post5.powspctrm,1)) = 1; > design(1,(size(gavgM1_post5.powspctrm,1)+1):(size(gavgM1_post5.powspctrm,1)+... > size(gavgM1_pre5.powspctrm,1))) = 2; > cfg.design = design; > cfg.ivar = 1; > > [stat] = ft_freqstatistics(cfg, gavgM1_post5, gavgM1_pre5); > > > For the clusterplot: > stat.raweffect = gavgM1_post5.powspctrm - gavgM1_pre5.powspctrm; > > cfg = []; > cfg.alpha = 0.025; > cfg.zparam = 'raweffect'; > cfg.zlim = [-1 1]; > cfg.layout = 'biosemi64.lay'; > ft_clusterplot(cfg, stat); > > Many thanks, > Mimma > > > >> Dear Mimma, >> >> Most likely, you specified a different alpha when calling >> ft_freqstatistics than when calling ft_clusterplot. Could you paste the >> cfg settings for both functions here, so that we can try to track down >> where exactly this error comes from? >> >> Best, >> Jörn >> >> >> On 4/1/2012 7:03 PM, veniero at med.unibs.it wrote: >>> Dear FieldTrip users, >>> I'm trying to run a cluster-based permutation tests on time-frequency >>> data. I get the result: >>> found 1 positive clusters in observed data found 0 negative clusters in >>> observed data, but I'm not able to use clusterplot because if the >>> following error: >>> ??? Error using ==> ft_clusterplot at 171 >>> no clusters present with a p-value lower than the specified alpha, >>> nothing >>> to plot >>> >>> Is this possible? Maybe it's just a trivial question. >>> >>> Many thanks, >>> Mimma >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> _______________________________________________ >> 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 -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From biomag.network.practical at gmail.com Mon Apr 2 17:12:03 2012 From: biomag.network.practical at gmail.com (Biomag Networks Satellite 25 Aug 2012) Date: Mon, 2 Apr 2012 17:12:03 +0200 Subject: [FieldTrip] Biomag Satellite Announcement: Open for Registration In-Reply-To: References: Message-ID: Dear Biomag community, We are pleased to announce that registration is now open for the Biomag 2012 Satellite Workshop on *"Studying the brain as a network using MEG: practical considerations." * * * *Date:* August 25, 2012 *Time:* 09:00-18:00 *Location:* ICM, the new Brain Institute at Hôpital Pitié-Salpêtrière; 47 Boulevard de l'Hôpital, 75013 Paris *Purpose of this Satellite:* It is becoming increasingly important to study the working brain as network both in cognitive and clinical neuroscience. MEG provides an excellent opportunity to study the functional interactions between various brain regions. There are now multiple approaches and tools available for doing this. The aim of the proposed workshop is to elucidate practical approaches for studying brain connectivity using MEG. This will be done by a set of presentations in which basics of connectivity and source space analysis are introduced. Then follows presentations by various toolbox developers. The toolbox presenters will be asked to 1) outline conceptually the types of connectivity approaches their toolboxes allow for and 2) describe how it practically can be done. Finally we will discuss how various connectivity measures can be tested using standardized data sets. Target audience: The workshop is targeted towards the advanced clinical or cognitive MEG user with an interest in embracing state-of-the-art methods for functional connectivity. Please see the satellite website for more details. You may register here. The registration deadline is June 30, 2012. Please note that there is a small (~10 euro) fee to cover costs, which you may pay at the door. For any further questions, you may send an email to the organizers at: biomag.network.practical at gmail.com We look forward to seeing you on August 25, 2012! Best regards, Ole Jensen, Sarang Dalal, and Johanna Zumer -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Mon Apr 2 21:18:19 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Mon, 2 Apr 2012 15:18:19 -0400 Subject: [FieldTrip] beamformer results smaller than brain In-Reply-To: References: Message-ID: Thanks, Arjen and Gio, I played around with cfg.inwardshift during ft_sourceanalysis, and adjusting it to somewhere between .25 and .5 gives decent results (it was originally set to 1), i.e. good coverage with no shrinkage. I'm actually a little confused about why one might need cfg.inwardshift parameter... Assuming the segmentation into different tissue types goes correctly, is it best to set the inwardshift parameters as close to 0 as possible (or not specify), since we'd want to put dipoles ranging the whole volume of the brain? Thanks! Akiko On Thu, Mar 29, 2012 at 5:13 AM, Gio Piantoni wrote: > Hi Akiko, > > Your headmodel looks pretty good and your beamformer plot seems to > cover most of the gray matter. > > However, it's good to check the location of your dipoles in respect to > your headmodel. For example, you can plot the .pos field of your > leadfield. Something like: > > ft_plot_mesh(bnd(3), 'facealpha', .5) > hold on > plot3(lead.pos(:,1), lead.pos(:,2), lead.pos(:,3), '.') > > It might well be that your grid is too coarse and some dipoles just > happen to be over the edge of the brain. Remember that your > "beamformer_result.png" is just an interpolation of the values of this > dipole grid. > > You can either try to make your grid more refined (but remember that > your computation time will significantly increase). Or you can > manipulate the way dipoles are considered inside or outside the brain > with "inwardshift" for ft_prepare_leadfield (although I'd advise > against using a negative value as some dipoles might really end up > outside of your brain mesh, with some numerical instabilities). > Another option (the easiest) is to nudge your grid by, say, a few > millimeters, so that the parietal dipoles will be just inside the > brain mesh. > > HTH, > > Gio > > -- > Giovanni Piantoni, MSc > Dept. Sleep & Cognition > Netherlands Institute for Neuroscience > Meibergdreef 47 > 1105 BA Amsterdam (NL) > > +31 20 5665492 > gio at gpiantoni.com > www.gpiantoni.com > > On Thu, Mar 29, 2012 at 00:22, Akiko Ikkai wrote: > > Hi Fieldtrip users, > > > > I'm hoping that someone could give me advice on segmentation and > beamformer > > on EEG data. I have EEG data set based on 128 channel cap. Thanks to the > > help I got in mid-Feb, I'm now able to create a decent > > segmentation (seg_results image attached) and volume conduction model. > > However, when I run beamformer based on these models, resulting > beamforming > > image is often smaller than the brain (beamformer_result attached). > > Particularly posterior parietal and occipital map is NaN. > > > > I have tried going back to segmentation and expanded brain by > using imdilate > > after ft_volumesegment such as: > > > > newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original > brain > > tissue from segmentation > > > > seg2.brain = newbrain; > > > > seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6; > > > > and run ft_prepare_mesh_new on seg2. Of course, I have to make sure > there is > > no intersect between different tissue types, so using imdilate has > > limitation. > > > > Could someone explain why this shrinkage might be happening, and how I > could > > fix it? > > > > Thanks in advance! Akiko > > > > -- > > Akiko Ikkai, Ph.D. > > Postdoctoral Fellow > > Department of Psychological and Brain Sciences > > Johns Hopkins University > > Ames Hall, 3400 N. Charles St. > > Baltimore, MD 21218 > > > > > > > > _______________________________________________ > > 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 > -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.vandenieuwenhuijzen at fcdonders.ru.nl Wed Apr 4 10:16:43 2012 From: m.vandenieuwenhuijzen at fcdonders.ru.nl (Marieke van de Nieuwenhuijzen) Date: Wed, 4 Apr 2012 10:16:43 +0200 (CEST) Subject: [FieldTrip] sudden errors in ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot In-Reply-To: <279226386.170300.1333525161466.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <1735698454.171384.1333527403632.JavaMail.root@draco.zimbra.ru.nl> Dear all, I have a problem with my beamforming script. The functions ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot all crash with the same main error, namely ??? Reference to non-existent field 'nChans'. Error in ==> ft_senstype at 188 elseif isheader && input.nChans==1 && ~isempty(regexp(input.label{1}, '^csc')) Error in ==> ft_convert_units at 56 if ft_senstype(obj, 'meg') Error in ==> ft_prepare_sourcemodel at 604 %(or of course ft_volumereslice, ft_volumesegment or ft_sourceplot, depending on the function) mri = ft_convert_units(mri); The only difference is that ft_volumereslice has the additional error layer Error in ==> ft_checkdata at 402 data = ft_convert_units(data); The code I am using is: cfg =[]; cfg.mri= subject.MRI; cfg.grid.warpmni = 'yes'; cfg.grid.resolution = 10; %resolution = 10 mm grid = ft_prepare_sourcemodel(cfg); mri = ft_read_mri(cfg.mri); mri.coordsys='ctf'; mri=ft_volumereslice([],mri); cfg = []; cfg.coordsys = 'ctf'; segmentedmri = ft_volumesegment(cfg, mri); mri.brainmask = segmentedmri.gray+segmentedmri.white+segmentedmri.csf; cfg = []; cfg.funparameter = 'brainmask'; figure; ft_sourceplot(cfg, mri); The curious thing is that this exact same code worked without any errors last week, but this week I am getting those errors. I am using the latest version of fieldtrip, and run ft_defaults before starting the script (although it also crashed when I didn't do that; I only started running ft_defaults when I got these errors). The fact that all errors seem to stem from the same error in ft_senstype, that this code has worked without any problems until last week, and that ft_senstype has been updated last Friday makes me suspect some bug during that update, but I am not sure about that. Does anyone have an idea as to what might be the problem here? Best, Marieke From r.oostenveld at donders.ru.nl Wed Apr 4 12:53:03 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 4 Apr 2012 12:53:03 +0200 Subject: [FieldTrip] sudden errors in ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot In-Reply-To: <1735698454.171384.1333527403632.JavaMail.root@draco.zimbra.ru.nl> References: <1735698454.171384.1333527403632.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <3B2F1399-1110-4339-A6EA-13DE99B083E6@donders.ru.nl> Dear Marieke The recently introduced bug has been tracked down and fixed. See http://bugzilla.fcdonders.nl/show_bug.cgi?id=1405 Sorry for the inconvenience. Robert On 4 Apr 2012, at 10:16, Marieke van de Nieuwenhuijzen wrote: > Dear all, > > I have a problem with my beamforming script. The functions ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot all crash with the same main error, namely > > ??? Reference to non-existent field 'nChans'. > > Error in ==> ft_senstype at 188 > elseif isheader && input.nChans==1 && ~isempty(regexp(input.label{1}, '^csc')) > > Error in ==> ft_convert_units at 56 > if ft_senstype(obj, 'meg') > > Error in ==> ft_prepare_sourcemodel at 604 %(or of course ft_volumereslice, ft_volumesegment or ft_sourceplot, depending on the function) > mri = ft_convert_units(mri); > > The only difference is that ft_volumereslice has the additional error layer > > Error in ==> ft_checkdata at 402 > data = ft_convert_units(data); > > The code I am using is: > > cfg =[]; > cfg.mri= subject.MRI; > cfg.grid.warpmni = 'yes'; > cfg.grid.resolution = 10; %resolution = 10 mm > grid = ft_prepare_sourcemodel(cfg); > > mri = ft_read_mri(cfg.mri); > mri.coordsys='ctf'; > mri=ft_volumereslice([],mri); > > cfg = []; > cfg.coordsys = 'ctf'; > segmentedmri = ft_volumesegment(cfg, mri); > > mri.brainmask = segmentedmri.gray+segmentedmri.white+segmentedmri.csf; > cfg = []; > cfg.funparameter = 'brainmask'; > figure; > ft_sourceplot(cfg, mri); > > The curious thing is that this exact same code worked without any errors last week, but this week I am getting those errors. > > I am using the latest version of fieldtrip, and run ft_defaults before starting the script (although it also crashed when I didn't do that; I only started running ft_defaults when I got these errors). > > The fact that all errors seem to stem from the same error in ft_senstype, that this code has worked without any problems until last week, and that ft_senstype has been updated last Friday makes me suspect some bug during that update, but I am not sure about that. > > Does anyone have an idea as to what might be the problem here? > > Best, > Marieke > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Wed Apr 4 12:56:09 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 4 Apr 2012 12:56:09 +0200 Subject: [FieldTrip] SPM-DCM course at the BIOMAG in Paris References: Message-ID: <60FE20C9-66C1-4682-B896-313A7E38E883@donders.ru.nl> Dear FieldTrip users Jean Daunizeau and Jeremie Mattout are organizing a DCM educational course at the BIOMAG conference in Paris in August. The registration for the course has just opened. Please see the attached flyer for further details best regards, Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Announcement_DCMcourse2012.pdf Type: application/pdf Size: 204397 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Fri Apr 6 20:05:56 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Fri, 6 Apr 2012 12:05:56 -0600 Subject: [FieldTrip] Removing channels from processed data Message-ID: Dear FieldTrippers, I'm using fieldtrip-20120405. I'm trying to remove a "bad" channel from a subject's processed data (output of ft_timelockanalysis and ft_freqanalysis). I've found the function ft_selectdata (which runs ft_selectdata_new), but when I define my cfg to remove the bad channel (cfg.channels={'all','-E59'}) and use the function, it also removes the dimord field which subsequent ft_* functions need (e.g., ft_multiplotER, ft_timelockgrandaverage). I could manually remove the channel, but I was hoping for a ft_* function that would modify the label field automatically. Manually replacing the channel with NaNs does not seem to be a solution because when I use ft_singleplotER to plot data from a ROI (i.e., multiple channels in a region) that includes this now-all-NaNs channel, nothing gets plotted (meaning a mean, and not a nanmean, function gets used to average over the ROI), so I fear the same thing will happen with other functions (e.g., ft_timelockstatistics). I also know I can use ft_rejectvisual early on in my processing, but I don't want to re-process my data (and I'm not currently using FT for artifact detection). So my question is: what's the best FieldTrip function-based way to remove a channel? Thanks, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Apr 6 20:50:11 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 6 Apr 2012 20:50:11 +0200 Subject: [FieldTrip] Removing channels from processed data In-Reply-To: References: Message-ID: <87CFA1EE-23A1-40B4-AF30-F96F63838BE7@donders.ru.nl> Dear Matt, It seems you have stumbled on some code that is still a bit under development, and apparently not really stable. ft_selectdata should be able to do the trick for you, but I suspect a bug in ft_selectdata_new, so I'd try ft_selectdata_old instead. To achieve this, you need to do something like this: selchan = ft_channelselection({'all' '-E59'}, data.label); data = ft_selectdata(data, 'channel', selchan); % notice the function's input now with key-value pairs, rather than a cfg. We hope to find some time to improve the ft_selectdata_new soon. For the time being, could you file a bug on this issue on our bugzilla website? (www.bugzilla.fcdonders.nl) Cheers, JM On Apr 6, 2012, at 8:05 PM, Matt Mollison wrote: > Dear FieldTrippers, > > I'm using fieldtrip-20120405. I'm trying to remove a "bad" channel from a subject's processed data (output of ft_timelockanalysis and ft_freqanalysis). I've found the function ft_selectdata (which runs ft_selectdata_new), but when I define my cfg to remove the bad channel (cfg.channels={'all','-E59'}) and use the function, it also removes the dimord field which subsequent ft_* functions need (e.g., ft_multiplotER, ft_timelockgrandaverage). > > I could manually remove the channel, but I was hoping for a ft_* function that would modify the label field automatically. Manually replacing the channel with NaNs does not seem to be a solution because when I use ft_singleplotER to plot data from a ROI (i.e., multiple channels in a region) that includes this now-all-NaNs channel, nothing gets plotted (meaning a mean, and not a nanmean, function gets used to average over the ROI), so I fear the same thing will happen with other functions (e.g., ft_timelockstatistics). I also know I can use ft_rejectvisual early on in my processing, but I don't want to re-process my data (and I'm not currently using FT for artifact detection). > > So my question is: what's the best FieldTrip function-based way to remove a channel? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Fri Apr 6 21:34:56 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Fri, 6 Apr 2012 13:34:56 -0600 Subject: [FieldTrip] Removing channels from processed data In-Reply-To: <87CFA1EE-23A1-40B4-AF30-F96F63838BE7@donders.ru.nl> References: <87CFA1EE-23A1-40B4-AF30-F96F63838BE7@donders.ru.nl> Message-ID: Thanks, JM. That seems to solve it. Bug submitted: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1409 Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Fri, Apr 6, 2012 at 12:50 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Matt, > > It seems you have stumbled on some code that is still a bit under > development, and apparently not really stable. > > ft_selectdata should be able to do the trick for you, but I suspect a bug > in ft_selectdata_new, so I'd try ft_selectdata_old instead. > > To achieve this, you need to do something like this: > > selchan = ft_channelselection({'all' '-E59'}, data.label); > data = ft_selectdata(data, 'channel', selchan); % notice the function's > input now with key-value pairs, rather than a cfg. > > We hope to find some time to improve the ft_selectdata_new soon. For the > time being, could you file a bug on this issue on our bugzilla website? ( > www.bugzilla.fcdonders.nl) > > Cheers, > > JM > > > On Apr 6, 2012, at 8:05 PM, Matt Mollison wrote: > > Dear FieldTrippers, > > I'm using fieldtrip-20120405. I'm trying to remove a "bad" channel from a > subject's processed data (output of ft_timelockanalysis and > ft_freqanalysis). I've found the function ft_selectdata (which runs > ft_selectdata_new), but when I define my cfg to remove the bad channel > (cfg.channels={'all','-E59'}) and use the function, it also removes the > dimord field which subsequent ft_* functions need (e.g., ft_multiplotER, > ft_timelockgrandaverage). > > I could manually remove the channel, but I was hoping for a ft_* function > that would modify the label field automatically. Manually replacing the > channel with NaNs does not seem to be a solution because when I use > ft_singleplotER to plot data from a ROI (i.e., multiple channels in a > region) that includes this now-all-NaNs channel, nothing gets plotted > (meaning a mean, and not a nanmean, function gets used to average over the > ROI), so I fear the same thing will happen with other functions (e.g., > ft_timelockstatistics). I also know I can use ft_rejectvisual early on in > my processing, but I don't want to re-process my data (and I'm not > currently using FT for artifact detection). > > So my question is: what's the best FieldTrip function-based way to remove > a channel? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > 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 dashiel.munding at gmail.com Sun Apr 8 20:52:40 2012 From: dashiel.munding at gmail.com (Dashiel Munding) Date: Sun, 8 Apr 2012 20:52:40 +0200 Subject: [FieldTrip] Problem reading trials into ft_rejectvisual Message-ID: Hello all, I'm trying to figure out a way of reading only selected trials into analysis without running through ft_rejectvisual every time. I have a list of trials that I have already rejected, and the documentation (http://fieldtrip.fcdonders.nl/reference/ft_rejectvisual) says that I should be able to use cfg.trials as a 1xN vector to put in a list of those trials that I want to use : cfg.trials = 'all' or a selection given as a 1xN vector (default = 'all') I've tried various formats for this vector (I'm new to both MATLAB and fieldtrip, so this might be a simple solve) but I can't get a positive result. I know I can save out the variable and read it in again at a later date, but this seems like a very inefficient way of doing it if all I need is a list of numbers, instead of a 1.5gb .m file... Has anyone come across/solved this problem? Can anyone provide me with an example of the syntax fieldtrip is expecting? I've tried: cfg.trials = {'all' '-56', '-151', '-232', '-53'}; cfg.trials = {'1','2','3','4','5','6','7','8','9','10','46'}; cfg.trials = {1,2,3,4,5,6,7,8,9,10,46}; and some other efforts to no avail! Thanks in advance, and sorry for naivety! Dashiel From dashiel.munding at gmail.com Sun Apr 8 20:56:22 2012 From: dashiel.munding at gmail.com (Dashiel Munding) Date: Sun, 8 Apr 2012 20:56:22 +0200 Subject: [FieldTrip] Problem reading trials into ft_rejectvisual In-Reply-To: References: Message-ID: Thought an example of the error message I'm getting might be useful in diagnosing the problem. I would delve further but I'm not an experienced MATLAB user, so I don't think my investigation would be very fruitful! --- Error using subsindex Function 'subsindex' is not defined for values of class 'cell'. Error in selfromraw (line 11) data.trial = data.trial(selrpt); Error in ft_selectdata_old (line 544) data = selfromraw(data, 'rpt', selrpt); Error in ft_selectdata (line 45) [varargout{1:nargout}] = ft_selectdata_old(varargin{:}); Error in ft_rejectvisual (line 196) data = ft_selectdata(data, 'rpt', cfg.trials); On 8 April 2012 20:52, Dashiel Munding wrote: > Hello all, > > I'm trying to figure out a way of reading only selected trials into > analysis without running through ft_rejectvisual every time. I have a > list of trials that I have already rejected, and the documentation > (http://fieldtrip.fcdonders.nl/reference/ft_rejectvisual) says that I > should be able to use cfg.trials as a 1xN vector to put in a list of > those trials that I want to use : > > cfg.trials      = 'all' or a selection given as a 1xN vector (default = 'all') > > I've tried various formats for this vector (I'm new to both MATLAB and > fieldtrip, so this might be a simple solve) but I can't get a positive > result. I know I can save out the variable and read it in again at a > later date, but this seems like a very inefficient way of doing it if > all I need is a list of numbers, instead of a 1.5gb .m file... > > Has anyone come across/solved this problem? Can anyone provide me with > an example of the syntax fieldtrip is expecting? > > I've tried: > > cfg.trials = {'all' '-56', '-151', '-232', '-53'}; > > cfg.trials = {'1','2','3','4','5','6','7','8','9','10','46'}; > > cfg.trials = {1,2,3,4,5,6,7,8,9,10,46}; > > and some other efforts to no avail! > > Thanks in advance, and sorry for naivety! > > Dashiel From matt.mollison at gmail.com Sun Apr 8 21:17:31 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Sun, 8 Apr 2012 13:17:31 -0600 Subject: [FieldTrip] Problem reading trials into ft_rejectvisual In-Reply-To: References: Message-ID: Dashiel, You're using curly braces {} for trial indexing; this creates a cell array, which you don't want. Try using brackets [] to form a vector: cfg.trials = [1,2,3,4,5,6,7,8,9,10,46]; Check out http://www.mathworks.com/help/techdoc/ref/specialcharacters.htmlfor more matlab character syntax. Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Sun, Apr 8, 2012 at 12:56 PM, Dashiel Munding wrote: > Thought an example of the error message I'm getting might be useful in > diagnosing the problem. I would delve further but I'm not an > experienced MATLAB user, so I don't think my investigation would be > very fruitful! > > --- > > Error using subsindex > Function 'subsindex' is not defined for values of class 'cell'. > > Error in selfromraw (line 11) > data.trial = data.trial(selrpt); > > Error in ft_selectdata_old (line 544) > data = selfromraw(data, 'rpt', selrpt); > > Error in ft_selectdata (line 45) > [varargout{1:nargout}] = ft_selectdata_old(varargin{:}); > > Error in ft_rejectvisual (line 196) > data = ft_selectdata(data, 'rpt', cfg.trials); > > On 8 April 2012 20:52, Dashiel Munding wrote: > > Hello all, > > > > I'm trying to figure out a way of reading only selected trials into > > analysis without running through ft_rejectvisual every time. I have a > > list of trials that I have already rejected, and the documentation > > (http://fieldtrip.fcdonders.nl/reference/ft_rejectvisual) says that I > > should be able to use cfg.trials as a 1xN vector to put in a list of > > those trials that I want to use : > > > > cfg.trials = 'all' or a selection given as a 1xN vector (default = > 'all') > > > > I've tried various formats for this vector (I'm new to both MATLAB and > > fieldtrip, so this might be a simple solve) but I can't get a positive > > result. I know I can save out the variable and read it in again at a > > later date, but this seems like a very inefficient way of doing it if > > all I need is a list of numbers, instead of a 1.5gb .m file... > > > > Has anyone come across/solved this problem? Can anyone provide me with > > an example of the syntax fieldtrip is expecting? > > > > I've tried: > > > > cfg.trials = {'all' '-56', '-151', '-232', '-53'}; > > > > cfg.trials = {'1','2','3','4','5','6','7','8','9','10','46'}; > > > > cfg.trials = {1,2,3,4,5,6,7,8,9,10,46}; > > > > and some other efforts to no avail! > > > > Thanks in advance, and sorry for naivety! > > > > Dashiel > > _______________________________________________ > 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 jarang.hahm at gmail.com Tue Apr 10 11:40:03 2012 From: jarang.hahm at gmail.com (Jarang Hahm) Date: Tue, 10 Apr 2012 18:40:03 +0900 Subject: [FieldTrip] =?utf-8?q?=5BFieldTrip=E2=80=8B=5D_Data_handling_afte?= =?utf-8?q?r_excluding_single_sensors_=28Neuromag=29?= Message-ID: Hi all, We are using Neuromag 306 sensors VectorView system. And only gradiometer sensors (204 sensors) are used for analysis. In the artifact rejection, I excluded four bad sensors, not as a pair, among 204 sensors. After time-frequency analysis, I got lost when combine the sensors. How can I deal with the data with a single sensor in part? Should I reject the sensor as a pair? Or, combine the signals only for the paired sensors? I want you to suggest the proper way to handle the data of one sensor in a pair. Thank you in advance, Jarang Hahm -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Tue Apr 10 13:16:47 2012 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Tue, 10 Apr 2012 13:16:47 +0200 Subject: [FieldTrip] =?utf-8?q?=5BFieldTrip=E2=80=8B=5D_Data_handling_afte?= =?utf-8?q?r_excluding_single_sensors_=28Neuromag=29?= In-Reply-To: References: Message-ID: Dear Jarang, I think there are two options: 1.) You exclude as a pair, as combining the two orthogonal sensors you want to capture the different directions of the magnetic field. 2.) Or you look at the horizontal and vertical gradiometers separately. The following script should allow you to extract the two different sensor types channel = ft_channelselection('MEG*2',data.label); index = match_str(data.label,channel); gradH_F = data; gradH_F.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); gradH_S = data; gradH_S.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); channel = ft_channelselection('MEG*3',data.label); index = match_str(data.label,channel); gradV_F = data; gradV_F.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); gradV_S = data; gradV_S.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); data is a grand mean time frequency matrix with keep individuals = yes. I hope that helps. Best, Stephan El 10/04/2012, a las 11:40, Jarang Hahm escribió: > Hi all, > > > We are using Neuromag 306 sensors VectorView system. > And only gradiometer sensors (204 sensors) are used for analysis. > > > > In the artifact rejection, I excluded four bad sensors, not as a pair, among 204 sensors. > > After time-frequency analysis, I got lost when combine the sensors. > > > > How can I deal with the data with a single sensor in part? > > Should I reject the sensor as a pair? Or, combine the signals only for the paired sensors? > > > I want you to suggest the proper way to handle the data of one sensor in a pair. > > > > > Thank you in advance, > > > > Jarang Hahm > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Tue Apr 10 21:58:18 2012 From: lihqih at gmail.com (qi li) Date: Tue, 10 Apr 2012 15:58:18 -0400 Subject: [FieldTrip] ft_multiplotER Message-ID: Hi there, I tried to plot with the instruction in the tutorial. cfg=[];cfg.layout='ctf275'; ft_multiplotER(cfg,data) and get the following message 'reading layout from file ctf275.lay Error using ft_prepare_layout>readlay (line 668) could not open layout file: ctf275.lay' Any hints to solve the issue would be highly appreciated! From eelke.spaak at donders.ru.nl Wed Apr 11 08:02:11 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 11 Apr 2012 08:02:11 +0200 Subject: [FieldTrip] ft_multiplotER In-Reply-To: References: Message-ID: Hi qi, Could you try: cfg.layout = 'CTF275.lay'; so, uppercase letters 'CTF' and include the extension. That should work (at least, if the data you are trying to plot is from a CTF 275 system, which I assume it is). Best, Eelke On 10 April 2012 21:58, qi li wrote: > Hi there, > > I tried to plot with the instruction in the tutorial. > > cfg=[];cfg.layout='ctf275'; > ft_multiplotER(cfg,data) > and get the following message > > 'reading layout from file ctf275.lay > Error using ft_prepare_layout>readlay (line 668) > could not open layout file: ctf275.lay' > > Any hints to solve the issue would be highly appreciated! > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lihqih at gmail.com Wed Apr 11 22:13:23 2012 From: lihqih at gmail.com (qi li) Date: Wed, 11 Apr 2012 16:13:23 -0400 Subject: [FieldTrip] question on the coordinate Message-ID: Hi there, Our MRI data was already alined to Talariach coordinate. Let me call it mri. I aligned the MRI coordinate to MEG by ft_volumerealign and produce a variable called mri_other. mri_other=ft_volumerealign(cfg,mri); Now I reslice by mrirs=ft_volumereslice(cfg,mri_other) and do segmentation by cfg.coordsys='ctf; seg=ft_volumesegment(cfg,mrirs); I found mrirs.transform is not equal to mri_other.transform. Is this correct? I think re-slicing and segmentation should not change the transformation matrix. The last question is since our mri data was already aligned to Talariach, do we need to realign segmented? Thank you all! Qi From explena at gmail.com Thu Apr 12 10:57:44 2012 From: explena at gmail.com (Shen-Mou Hsu) Date: Thu, 12 Apr 2012 16:57:44 +0800 Subject: [FieldTrip] [problem] zero plv Message-ID: Dear Users, I try to calculate the phase locking values following the tutorial and encounter a problem. First, I ran freqanalysis as follows: cfg = []; cfg.channel = 'EEG'; cfg.method = 'mtmfft'; cfg.foi = 8:1:120; cfg.keeptrials = 'yes'; cfg.ouput = 'fourier'; cfg.tapsmofrq = 2; Phase= ft_freqanalysis(cfg, data); I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) Then, I ran connectivity analysis as follows cfg = []; cfg.method = 'plv'; PLV = ft_connectivityanalysis(cfg, Phase); Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: [0x113 double] I wondered if there is anything wrong with the previous steps. Many thanks! Shen-Mou Hsu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 12 11:37:04 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 12 Apr 2012 11:37:04 +0200 Subject: [FieldTrip] [problem] zero plv In-Reply-To: References: Message-ID: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> Hi Shen-Mou, There's a typo in the cfg that you supply to ft_freqanalysis -> cfg.ouput should read cfg.output BW, JM On Apr 12, 2012, at 10:57 AM, Shen-Mou Hsu wrote: > Dear Users, > > I try to calculate the phase locking values following the tutorial and encounter a problem. > > First, I ran freqanalysis as follows: > cfg = []; > cfg.channel = 'EEG'; > cfg.method = 'mtmfft'; > cfg.foi = 8:1:120; > cfg.keeptrials = 'yes'; > cfg.ouput = 'fourier'; > cfg.tapsmofrq = 2; > Phase= ft_freqanalysis(cfg, data); > > I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) > > Then, I ran connectivity analysis as follows > cfg = []; > cfg.method = 'plv'; > PLV = ft_connectivityanalysis(cfg, Phase); > > Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: [0x113 double] > > I wondered if there is anything wrong with the previous steps. Many thanks! > > Shen-Mou Hsu > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From explena at gmail.com Thu Apr 12 12:15:40 2012 From: explena at gmail.com (Shen-Mou Hsu) Date: Thu, 12 Apr 2012 18:15:40 +0800 Subject: [FieldTrip] [problem] zero plv In-Reply-To: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> References: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> Message-ID: Hi JM, Apologize for such a stupid mistake. However, I have amended the typo and the results are the same. Both cumsumcnt and cumtapcnt returned constant values, 1101 (timepoints) and 3, respectively. I am indebted to your kindness in this matter. Shen-Mou On Thu, Apr 12, 2012 at 5:37 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Shen-Mou, > > There's a typo in the cfg that you supply to ft_freqanalysis -> cfg.ouput > should read cfg.output > > BW, > > JM > > On Apr 12, 2012, at 10:57 AM, Shen-Mou Hsu wrote: > > Dear Users, > > I try to calculate the phase locking values following the tutorial and > encounter a problem. > > First, I ran freqanalysis as follows: > cfg = []; > cfg.channel = 'EEG'; > cfg.method = 'mtmfft'; > cfg.foi = 8:1:120; > cfg.keeptrials = 'yes'; > cfg.ouput = 'fourier'; > cfg.tapsmofrq = 2; > Phase= ft_freqanalysis(cfg, data); > > I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are > constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) > > Then, I ran connectivity analysis as follows > cfg = []; > cfg.method = 'plv'; > PLV = ft_connectivityanalysis(cfg, Phase); > > Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: > [0x113 double] > > I wondered if there is anything wrong with the previous steps. Many thanks! > > Shen-Mou Hsu > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > 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 explena at gmail.com Thu Apr 12 12:57:18 2012 From: explena at gmail.com (Shen-Mou Hsu) Date: Thu, 12 Apr 2012 18:57:18 +0800 Subject: [FieldTrip] [problem] zero plv In-Reply-To: References: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> Message-ID: Dear JM, After correcting the typo you pointed out, I do get the plv. Many thanks indeed! Shen-Mou On Thu, Apr 12, 2012 at 6:15 PM, Shen-Mou Hsu wrote: > Hi JM, > > Apologize for such a stupid mistake. However, I have amended the typo and > the results are the same. Both cumsumcnt and cumtapcnt returned constant > values, 1101 (timepoints) and 3, respectively. I am indebted to your > kindness in this matter. > > Shen-Mou > > > On Thu, Apr 12, 2012 at 5:37 PM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Shen-Mou, >> >> There's a typo in the cfg that you supply to ft_freqanalysis -> cfg.ouput >> should read cfg.output >> >> BW, >> >> JM >> >> On Apr 12, 2012, at 10:57 AM, Shen-Mou Hsu wrote: >> >> Dear Users, >> >> I try to calculate the phase locking values following the tutorial and >> encounter a problem. >> >> First, I ran freqanalysis as follows: >> cfg = []; >> cfg.channel = 'EEG'; >> cfg.method = 'mtmfft'; >> cfg.foi = 8:1:120; >> cfg.keeptrials = 'yes'; >> cfg.ouput = 'fourier'; >> cfg.tapsmofrq = 2; >> Phase= ft_freqanalysis(cfg, data); >> >> I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are >> constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) >> >> Then, I ran connectivity analysis as follows >> cfg = []; >> cfg.method = 'plv'; >> PLV = ft_connectivityanalysis(cfg, Phase); >> >> Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: >> [0x113 double] >> >> I wondered if there is anything wrong with the previous steps. Many >> thanks! >> >> Shen-Mou Hsu >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> 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 fredericroux at hotmail.de Thu Apr 12 19:01:49 2012 From: fredericroux at hotmail.de (Frederic Roux) Date: Thu, 12 Apr 2012 19:01:49 +0200 Subject: [FieldTrip] randomization vs permutation using ft_sourceanalysis Message-ID: Dear all, I would like to compute first level statistics of resting state source activity during eyes open and eyes closed to be able to compare this contrast across a group of subjects with different ages. I noticed that ft_sourceanalysis offers the possibility to contrast two conditions using cfg.randomization or cfg.permutation. The help documentation mentions that these options are required if one wants to contrast two conditions and apparently they do something different since they are mutually exclusive (one can not call ft_sourcenalysis with both). However, it is not clear to me how both options differ and how the data structure that is being returned can be used with ft_sourcestatistics. Any help would be as always highly appreciated. Best, Fred -- Frédéric Roux, PhD student Department of Neurophysiology Max Planck Institute for Brain Research D-60529 Frankfurt am Main Frederic.Roux at brain.mpg.de +49(0)69630183225 -------------- next part -------------- An HTML attachment was scrubbed... URL: From candida at nmr.mgh.harvard.edu Thu Apr 12 19:21:38 2012 From: candida at nmr.mgh.harvard.edu (Candida Jane Maria Ustine) Date: Thu, 12 Apr 2012 13:21:38 -0400 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data Message-ID: Hello All, I have just started reading about fieldtrip and I am learning a lot of exciting things. I have MEG data using the neuromag system and I wanted to run the Independent Component Analysis on the .fif files to remove the EOG and ECG artifact from them. I see that the documentation provided in the website( http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts) has resources to handle CTF datasets, and I was wondering if anyone has looked into the option of using the .fif files directly. Or is there a way to convert the *.fif files to the CTF format as there is an MNE utility to do the reverse mne_ctf2fif? Thanks much for your time and help! Best, Candida -- Candida Jane Maria Ustine Martinos Center for Biomedical Imaging MGH Kuperberg Lab The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Thu Apr 12 20:34:54 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Thu, 12 Apr 2012 13:34:54 -0500 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact Message-ID: Hi Candida, Welcome to FieldTrip. It seems you can import Neuromag data directly into FieldTrip: see http://fieldtrip.fcdonders.nl/getting_started/neuromag . Once the data are read into FieldTrip you can just save them as MATLAB files and you should be able to treat them the same as data from any other source once they're in FieldTrip's format. Best, Steve Politzer-Ahles On Thu, Apr 12, 2012 at 12:22 PM, wrote: > > Message: 4 > Date: Thu, 12 Apr 2012 13:21:38 -0400 > From: Candida Jane Maria Ustine > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact > on Neuromag(*.fif) data > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello All, > > I have just started reading about fieldtrip and I am learning a lot of > exciting things. > > I have MEG data using the neuromag system and I wanted to run the > Independent Component Analysis on the .fif files to remove the EOG and ECG > artifact from them. I see that the documentation provided in the website( > > http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts > ) > has resources to handle CTF datasets, and I was wondering if anyone has > looked into the option of using the .fif files directly. > Or is there a way to convert the *.fif files to the CTF format as there is > an MNE utility to do the reverse mne_ctf2fif? > > Thanks much for your time and help! > > Best, > Candida > > > > -- > Candida Jane Maria Ustine > Martinos Center for Biomedical Imaging > MGH > Kuperberg Lab > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Partners Compliance > HelpLine at http://www.partners.org/complianceline . If the e-mail was > sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120412/f79ae1c8/attachment.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 17, Issue 11 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rapela at ucsd.edu Thu Apr 12 21:41:54 2012 From: rapela at ucsd.edu (Joaquin Rapela) Date: Thu, 12 Apr 2012 12:41:54 -0700 Subject: [FieldTrip] Postdoctoral position in motor control Message-ID: <20120412194154.GA17424@dreaming.ucsd.edu> Please contact Prof. Della-Maggiore (vdellamaggiore at fmed.uba.ar) if you are interested in the following postdoctoral position in the lively city of Buenos Aires, Argentina. Cordially, Joaquin The Physiology of Action Lab (www.physiologyofactionlab.info) is looking for a candidate to fill a postdoctoral position in the Department of Physiology of the University of Buenos Aires, Argentina. The Labortory focuses on Human Behavioral Neuroscience, particularly in the area of motor control. We use Transcranial Magnetic Stimulation, Magnetic Resonance Imaging, EEG and psychophysics to study the neural mechanisms at the basis of different aspects of motor control. These include motor resonance and action understanding during action observation, online motor control and motor learning. Plastic changes induced by learning and stroke are also main interests of the lab. We are looking for a Ph.D. with a background in Neuroscience and, preferably, with experience in one ore more of the techniques used in the lab, and data analysis. Candidates with knowledge of Matlab would have priority. The postdoc is funded by a fellowship from the National Agency for the Promotion of Science and Technology (Argentina). Interested candidates could contact Dr. Valeria Della Maggiore at vdellamaggiore at fmed.uba.ar with a CV, a letter of interest and one or two references (email). Many thanks -- Valeria Della-Maggiore, Ph. D Department of Physiology, School of Medicine University of Buenos Aires Paraguay 2155, Capital Federal Buenos Aires, C1121ABG Argentina phone 54 11 5 950 9500 (2132) http://www.physiologyofactionlab.info ------------------------------------------------------------ being wild and disciplined at the same time.... -- Joaquin Rapela, PhD Swartz Center for Computational Neuroscience University of California San Diego 9500 Gilman Drive, San Diego, CA 92093-0559 tel: (858) 822-7536 fax: (858) 822-7556 http://sccn.ucsd.edu/~rapela ---------------------------------- the gods do not grant men all their gifts at once Nestor in The Iliad From alexandre.gramfort at inria.fr Fri Apr 13 08:50:39 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 13 Apr 2012 08:50:39 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: Message-ID: hi Candida, you should be able to import your fif files into fieldtrip but be careful when applying ICA on neuromag data as channels have different types and you have signals with 2 orders of magnitude difference between gradiometers and magnetometers. I am curious to know if fieldtrip handles this properly? and if so how. Also can Fieldtrip write data back into fif files keeping intact all the measurement info? thanks Alex -- Alexandre Gramfort, PhD alexandre.gramfort at inria.fr INRIA Parietal Project Team, NeuroSpin CEA Saclay Bat. 145, PC 156 91191 Gif-sur-Yvette, France http://alexandre.gramfort.net On Thu, Apr 12, 2012 at 7:21 PM, Candida Jane Maria Ustine wrote: > Hello All, > > I have just started reading about fieldtrip and I am learning a lot of > exciting things. > > I have MEG data using the neuromag system and I wanted to run the > Independent Component Analysis on the .fif files to remove the EOG and ECG > artifact from them. I see that the documentation provided in the > website(http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts) > has resources to handle CTF datasets, and I was wondering if anyone has > looked into the option of using the .fif files directly. > Or is there a way to convert the *.fif files to the CTF format as there is > an MNE utility to do the reverse mne_ctf2fif? > > Thanks much for your time and help! > > Best, > Candida > > > > -- > Candida Jane Maria Ustine > Martinos Center for Biomedical Imaging > MGH > Kuperberg Lab > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Partners Compliance > HelpLine at http://www.partners.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact the > sender and properly dispose of the e-mail. > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From jan.schoffelen at donders.ru.nl Fri Apr 13 09:01:40 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 Apr 2012 09:01:40 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: Message-ID: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> Hi Alex, > I am curious to know if fieldtrip handles this properly? and if so how. It depends a bit on the exact algorithm that is used, but for example the runica implementation (we use the EEGlab code for this) performs a whitening of the data prior to the decomposition. This would address the difference in magnitude issue, wouldn't it? > Also can Fieldtrip write data back into fif files keeping intact > all the measurement info? Not really; I have some code of Lauri's (which is not yet in FT), which can write epoched data to a fif-file. However, most of the measurement info is lost along the way. Also, since we're not fif-experts, it's not trivial for us to find out how the measurement info should be formatted. Of course it is possible to reverse engineer this from the mne-code, but this is heavily geared towards elekta hardware. Yet, I could imagine that this functionality could be valuable, because it would enable two-way traffic of data between FT and MNE-suite. Do you happen to have any code that writes meaningful measurement info? Best, Jan-Mathijs > > thanks > > Alex > -- > Alexandre Gramfort, PhD > alexandre.gramfort at inria.fr > INRIA Parietal Project Team, NeuroSpin CEA Saclay > Bat. 145, PC 156 > 91191 Gif-sur-Yvette, France > http://alexandre.gramfort.net > > On Thu, Apr 12, 2012 at 7:21 PM, Candida Jane Maria Ustine > wrote: >> Hello All, >> >> I have just started reading about fieldtrip and I am learning a lot of >> exciting things. >> >> I have MEG data using the neuromag system and I wanted to run the >> Independent Component Analysis on the .fif files to remove the EOG and ECG >> artifact from them. I see that the documentation provided in the >> website(http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts) >> has resources to handle CTF datasets, and I was wondering if anyone has >> looked into the option of using the .fif files directly. >> Or is there a way to convert the *.fif files to the CTF format as there is >> an MNE utility to do the reverse mne_ctf2fif? >> >> Thanks much for your time and help! >> >> Best, >> Candida >> >> >> >> -- >> Candida Jane Maria Ustine >> Martinos Center for Biomedical Imaging >> MGH >> Kuperberg Lab >> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Partners Compliance >> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent >> to you in error but does not contain patient information, please contact the >> sender and properly dispose of the e-mail. >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Fri Apr 13 09:22:53 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 13 Apr 2012 09:22:53 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> References: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> Message-ID: hi Jan-Mathijs, thanks for the quick answer. > It depends a bit on the exact algorithm that is used, but for example the > runica implementation (we use the EEGlab code for this) performs a whitening > of the data prior to the decomposition. This would address the difference in > magnitude issue, wouldn't it? it does yes. My question is then how do you compute the withering matrix? > Also can Fieldtrip write data back into fif files keeping intact > all the measurement info? > > Not really; I have some code of Lauri's (which is not yet in FT), which can > write epoched data to a fif-file. However, most of the measurement info is > lost along the way. that's what I feared. > Also, since we're not fif-experts, it's not trivial for > us to find out how the measurement info should be formatted. Of course it is > possible to reverse engineer this from the mne-code, but this is heavily > geared towards elekta hardware. Yet, I could imagine that this functionality > could be valuable, because it would enable two-way traffic of data between > FT and MNE-suite. that would be very valuable indeed. > Do you happen to have any code that writes meaningful > measurement info? not in one function or at least not in matlab. one should have a fiff_write_meas_info.m that does the opposite to: https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_read_meas_info.m part of the answer is in: https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_write_evoked.m a python example is in : https://github.com/mne-tools/mne-python/blob/master/mne/fiff/meas_info.py#L235 but I agree you need a fairly good understanding of the fif format… we might have to sit down together to do this. Alex From Andrew.Dykstra at med.uni-heidelberg.de Fri Apr 13 09:51:01 2012 From: Andrew.Dykstra at med.uni-heidelberg.de (Andrew R. Dykstra) Date: Fri, 13 Apr 2012 09:51:01 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data Message-ID: Hi Candida, An alternative to using fieldtrip would be EEGLAB (I believe Fieldtrip using the code there anyway). I was able to run ICA on my combined EEG/Neuromag-122 data using a combination of the MNE MATLAB toolbox (specifically, fiff_setup_read_raw & fiff_read_raw_segment) and EEGLAB's import from MATLAB matrix functionality. More work would be required to retain the sensor locations and resulting component topographies. Then, along the lines of Alex's concerns, you could run the decomposition separately for each sensor type (Mags/Grads/EEG). This may be unnecessary if the runica algorithm handles this properly (assuming you have imported the sensor types along with the time series data into EEGLAB). After subtracting out the artifact components, you could then replace the appropriate entires of your original data matrix and use fiff_write_raw_segment (from the nightly build of the MNE suite). Hope this helps, Andy -- Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov -------------- next part -------------- An HTML attachment was scrubbed... URL: From grion at sissa.it Fri Apr 13 11:14:08 2012 From: grion at sissa.it (Natalia Grion) Date: Fri, 13 Apr 2012 11:14:08 +0200 Subject: [FieldTrip] PLV definition and implementation Message-ID: <20120413111408.Horde.eLHMRh8V4mxPh_5gqW4WfWA@webmail.sissa.it> Dear Fieldtripers, I would like to know how you define and implement 'plv' (phase locking value) in the fieldtrip. I do not see any documentation on this issue of reference paper and I'm confused by the fact that this definition was used by Lachaux (1999) and fieldtrip is taking the cross-spectrum and doing some treatment (difficult to follow in the series of functions involved) to ignore amplitude consistency (I guess a different treatment from coherence 'coh' function). Could you clarify this to me or give me a reference paper? Thanks! Natalia From jan.schoffelen at donders.ru.nl Fri Apr 13 11:57:56 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 Apr 2012 11:57:56 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> Message-ID: <5DB5ADAB-2E6A-4B90-B8AD-69D7CF315BB4@donders.ru.nl> Hi Alex, > it does yes. My question is then how do you compute the withering matrix? That's the magic of EEGlab ;-). I did not look into the code but I would assume based on the estimate of the precision matrix. Do you think the magnitude problem will lead to numerical issues upon inversion of the covariance matrix? >> Also can Fieldtrip write data back into fif files keeping intact >> all the measurement info? >> >> Not really; I have some code of Lauri's (which is not yet in FT), which can >> write epoched data to a fif-file. However, most of the measurement info is >> lost along the way. > > that's what I feared. > >> Also, since we're not fif-experts, it's not trivial for >> us to find out how the measurement info should be formatted. Of course it is >> possible to reverse engineer this from the mne-code, but this is heavily >> geared towards elekta hardware. Yet, I could imagine that this functionality >> could be valuable, because it would enable two-way traffic of data between >> FT and MNE-suite. > > that would be very valuable indeed. > >> Do you happen to have any code that writes meaningful >> measurement info? > > not in one function or at least not in matlab. > > one should have a fiff_write_meas_info.m that does the opposite to: > > https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_read_meas_info.m > > part of the answer is in: > > https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_write_evoked.m > > a python example is in : > > https://github.com/mne-tools/mne-python/blob/master/mne/fiff/meas_info.py#L235 > > but I agree you need a fairly good understanding of the fif format… > > we might have to sit down together to do this. I am afraid so. Well, I would certainly be up for it, because it would further strengthen both packages. Shall I come to you, or will you come to me ;-)? JM > Alex > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Fri Apr 13 12:08:10 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 13 Apr 2012 12:08:10 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: <5DB5ADAB-2E6A-4B90-B8AD-69D7CF315BB4@donders.ru.nl> References: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> <5DB5ADAB-2E6A-4B90-B8AD-69D7CF315BB4@donders.ru.nl> Message-ID: hi JM, > That's the magic of EEGlab ;-). I did not look into the code but I would > assume based on the estimate of the precision matrix. Do you think the > magnitude problem will lead to numerical issues upon inversion of the > covariance matrix? probably not. > I am afraid so. Well, I would certainly be up for it, because it would > further strengthen both packages. Shall I come to you, or will you come to > me ;-)? Unless I come to you first, you'll come to me for Biomag in august I guess. Alex From Panagiotis.Tsiatsis at Tuebingen.MPG.de Fri Apr 13 19:00:14 2012 From: Panagiotis.Tsiatsis at Tuebingen.MPG.de (Panagiotis Tsiatsis) Date: Fri, 13 Apr 2012 19:00:14 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: Message-ID: <4F885B9E.6000307@Tuebingen.MPG.de> On 4/13/2012 8:50 AM, Alexandre Gramfort wrote: > but be careful when applying ICA on neuromag data as > channels have different types and you have signals > with 2 orders of magnitude difference between gradiometers > and magnetometers. > > I am curious to know if fieldtrip handles this properly? and if so how. Hi all, I am also working with CTF MEG data. What I ve been basically doing up to now was to split the datasets in two subsets: one containing only the MEGGRAD sensors (let s call it A) and another containing all the rest (let it be B). Then I would apply ICA only on the set containing the main MEG sensors, subtract the EOG-related components and re-construct the data without them (A'). Finally, I would merge A' with B. This works fine and the results that I am getting are convincing, the only problem is that of course the reference channels are still contaminated. I don t know if this would be a problem in subsequent analysis, ie source localization, maybe somebody who has more experience further down this road could comment on that. Best, Panagiotis -- Panagiotis S. Tsiatsis Max Planck Institute for Biological Cybernetics Cognitive NeuroImaging Group Tuebingen, Germany From cas243 at georgetown.edu Fri Apr 13 19:52:47 2012 From: cas243 at georgetown.edu (Clara A. Scholl) Date: Fri, 13 Apr 2012 13:52:47 -0400 Subject: [FieldTrip] dimensions for coherence Message-ID: Dear Fieldtrip users, I'm encountering a problem with calculating coherence between two time courses. I suspect I'm misunderstanding something very basic. When I calculate the coherence using data with multiple trials -- with dimensions rpttap_chan_freq, everything works fine (I get a coherence spectrum calculation that is averaged over the rpt dimension). However if I want to limit the calculation to data with dimensions chan_freq (i.e. find the coherence between the fourier spectra (containing both amplitude and phase info) of a single timecourse on two different channels (where those channels are specified using cfg.channelcmb)), I get an error. I've tried to do this two different ways. If I still use the rpttap_chan_freq data, I tried specifying cfg.trials=1 in the connectivity analysis input, and the error given is: ??? Index exceeds matrix dimensions. Error in ==> ft_connectivity_corr at 131 p1 = reshape(input(j,powindx(:,1),:,:,:), siz(2:end)); Error in ==> ft_connectivityanalysis at 471 [datout, varout, nrpt] = ft_connectivity_corr(data.(inparam), optarg{:}); ->>If I input frequency data with dimensions chan_freq into ft_connectivityanalysis (still only specifying cfg.method='coh' and the channel combinations I'm interested in with cfg.channelcmb) the output is: ??? Index exceeds matrix dimensions. Error in ==> ft_checkdata>fixcsd at 843 tmpdat1 = data.fourierspctrm(indx,cmbindx(:,1),:,:); Error in ==> ft_checkdata at 629 data = fixcsd(data, cmbrepresentation, channelcmb); Error in ==> univariate2bivariate at 37 data = ft_checkdata(data, 'cmbrepresentation', 'sparse', 'channelcmb', cmb); Error in ==> ft_connectivityanalysis at 320 [data, powindx, hasrpt] = univariate2bivariate(data, 'fourierspctrm', 'crsspctrm', dtype, 'cmb', cfg.channelcmb, 'keeprpt', normrpt); ->>Does the coherence calculation appear to require more than one (complex) value at each channel & frequency band of interest? Am I confused about what the rpttap dimension contains? My time window is narrow and my fft calculation only has 1 taper, is that a problem? Because the fourier calculation at each channel_frequency point contains both amplitude and phase information, wouldn't data with chan_freq dimensions be sufficient to calculate the cross spectral densities between the fourier transforms of two channels? Thanks for any guidance, Clara From jan.schoffelen at donders.ru.nl Fri Apr 13 20:28:31 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 Apr 2012 20:28:31 +0200 Subject: [FieldTrip] dimensions for coherence In-Reply-To: References: Message-ID: Hi Clara, Did you check the tutorial on the website? http://fieldtrip.fcdonders.nl/tutorial/connectivity The input data to ft_connectivityanalysis has some requirements. For coherence, you either need a freq-structure containing a 'fourierspctrm' field, or a 'crsspctrm' (+ 'powspctrm') field. The 'fourierspctrm' by definition should have a dimord of 'rpttap_chan_freq(_time', and the 'crsspctrm' may have lost the 'rpt' or 'rpttap' dimension. If your freq data looks different, you will not be able to compute coherence. Admittedly, the error messages you get are quite unspecific, but given the scarce information you are providing with respect to what exactly you have been doing, I can only give some general advice and point you to the documentation. Best, Jan-Mathijs On Apr 13, 2012, at 7:52 PM, Clara A. Scholl wrote: > Dear Fieldtrip users, > > I'm encountering a problem with calculating coherence between two time > courses. I suspect I'm misunderstanding something very basic. > > When I calculate the coherence using data with multiple trials -- with > dimensions rpttap_chan_freq, everything works fine (I get a coherence > spectrum calculation that is averaged over the rpt dimension). > However if I want to limit the calculation to data with dimensions > chan_freq (i.e. find the coherence between the fourier spectra > (containing both amplitude and phase info) of a single timecourse on > two different channels (where those channels are specified using > cfg.channelcmb)), I get an error. I've tried to do this two different > ways. If I still use the rpttap_chan_freq data, I tried specifying > cfg.trials=1 in the connectivity analysis input, and the error given > is: > ??? Index exceeds matrix dimensions. > > Error in ==> ft_connectivity_corr at 131 > p1 = reshape(input(j,powindx(:,1),:,:,:), siz(2:end)); > > Error in ==> ft_connectivityanalysis at 471 > [datout, varout, nrpt] = ft_connectivity_corr(data.(inparam), optarg{:}); > > > ->>If I input frequency data with dimensions chan_freq into > ft_connectivityanalysis (still only specifying cfg.method='coh' and > the channel combinations I'm interested in with cfg.channelcmb) the > output is: > > ??? Index exceeds matrix dimensions. > > Error in ==> ft_checkdata>fixcsd at 843 > tmpdat1 = data.fourierspctrm(indx,cmbindx(:,1),:,:); > > Error in ==> ft_checkdata at 629 > data = fixcsd(data, cmbrepresentation, channelcmb); > > Error in ==> univariate2bivariate at 37 > data = ft_checkdata(data, 'cmbrepresentation', 'sparse', > 'channelcmb', cmb); > > Error in ==> ft_connectivityanalysis at 320 > [data, powindx, hasrpt] = univariate2bivariate(data, > 'fourierspctrm', 'crsspctrm', dtype, 'cmb', cfg.channelcmb, 'keeprpt', > normrpt); > > > ->>Does the coherence calculation appear to require more than one > (complex) value at each channel & frequency band of interest? Am I > confused about what the rpttap dimension contains? My time window is > narrow and my fft calculation only has 1 taper, is that a problem? > Because the fourier calculation at each channel_frequency point > contains both amplitude and phase information, wouldn't data with > chan_freq dimensions be sufficient to calculate the cross spectral > densities between the fourier transforms of two channels? > > Thanks for any guidance, > Clara > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cas243 at georgetown.edu Fri Apr 13 21:01:34 2012 From: cas243 at georgetown.edu (Clara A. Scholl) Date: Fri, 13 Apr 2012 15:01:34 -0400 Subject: [FieldTrip] dimensions for coherence In-Reply-To: References: Message-ID: Thank you Jan-Mathijs! I was using the the coherence tutorial (http://fieldtrip.fcdonders.nl/tutorial/coherence) but after reading the connectivity tutorial I'm still confused. A more parsimonious way to phrase my question would be: Why do I get an error when my fourierspctrm with dimord rpttap_chan_freq has dimensions of 1 x 128 x 10 (the key being, just 1 rpttap value for each channel x frequency combination)? At each channel & frequency, fourierspctrum contains a complex value so the data structure contains the phase and amplitude information at each channel and frequency, which I think -- perhaps incorrectly -- should be sufficient to calculate the coherence. I'll paste below an example of the error I'm getting, beginning with the initial data structure through the ft_connectivityanalysis error. IF the initial data structure (called tmp in this example) has rpt size > 1, then I don't get the error. Thanks, Clara tmp = label: {128x1 cell} time: [0.3380 0.3400 0.3420 0.3440 0.3460 0.3480 0.3500 0.3520 0.3540 0.3560 0.3580 0.3600 0.3620 0.3640 0.3660 0.3680 0.3700 0.3720] cfg: [1x1 struct] trial: [1x128x18 double] sampleinfo: [1 18] dimord: 'rpt_chan_time' >> cfg=[]; cfg.output='fourier'; cfg.method='mtmfft'; cfg.tapsmofrq=28; cfg.channel={'all'}; freqm0=ft_freqanalysis(cfg, tmp) the input is timelock data with 128 channels and 18 timebins processing trials Warning: using only one taper for specified smoothing > In specest/private/warning_once at 75 In ft_specest_mtmfft at 96 In ft_freqanalysis at 519 processing trial 1/1 nfft: 18 samples, datalength: 18 samples, 1 tapers the call to "ft_freqanalysis" took 0 seconds and an estimated 0 MB freqm0 = label: {128x1 cell} dimord: 'rpttap_chan_freq' freq: [0 27.7778 55.5556 83.3333 111.1111 138.8889 166.6667 194.4444 222.2222 250.0000] fourierspctrm: [1x128x10 double] cumsumcnt: 18 cumtapcnt: 1 cfg: [1x1 struct] >> cfg=[]; cfg.method='coh'; cfg.channelcmb={'E34', 'E98'}; fdm0=ft_connectivityanalysis(cfg, freqm0) selection fourierspctrm along dimension 2 ??? Index exceeds matrix dimensions. Error in ==> ft_connectivity_corr at 131 p1 = reshape(input(j,powindx(:,1),:,:,:), siz(2:end)); Error in ==> ft_connectivityanalysis at 471 [datout, varout, nrpt] = ft_connectivity_corr(data.(inparam), optarg{:}); From alexandre.gramfort at inria.fr Sun Apr 15 14:34:44 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Sun, 15 Apr 2012 14:34:44 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: <4F885B9E.6000307@Tuebingen.MPG.de> References: <4F885B9E.6000307@Tuebingen.MPG.de> Message-ID: Dear Panagiotis, the only potential caveat I see for the inverse problem is that you reduce the rank of your data but using ICA. To take care of this you make sure that your inverse solver takes it into account via the whitening noise covariance matrix that should also be applied to the gain/leadfield matrix. Alex On Fri, Apr 13, 2012 at 7:00 PM, Panagiotis Tsiatsis wrote: > On 4/13/2012 8:50 AM, Alexandre Gramfort wrote: >> >> but be careful when applying ICA on neuromag data as >> channels have different types and you have signals >> with 2 orders of magnitude difference between gradiometers >> and magnetometers. >> >> I am curious to know if fieldtrip handles this properly? and if so how. > > Hi all, > > I am also working with CTF MEG data. What I ve been basically doing up to > now was to split the datasets in two subsets: one containing only the > MEGGRAD sensors (let s call it A)  and another containing all the rest (let > it be B). Then I would apply ICA only on the set containing the main MEG > sensors, subtract the EOG-related components and re-construct the data > without them (A'). Finally, I would merge A' with B. This works fine and the > results that I am getting are convincing, the only problem is that of course > the reference channels are still contaminated. I don t know if this would be > a problem in subsequent analysis, ie source localization, maybe somebody who > has more experience further down this road could comment on that. > > > Best, > Panagiotis > > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From B.Haendel at gmx.net Mon Apr 16 15:56:13 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Mon, 16 Apr 2012 15:56:13 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad Message-ID: <20120416135613.3220@gmx.net> Dear fieldtrip users, has anyone experience in using ft_denoise_synthetic? If I try to calculate 3rd order grads in the below specified way the data does not change with respect to the input data (which has no synthetic gradiometer applied). Is there some obvious misunderstanding on my side of how to use this function or is our environment truly noiseless :) Cheers, Barbara cfg=[]; cfg.gradient ='G3BR'; cfg.trials = 'all'; data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); >> data_3rdorder.grad.balance ans = G1BR: [1x1 struct] G2BR: [1x1 struct] G3BR: [1x1 struct] current: 'G3BR' previous: {'none'} >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) ans = 0 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From michael.wibral at web.de Mon Apr 16 16:46:27 2012 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 16 Apr 2012 16:46:27 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <20120416135613.3220@gmx.net> References: <20120416135613.3220@gmx.net> Message-ID: An HTML attachment was scrubbed... URL: From stan.vanpelt at fcdonders.ru.nl Mon Apr 16 16:59:25 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Mon, 16 Apr 2012 16:59:25 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: Message-ID: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> Hi Barbara, I can replicate your finding, but am unsure what is causing it. Maybe the difference/correction is lower than the Matlab or CTF precision? In any case, i f the 3rd order gradients were on, ft_denoise_synthetic would undo the G3BR-balancing, ergo it toggles. Best, Stan ----- Oorspronkelijk bericht ----- > Van: "Michael Wibral" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Maandag 16 april 2012 16:46:27 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hi Barbara, > are you certain that the original data do not have 3rd gradients > enabled? - looking at them once in dataEditor, switching to 3rd grads > and accidentally forgetting to unclick 'save parameters with dataset' > will make them have 3rd grads... > When I last used ft_denoise_synthetic it worked pretty much as > described (??). > Michael > Gesendet: Montag, 16. April 2012 um 15:56 Uhr > Von: "Barbara Haendel" > An: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] ft_denoise_synthetic 3rd order grad > Dear fieldtrip users, > has anyone experience in using ft_denoise_synthetic? If I try to > calculate 3rd order grads in the below specified way the data does not > change with respect to the input data (which has no synthetic > gradiometer applied). Is there some obvious misunderstanding on my > side of how to use this function or is our environment truly noiseless > :) > Cheers, > Barbara > cfg=[]; > cfg.gradient ='G3BR'; > cfg.trials = 'all'; > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > >> data_3rdorder.grad.balance > ans = > G1BR: [1x1 struct] > G2BR: [1x1 struct] > G3BR: [1x1 struct] > current: 'G3BR' > previous: {'none'} > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > ans = 0 > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 -- Stan van Pelt Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 10981 Fax: (+31) (0)24 36 10989 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Panagiotis.Tsiatsis at Tuebingen.MPG.de Mon Apr 16 17:53:56 2012 From: Panagiotis.Tsiatsis at Tuebingen.MPG.de (Panagiotis Tsiatsis) Date: Mon, 16 Apr 2012 17:53:56 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <4F8C4094.2020707@Tuebingen.MPG.de> Hello girls and guys, It is working for my CTF MEG data - the version that I have is v4692 2011-11-07. The other thing that might cause a problem could be ommiting the reference channels definition before the ft_ preprocessing command that gave you your "dataprepro" i.e maybe you might need something like this cfg = []; ... //various preprocessing parameters ... cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; dataprepro = ft_preprocessing(cfg); Hope you are lucky :) Best, Panagiotis On 4/16/2012 4:59 PM, Stan van Pelt wrote: > Hi Barbara, > > I can replicate your finding, but am unsure what is causing it. Maybe > the difference/correction is lower than the Matlab or CTF precision? > In any case, if the 3rd order gradients were on, ft_denoise_synthetic > would undo the G3BR-balancing, ergo it toggles. > > Best, > Stan > > > ------------------------------------------------------------------------ > > *Van: *"Michael Wibral" > *Aan: *"Email discussion list for the FieldTrip project" > > *Verzonden: *Maandag 16 april 2012 16:46:27 > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > Hi Barbara, > > are you certain that the original data do not have 3rd gradients > enabled? - looking at them once in dataEditor, switching to 3rd > grads and accidentally forgetting to unclick 'save parameters with > dataset' will make them have 3rd grads... > > When I last used ft_denoise_synthetic it worked pretty much as > described (??). > > Michael > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > *Von:* "Barbara Haendel" > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > Dear fieldtrip users, > > has anyone experience in using ft_denoise_synthetic? If I try to > calculate 3rd order grads in the below specified way the data does > not change with respect to the input data (which has no synthetic > gradiometer applied). Is there some obvious misunderstanding on my > side of how to use this function or is our environment truly > noiseless :) > > Cheers, > Barbara > > cfg=[]; > cfg.gradient ='G3BR'; > cfg.trials = 'all'; > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > >> data_3rdorder.grad.balance > > ans = > > G1BR: [1x1 struct] > G2BR: [1x1 struct] > G3BR: [1x1 struct] > current: 'G3BR' > previous: {'none'} > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > ans = 0 > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 > > > > > -- > Stan van Pelt > > Donders Institute for Brain, Cognition and Behaviour, Radboud > University Nijmegen > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > E-mail: stan.vanpelt at donders.ru.nl > Website: www.ru.nl/donders/ > Phone: (+31) (0)24 36 10981 > Fax: (+31) (0)24 36 10989 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Panagiotis S. Tsiatsis Max Planck Institute for Biological Cybernetics Cognitive NeuroImaging Group Tuebingen, Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue Apr 17 00:07:45 2012 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 17 Apr 2012 00:07:45 +0200 Subject: [FieldTrip] NeuroScan QuikCap64 Message-ID: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> Hi, I have recently started using a NeuroScan 64 Channel SynAmps2 System with a QuikCap. Does anyone know how to prepare a layout for this cap? From the Scan4.2. software, I only get x and y coordinates, but no z coordinates, and on the setup CD I can only find PDF files with the layout. Any suggestions are welcome. Thanks a lot, Julian ******************************************** Julian Keil International Laboratory for Brain Music and Sound Research (BRAMS) Pavillon 1430 Mont-Royal Université de Montréal Montréal, Québec Canada, H2V 4P3 julian.keil at uni-konstanz.de +1-514-343-6111-29653 www.brams.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Tue Apr 17 08:41:01 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Tue, 17 Apr 2012 09:41:01 +0300 Subject: [FieldTrip] Signal viewer + Biosemi Message-ID: Hello, I looked I the Signal viewer example in the following page: http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer I just want to know how could I view a signal coming directly from the biosemi device? (I think the following line should be changed: cfg.dataset = 'buffer://localhost:1972'; but I don't know what to put) Thanks for your help -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From diana.ibanescu at gmail.com Tue Apr 17 10:33:11 2012 From: diana.ibanescu at gmail.com (Diana Ibanescu) Date: Tue, 17 Apr 2012 10:33:11 +0200 Subject: [FieldTrip] Function ft_prepare_bemmodel deprecated... Message-ID: Hello, I am interested in an example how to compute an EEG leadfield with OpenMEEG in the Fieldtrip toolbox. I found a demo script here: http://fieldtrip.fcdonders.nl/example/testing_bem_created_leadfields When I call the function ft_prepare_bemmodel(cfg, vol) I receive the following warning: "Warning: FT_PREPARE_BEMMODEL is deprecated, please use FT_HEADMODEL_BEM_... with cfg.method = 'bem_bladeebla' instead." The function ft_headmodel_bem_openmeeg receive as parameter "geom" while ft_prepare_bemmodel receive other parameters: vol = ft_headmodel_openmeeg(geom, ...) Optional input arguments should be specified in key-value pairs and can include isolatedsource = string, 'yes' or 'no' hdmfile = string, filename with BEM headmodel conductivity = vector, conductivity of each compartment Are the 2 functions similar? Is there any demo updated after the function ft_prepare_bemmodel became deprecated? What function can I use instead? Thank you, Diana. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue Apr 17 11:35:17 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 17 Apr 2012 11:35:17 +0200 Subject: [FieldTrip] NeuroScan QuikCap64 In-Reply-To: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> References: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> Message-ID: Hi Julian, Have a look at our layout tutorial: http://fieldtrip.fcdonders.nl/tutorial/layout Starting from the PDF files (or bitmap (jpg/png) files based on them) you should be able to easily create a layout using ft_prepare_layout. Best, Eelke On 17 April 2012 00:07, Julian Keil wrote: > Hi, > > I have recently started using a NeuroScan 64 Channel SynAmps2 System with a > QuikCap. > Does anyone know how to prepare a layout for this cap? > From the Scan4.2. software, I only get x and y coordinates, but no z > coordinates, and on the setup CD I can only find PDF files with the layout. > > Any suggestions are welcome. > > Thanks a lot, > > Julian > > > > ******************************************** > Julian Keil > > International Laboratory for Brain > Music and Sound Research (BRAMS) > > Pavillon 1430 Mont-Royal > Université de Montréal > Montréal, Québec > Canada,  H2V 4P3 > > julian.keil at uni-konstanz.de > +1-514-343-6111-29653 > www.brams.org > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Tue Apr 17 12:57:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 17 Apr 2012 12:57:37 +0200 Subject: [FieldTrip] NeuroScan QuikCap64 In-Reply-To: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> References: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> Message-ID: <4F8D4CA1.2050108@donders.ru.nl> Hi Julian, layout-files are in 2D, thus there is no need for a third dimenstion. You can use the x- and y-coordinates from your software package. If you got a third coordinate, you can try to build an elect-structure, see: http://fieldtrip.fcdonders.nl/faq/how_are_electrodes_magnetometers_or_gradiometers_described In case you got no third dimension, you can just set the z-coordinates to 0 for the elect-structure. It won't be 100% correct though, but the best you can do when only having a 2D layout at hand. You can also try one of the other layouts that we have that look similar, i.e. any layout that obeys the 1020-system (I am using easycapM11.lay, just try ft_prepare_layout while setting cfg.feedback='yes') Best, Jörn On 4/17/2012 12:07 AM, Julian Keil wrote: > Hi, > > I have recently started using a NeuroScan 64 Channel SynAmps2 System > with a QuikCap. > Does anyone know how to prepare a layout for this cap? > From the Scan4.2. software, I only get x and y coordinates, but no z > coordinates, and on the setup CD I can only find PDF files with the > layout. > > Any suggestions are welcome. > > Thanks a lot, > > Julian > > > > ********************************************** > *Julian Keil* > * > * > /International Laboratory for Brain/ > /Music and Sound Research (BRAMS)/ > > Pavillon 1430 Mont-Royal > Université de Montréal > Montréal, Québec > Canada, H2V 4P3 > > julian.keil at uni-konstanz.de > +1-514-343-6111-29653 > www.brams.org > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.severens at maartenskliniek.nl Tue Apr 17 14:51:41 2012 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Tue, 17 Apr 2012 14:51:41 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Hi Hamza You first need to start a buffer to read the data from de biosemi device, so start the biosemi2ft, see here http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. Then if you do not change the defaults you do not need to change the cfg.dataset field for the signal viewer. There is also a signal viewer based on c code (so no extra matlab session is necessary). You can find it here: fieldtrip/realtime/utilities/viewer Best, Marianne ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] Sent: Tuesday, April 17, 2012 8:41 AM To: Email discussion list for the FieldTrip project Subject: [FieldTrip] Signal viewer + Biosemi Hello, I looked I the Signal viewer example in the following page: http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer I just want to know how could I view a signal coming directly from the biosemi device? (I think the following line should be changed: cfg.dataset = 'buffer://localhost:1972'; but I don't know what to put) Thanks for your help -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From giulia.rizza at tiscali.it Tue Apr 17 15:04:23 2012 From: giulia.rizza at tiscali.it (Giulia Rizza) Date: Tue, 17 Apr 2012 15:04:23 +0200 (CEST) Subject: [FieldTrip] R: NeuroScan QuikCap64 Message-ID: <29197848.94691334667863183.JavaMail.defaultUser@defaultHost> Hi Julian I had the same problem some time ago and I found a list of the coordinates for all the channels in the download session of this link (then I followed the instructions in the FT tutorial): http://robertoostenveld. ruhosting.nl/index.php/electrode/#aes1994 Hope this helps Giulia >---- Messaggio originale---- >Da: julian.keil at gmail.com >Data: 17/04/2012 0.07 >A: "Email discussion list for the FieldTrip project" >Ogg: [FieldTrip] NeuroScan QuikCap64 > >Hi, > >I have recently started using a NeuroScan 64 Channel SynAmps2 System with a QuikCap. >Does anyone know how to prepare a layout for this cap? >From the Scan4.2. software, I only get x and y coordinates, but no z coordinates, and on the setup CD I can only find PDF files with the layout. > >Any suggestions are welcome. > >Thanks a lot, > >Julian > > > >******************************************** >Julian Keil > >International Laboratory for Brain >Music and Sound Research (BRAMS) > >Pavillon 1430 Mont-Royal >Université de Montréal >Montréal, Québec >Canada, H2V 4P3 > >julian.keil at uni-konstanz.de >+1-514-343-6111-29653 >www.brams.org > > > > > > >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru. nl/mailman/listinfo/fieldtrip Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più di uno spot in TV.Per ogni nuovo abbonato 30 € di premio per te e per lui! Un amico al mese e parli e navighisempre gratis: http://freelosophy.tiscali.it/ From julian.keil at gmail.com Tue Apr 17 15:21:16 2012 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 17 Apr 2012 15:21:16 +0200 Subject: [FieldTrip] R: NeuroScan QuikCap64 In-Reply-To: <29197848.94691334667863183.JavaMail.defaultUser@defaultHost> References: <29197848.94691334667863183.JavaMail.defaultUser@defaultHost> Message-ID: <4A1B2E1E-A2CE-4381-AF8F-20EE9A83A7E7@gmail.com> Hi, thanks a lot you all! Out of laziness, I wanted to avoid doing the layout by hand from the image file :-) And thanks to Catarina, who sent me the 3D-Positions, I didn't have to. So if anyone ever runs into the same problem, here's a .mat-file with labels, positions (as provided by NeuroScan) and the created layout. Best, Julian ******************************************** Julian Keil International Laboratory for Brain Music and Sound Research (BRAMS) Pavillon 1430 Mont-Royal Université de Montréal Montréal, Québec Canada, H2V 4P3 julian.keil at uni-konstanz.de +1-514-343-6111-29653 www.brams.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NeuroScan64.mat Type: application/x-matlab-workspace Size: 4265 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at fcdonders.ru.nl Tue Apr 17 16:13:46 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Tue, 17 Apr 2012 16:13:46 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <4F8C4094.2020707@Tuebingen.MPG.de> Message-ID: <2082724711.41482.1334672026438.JavaMail.root@sculptor.zimbra.ru.nl> Hi Panagiotis, Good point, thanks. It works for me now. Best, Stan ----- Oorspronkelijk bericht ----- > Van: "Panagiotis Tsiatsis" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Maandag 16 april 2012 17:53:56 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hello girls and guys, > It is working for my CTF MEG data - the version that I have is v4692 > 2011-11-07. > The other thing that might cause a problem could be ommiting the > reference channels definition before the ft_ preprocessing command > that gave you your "dataprepro" > i.e maybe you might need something like this > cfg = []; > ... > //various preprocessing parameters > ... > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > dataprepro = ft_preprocessing(cfg); > Hope you are lucky :) > Best, > Panagiotis > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > Hi Barbara, > > I can replicate your finding, but am unsure what is causing it. > > Maybe > > the difference/correction is lower than the Matlab or CTF precision? > > In any case, if the 3rd order gradients were on, > > ft_denoise_synthetic > > would undo the G3BR-balancing, ergo it toggles. > > Best, > > Stan > > ----- Oorspronkelijk bericht ----- > > > Van: "Michael Wibral" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > > Verzonden: Maandag 16 april 2012 16:46:27 > > > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Hi Barbara, > > > are you certain that the original data do not have 3rd gradients > > > enabled? - looking at them once in dataEditor, switching to 3rd > > > grads > > > and accidentally forgetting to unclick 'save parameters with > > > dataset' > > > will make them have 3rd grads... > > > When I last used ft_denoise_synthetic it worked pretty much as > > > described (??). > > > Michael > > > Gesendet: Montag, 16. April 2012 um 15:56 Uhr > > > Von: "Barbara Haendel" > > > An: fieldtrip at donders.ru.nl > > > Betreff: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Dear fieldtrip users, > > > has anyone experience in using ft_denoise_synthetic? If I try to > > > calculate 3rd order grads in the below specified way the data does > > > not > > > change with respect to the input data (which has no synthetic > > > gradiometer applied). Is there some obvious misunderstanding on my > > > side of how to use this function or is our environment truly > > > noiseless > > > :) > > > Cheers, > > > Barbara > > > cfg=[]; > > > cfg.gradient ='G3BR'; > > > cfg.trials = 'all'; > > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > >> data_3rdorder.grad.balance > > > ans = > > > G1BR: [1x1 struct] > > > G2BR: [1x1 struct] > > > G3BR: [1x1 struct] > > > current: 'G3BR' > > > previous: {'none'} > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > ans = 0 > > > -- > > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > > Jetzt informieren: > > > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > > _______________________________________________ > > > 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 > > -- > > Stan van Pelt > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > University Nijmegen > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > E-mail: stan.vanpelt at donders.ru.nl > > Website: www.ru.nl/donders/ > > Phone: (+31) (0)24 36 10981 > > Fax: (+31) (0)24 36 10989 > > _______________________________________________ > > fieldtrip mailing list fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Stan van Pelt Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 10981 Fax: (+31) (0)24 36 10989 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at mac.com Tue Apr 17 22:39:48 2012 From: nathanweisz at mac.com (Nathan Weisz) Date: Tue, 17 Apr 2012 22:39:48 +0200 Subject: [FieldTrip] postdoc positions @ CIMeC Message-ID: Dear all, not directly fieldtrip related ... I will be soon posting calls for postdoc positions at my new institution: http://www.unitn.it/cimec The postdoc positions will be within a new ERC-funded project (http://cordis.europa.eu/projects/rcn/103253_en.html), which will investigate the role of ongoing oscillatory activity patterns on perception. The studies conducted within this project will mainly use MEG and combined EEG / TMS. Apart from offline studies, relevant brain activity patterns will be used to control experiments in "realtime". I would be interested in getting in touch with postdocs or soon-to-be-postdocs who may be interested in working in such a project. The CIMeC offers access to state-of-the-art neuroimaging / -stimulation facilities along with an international and academically stimulating flair. Needless to say that it is located in a beautiful surrounding for the out-of-the-lab times (especially for mountain and water-sport lovers) and wine + food are not too bad as well. The salary is internationally competetive. Please pass this on to anyone you think might be interested. Best, Nathan -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Wed Apr 18 09:18:04 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 18 Apr 2012 10:18:04 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: Thank you Marianne I did not ask for just viewing the signal only, but to do realtime processing in general. Thanks again Hamza On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne < m.severens at maartenskliniek.nl> wrote: > Hi Hamza > > You first need to start a buffer to read the data from de biosemi device, > so start the biosemi2ft, see here > http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. > Then if you do not change the defaults you do not need to change the > cfg.dataset field for the signal viewer. > > There is also a signal viewer based on c code (so no extra matlab session > is necessary). You can find it here: fieldtrip/realtime/utilities/viewer > > Best, Marianne > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] > Sent: Tuesday, April 17, 2012 8:41 AM > To: Email discussion list for the FieldTrip project > Subject: [FieldTrip] Signal viewer + Biosemi > > Hello, > > I looked I the Signal viewer example in the following page: > http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer > > I just want to know how could I view a signal coming directly from the > biosemi device? > (I think the following line should be changed: > cfg.dataset = 'buffer://localhost:1972'; > but I don't know what to put) > > Thanks for your help > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is > geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking > van deze informatie is conform het Privacy reglement van de Sint > Maartenskliniek. De informatie is uitsluitend bestemd voor de > geadresseerde. Gebruik van deze informatie door anderen dan de > geadresseerde is, zonder voorafgaande schriftelijke toestemming van de > rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de > juiste en volledige overbrenging van de inhoud van een gezonden e-mail, > noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.vandenbroek at donders.ru.nl Wed Apr 18 10:04:34 2012 From: p.vandenbroek at donders.ru.nl (Philip van den Broek) Date: Wed, 18 Apr 2012 10:04:34 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> Hi Hamza, In that case you might be interested in BrainStream (for documentation, see website www.brainstream.nu), which also contains a section about how we connect to all fieldtrip supported devices. Might you be interested in BrainStream, the code can be downloaded from (http://code.google.com/p/brainstream/). Kind Regards Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > Thank you Marianne > > I did not ask for just viewing the signal only, but to do realtime processing in general. > > Thanks again > > Hamza > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne wrote: > Hi Hamza > > You first need to start a buffer to read the data from de biosemi device, so start the biosemi2ft, see here http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. Then if you do not change the defaults you do not need to change the cfg.dataset field for the signal viewer. > > There is also a signal viewer based on c code (so no extra matlab session is necessary). You can find it here: fieldtrip/realtime/utilities/viewer > > Best, Marianne > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] > Sent: Tuesday, April 17, 2012 8:41 AM > To: Email discussion list for the FieldTrip project > Subject: [FieldTrip] Signal viewer + Biosemi > > Hello, > > I looked I the Signal viewer example in the following page: > http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer > > I just want to know how could I view a signal coming directly from the biosemi device? > (I think the following line should be changed: > cfg.dataset = 'buffer://localhost:1972'; > but I don't know what to put) > > Thanks for your help > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 hamzaf at sabanciuniv.edu Wed Apr 18 10:52:16 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 18 Apr 2012 11:52:16 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> Message-ID: Thanks Philip I downloaded the BrainStream code but I did not work with it yet. But when you recommend me to use BrainStream is it because it contains things that fieldtrip functions cannot do or because it is just another alternative for making online experiments? I did not looked carefully at BrainStream webpage, but I feel that fieldtrip is more flexible regarding help and mailing. Regards Hamza On Wed, Apr 18, 2012 at 11:04 AM, Philip van den Broek < p.vandenbroek at donders.ru.nl> wrote: > Hi Hamza, > > In that case you might be interested in BrainStream (for documentation, > see website www.brainstream.nu), which also contains a section about how > we connect to all fieldtrip supported devices. Might you be interested in > BrainStream, the code can be downloaded from ( > http://code.google.com/p/brainstream/). > > Kind Regards > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > > Thank you Marianne > > I did not ask for just viewing the signal only, but to do realtime > processing in general. > > Thanks again > > Hamza > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne < > m.severens at maartenskliniek.nl> wrote: > >> Hi Hamza >> >> You first need to start a buffer to read the data from de biosemi device, >> so start the biosemi2ft, see here >> http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. >> Then if you do not change the defaults you do not need to change the >> cfg.dataset field for the signal viewer. >> >> There is also a signal viewer based on c code (so no extra matlab session >> is necessary). You can find it here: fieldtrip/realtime/utilities/viewer >> >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] >> On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >> Sent: Tuesday, April 17, 2012 8:41 AM >> To: Email discussion list for the FieldTrip project >> Subject: [FieldTrip] Signal viewer + Biosemi >> >> Hello, >> >> I looked I the Signal viewer example in the following page: >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >> >> I just want to know how could I view a signal coming directly from the >> biosemi device? >> (I think the following line should be changed: >> cfg.dataset = 'buffer://localhost:1972'; >> but I don't know what to put) >> >> Thanks for your help >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking >> van deze informatie is conform het Privacy reglement van de Sint >> Maartenskliniek. De informatie is uitsluitend bestemd voor de >> geadresseerde. Gebruik van deze informatie door anderen dan de >> geadresseerde is, zonder voorafgaande schriftelijke toestemming van de >> rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de >> juiste en volledige overbrenging van de inhoud van een gezonden e-mail, >> noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.vandenbroek at donders.ru.nl Wed Apr 18 12:10:54 2012 From: p.vandenbroek at donders.ru.nl (Philip van den Broek) Date: Wed, 18 Apr 2012 12:10:54 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> Message-ID: <2ADC0647-2CD2-4F84-8A1D-BAB78AB57E68@donders.ru.nl> Hi Hamza, > But when you recommend me to use BrainStream is it because it contains things that fieldtrip functions cannot do or because it is just another alternative for making online experiments? No, you should be able to do everything with fieldtrip. It is indeed another alternative for making online experiments with a different approach, which I thought might be of interest to you (or in general to anyone else involved in conducting real-time (BCI) experiments), but in the end off course that's something you can only decide. BrainStream is designed specifically for defining and executing real-time experiments and uses fieldtrips realtime buffer and hardware interfacing solutions (i.e., biosemi2ft, tmsi2ft etc.). It has all kind of built-in solutions for starting extra Matlab clients, automatic parallel execution, easy access to and switching between devices, information exchange, simulating from file or random data. In the design, you can use any Matlab code, including fieldtrip functions. However, you need to learn its specific way of defining experiments. Kind regards Philip > > Regards > > Hamza > > On Wed, Apr 18, 2012 at 11:04 AM, Philip van den Broek wrote: > Hi Hamza, > > In that case you might be interested in BrainStream (for documentation, see website www.brainstream.nu), which also contains a section about how we connect to all fieldtrip supported devices. Might you be interested in BrainStream, the code can be downloaded from (http://code.google.com/p/brainstream/). > > Kind Regards > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > >> Thank you Marianne >> >> I did not ask for just viewing the signal only, but to do realtime processing in general. >> >> Thanks again >> >> Hamza >> >> On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne wrote: >> Hi Hamza >> >> You first need to start a buffer to read the data from de biosemi device, so start the biosemi2ft, see here http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. Then if you do not change the defaults you do not need to change the cfg.dataset field for the signal viewer. >> >> There is also a signal viewer based on c code (so no extra matlab session is necessary). You can find it here: fieldtrip/realtime/utilities/viewer >> >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >> Sent: Tuesday, April 17, 2012 8:41 AM >> To: Email discussion list for the FieldTrip project >> Subject: [FieldTrip] Signal viewer + Biosemi >> >> Hello, >> >> I looked I the Signal viewer example in the following page: >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >> >> I just want to know how could I view a signal coming directly from the biosemi device? >> (I think the following line should be changed: >> cfg.dataset = 'buffer://localhost:1972'; >> but I don't know what to put) >> >> Thanks for your help >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> _______________________________________________ >> 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 > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 hamzaf at sabanciuniv.edu Wed Apr 18 16:30:55 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 18 Apr 2012 17:30:55 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: <2ADC0647-2CD2-4F84-8A1D-BAB78AB57E68@donders.ru.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> <2ADC0647-2CD2-4F84-8A1D-BAB78AB57E68@donders.ru.nl> Message-ID: Thanks a lot Philip for the information. Regards Hamza On Wed, Apr 18, 2012 at 1:10 PM, Philip van den Broek < p.vandenbroek at donders.ru.nl> wrote: > Hi Hamza, > > But when you recommend me to use BrainStream is it because it contains > things that fieldtrip functions cannot do or because it is just another > alternative for making online experiments? > > No, you should be able to do everything with fieldtrip. It is indeed > another alternative for making online experiments with a different > approach, which I thought might be of interest to you (or in general to > anyone else involved in conducting real-time (BCI) experiments), but in the > end off course that's something you can only decide. > BrainStream is designed specifically for defining and executing real-time > experiments and uses fieldtrips realtime buffer and hardware interfacing > solutions (i.e., biosemi2ft, tmsi2ft etc.). It has all kind of built-in > solutions for starting extra Matlab clients, automatic parallel execution, > easy access to and switching between devices, information exchange, > simulating from file or random data. In the design, you can use any Matlab > code, including fieldtrip functions. However, you need to learn its > specific way of defining experiments. > > Kind regards > Philip > > > > Regards > > Hamza > > On Wed, Apr 18, 2012 at 11:04 AM, Philip van den Broek < > p.vandenbroek at donders.ru.nl> wrote: > >> Hi Hamza, >> >> In that case you might be interested in BrainStream (for documentation, >> see website www.brainstream.nu), which also contains a section about how >> we connect to all fieldtrip supported devices. Might you be interested in >> BrainStream, the code can be downloaded from ( >> http://code.google.com/p/brainstream/). >> >> Kind Regards >> >> Philip van den Broek >> Radboud University Nijmegen >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> >> On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: >> >> Thank you Marianne >> >> I did not ask for just viewing the signal only, but to do realtime >> processing in general. >> >> Thanks again >> >> Hamza >> >> On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne < >> m.severens at maartenskliniek.nl> wrote: >> >>> Hi Hamza >>> >>> You first need to start a buffer to read the data from de biosemi >>> device, so start the biosemi2ft, see here >>> http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. >>> Then if you do not change the defaults you do not need to change the >>> cfg.dataset field for the signal viewer. >>> >>> There is also a signal viewer based on c code (so no extra matlab >>> session is necessary). You can find it here: >>> fieldtrip/realtime/utilities/viewer >>> >>> Best, Marianne >>> ________________________________________ >>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] >>> On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >>> Sent: Tuesday, April 17, 2012 8:41 AM >>> To: Email discussion list for the FieldTrip project >>> Subject: [FieldTrip] Signal viewer + Biosemi >>> >>> Hello, >>> >>> I looked I the Signal viewer example in the following page: >>> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >>> >>> I just want to know how could I view a signal coming directly from the >>> biosemi device? >>> (I think the following line should be changed: >>> cfg.dataset = 'buffer://localhost:1972'; >>> but I don't know what to put) >>> >>> Thanks for your help >>> >>> >>> -- >>> Hamza Fawzi Altakroury >>> Graduate student - MA >>> Faculty of Engineering and Natural Sciences >>> Sabancı University >>> >>> Disclaimer >>> Vrijgave van de informatie verzonden met dit e-mail bericht is >>> geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking >>> van deze informatie is conform het Privacy reglement van de Sint >>> Maartenskliniek. De informatie is uitsluitend bestemd voor de >>> geadresseerde. Gebruik van deze informatie door anderen dan de >>> geadresseerde is, zonder voorafgaande schriftelijke toestemming van de >>> rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de >>> juiste en volledige overbrenging van de inhoud van een gezonden e-mail, >>> noch voor de ontvangst daarvan. >>> >>> Sint Maartenskliniek >>> Hengstdal 3, >>> 6574 NA Ubbergen (bij Nijmegen) >>> Telefoon 024-3659 911 >>> Telefax 024-3659 204 >>> KvK nummer 41055111 >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> _______________________________________________ >> 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 >> > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Wed Apr 18 23:02:49 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Wed, 18 Apr 2012 23:02:49 +0200 Subject: [FieldTrip] Function ft_prepare_bemmodel deprecated... In-Reply-To: References: Message-ID: Hello diana, thanks for reporting the API change. I'll see if I can update the scripts: openmeeg_eeg_leadfield_example.m openmeeg_meg_leadfield_example.m feel free to give it a try if I am not too reactive... Alex On Tue, Apr 17, 2012 at 10:33 AM, Diana Ibanescu wrote: > Hello, > > I am interested in an example how to compute an EEG leadfield with OpenMEEG > in the Fieldtrip toolbox. I found a demo script here: > http://fieldtrip.fcdonders.nl/example/testing_bem_created_leadfields > When I call the function ft_prepare_bemmodel(cfg, vol) I receive the > following warning: > "Warning: FT_PREPARE_BEMMODEL is deprecated, please use FT_HEADMODEL_BEM_... > with cfg.method = 'bem_bladeebla' > instead." > The function ft_headmodel_bem_openmeeg receive as parameter "geom" while > ft_prepare_bemmodel receive other parameters: >  vol = ft_headmodel_openmeeg(geom, ...) > >   Optional input arguments should be specified in key-value pairs and can >   include >     isolatedsource   = string, 'yes' or 'no' >     hdmfile          = string, filename with BEM headmodel >     conductivity     = vector, conductivity of each compartment > > Are the 2 functions similar? Is there any demo updated after the function > ft_prepare_bemmodel became deprecated? What function can I use instead? > > Thank you, > Diana. > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From B.Haendel at gmx.net Thu Apr 19 08:59:39 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Thu, 19 Apr 2012 08:59:39 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <4F8C4094.2020707@Tuebingen.MPG.de> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de> Message-ID: <20120419065939.195940@gmx.net> Hey there, thanks a lot for the replies! Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. Thanks again, Barbara -------- Original-Nachricht -------- > Datum: Mon, 16 Apr 2012 17:53:56 +0200 > Von: Panagiotis Tsiatsis > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hello girls and guys, > > It is working for my CTF MEG data - the version that I have is v4692 > 2011-11-07. > > The other thing that might cause a problem could be ommiting the > reference channels definition before the ft_ preprocessing command that > gave you your "dataprepro" > > i.e maybe you might need something like this > > cfg = []; > > ... > //various preprocessing parameters > ... > > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > > dataprepro = ft_preprocessing(cfg); > > > Hope you are lucky :) > > Best, > Panagiotis > > > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > Hi Barbara, > > > > I can replicate your finding, but am unsure what is causing it. Maybe > > the difference/correction is lower than the Matlab or CTF precision? > > In any case, if the 3rd order gradients were on, ft_denoise_synthetic > > would undo the G3BR-balancing, ergo it toggles. > > > > Best, > > Stan > > > > > > ------------------------------------------------------------------------ > > > > *Van: *"Michael Wibral" > > *Aan: *"Email discussion list for the FieldTrip project" > > > > *Verzonden: *Maandag 16 april 2012 16:46:27 > > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Hi Barbara, > > > > are you certain that the original data do not have 3rd gradients > > enabled? - looking at them once in dataEditor, switching to 3rd > > grads and accidentally forgetting to unclick 'save parameters with > > dataset' will make them have 3rd grads... > > > > When I last used ft_denoise_synthetic it worked pretty much as > > described (??). > > > > Michael > > > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > > *Von:* "Barbara Haendel" > > *An:* fieldtrip at donders.ru.nl > > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Dear fieldtrip users, > > > > has anyone experience in using ft_denoise_synthetic? If I try to > > calculate 3rd order grads in the below specified way the data does > > not change with respect to the input data (which has no synthetic > > gradiometer applied). Is there some obvious misunderstanding on my > > side of how to use this function or is our environment truly > > noiseless :) > > > > Cheers, > > Barbara > > > > cfg=[]; > > cfg.gradient ='G3BR'; > > cfg.trials = 'all'; > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > > > > >> data_3rdorder.grad.balance > > > > ans = > > > > G1BR: [1x1 struct] > > G2BR: [1x1 struct] > > G3BR: [1x1 struct] > > current: 'G3BR' > > previous: {'none'} > > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > > ans = 0 > > > > -- > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > Jetzt informieren: > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > _______________________________________________ > > 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 > > > > > > > > > > -- > > Stan van Pelt > > > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > University Nijmegen > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > E-mail: stan.vanpelt at donders.ru.nl > > Website: www.ru.nl/donders/ > > Phone: (+31) (0)24 36 10981 > > Fax: (+31) (0)24 36 10989 > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From B.Haendel at gmx.net Thu Apr 19 08:59:39 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Thu, 19 Apr 2012 08:59:39 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <4F8C4094.2020707@Tuebingen.MPG.de> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de> Message-ID: <20120419065939.195940@gmx.net> Hey there, thanks a lot for the replies! Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. Thanks again, Barbara -------- Original-Nachricht -------- > Datum: Mon, 16 Apr 2012 17:53:56 +0200 > Von: Panagiotis Tsiatsis > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hello girls and guys, > > It is working for my CTF MEG data - the version that I have is v4692 > 2011-11-07. > > The other thing that might cause a problem could be ommiting the > reference channels definition before the ft_ preprocessing command that > gave you your "dataprepro" > > i.e maybe you might need something like this > > cfg = []; > > ... > //various preprocessing parameters > ... > > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > > dataprepro = ft_preprocessing(cfg); > > > Hope you are lucky :) > > Best, > Panagiotis > > > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > Hi Barbara, > > > > I can replicate your finding, but am unsure what is causing it. Maybe > > the difference/correction is lower than the Matlab or CTF precision? > > In any case, if the 3rd order gradients were on, ft_denoise_synthetic > > would undo the G3BR-balancing, ergo it toggles. > > > > Best, > > Stan > > > > > > ------------------------------------------------------------------------ > > > > *Van: *"Michael Wibral" > > *Aan: *"Email discussion list for the FieldTrip project" > > > > *Verzonden: *Maandag 16 april 2012 16:46:27 > > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Hi Barbara, > > > > are you certain that the original data do not have 3rd gradients > > enabled? - looking at them once in dataEditor, switching to 3rd > > grads and accidentally forgetting to unclick 'save parameters with > > dataset' will make them have 3rd grads... > > > > When I last used ft_denoise_synthetic it worked pretty much as > > described (??). > > > > Michael > > > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > > *Von:* "Barbara Haendel" > > *An:* fieldtrip at donders.ru.nl > > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Dear fieldtrip users, > > > > has anyone experience in using ft_denoise_synthetic? If I try to > > calculate 3rd order grads in the below specified way the data does > > not change with respect to the input data (which has no synthetic > > gradiometer applied). Is there some obvious misunderstanding on my > > side of how to use this function or is our environment truly > > noiseless :) > > > > Cheers, > > Barbara > > > > cfg=[]; > > cfg.gradient ='G3BR'; > > cfg.trials = 'all'; > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > > > > >> data_3rdorder.grad.balance > > > > ans = > > > > G1BR: [1x1 struct] > > G2BR: [1x1 struct] > > G3BR: [1x1 struct] > > current: 'G3BR' > > previous: {'none'} > > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > > ans = 0 > > > > -- > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > Jetzt informieren: > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > _______________________________________________ > > 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 > > > > > > > > > > -- > > Stan van Pelt > > > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > University Nijmegen > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > E-mail: stan.vanpelt at donders.ru.nl > > Website: www.ru.nl/donders/ > > Phone: (+31) (0)24 36 10981 > > Fax: (+31) (0)24 36 10989 > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From jan.schoffelen at donders.ru.nl Thu Apr 19 10:02:43 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 19 Apr 2012 10:02:43 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <20120419065939.195940@gmx.net> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de> <20120419065939.195940@gmx.net> Message-ID: Hi Barbara, Good plan to adjust the code a bit in this respect. Could you please file a bug about this on our bugzilla list: bugzilla.fcdonders.nl Best wishes, Jan-Mathijs On Apr 19, 2012, at 8:59 AM, Barbara Haendel wrote: > > > Hey there, thanks a lot for the replies! > > Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. > > Thanks again, > Barbara > > > > > -------- Original-Nachricht -------- >> Datum: Mon, 16 Apr 2012 17:53:56 +0200 >> Von: Panagiotis Tsiatsis >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > >> Hello girls and guys, >> >> It is working for my CTF MEG data - the version that I have is v4692 >> 2011-11-07. >> >> The other thing that might cause a problem could be ommiting the >> reference channels definition before the ft_ preprocessing command that >> gave you your "dataprepro" >> >> i.e maybe you might need something like this >> >> cfg = []; >> >> ... >> //various preprocessing parameters >> ... >> >> cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; >> >> dataprepro = ft_preprocessing(cfg); >> >> >> Hope you are lucky :) >> >> Best, >> Panagiotis >> >> >> On 4/16/2012 4:59 PM, Stan van Pelt wrote: >>> Hi Barbara, >>> >>> I can replicate your finding, but am unsure what is causing it. Maybe >>> the difference/correction is lower than the Matlab or CTF precision? >>> In any case, if the 3rd order gradients were on, ft_denoise_synthetic >>> would undo the G3BR-balancing, ergo it toggles. >>> >>> Best, >>> Stan >>> >>> >>> ------------------------------------------------------------------------ >>> >>> *Van: *"Michael Wibral" >>> *Aan: *"Email discussion list for the FieldTrip project" >>> >>> *Verzonden: *Maandag 16 april 2012 16:46:27 >>> *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad >>> >>> Hi Barbara, >>> >>> are you certain that the original data do not have 3rd gradients >>> enabled? - looking at them once in dataEditor, switching to 3rd >>> grads and accidentally forgetting to unclick 'save parameters with >>> dataset' will make them have 3rd grads... >>> >>> When I last used ft_denoise_synthetic it worked pretty much as >>> described (??). >>> >>> Michael >>> >>> *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr >>> *Von:* "Barbara Haendel" >>> *An:* fieldtrip at donders.ru.nl >>> *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad >>> >>> Dear fieldtrip users, >>> >>> has anyone experience in using ft_denoise_synthetic? If I try to >>> calculate 3rd order grads in the below specified way the data does >>> not change with respect to the input data (which has no synthetic >>> gradiometer applied). Is there some obvious misunderstanding on my >>> side of how to use this function or is our environment truly >>> noiseless :) >>> >>> Cheers, >>> Barbara >>> >>> cfg=[]; >>> cfg.gradient ='G3BR'; >>> cfg.trials = 'all'; >>> data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); >>> >>> >>>>> data_3rdorder.grad.balance >>> >>> ans = >>> >>> G1BR: [1x1 struct] >>> G2BR: [1x1 struct] >>> G3BR: [1x1 struct] >>> current: 'G3BR' >>> previous: {'none'} >>> >>>>> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) >>> >>> ans = 0 >>> >>> -- >>> NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! >>> Jetzt informieren: >> http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a >>> _______________________________________________ >>> 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 >>> >>> >>> >>> >>> -- >>> Stan van Pelt >>> >>> Donders Institute for Brain, Cognition and Behaviour, Radboud >>> University Nijmegen >>> Kapittelweg 29, 6525 EN Nijmegen, Netherlands >>> E-mail: stan.vanpelt at donders.ru.nl >>> Website: www.ru.nl/donders/ >>> Phone: (+31) (0)24 36 10981 >>> Fax: (+31) (0)24 36 10989 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Panagiotis S. Tsiatsis >> Max Planck Institute for Biological Cybernetics >> Cognitive NeuroImaging Group >> Tuebingen, Germany >> > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Thu Apr 19 10:24:57 2012 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 19 Apr 2012 10:24:57 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <20120419065939.195940@gmx.net> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de>, <20120419065939.195940@gmx.net> Message-ID: An HTML attachment was scrubbed... URL: From B.Haendel at gmx.net Thu Apr 19 11:01:59 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Thu, 19 Apr 2012 11:01:59 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de>, <20120419065939.195940@gmx.net> Message-ID: <20120419090159.195980@gmx.net> Hey Michael, I completely agree that there should be a warning especially because the specification in data.grad.balance.current is consequently wrong. As Jan-Mathijs suggested I filed a bug report to fieldtrip. Best, Barbara -------- Original-Nachricht -------- > Datum: Thu, 19 Apr 2012 10:24:57 +0200 (CEST) > Von: "Michael Wibral" > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de From b.reuderink at donders.ru.nl Thu Apr 19 12:48:03 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 19 Apr 2012 12:48:03 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: Dear Hamza, Could you perhaps elaborate on your question? I was also under the impression that you asked how to view the (real time) Biosemi signals --- which Marianne explained. What are you trying to achieve, what is your approach, and on what aspect are you asking for help? Best, Boris On Wed, Apr 18, 2012 at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > Thank you Marianne > > I did not ask for just viewing the signal only, but to do realtime > processing in general. > > Thanks again > > Hamza > > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne > wrote: >> >> Hi Hamza >> >> You first need to start a buffer to read the data from de biosemi device, >> so start the biosemi2ft, see here >> http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. >> Then if you do not change the defaults you do not need to change the >> cfg.dataset field for the signal viewer. >> >> There is also a signal viewer based on c code (so no extra matlab session >> is necessary). You can find it here: fieldtrip/realtime/utilities/viewer >> >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On >> Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >> Sent: Tuesday, April 17, 2012 8:41 AM >> To: Email discussion list for the FieldTrip project >> Subject: [FieldTrip] Signal viewer + Biosemi >> >> Hello, >> >> I looked I the Signal viewer example in the following page: >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >> >> I just want to know how could I view a signal coming directly from the >> biosemi device? >> (I think the following line should be changed: >>  cfg.dataset        = 'buffer://localhost:1972'; >> but I don't know what to put) >> >> Thanks for your help >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van >> deze informatie is conform het Privacy reglement van de Sint >> Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. >> Gebruik van deze informatie door anderen dan de geadresseerde is, zonder >> voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De >> Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging >> van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From alexandre.gramfort at inria.fr Fri Apr 20 09:13:33 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 20 Apr 2012 09:13:33 +0200 Subject: [FieldTrip] Function ft_prepare_bemmodel deprecated... In-Reply-To: References: Message-ID: Hello Diana, I've just fixed on the svn the OpenMEEG demo scripts which had accidentally been broken. Once you update your version, you should now be able to run: openmeeg_eeg_leadfield_example.m  openmeeg_meg_leadfield_example.m which will confirm that OpenMEEG works as expected. Best, Alex On Wed, Apr 18, 2012 at 11:02 PM, Alexandre Gramfort wrote: > Hello diana, > > thanks for reporting the API change. > > I'll see if I can update the scripts: > > openmeeg_eeg_leadfield_example.m  openmeeg_meg_leadfield_example.m > > feel free to give it a try if I am not too reactive... > > Alex > > On Tue, Apr 17, 2012 at 10:33 AM, Diana Ibanescu > wrote: >> Hello, >> >> I am interested in an example how to compute an EEG leadfield with OpenMEEG >> in the Fieldtrip toolbox. I found a demo script here: >> http://fieldtrip.fcdonders.nl/example/testing_bem_created_leadfields >> When I call the function ft_prepare_bemmodel(cfg, vol) I receive the >> following warning: >> "Warning: FT_PREPARE_BEMMODEL is deprecated, please use FT_HEADMODEL_BEM_... >> with cfg.method = 'bem_bladeebla' >> instead." >> The function ft_headmodel_bem_openmeeg receive as parameter "geom" while >> ft_prepare_bemmodel receive other parameters: >>  vol = ft_headmodel_openmeeg(geom, ...) >> >>   Optional input arguments should be specified in key-value pairs and can >>   include >>     isolatedsource   = string, 'yes' or 'no' >>     hdmfile          = string, filename with BEM headmodel >>     conductivity     = vector, conductivity of each compartment >> >> Are the 2 functions similar? Is there any demo updated after the function >> ft_prepare_bemmodel became deprecated? What function can I use instead? >> >> Thank you, >> Diana. >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> From hamzaf at sabanciuniv.edu Sat Apr 21 09:28:57 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 21 Apr 2012 10:28:57 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: Dear Boris Due to my misunderstanding I thought the realtime processing is done by reading the data from a gdf file that is created by the biosemi2ft function. Reading the signal viewer discription on your site made me understand the realtime processing and reading from a buffter. To read the data from the biosemi I thought I should change the address (cfg.dataset = 'buffer://localhost:1972';), but, thanks to Marianne, I could view the signals easily from biosemi by keeping the line as it is. The command lines that I typed are: In cmd: *biosemi2ft example.config.txt out - *In MatLab: *cfg = []; * *cfg.blocksize = 1; % seconds * *cfg.dataset = 'buffer://localhost:1972'; % where to read the data* Best, Hamza On Thu, Apr 19, 2012 at 1:48 PM, Boris Reuderink wrote: > Dear Hamza, > > Could you perhaps elaborate on your question? I was also under the > impression that you asked how to view the (real time) Biosemi signals > --- which Marianne explained. What are you trying to achieve, what is > your approach, and on what aspect are you asking for help? > > Best, > > Boris > > On Wed, Apr 18, 2012 at 9:18 AM, Hamza Fawzi Altakroury (Student) > wrote: > > Thank you Marianne > > > > I did not ask for just viewing the signal only, but to do realtime > > processing in general. > > > > Thanks again > > > > Hamza > > > > > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne > > wrote: > >> > >> Hi Hamza > >> > >> You first need to start a buffer to read the data from de biosemi > device, > >> so start the biosemi2ft, see here > >> > http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. > >> Then if you do not change the defaults you do not need to change the > >> cfg.dataset field for the signal viewer. > >> > >> There is also a signal viewer based on c code (so no extra matlab > session > >> is necessary). You can find it here: fieldtrip/realtime/utilities/viewer > >> > >> Best, Marianne > >> ________________________________________ > >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > On > >> Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] > >> Sent: Tuesday, April 17, 2012 8:41 AM > >> To: Email discussion list for the FieldTrip project > >> Subject: [FieldTrip] Signal viewer + Biosemi > >> > >> Hello, > >> > >> I looked I the Signal viewer example in the following page: > >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer > >> > >> I just want to know how could I view a signal coming directly from the > >> biosemi device? > >> (I think the following line should be changed: > >> cfg.dataset = 'buffer://localhost:1972'; > >> but I don't know what to put) > >> > >> Thanks for your help > >> > >> > >> -- > >> Hamza Fawzi Altakroury > >> Graduate student - MA > >> Faculty of Engineering and Natural Sciences > >> Sabancı University > >> > >> Disclaimer > >> Vrijgave van de informatie verzonden met dit e-mail bericht is > >> geaccordeerd door de ontvanger en/of zijn behandelend arts. > Verstrekking van > >> deze informatie is conform het Privacy reglement van de Sint > >> Maartenskliniek. De informatie is uitsluitend bestemd voor de > geadresseerde. > >> Gebruik van deze informatie door anderen dan de geadresseerde is, zonder > >> voorafgaande schriftelijke toestemming van de rechthebbende , verboden. > De > >> Sint Maartenskliniek staat niet in voor de juiste en volledige > overbrenging > >> van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > >> > >> Sint Maartenskliniek > >> Hengstdal 3, > >> 6574 NA Ubbergen (bij Nijmegen) > >> Telefoon 024-3659 911 > >> Telefax 024-3659 204 > >> KvK nummer 41055111 > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > twitter.com/#!/breuderink | > github.com/breuderink | borisreuderink.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at gmx.de Sun Apr 22 09:07:06 2012 From: paul_c at gmx.de (Paul Czienskowski) Date: Sun, 22 Apr 2012 09:07:06 +0200 Subject: [FieldTrip] Question concerning ft_headmodel_bem_openmeeg Message-ID: <4F93AE1A.50405@gmx.de> Dear all, I want to create headmodels with the ft_headmodel_bem_openmeeg function, and - for I formerly used the ft_prepare_bemmodel function - decided to delve into the new function first, to see how it works. Anyway, I stumbled upon something that puzzled me a bit. In line 96 to 106, the boundaries are rearranged to be inside first, which to my understanding means, that the first boundary in the array of boundaries will be the innermost one (i.e. the brain in my case) and the last boundary will be the outermost one (i.e. skin). Everything's fine hitherto. But from line 108 on, things become quite odd. Line 108 and 109 define the first compartment to be the skin and the last to be the source compartment. This is cross-checked again in line 127 to 129. To my understanding this is a contradiction and I would appreciate, if anybody could tell me if I got something completely wrong, or if the function does odd things. If the function is correct, there should at least be a comment explaining why this contradiction makes sense anyway. Best regards, Paul From matt.mollison at gmail.com Mon Apr 23 05:54:33 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Sun, 22 Apr 2012 21:54:33 -0600 Subject: [FieldTrip] Oscillatory power normalization Message-ID: Hi FieldTrippers, In almost all the papers I've read involving oscillatory power, some kind of transformation is done to the data due to the 1/f power spectrum effect (power decreases as frequency increases). I'm mostly looking at within-subjects experiments (every subject behaved in all conditions) comparing conditions across subjects, but it seems like normalizing the power spectrum should apply in any case (especially if any kind of parametric stats are done—right?). Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis to make these transformations (e.g., log10 normalization, dB normalization [EEGLab does this], vector length normalization, etc.; the only thing I see is in ft_sourcedescriptives, but I'm not doing source analyses), and it confuses me why this is the case. I can't find much discussion regarding the 1/f issue on the FT wiki or the mailing list. This seems like an important step that is missing from any frequency analysis workflow. Am I missing something (meaning I just don't see the option), am I misunderstanding something (meaning I'm incorrect in this assumption), or is this an issue that needs to be fixed? Thanks, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon Apr 23 08:49:00 2012 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Mon, 23 Apr 2012 08:49:00 +0200 Subject: [FieldTrip] Oscillatory power normalization In-Reply-To: References: Message-ID: <6CC16DD9-C72B-4CA4-A7C9-D504BBCF9447@psi.ucm.es> Hi Matt, I think Fieltrip does not do these transformations. However you could do cfg.baselinetype = 'relative' (power post/power pre) and take the log10 and multiply by 10 (TF.powerspctrm). Then you should have dB. best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 23/04/2012, a las 05:54, Matt Mollison escribió: > Hi FieldTrippers, > > In almost all the papers I've read involving oscillatory power, some kind of transformation is done to the data due to the 1/f power spectrum effect (power decreases as frequency increases). I'm mostly looking at within-subjects experiments (every subject behaved in all conditions) comparing conditions across subjects, but it seems like normalizing the power spectrum should apply in any case (especially if any kind of parametric stats are done—right?). > > Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis to make these transformations (e.g., log10 normalization, dB normalization [EEGLab does this], vector length normalization, etc.; the only thing I see is in ft_sourcedescriptives, but I'm not doing source analyses), and it confuses me why this is the case. I can't find much discussion regarding the 1/f issue on the FT wiki or the mailing list. This seems like an important step that is missing from any frequency analysis workflow. Am I missing something (meaning I just don't see the option), am I misunderstanding something (meaning I'm incorrect in this assumption), or is this an issue that needs to be fixed? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > _______________________________________________ > 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 eelke.spaak at donders.ru.nl Mon Apr 23 11:54:42 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 23 Apr 2012 11:54:42 +0200 Subject: [FieldTrip] Oscillatory power normalization In-Reply-To: References: Message-ID: Hi Matt, When you are comparing power across conditions, it is not really necessary to apply an explicit correction for the dominant 1/f component of the raw spectrum. Since this 1/f component is present in both conditions, when you subtract power in one condition from power in another condition (or compute the ratio, or log-ratio, or relative change, or whatever), the 1/f will cancel out and you will only be left with whatever is due to your experimental manipulation. This is true because the contrast is done per frequency. (Note that comparing activity versus baseline is just a special case of looking at a contrast between conditions, so the same argument holds there.) The only time when an explicit correction for 1/f is useful, is when you want to look at raw power. The most dominant oscillatory features (visual alpha, visual contrast induced gamma...) will usually be evident in raw spectra without such a correction, by the way. Correcting for 1/f can be done in many ways, the most simple one is simply taking the logarithm of power, something like: freqCorrected = freqUncorrected; freqCorrected.powspctrm = log10(freqCorrected.powspctrm); Or you could take the first derivative in the time domain (equivalent to multiplying the spectrum with f, search for post by Robert on this on the FT list). Or you could take the log of both the frequency- and power axes, then fit a line, and subtract it, then transform back (10^corrected data). But, the main point is: in the vast majority of typical cognitive experiments, correcting for 1/f is not needed. Best, Eelke On 23 April 2012 05:54, Matt Mollison wrote: > Hi FieldTrippers, > > In almost all the papers I've read involving oscillatory power, some kind of > transformation is done to the data due to the 1/f power spectrum effect > (power decreases as frequency increases). I'm mostly looking at > within-subjects experiments (every subject behaved in all conditions) > comparing conditions across subjects, but it seems like normalizing the > power spectrum should apply in any case (especially if any kind of > parametric stats are done—right?). > > Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis > to make these transformations (e.g., log10 normalization, dB normalization > [EEGLab does this], vector length normalization, etc.; the only thing I see > is in ft_sourcedescriptives, but I'm not doing source analyses), and it > confuses me why this is the case. I can't find much discussion regarding the > 1/f issue on the FT wiki or the mailing list. This seems like an important > step that is missing from any frequency analysis workflow. Am I missing > something (meaning I just don't see the option), am I misunderstanding > something (meaning I'm incorrect in this assumption), or is this an issue > that needs to be fixed? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jdien07 at mac.com Tue Apr 24 08:41:20 2012 From: jdien07 at mac.com (Joseph Dien) Date: Tue, 24 Apr 2012 02:41:20 -0400 Subject: [FieldTrip] Oscillatory power normalization In-Reply-To: References: Message-ID: <454AC917-60FD-4CF6-BF21-242DF4B5B4D0@mac.com> I'm new to spectral analysis so take anything I say with a grain of salt: 1) If one intends on taking the average of a band (like 8-12Hz for alpha), seems like maybe helpful to correct for 1/f so the lower bands don't dominate? 2) Another issue is spectral density (correcting for frequency bin width for discrete Fourier). As far as I can tell, FieldTrip isn't doing this. Seems like it should be standard. Or at least it should say in the documentation whether it is being done. Am I wrong? Cheers! Joe On Apr 23, 2012, at 5:54 AM, Eelke Spaak wrote: > Hi Matt, > > When you are comparing power across conditions, it is not really > necessary to apply an explicit correction for the dominant 1/f > component of the raw spectrum. Since this 1/f component is present in > both conditions, when you subtract power in one condition from power > in another condition (or compute the ratio, or log-ratio, or relative > change, or whatever), the 1/f will cancel out and you will only be > left with whatever is due to your experimental manipulation. This is > true because the contrast is done per frequency. (Note that comparing > activity versus baseline is just a special case of looking at a > contrast between conditions, so the same argument holds there.) > > The only time when an explicit correction for 1/f is useful, is when > you want to look at raw power. The most dominant oscillatory features > (visual alpha, visual contrast induced gamma...) will usually be > evident in raw spectra without such a correction, by the way. > Correcting for 1/f can be done in many ways, the most simple one is > simply taking the logarithm of power, something like: > > freqCorrected = freqUncorrected; > freqCorrected.powspctrm = log10(freqCorrected.powspctrm); > > Or you could take the first derivative in the time domain (equivalent > to multiplying the spectrum with f, search for post by Robert on this > on the FT list). Or you could take the log of both the frequency- and > power axes, then fit a line, and subtract it, then transform back > (10^corrected data). > > But, the main point is: in the vast majority of typical cognitive > experiments, correcting for 1/f is not needed. > > Best, > Eelke > > On 23 April 2012 05:54, Matt Mollison wrote: >> Hi FieldTrippers, >> >> In almost all the papers I've read involving oscillatory power, some kind of >> transformation is done to the data due to the 1/f power spectrum effect >> (power decreases as frequency increases). I'm mostly looking at >> within-subjects experiments (every subject behaved in all conditions) >> comparing conditions across subjects, but it seems like normalizing the >> power spectrum should apply in any case (especially if any kind of >> parametric stats are done—right?). >> >> Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis >> to make these transformations (e.g., log10 normalization, dB normalization >> [EEGLab does this], vector length normalization, etc.; the only thing I see >> is in ft_sourcedescriptives, but I'm not doing source analyses), and it >> confuses me why this is the case. I can't find much discussion regarding the >> 1/f issue on the FT wiki or the mailing list. This seems like an important >> step that is missing from any frequency analysis workflow. Am I missing >> something (meaning I just don't see the option), am I misunderstanding >> something (meaning I'm incorrect in this assumption), or is this an issue >> that needs to be fixed? >> >> Thanks, >> Matt >> >> -- >> Univ. of Colorado at Boulder >> Dept. of Psychology and Neuroscience >> matthew.mollison at colorado.edu >> http://psych.colorado.edu/~mollison/ >> >> _______________________________________________ >> 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 -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ From stan.vanpelt at fcdonders.ru.nl Tue Apr 24 10:14:54 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Tue, 24 Apr 2012 10:14:54 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: Message-ID: <506536226.7942.1335255294672.JavaMail.root@sculptor.zimbra.ru.nl> Hi all, A follow-up question on the implementation of 3rd-order gradiometer correction in FT: I am puzzling how one can do both 3-order grad. correction and dft-filtering properly using FT. the logical sequency would be to do ft_denoise_synthetic first, and subsequently dft-filtering using ft_preprocessing. However, in that case it is no longer possible to pad the data when calling ft_preprocessing, because it now processes trial-data (output from ft_denoise_synthetic), and doesn't read in the original dataset anymore. or am I mistaken here? I could see 3 alternatives, which seem to be more like (computationally) suboptimal workarounds: - Apply ft_denoise_synthetic on the entire dataset, then dft-filter the entire dataset, and then run ft_redefinetrial to cut the data into actual trials - Adjust the trial definition such that longer data segments are read in, equivalent to your padding size. Then apply ft_denoise_synthetic on these trials, then dft-filter them, and then run ft_redefinetrial to cut the data into actual trials - Doing the 3-rd order grad. correction first using the DataEditor, and then process it further using FT. Any thoughts? Best, Stan ----- Oorspronkelijk bericht ----- > Van: "Michael Wibral" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Donderdag 19 april 2012 10:24:57 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hey there, > sorry for not thinking about it any earlier, indeed I can confirm that > ft_denoise.. needs the reference channels to function properly. I > remember having to preprocess in a funny order in old ft versions, to > do artefcat rejection without the refs and denoising with the refs. > Personally, I think the code should check whether the refs are there > and otherwise throw an error. Since ft_denoise.. only concerns CTF > (and bti??) systems, where the refs have fixed names this could be > easily implemented, or am I mistaken? > Best, > Michael > Gesendet: Donnerstag, 19. April 2012 um 08:59 Uhr > Von: "Barbara Haendel" > An: "Email discussion list for the FieldTrip project" > , fieldtrip at donders.ru.nl > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hey there, thanks a lot for the replies! > Panagiotis hit the mark. Indeed the reference channels were excluded > in the first round of preprocessing. May be one could include a short > note on that in the ft_denoise m-file description since only including > relevant channels is the normal way to treat data in preprocessing. > Thanks again, > Barbara > -------- Original-Nachricht -------- > > Datum: Mon, 16 Apr 2012 17:53:56 +0200 > > Von: Panagiotis Tsiatsis > > An: Email discussion list for the FieldTrip project > > > > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > Hello girls and guys, > > > > It is working for my CTF MEG data - the version that I have is v4692 > > 2011-11-07. > > > > The other thing that might cause a problem could be ommiting the > > reference channels definition before the ft_ preprocessing command > > that > > gave you your "dataprepro" > > > > i.e maybe you might need something like this > > > > cfg = []; > > > > ... > > //various preprocessing parameters > > ... > > > > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > > > > dataprepro = ft_preprocessing(cfg); > > > > > > Hope you are lucky :) > > > > Best, > > Panagiotis > > > > > > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > > Hi Barbara, > > > > > > I can replicate your finding, but am unsure what is causing it. > > > Maybe > > > the difference/correction is lower than the Matlab or CTF > > > precision? > > > In any case, if the 3rd order gradients were on, > > > ft_denoise_synthetic > > > would undo the G3BR-balancing, ergo it toggles. > > > > > > Best, > > > Stan > > > > > > > > > ------------------------------------------------------------------------ > > > > > > *Van: *"Michael Wibral" > > > *Aan: *"Email discussion list for the FieldTrip project" > > > > > > *Verzonden: *Maandag 16 april 2012 16:46:27 > > > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > > > Hi Barbara, > > > > > > are you certain that the original data do not have 3rd gradients > > > enabled? - looking at them once in dataEditor, switching to 3rd > > > grads and accidentally forgetting to unclick 'save parameters with > > > dataset' will make them have 3rd grads... > > > > > > When I last used ft_denoise_synthetic it worked pretty much as > > > described (??). > > > > > > Michael > > > > > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > > > *Von:* "Barbara Haendel" > > > *An:* fieldtrip at donders.ru.nl > > > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > > > Dear fieldtrip users, > > > > > > has anyone experience in using ft_denoise_synthetic? If I try to > > > calculate 3rd order grads in the below specified way the data does > > > not change with respect to the input data (which has no synthetic > > > gradiometer applied). Is there some obvious misunderstanding on my > > > side of how to use this function or is our environment truly > > > noiseless :) > > > > > > Cheers, > > > Barbara > > > > > > cfg=[]; > > > cfg.gradient ='G3BR'; > > > cfg.trials = 'all'; > > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > > > > > > > >> data_3rdorder.grad.balance > > > > > > ans = > > > > > > G1BR: [1x1 struct] > > > G2BR: [1x1 struct] > > > G3BR: [1x1 struct] > > > current: 'G3BR' > > > previous: {'none'} > > > > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > > > > ans = 0 > > > > > > -- > > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > > Jetzt informieren: > > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > > _______________________________________________ > > > 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 > > > > > > > > > > > > > > > -- > > > Stan van Pelt > > > > > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > > University Nijmegen > > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > > E-mail: stan.vanpelt at donders.ru.nl > > > Website: www.ru.nl/donders/ > > > Phone: (+31) (0)24 36 10981 > > > Fax: (+31) (0)24 36 10989 > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > > Panagiotis S. Tsiatsis > > Max Planck Institute for Biological Cybernetics > > Cognitive NeuroImaging Group > > Tuebingen, Germany > > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 -- Stan van Pelt Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 10981 Fax: (+31) (0)24 36 10989 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue Apr 24 10:26:18 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 24 Apr 2012 10:26:18 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <506536226.7942.1335255294672.JavaMail.root@sculptor.zimbra.ru.nl> References: <506536226.7942.1335255294672.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Hi Stan, To me, it seems all three options would be fine, and I actually don't think they are computationally suboptimal. I would probably go for option 2, and have done so with a similar problem in the past. This worked well for me. Best, Eelke On 24 April 2012 10:14, Stan van Pelt wrote: > Hi all, > > A follow-up question on the implementation of 3rd-order gradiometer > correction in FT: > > I am puzzling how one can do both 3-order grad. correction and dft-filtering > properly using FT. the logical sequency would be to do ft_denoise_synthetic > first, and subsequently dft-filtering using ft_preprocessing. However, in > that case it is no longer possible to pad the data when calling > ft_preprocessing, because it now processes trial-data (output from > ft_denoise_synthetic), and doesn't read in the original dataset anymore. or > am I mistaken here? > > I could see 3 alternatives, which seem to be more > like (computationally) suboptimal workarounds: > - Apply ft_denoise_synthetic on the entire dataset, then dft-filter the > entire dataset, and then run ft_redefinetrial to cut the data into actual > trials > - Adjust the trial definition such that longer data segments are read in, > equivalent to your padding size. Then apply ft_denoise_synthetic on these > trials, then dft-filter them, and then run ft_redefinetrial to cut the data > into actual trials > - Doing the 3-rd order grad. correction first using the DataEditor, and then > process it further using FT. > > Any thoughts? > > Best, Stan > > > ________________________________ > > Van: "Michael Wibral" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Donderdag 19 april 2012 10:24:57 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Hey there, > > sorry for not thinking about it any earlier, indeed I can confirm that > ft_denoise.. needs the reference channels to function properly. I remember > having to preprocess in a funny order in old ft versions, to do artefcat > rejection without the refs and denoising with the refs. > > Personally, I think the code should check whether the refs are there and > otherwise throw an error. Since ft_denoise.. only concerns CTF (and bti??) > systems, where the refs have fixed names this could be easily implemented, > or am I mistaken? > > Best, > Michael > Gesendet: Donnerstag, 19. April 2012 um 08:59 Uhr > Von: "Barbara Haendel" > An: "Email discussion list for the FieldTrip project" > , fieldtrip at donders.ru.nl > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Hey there, thanks a lot for the replies! > > Panagiotis hit the mark. Indeed the reference channels were excluded in the > first round of preprocessing. May be one could include a short note on that > in the ft_denoise m-file description since only including relevant channels > is the normal way to treat data in preprocessing. > > Thanks again, > Barbara > > > > > -------- Original-Nachricht -------- >> Datum: Mon, 16 Apr 2012 17:53:56 +0200 >> Von: Panagiotis Tsiatsis >> An: Email discussion list for the FieldTrip project >> >> Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > >> Hello girls and guys, >> >> It is working for my CTF MEG data - the version that I have is v4692 >> 2011-11-07. >> >> The other thing that might cause a problem could be ommiting the >> reference channels definition before the ft_ preprocessing command that >> gave you your "dataprepro" >> >> i.e maybe you might need something like this >> >> cfg = []; >> >> ... >> //various preprocessing parameters >> ... >> >> cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; >> >> dataprepro = ft_preprocessing(cfg); >> >> >> Hope you are lucky :) >> >> Best, >> Panagiotis >> >> >> On 4/16/2012 4:59 PM, Stan van Pelt wrote: >> > Hi Barbara, >> > >> > I can replicate your finding, but am unsure what is causing it. Maybe >> > the difference/correction is lower than the Matlab or CTF precision? >> > In any case, if the 3rd order gradients were on, ft_denoise_synthetic >> > would undo the G3BR-balancing, ergo it toggles. >> > >> > Best, >> > Stan >> > >> > >> > ------------------------------------------------------------------------ >> > >> > *Van: *"Michael Wibral" >> > *Aan: *"Email discussion list for the FieldTrip project" >> > >> > *Verzonden: *Maandag 16 april 2012 16:46:27 >> > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad >> > >> > Hi Barbara, >> > >> > are you certain that the original data do not have 3rd gradients >> > enabled? - looking at them once in dataEditor, switching to 3rd >> > grads and accidentally forgetting to unclick 'save parameters with >> > dataset' will make them have 3rd grads... >> > >> > When I last used ft_denoise_synthetic it worked pretty much as >> > described (??). >> > >> > Michael >> > >> > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr >> > *Von:* "Barbara Haendel" >> > *An:* fieldtrip at donders.ru.nl >> > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad >> > >> > Dear fieldtrip users, >> > >> > has anyone experience in using ft_denoise_synthetic? If I try to >> > calculate 3rd order grads in the below specified way the data does >> > not change with respect to the input data (which has no synthetic >> > gradiometer applied). Is there some obvious misunderstanding on my >> > side of how to use this function or is our environment truly >> > noiseless :) >> > >> > Cheers, >> > Barbara >> > >> > cfg=[]; >> > cfg.gradient ='G3BR'; >> > cfg.trials = 'all'; >> > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); >> > >> > >> > >> data_3rdorder.grad.balance >> > >> > ans = >> > >> > G1BR: [1x1 struct] >> > G2BR: [1x1 struct] >> > G3BR: [1x1 struct] >> > current: 'G3BR' >> > previous: {'none'} >> > >> > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) >> > >> > ans = 0 >> > >> > -- >> > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! >> > Jetzt informieren: >> http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a >> > _______________________________________________ >> > 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 >> > >> > >> > >> > >> > -- >> > Stan van Pelt >> > >> > Donders Institute for Brain, Cognition and Behaviour, Radboud >> > University Nijmegen >> > Kapittelweg 29, 6525 EN Nijmegen, Netherlands >> > E-mail: stan.vanpelt at donders.ru.nl >> > Website: www.ru.nl/donders/ >> > Phone: (+31) (0)24 36 10981 >> > Fax: (+31) (0)24 36 10989 >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Panagiotis S. Tsiatsis >> Max Planck Institute for Biological Cybernetics >> Cognitive NeuroImaging Group >> Tuebingen, Germany >> > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 > > > > > -- > Stan van Pelt > > Donders Institute for Brain, Cognition and Behaviour, Radboud University > Nijmegen > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > E-mail:  stan.vanpelt at donders.ru.nl > Website: www.ru.nl/donders/ > Phone:  (+31) (0)24 36 10981 > Fax:    (+31) (0)24 36 10989 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From alexandre.gramfort at inria.fr Wed Apr 25 09:07:07 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Wed, 25 Apr 2012 09:07:07 +0200 Subject: [FieldTrip] Question concerning ft_headmodel_bem_openmeeg In-Reply-To: <4F93AE1A.50405@gmx.de> References: <4F93AE1A.50405@gmx.de> Message-ID: Hi Paul, I've not looked into the new functions yet and I am not sure it has been ever tested for openmeeg (robert, cristiano?). I'd stick to the old functions for urgent matters. Feel free to send me a patch if you end up fixing problems with the new ones. I'll review the changes ASAP. Best, Alex On Sun, Apr 22, 2012 at 9:07 AM, Paul Czienskowski wrote: > Dear all, > > I want to create headmodels with the ft_headmodel_bem_openmeeg function, and > - for I formerly used the ft_prepare_bemmodel function - decided to delve > into the new function first, to see how it works. Anyway, I stumbled upon > something that puzzled me a bit. In line 96 to 106, the boundaries are > rearranged to be inside first, which to my understanding means, that the > first boundary in the array of boundaries will be the innermost one (i.e. > the brain in my case) and the last boundary will be the outermost one (i.e. > skin). Everything's fine hitherto. But from line 108 on, things become quite > odd. Line 108 and 109 define the first compartment to be the skin and the > last to be the source compartment. This is cross-checked again in line 127 > to 129. To my understanding this is a contradiction and I would appreciate, > if anybody could tell me if I got something completely wrong, or if the > function does odd things. If the function is correct, there should at least > be a comment explaining why this contradiction makes sense anyway. > > Best regards, > Paul > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From v.poghosyan at humanbraindynamics.com Wed Apr 25 13:29:25 2012 From: v.poghosyan at humanbraindynamics.com (Vahe Poghosyan) Date: Wed, 25 Apr 2012 14:29:25 +0300 Subject: [FieldTrip] General questions In-Reply-To: References: <4F93AE1A.50405@gmx.de> Message-ID: <00ec01cd22d6$ad53fa00$07fbee00$@poghosyan@humanbraindynamics.com> Dear fieldtrip users and developer, I am new to fieldtrip. I think it's an excellent toolbox (thanks to the developers), but have few general questions: 1. I understand that fieldtrip is a data analysis toolbox, however the results of the analysis need to be visualized. I find the fieldtrip visualization functions, especially of the source analysis results (e.g. ft_sourceplot, ft_sourceinterpolate, ft_sourcemovie) inadequate. My question is how do you usually visualize the results of the source analysis? Do you write your own matlab functions, including font-ends to fieldtrip plotting functions or you use other freely/commercially available tools that can import fieldtrip structures or you are satisfied with what is provided in the fieldtrip toolbox? 2. It seems that the documentation provided on the fieldtrip website is not very up-to-date and the descriptions of many configuration options in the *.m files are not documented. At the moment to understand all the available configuration options, and what different functions are doing and how they are implemented, I am debugging them step-by-step. Short of debugging or every time asking questions in this list, is there another way of getting information about all the available configuration options for different fieldtrip functions and their implementation details? 3. I found some functions in the fieldtrip's SVN (trunc) version (on googlecode), which are not available in the daily releases on the ftp server (e.g. ft_surfacecheck). Is it safe to use those functions (I understand that the toolbox is released under GPL)? 4. Are the measurement units used throughout fieldtrip functions basic SI (International System of Units) units? More specifically, what are the units of the inputs to ft_dipolesimulation (cfg.dip.signal, cfg.dip.amplitude)? Are they A*m or nA*m or something else? What are the units of the output from the minimumnormestimate? A/m? Thanks in advance Vahe Poghosyan, Ph.D. Senior Scientist Lab. for Human Brain Dynamics AAI Scientific Cultural Services Ltd. http://aaiscs.com/LHBD/ From jpnv2006 at gmail.com Wed Apr 25 16:39:05 2012 From: jpnv2006 at gmail.com (Juan Pablo Neira) Date: Wed, 25 Apr 2012 16:39:05 +0200 Subject: [FieldTrip] Individual MRI - Atlas Message-ID: Hello, I would like to know if it is possible to use the ft_sourceplot function with an individual MRI (coordsys: ctf) and an Atlas A tried to use one atlas from the Faq "aal_MNI_V4.img". After ft_prepare_atlas the coordinate system was coord:mni. When I used the ft_sourceplot function (ortho method), there were some warnings about labels not found and points outside the atlas, but I always clicked in inside my MRI. Should I have my MRI and the atlas in the same coordinate system (mni)? Regards, Juan Pablo Neira Vesga From yuvharpaz at gmail.com Wed Apr 25 20:13:10 2012 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Wed, 25 Apr 2012 21:13:10 +0300 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: References: Message-ID: Hi there I had left to right error with this atlas in sourceplot. download the newer .nii version. http://fmri.wfubmc.edu/software/PickAtlas yuval On 25 April 2012 17:39, Juan Pablo Neira wrote: > Hello, > > I would like to know if it is possible to use the ft_sourceplot > function with an individual MRI (coordsys: ctf) and an Atlas > > A tried to use one atlas from the Faq "aal_MNI_V4.img". After > ft_prepare_atlas the coordinate system was coord:mni. > > When I used the ft_sourceplot function (ortho method), there were some > warnings about labels not found and points outside the atlas, but I > always clicked in inside my MRI. Should I have my MRI and the atlas > in the same coordinate system (mni)? > > Regards, > > Juan Pablo Neira Vesga > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Apr 26 00:04:12 2012 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Wed, 25 Apr 2012 22:04:12 +0000 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <7270aa3bcbfd9.4f574cba@mail.uh.edu> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>, <7270aa3bcbfd9.4f574cba@mail.uh.edu> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> Hi I encounted the same problem with ft_databrowser: ************* fetching artifacts... Error using ft_fetch_data (line 57) data does not contain a consistent trial definition, fetching data is not possible Error in ft_databrowser>redraw_cb (line 1159) art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); Error in ft_databrowser (line 535) redraw_cb(h); **************** The same data works OK with [data] = ft_rejectvisual(cfg, data) I have: MacOS 10.6.8 MATLAB 7.13.0.564 (R2011b) Matlab re-installation did not help in my case. I would be grateful for any tips. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] Sent: Wednesday, March 07, 2012 6:55 PM To: Email discussion list for the FieldTrip project Cc: fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] Error -> ft_databrowser Hi Michael, I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution. But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution. Mehmet ----- Original Message ----- From: "Epstein, Michael" Date: Wednesday, March 7, 2012 11:29 am Subject: Re: [FieldTrip] Error -> ft_databrowser To: fieldtrip at donders.ru.nl > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list. > > -Michael > > > ________________________________ > Dear Fieldtrippers, > > > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? > > > fieldtrip version 20120130, matlab version R2010a, operating system windows 7. > > > Thanks in advance for any suggestions. > > > > ??? Error using ==> ft_fetch_data at 57 > data does not contain a consistent trial definition, fetching data is not > possible > > > Error in ==> ft_databrowser>redraw_cb at 1159 > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); > > > Error in ==> ft_databrowser at 535 > redraw_cb(h); > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > _______________________________________________ > 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 r.vandermeij at donders.ru.nl Thu Apr 26 10:13:18 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Thu, 26 Apr 2012 10:13:18 +0200 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org> <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> Message-ID: Hi Elena, >From the looks of it you are using an old version of FieldTrip. Could you download the latest version and see if the problem persists? Best, Roemer On Thu, Apr 26, 2012 at 12:04 AM, Elena Orekhova wrote: > Hi > I encounted the same problem with ft_databrowser: > > ************* > fetching artifacts... Error using ft_fetch_data (line 57) > > data does not contain a consistent trial definition, fetching data is not > possible > > Error in ft_databrowser>redraw_cb (line 1159) > > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > Error in ft_databrowser (line 535) > redraw_cb(h); > **************** > > The same data works OK with > [data] = ft_rejectvisual(cfg, data) > > I have: > MacOS 10.6.8 > MATLAB 7.13.0.564 (R2011b) > > Matlab re-installation did not help in my case. > I would be grateful for any tips. > > Elena > ------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] > *Sent:* Wednesday, March 07, 2012 6:55 PM > > *To:* Email discussion list for the FieldTrip project > *Cc:* fieldtrip at donders.ru.nl > *Subject:* Re: [FieldTrip] Error -> ft_databrowser > > Hi Michael, > > > I have posted the question actually but I didn't hear any suggestions > about it. The same error was posted yesterday by someone else. > > > just to repeat what i have replied in the other post, i tried many things > to solve it (changed the code, run the databrowser code line by line, > updated fieldtrip version at etc.), but none of them solved the problem. I > started getting the error after I tried using parallel processing scripts > in matlab. But as i said, i have no basis to say that this caused the > problem. So basically, i do not know any scientific solution. > > > But an old school method solved the problem in my case. Simply i > uninstalled and re-installed matlab. Never got the error again. You may > want to try this. I have no other solution. > > > Mehmet > > > > > > ----- Original Message ----- > From: "Epstein, Michael" > Date: Wednesday, March 7, 2012 11:29 am > Subject: Re: [FieldTrip] Error -> ft_databrowser > To: fieldtrip at donders.ru.nl > > > Hi - I am actually encountering the same error with databrowser, > and was wondering if you ever came up with a solution to this problem - or > if anyone else has a solution - I didn't find a response on the mailing > list. > > > > > > -Michael > > > > > > > > > > ------------------------------ > > > Dear Fieldtrippers, > > > > > > > > > I am encountering a strange error while i try to use ft_databrowser. > The error code is as below. I have never seen this error earlier. I used > ft_databrowser many times and its only last 2 days that i am getting the > error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and > used the newer version but still the same error. Strangely, i dont get this > error when i tried with other computers (same matlab version (R2010a), same > operating system (windows 7) on both computers. Has anyone got this error > before? what may cause this error? > > > > > > > > > fieldtrip version 20120130, matlab version R2010a, operating system > windows 7. > > > > > > > > > Thanks in advance for any suggestions. > > > > > > > > > > > > ??? Error using ==> ft_fetch_data at 57 > > > data does not contain a consistent trial definition, fetching data is > not > > > possible > > > > > > > > > Error in ==> ft_databrowser>redraw_cb at 1159 > > > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > > > > > > > > Error in ==> ft_databrowser at 535 > > > redraw_cb(h); > > > > > ------------------------------ > > Conserve Resources. Print only when necessary. > > > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended > recipient. It may contain confidential information which is legally > privilegedor otherwise protected by law. If you received this e-mail in > error or from someone who is not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or > copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your > cooperation. > > > _______________________________________________ > > 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 > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Apr 26 10:19:56 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 26 Apr 2012 10:19:56 +0200 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>, <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> Message-ID: <4F99052C.1010508@donders.ru.nl> Hi Elena, most likely your data has trials with overlapping sample points. Unfortunately, the databrowser does not support this, or to be more specific ft_fetch_data does not support this. The reason for this is that a specific segment in time is defined twice in your data, and it is not clear what segment it is you would like to look at (due to filter artifacts and other preprocessing steps, the data will most likely have different values for the same sample points). For non-continuous data (already preprocessed data), it should be able to implement this nonetheless, but that's on our todo list. The best way for now is to call ft_redefinetrial and cut out the overlapping segments. You could also hack your way around this by removing data.sampleinfo. FieldTrip will then make up arbitrary, meaningless sample numbers. Keep in mind that we do not recommend this though. There is no way that the reconstructed sample numbers can be traced back to your original data! (well... if your programming skills are reasonable enough, it is possible, but that requires some further hacking, and a lot of effort). Best, Jörn On 4/26/2012 12:04 AM, Elena Orekhova wrote: > Hi > I encounted the same problem with ft_databrowser: > > ************* > fetching artifacts... Error using ft_fetch_data (line 57) > data does not contain a consistent trial definition, fetching data is not > possible > > Error in ft_databrowser>redraw_cb (line 1159) > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > Error in ft_databrowser (line 535) > redraw_cb(h); > **************** > > The same data works OK with > [data] = ft_rejectvisual(cfg, data) > > I have: > MacOS 10.6.8 > MATLAB 7.13.0.564 (R2011b) > > Matlab re-installation did not help in my case. > I would be grateful for any tips. > > Elena > ------------------------------------------------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun > [mcoskun at mail.uh.edu] > *Sent:* Wednesday, March 07, 2012 6:55 PM > *To:* Email discussion list for the FieldTrip project > *Cc:* fieldtrip at donders.ru.nl > *Subject:* Re: [FieldTrip] Error -> ft_databrowser > > Hi Michael, > > > I have posted the question actually but I didn't hear any suggestions > about it. The same error was posted yesterday by someone else. > > > just to repeat what i have replied in the other post, i tried many > things to solve it (changed the code, run the databrowser code line by > line, updated fieldtrip version at etc.), but none of them solved the > problem. I started getting the error after I tried using parallel > processing scripts in matlab. But as i said, i have no basis to say > that this caused the problem. So basically, i do not know any > scientific solution. > > > But an old school method solved the problem in my case. Simply i > uninstalled and re-installed matlab. Never got the error again. You > may want to try this. I have no other solution. > > > Mehmet > > > > > > ----- Original Message ----- > From: "Epstein, Michael" > Date: Wednesday, March 7, 2012 11:29 am > Subject: Re: [FieldTrip] Error -> ft_databrowser > To: fieldtrip at donders.ru.nl > > > Hi - I am actually encountering the same error with databrowser, and > was wondering if you ever came up with a solution to this problem - or > if anyone else has a solution - I didn't find a response on the > mailing list. > > > > > > -Michael > > > > > > > > > > > ------------------------------------------------------------------------ > > > Dear Fieldtrippers, > > > > > > > > > I am encountering a strange error while i try to use ft_databrowser. > The error code is as below. I have never seen this error earlier. I > used ft_databrowser many times and its only last 2 days that i am > getting the error. I downloaded a newer version of fieldtrip > (fieldtrip-20120130) and used the newer version but still the same > error. Strangely, i dont get this error when i tried with other > computers (same matlab version (R2010a), same operating system > (windows 7) on both computers. Has anyone got this error before? what > may cause this error? > > > > > > > > > fieldtrip version 20120130, matlab version R2010a, operating system > windows 7. > > > > > > > > > Thanks in advance for any suggestions. > > > > > > > > > > > > ??? Error using ==> ft_fetch_data at 57 > > > data does not contain a consistent trial definition, fetching data is not > > > possible > > > > > > > > > Error in ==> ft_databrowser>redraw_cb at 1159 > > > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > > > > > > > > Error in ==> ft_databrowser at 535 > > > redraw_cb(h); > > > > > > ------------------------------------------------------------------------ > > Conserve Resources. Print only when necessary. > > > > IMPORTANT NOTICE: This e-mail is meant only for the use of the > intended recipient. It may contain confidential information which is > legally privilegedor otherwise protected by law. If you received this > e-mail in error or from someone who is not authorized to send it to > you, you are strictly prohibited from reviewing, using, disseminating, > distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF > THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. > Thank you for your cooperation. > > > _______________________________________________ > > 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 -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Apr 26 10:47:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 26 Apr 2012 10:47:37 +0200 Subject: [FieldTrip] General questions In-Reply-To: <00ec01cd22d6$ad53fa00$07fbee00$@poghosyan@humanbraindynamics.com> References: <4F93AE1A.50405@gmx.de> <00ec01cd22d6$ad53fa00$07fbee00$@poghosyan@humanbraindynamics.com> Message-ID: <4F990BA9.5030709@donders.ru.nl> Dear Vahe, thanks for your elaborate feedback. Of course, we are working hard to make FieldTrip more intuitive and user-friendly. We are quite aware that there are lot of things which are suboptimal, some of them that you also pointed out. Here's my comments on your points: > 1. I understand that fieldtrip is a data analysis toolbox, however the > results of the analysis need to be visualized. I find the fieldtrip > visualization functions, especially of the source analysis results (e.g. > ft_sourceplot, ft_sourceinterpolate, ft_sourcemovie) inadequate. > My question is how do you usually visualize the results of the source > analysis? Do you write your own matlab functions, including font-ends to > fieldtrip plotting functions or you use other freely/commercially available > tools that can import fieldtrip structures or you are satisfied with what is > provided in the fieldtrip toolbox? What exactly do you find inadequate? The way the plots look like or the way you need to call the functions? I have to admit that plotting results in sourcespace is more complex than plotting in sensor space. This is simply because there are so many more options and parameters. The intention of FT is not to provide the user with an easy-to-click GUI which hides important options, but to require the user to think him-/herself about important options like downsampling, interpolation options, normalization, etc. (to answer your question on my behalf: I am satisfied, once I found out how to plot - which took some time). > 2. It seems that the documentation provided on the fieldtrip website is not > very up-to-date and the descriptions of many configuration options in the > *.m files are not documented. At the moment to understand all the available > configuration options, and what different functions are doing and how they > are implemented, I am debugging them step-by-step. > Short of debugging or every time asking questions in this list, is there > another way of getting information about all the available configuration > options for different fieldtrip functions and their implementation details? Yes, there is an overview other than what the help is showing: http://fieldtrip.fcdonders.nl/reference/index For a function overview: http://fieldtrip.fcdonders.nl/reference The function and configuration reference of the FieldTrip wiki is literally a collection of all the helps. Note that for some functions, there are undocumented functions (which has a reason), they are mostly hidden and explained in the comments below the help. We (will) try to make the naming consistent throughout FieldTrip, so that, once acquainted with the naming scheme, the cfg options should be self-explanatory. Can you point to a particular example where the cfg-options are not documented adequately? This is for us sometimes a bit hard to figure out, because we know FT already quite well and thus need to rely on feedback of new users. But if you have any questions how a certain function works, or about the algorithm behind, feel free to just write a mail to this list - that's what it is there for ;) > 3. I found some functions in the fieldtrip's SVN (trunc) version (on > googlecode), which are not available in the daily releases on the ftp server > (e.g. ft_surfacecheck). > Is it safe to use those functions (I understand that the toolbox is released > under GPL)? Sorry, I don't know as I have neither written nor used these functions. > 4. Are the measurement units used throughout fieldtrip functions basic SI > (International System of Units) units? More specifically, what are the units > of the inputs to ft_dipolesimulation (cfg.dip.signal, cfg.dip.amplitude)? > Are they A*m or nA*m or something else? What are the units of the output > from the minimumnormestimate? A/m? I also cannot be of much help here, but as far as I know unit declaration are a consistent problem throughout FieldTrip, and currently we are working on restructuring the code and making this clearer. I would be tempted to say that the unit is a 'what-you-put-in-comes-out', i.e. if your data is measured in nA and the distance measured in cm, then the unit will be nA*cm. But, I don't know exactly. You can try to search the FieldTrip wiki for 'units' or any related search term, but I am afraid that most pages will be rather a collection of To-Dos for/from one of us. Maybe mire helpful might be this to search in the mailinglist for old posts on units (I couldn't find any, sorry)" http://fieldtrip.fcdonders.nl/discussion_list I hope Robert or Jan-Mathijs (currently on vacation) can give you more elaborate feedback on the last two question of yours. Best, Jörn > > > Thanks in advance > > Vahe Poghosyan, Ph.D. > Senior Scientist > Lab. for Human Brain Dynamics > AAI Scientific Cultural Services Ltd. > http://aaiscs.com/LHBD/ > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From Elena.Orekhova at neuro.gu.se Thu Apr 26 11:20:05 2012 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 26 Apr 2012 09:20:05 +0000 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org> <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se>, Message-ID: <32CC77C0C8A7AD4B9410934642608E1F25391E36@exchccr1.neuro.gu.se> Indeed it works OK for the latest version. Thank you! Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Roemer van der Meij [r.vandermeij at donders.ru.nl] Sent: Thursday, April 26, 2012 10:13 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] Error -> ft_databrowser Hi Elena, >From the looks of it you are using an old version of FieldTrip. Could you download the latest version and see if the problem persists? Best, Roemer On Thu, Apr 26, 2012 at 12:04 AM, Elena Orekhova > wrote: Hi I encounted the same problem with ft_databrowser: ************* fetching artifacts... Error using ft_fetch_data (line 57) data does not contain a consistent trial definition, fetching data is not possible Error in ft_databrowser>redraw_cb (line 1159) art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); Error in ft_databrowser (line 535) redraw_cb(h); **************** The same data works OK with [data] = ft_rejectvisual(cfg, data) I have: MacOS 10.6.8 MATLAB 7.13.0.564 (R2011b) Matlab re-installation did not help in my case. I would be grateful for any tips. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] Sent: Wednesday, March 07, 2012 6:55 PM To: Email discussion list for the FieldTrip project Cc: fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] Error -> ft_databrowser Hi Michael, I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution. But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution. Mehmet ----- Original Message ----- From: "Epstein, Michael" > Date: Wednesday, March 7, 2012 11:29 am Subject: Re: [FieldTrip] Error -> ft_databrowser To: fieldtrip at donders.ru.nl > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list. > > -Michael > > > ________________________________ > Dear Fieldtrippers, > > > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? > > > fieldtrip version 20120130, matlab version R2010a, operating system windows 7. > > > Thanks in advance for any suggestions. > > > > ??? Error using ==> ft_fetch_data at 57 > data does not contain a consistent trial definition, fetching data is not > possible > > > Error in ==> ft_databrowser>redraw_cb at 1159 > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); > > > Error in ==> ft_databrowser at 535 > redraw_cb(h); > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > _______________________________________________ > 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 -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From bibi.raquel at gmail.com Thu Apr 26 14:30:14 2012 From: bibi.raquel at gmail.com (Raquel Bibi) Date: Thu, 26 Apr 2012 08:30:14 -0400 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <4F99052C.1010508@donders.ru.nl> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org> <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> <4F99052C.1010508@donders.ru.nl> Message-ID: <6FA6AC40-1549-475F-93C3-80681B6BDAF5@gmail.com> Another way of knowing sample information is to include it again in the trl definition of your trial function so that the 4th ( any column after the first three) column reads event(i).sample. The information will always be available in the trialinfo field of the data. Regards, Raquel Sent from my iPhone On Apr 26, 2012, at 4:19 AM, "Jörn M. Horschig" wrote: > Hi Elena, > > most likely your data has trials with overlapping sample points. Unfortunately, the databrowser does not support this, or to be more specific ft_fetch_data does not support this. The reason for this is that a specific segment in time is defined twice in your data, and it is not clear what segment it is you would like to look at (due to filter artifacts and other preprocessing steps, the data will most likely have different values for the same sample points). For non-continuous data (already preprocessed data), it should be able to implement this nonetheless, but that's on our todo list. The best way for now is to call ft_redefinetrial and cut out the overlapping segments. > > You could also hack your way around this by removing data.sampleinfo. FieldTrip will then make up arbitrary, meaningless sample numbers. Keep in mind that we do not recommend this though. There is no way that the reconstructed sample numbers can be traced back to your original data! (well... if your programming skills are reasonable enough, it is possible, but that requires some further hacking, and a lot of effort). > > Best, > Jörn > > On 4/26/2012 12:04 AM, Elena Orekhova wrote: >> >> Hi >> I encounted the same problem with ft_databrowser: >> >> ************* >> fetching artifacts... Error using ft_fetch_data (line 57) >> data does not contain a consistent trial definition, fetching data is not >> possible >> >> Error in ft_databrowser>redraw_cb (line 1159) >> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', >> endsample); >> >> Error in ft_databrowser (line 535) >> redraw_cb(h); >> **************** >> >> The same data works OK with >> [data] = ft_rejectvisual(cfg, data) >> >> I have: >> MacOS 10.6.8 >> MATLAB 7.13.0.564 (R2011b) >> >> Matlab re-installation did not help in my case. >> I would be grateful for any tips. >> >> Elena >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] >> Sent: Wednesday, March 07, 2012 6:55 PM >> To: Email discussion list for the FieldTrip project >> Cc: fieldtrip at donders.ru.nl >> Subject: Re: [FieldTrip] Error -> ft_databrowser >> >> Hi Michael, >> >> >> I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. >> >> >> just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution. >> >> >> But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution. >> >> >> Mehmet >> >> >> >> >> >> ----- Original Message ----- >> From: "Epstein, Michael" >> Date: Wednesday, March 7, 2012 11:29 am >> Subject: Re: [FieldTrip] Error -> ft_databrowser >> To: fieldtrip at donders.ru.nl >> >> > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list. >> > >> > -Michael >> > >> > >> > >> > Dear Fieldtrippers, >> > >> > >> > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? >> > >> > >> > fieldtrip version 20120130, matlab version R2010a, operating system windows 7. >> > > > _______________________________________________ > 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 r.oostenveld at donders.ru.nl Thu Apr 26 23:35:31 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 26 Apr 2012 23:35:31 +0200 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: References: Message-ID: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> Hi Juan You should indeed have the data and the atlas in the same coordinate system (e.g. MNI). They don't need to have the same resolution. best Robert On 25 Apr 2012, at 16:39, Juan Pablo Neira wrote: > Hello, > > I would like to know if it is possible to use the ft_sourceplot > function with an individual MRI (coordsys: ctf) and an Atlas > > A tried to use one atlas from the Faq "aal_MNI_V4.img". After > ft_prepare_atlas the coordinate system was coord:mni. > > When I used the ft_sourceplot function (ortho method), there were some > warnings about labels not found and points outside the atlas, but I > always clicked in inside my MRI. Should I have my MRI and the atlas > in the same coordinate system (mni)? > > Regards, > > Juan Pablo Neira Vesga > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From anokhina at psychiatry.wustl.edu Thu Apr 26 23:38:05 2012 From: anokhina at psychiatry.wustl.edu (Anokhin, Andrey) Date: Thu, 26 Apr 2012 21:38:05 +0000 Subject: [FieldTrip] POSTDOC POSITION Message-ID: A postdoctoral training position is available in the Department of Psychiatry at Washington University School of Medicine. The successful candidate will participate in an interdisciplinary research program linking genetics, brain function, and behavior in order to understand the etiology of addiction and related characteristics such as impulsivity and reward dysregulation. We are seeking a psychophysiologist/neuroscientist/biomedical engineer with a strong background in the analysis of EEG, ERP, and/or fMRI data. This position is available within National Institute on Drug Abuse funded Institutional National Research Service Award to support multi-disciplinary training in drug abuse (including nicotine and tobacco dependence) research. The primary focus of this position will be on advanced analysis of brain electrophysiology and fMRI data obtained in large genetically informative samples (twins, genotyping data). The overall goal of his research is to investigate brain mechanisms mediating genetic influences on individual differences in self-regulation of behavior, including inhibitory control, performance monitoring, decision making, and reinforcement learning. The candidate will have opportunity to interact with multi-disciplinary faculty and obtain research training in different areas including statistical/quantitative, molecular and genetic epidemiologic, clinical and neuroscience aspects of research on substance use disorders. The position is available immediately, and applications will be accepted until the position is filled. Washington University in St. Louis is an Affirmative Action/Equal Opportunity Employer. To apply, please contact Andrey Anokhin (Andrey at wustl.edu). ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jpnv2006 at gmail.com Fri Apr 27 09:53:03 2012 From: jpnv2006 at gmail.com (Juan Pablo Neira) Date: Fri, 27 Apr 2012 09:53:03 +0200 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> References: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> Message-ID: Thank you for your help, But is there any possibility of not using an MNI (average) brain and take advantage of the atlas.? We are working with individual MRIs and we do not want to visualize results in the MNI brain. We could build an atlas, based on our MRI, with other toolbox. But now we would like to use this atlas in the ft_sourceplot and ft_volumelookup functions. Thanks in advance, Juan Pablo Neira On Thu, Apr 26, 2012 at 11:35 PM, Robert Oostenveld wrote: > Hi Juan > > You should indeed have the data and the atlas in the same coordinate system (e.g. MNI). They don't need to have the same resolution. > > best > Robert > > > On 25 Apr 2012, at 16:39, Juan Pablo Neira wrote: > >> Hello, >> >> I would like to know if it is possible to use the ft_sourceplot >> function with an individual MRI (coordsys: ctf) and an Atlas >> >> A tried to use one atlas from the Faq "aal_MNI_V4.img".  After >> ft_prepare_atlas the coordinate system was coord:mni. >> >> When I used the ft_sourceplot function (ortho method), there were some >> warnings about labels not found and points outside the atlas, but I >> always clicked in inside my MRI.  Should I have my MRI and the atlas >> in the same coordinate system (mni)? >> >> Regards, >> >> Juan Pablo Neira Vesga >> _______________________________________________ >> 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 Elena.Orekhova at neuro.gu.se Fri Apr 27 11:07:18 2012 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 27 Apr 2012 09:07:18 +0000 Subject: [FieldTrip] ft_volumereslice problem Message-ID: <32CC77C0C8A7AD4B9410934642608E1F25391F48@exchccr1.neuro.gu.se> Hi, I try to reslice MRI from [157 204 203] to [256 256 256] I do: cfg = []; cfg.dim = [256 256 256]; mri_resl = ft_volumereslice(cfg, mri); but I get the error (see below) I use latest FT version with Mac OS 10.6.8 and Matlab 7.13.0.564 (R2011b) Thanks in advance Elena ********************* the input is volume data with dimensions [157 204 203] reslicing from [157 204 203] to [256 256 256] the input is volume data with dimensions [157 204 203] the input is volume data with dimensions [256 256 256] 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 (line 467) ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ft_sourceinterpolate (line 376) av( sel) = my_interpn(fv, ax(sel), ay(sel), az(sel), cfg.interpmethod, cfg.feedback); Error in ft_volumereslice (line 147) reslice = ft_sourceinterpolate(tmpcfg, mri, reslice); -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuvharpaz at gmail.com Fri Apr 27 18:02:35 2012 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Fri, 27 Apr 2012 19:02:35 +0300 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: References: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> Message-ID: Dear Juan Pablo Neira I think what has to be done in this case is first to transfer the MRI to MNI space following steps described here. http://fieldtrip.fcdonders.nl/development/minimum_norm_estimate_new?s[]=mri&s[]=mni then you use the transformation in reverse on the atlas so you end up with an MNI atlas reshaped according to the individual MRI. then you can set sourceplot to use the atlas and give you names of regions when using the plot (ortho mode) interactively. you can also generate masks to color regions etc. I haven't done it but it should be possible. Yuval On 27 April 2012 10:53, Juan Pablo Neira wrote: > Thank you for your help, > > But is there any possibility of not using an MNI (average) brain and > take advantage of the atlas.? We are working with individual MRIs and > we do not want to visualize results in the MNI brain. > > We could build an atlas, based on our MRI, with other toolbox. But > now we would like to use this atlas in the ft_sourceplot and > ft_volumelookup functions. > > Thanks in advance, > > Juan Pablo Neira > > On Thu, Apr 26, 2012 at 11:35 PM, Robert Oostenveld > wrote: > > Hi Juan > > > > You should indeed have the data and the atlas in the same coordinate > system (e.g. MNI). They don't need to have the same resolution. > > > > best > > Robert > > > > > > On 25 Apr 2012, at 16:39, Juan Pablo Neira wrote: > > > >> Hello, > >> > >> I would like to know if it is possible to use the ft_sourceplot > >> function with an individual MRI (coordsys: ctf) and an Atlas > >> > >> A tried to use one atlas from the Faq "aal_MNI_V4.img". After > >> ft_prepare_atlas the coordinate system was coord:mni. > >> > >> When I used the ft_sourceplot function (ortho method), there were some > >> warnings about labels not found and points outside the atlas, but I > >> always clicked in inside my MRI. Should I have my MRI and the atlas > >> in the same coordinate system (mni)? > >> > >> Regards, > >> > >> Juan Pablo Neira Vesga > >> _______________________________________________ > >> 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 > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.N.Maijers at student.ru.nl Sat Apr 28 16:01:25 2012 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Sat, 28 Apr 2012 16:01:25 +0200 Subject: [FieldTrip] Problem in ft_timelockstatistics() phase Message-ID: <20120428160125.521cf366@sander-H57M-USB3> Hi, I am trying to rework a small FieldTrip experiment I did last year (reproduction of larger experiment done by Irina Simanova). Calling ft_timelockstatistics() on two ERP data partitions results in an error: "Undefined function 'fieldnames' for input arguments of type 'cell'." I'm running FieldTrip under MATLAB R2011b 64-bit on Linux. I see a possible cause of the problem, in that these data we pre-analysed with ft_timelockanalysis() a year ago, or longer. I read them from parts of the data set I was supplied with. Maybe there have been breaking changes to this function in the meantime? The cfg struct that I pass as parameter seems in line with the current documentation, though. LOG: >> main() data_set_location = /media/SAMSUNG/0,data_set/EEG/0 MATLAB output_dir = /tmp/EEG Data set part file: timelock10_lp Data set part file: timelock11_lp CONTRAST [class 1, size = 220]: participant timelock10_lp on condition avg_anm_aud_lp [class 2, size = 224]: participant timelock10_lp on condition avg_tls_aud_lp cfg method: 'crossvalidate' latency: [0 0.7000] channel: {1x60 cell} nfolds: 5 mva: {2x1 cell} design: [444x1 double] class_1_data__struct avg: [62x501 double] var: [62x501 double] fsample: 500 time: [1x501 double] dof: [62x501 double] label: {62x1 cell} trial: [220x62x501 double] dimord: 'rpt_chan_time' cfg: [1x1 struct] class_2_data__struct avg: [62x501 double] var: [62x501 double] fsample: 500 time: [1x501 double] dof: [62x501 double] label: {62x1 cell} trial: [224x62x501 double] dimord: 'rpt_chan_time' cfg: [1x1 struct] selected 60 channels selected 351 time bins selected 1 frequency bins using "ft_statistics_crossvalidate" for the statistical testing fixing random number generator for reproducibility creating sample indices using 5-fold cross-validation validating fold 1 of 5 for 1 datasets validating fold 2 of 5 for 1 datasets validating fold 3 of 5 for 1 datasets validating fold 4 of 5 for 1 datasets validating fold 5 of 5 for 1 datasets Undefined function 'fieldnames' for input arguments of type 'cell'. Error in ft_statistics_crossvalidate (line 84) fn = fieldnames(stat.model{1}); Error in statistics_wrapper (line 298) [stat] = statmethod(cfg, dat, design); Error in ft_timelockstatistics (line 110) [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Error in main/modeling (line 203) stat = ft_timelockstatistics(cfg, class_1_datastruct, class_2_datastruct); Error in main/statistics (line 225) stat = modeling(data_set, method, obj_class_1_and_2); Error in main/ERP_experiment (line 374) stats = statistics(data_set, contrasts, method); Error in main (line 401) stats_x = ERP_experiment(data_set_location, 'RR', output_dir) Any suggestions would be welcom! Kind regards, Sander Maijers From hamzaf at sabanciuniv.edu Sat Apr 28 18:08:16 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 28 Apr 2012 19:08:16 +0300 Subject: [FieldTrip] Error in a given example Message-ID: Hello, While trying to understand the ft_deinetrial I tried the following example from the page ( http://fieldtrip.fcdonders.nl/tutorial/preprocessing) cfg = []; cfg.dataset = 'Subject01.ds'; cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for fully incongruent (FIC). cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 2; % in seconds cfg = ft_definetrial(cfg); I get the following error readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) reading the events from 'Subject01.ds\Subject01.res4' readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) ??? Error using ==> ft_definetrial at 185 no trials were defined, see FT_DEFINETRIAL for help I wonder why? Best -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sat Apr 28 18:12:20 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 28 Apr 2012 19:12:20 +0300 Subject: [FieldTrip] cfg.trialdef.eventtype Message-ID: Hello, I wonder what should be written after in this variable (cfg.trialdef.eventtype) ? and what is meant by '?' ? Best -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Apr 29 07:01:00 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 29 Apr 2012 08:01:00 +0300 Subject: [FieldTrip] Error in a given example In-Reply-To: References: Message-ID: Hello, I discovered the solution, I should but the full path of 'Subject01.ds'. I did not saw that in the tutorial but I found that in the previous messages. Best On Sat, Apr 28, 2012 at 7:08 PM, Hamza Fawzi Altakroury (Student) < hamzaf at sabanciuniv.edu> wrote: > Hello, > > While trying to understand the ft_deinetrial > > I tried the following example from the page ( > http://fieldtrip.fcdonders.nl/tutorial/preprocessing) > > cfg = []; > cfg.dataset = 'Subject01.ds'; > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for > fully incongruent (FIC). > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 2; % in seconds > cfg = ft_definetrial(cfg); > > I get the following error > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > reading the events from 'Subject01.ds\Subject01.res4' > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > ??? Error using ==> ft_definetrial at 185 > no trials were defined, see FT_DEFINETRIAL for help > > > I wonder why? > > Best > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Apr 29 07:07:55 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 29 Apr 2012 08:07:55 +0300 Subject: [FieldTrip] cfg.trialdef.eventtype In-Reply-To: References: Message-ID: Sorry in being rush in asking questions, I found the solution By typing '?' we get info about the file, one of them the eventtype. Hamza On Sat, Apr 28, 2012 at 7:12 PM, Hamza Fawzi Altakroury (Student) < hamzaf at sabanciuniv.edu> wrote: > Hello, > > I wonder what should be written after in this variable > (cfg.trialdef.eventtype) ? > and what is meant by '?' ? > > Best > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From vitoria.piai at gmail.com Sun Apr 29 15:19:16 2012 From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=) Date: Sun, 29 Apr 2012 15:19:16 +0200 Subject: [FieldTrip] error in ft_databrowser Message-ID: <4F9D3FD4.2050301@gmail.com> Hi there, I'm getting the following error when trying ft_databrowser on the output of ft_componentanalysis (ft_topoplotIC on the same dataset works fine): ??? Error using ==> keyvalcheck at 77 the input argument 'tag' is forbidden Error in ==> ft_plot_text at 44 keyvalcheck(varargin, 'optional', {'hpos', 'vpos', 'width', 'height', 'hlim', 'vlim', 'Color', .... Error in ==> ft_databrowser>redraw_cb at 1346 ft_plot_text(labelx(laysel), labely(laysel), opt.hdr.label(chanindx(i)), 'tag', 'timecourse', 'HorizontalAlignment', 'right'); Error in ==> ft_databrowser at 548 redraw_cb(h); I'm using the ft_databrowser version updated on the 25th of April. Is this a bug? Thank you, Vitória -- ** Please consider the environment - do you really need to print? ** From veniero at med.unibs.it Sun Apr 1 19:03:51 2012 From: veniero at med.unibs.it (veniero at med.unibs.it) Date: Sun, 1 Apr 2012 19:03:51 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: References: Message-ID: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> Dear FieldTrip users, I'm trying to run a cluster-based permutation tests on time-frequency data. I get the result: found 1 positive clusters in observed data found 0 negative clusters in observed data, but I'm not able to use clusterplot because if the following error: ??? Error using ==> ft_clusterplot at 171 no clusters present with a p-value lower than the specified alpha, nothing to plot Is this possible? Maybe it's just a trivial question. Many thanks, Mimma From Lilla.Magyari at mpi.nl Sun Apr 1 19:58:55 2012 From: Lilla.Magyari at mpi.nl (Magyari, Lilla) Date: Sun, 01 Apr 2012 19:58:55 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> Message-ID: <4F78975F.10607@mpi.nl> Dear Mimma, I am not exactly sure about what "found 1 positive clusters in observed data found 0 negative clusters in observed data" means but I would guess that it means only the number of clusters that you got after your test. This doesn't mean that these clusters are significant. Have you checked in the output of ft_freqstatistics if you have any significant clusters? (You can check it in the field stat.posclusters or stat.negclusters). Hope this helps Lilla veniero at med.unibs.it wrote: > Dear FieldTrip users, > I'm trying to run a cluster-based permutation tests on time-frequency > data. I get the result: > found 1 positive clusters in observed data found 0 negative clusters in > observed data, but I'm not able to use clusterplot because if the > following error: > ??? Error using ==> ft_clusterplot at 171 > no clusters present with a p-value lower than the specified alpha, nothing > to plot > > Is this possible? Maybe it's just a trivial question. > > Many thanks, > Mimma > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Mon Apr 2 09:24:35 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 02 Apr 2012 09:24:35 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> Message-ID: <4F795433.6000007@donders.ru.nl> Dear Mimma, Most likely, you specified a different alpha when calling ft_freqstatistics than when calling ft_clusterplot. Could you paste the cfg settings for both functions here, so that we can try to track down where exactly this error comes from? Best, Jörn On 4/1/2012 7:03 PM, veniero at med.unibs.it wrote: > Dear FieldTrip users, > I'm trying to run a cluster-based permutation tests on time-frequency > data. I get the result: > found 1 positive clusters in observed data found 0 negative clusters in > observed data, but I'm not able to use clusterplot because if the > following error: > ??? Error using ==> ft_clusterplot at 171 > no clusters present with a p-value lower than the specified alpha, nothing > to plot > > Is this possible? Maybe it's just a trivial question. > > Many thanks, > Mimma > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From veniero at med.unibs.it Mon Apr 2 11:11:30 2012 From: veniero at med.unibs.it (veniero at med.unibs.it) Date: Mon, 2 Apr 2012 11:11:30 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <4F795433.6000007@donders.ru.nl> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> <4F795433.6000007@donders.ru.nl> Message-ID: <3a64b4c61afcca813c6c64d8fed5a5b1.squirrel@mail.med.unibs.it> Dear Jörn, I'm copmparing two conditions gavgM1_post5 and gavgM1_pre5. Here the settings I'm using: cfg = []; cfg.channel = {'EEG'}; cfg.layout= 'biosemi64.lay'; cfg.latency = 'all'; cfg.frequency = [20 20]; cfg.avgeoverfreq = 'yes'; cfg.method = 'montecarlo'; cfg.statistic = '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; design = zeros(1,size(gavgM1_post5.powspctrm,1) + size(gavgM1_pre5.powspctrm,1)); design(1,1:size(gavgM1_post5.powspctrm,1)) = 1; design(1,(size(gavgM1_post5.powspctrm,1)+1):(size(gavgM1_post5.powspctrm,1)+... size(gavgM1_pre5.powspctrm,1))) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_freqstatistics(cfg, gavgM1_post5, gavgM1_pre5); For the clusterplot: stat.raweffect = gavgM1_post5.powspctrm - gavgM1_pre5.powspctrm; cfg = []; cfg.alpha = 0.025; cfg.zparam = 'raweffect'; cfg.zlim = [-1 1]; cfg.layout = 'biosemi64.lay'; ft_clusterplot(cfg, stat); Many thanks, Mimma > Dear Mimma, > > Most likely, you specified a different alpha when calling > ft_freqstatistics than when calling ft_clusterplot. Could you paste the > cfg settings for both functions here, so that we can try to track down > where exactly this error comes from? > > Best, > Jörn > > > On 4/1/2012 7:03 PM, veniero at med.unibs.it wrote: >> Dear FieldTrip users, >> I'm trying to run a cluster-based permutation tests on time-frequency >> data. I get the result: >> found 1 positive clusters in observed data found 0 negative clusters in >> observed data, but I'm not able to use clusterplot because if the >> following error: >> ??? Error using ==> ft_clusterplot at 171 >> no clusters present with a p-value lower than the specified alpha, >> nothing >> to plot >> >> Is this possible? Maybe it's just a trivial question. >> >> Many thanks, >> Mimma >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From jm.horschig at donders.ru.nl Mon Apr 2 16:34:16 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 02 Apr 2012 16:34:16 +0200 Subject: [FieldTrip] problem with clusterplot? In-Reply-To: <3a64b4c61afcca813c6c64d8fed5a5b1.squirrel@mail.med.unibs.it> References: <0357c9afdc8fd91c873b2c9d0fd20207.squirrel@mail.med.unibs.it> <4F795433.6000007@donders.ru.nl> <3a64b4c61afcca813c6c64d8fed5a5b1.squirrel@mail.med.unibs.it> Message-ID: <4F79B8E8.3010807@donders.ru.nl> Dear Mimma, okay, I see. First of all, behaviour of ft_clusterplot is perfectly fine. The way ft_freqstatistics works is that it first computes a t-value for all datapoints, and then computes clusters in time, space and/or frequency, depending on whether you set cfg.avgovertime or cfg.avgoverfreq to 'yes'. All these t-values are uncorrected t-values, therefore the reliability of the statistics will suffer from multiple comparisons (as a side note, this might be an interesting read: http://www.danielbor.com/dilemma-weak-neuroimaging/ ). The test you specified will compute permutations of your data and then compare the actual observed t-value (as described above) with the distribution of the random permutations. Only if your observation lies in the significant head or tail of the permutation distribution (as defined by the first/last 2.5%, i.e. your alpha value), the found cluster will be considered to be significant. Thus, even if the t-value might be significant, it will be corrected thereafter by the cluster permutation. For a detailled description, I would advise you to read this paper on which the whole method is based on: http://www.sciencedirect.com/science/article/pii/S016502700700074X In your data, the observed cluster is not significant anymore after the cluster-based correction. You can also check it by typing stat.posclusters.prob, which will return a value > 0.025 Hope I described it somewhat comprehensible. Best, Jörn On 4/2/2012 11:11 AM, veniero at med.unibs.it wrote: > Dear Jörn, > I'm copmparing two conditions gavgM1_post5 and gavgM1_pre5. > Here the settings I'm using: > > cfg = []; > cfg.channel = {'EEG'}; > cfg.layout= 'biosemi64.lay'; > cfg.latency = 'all'; > cfg.frequency = [20 20]; > cfg.avgeoverfreq = 'yes'; > cfg.method = 'montecarlo'; > cfg.statistic = '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; > design = zeros(1,size(gavgM1_post5.powspctrm,1) + > size(gavgM1_pre5.powspctrm,1)); > design(1,1:size(gavgM1_post5.powspctrm,1)) = 1; > design(1,(size(gavgM1_post5.powspctrm,1)+1):(size(gavgM1_post5.powspctrm,1)+... > size(gavgM1_pre5.powspctrm,1))) = 2; > cfg.design = design; > cfg.ivar = 1; > > [stat] = ft_freqstatistics(cfg, gavgM1_post5, gavgM1_pre5); > > > For the clusterplot: > stat.raweffect = gavgM1_post5.powspctrm - gavgM1_pre5.powspctrm; > > cfg = []; > cfg.alpha = 0.025; > cfg.zparam = 'raweffect'; > cfg.zlim = [-1 1]; > cfg.layout = 'biosemi64.lay'; > ft_clusterplot(cfg, stat); > > Many thanks, > Mimma > > > >> Dear Mimma, >> >> Most likely, you specified a different alpha when calling >> ft_freqstatistics than when calling ft_clusterplot. Could you paste the >> cfg settings for both functions here, so that we can try to track down >> where exactly this error comes from? >> >> Best, >> Jörn >> >> >> On 4/1/2012 7:03 PM, veniero at med.unibs.it wrote: >>> Dear FieldTrip users, >>> I'm trying to run a cluster-based permutation tests on time-frequency >>> data. I get the result: >>> found 1 positive clusters in observed data found 0 negative clusters in >>> observed data, but I'm not able to use clusterplot because if the >>> following error: >>> ??? Error using ==> ft_clusterplot at 171 >>> no clusters present with a p-value lower than the specified alpha, >>> nothing >>> to plot >>> >>> Is this possible? Maybe it's just a trivial question. >>> >>> Many thanks, >>> Mimma >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> _______________________________________________ >> 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 -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From biomag.network.practical at gmail.com Mon Apr 2 17:12:03 2012 From: biomag.network.practical at gmail.com (Biomag Networks Satellite 25 Aug 2012) Date: Mon, 2 Apr 2012 17:12:03 +0200 Subject: [FieldTrip] Biomag Satellite Announcement: Open for Registration In-Reply-To: References: Message-ID: Dear Biomag community, We are pleased to announce that registration is now open for the Biomag 2012 Satellite Workshop on *"Studying the brain as a network using MEG: practical considerations." * * * *Date:* August 25, 2012 *Time:* 09:00-18:00 *Location:* ICM, the new Brain Institute at Hôpital Pitié-Salpêtrière; 47 Boulevard de l'Hôpital, 75013 Paris *Purpose of this Satellite:* It is becoming increasingly important to study the working brain as network both in cognitive and clinical neuroscience. MEG provides an excellent opportunity to study the functional interactions between various brain regions. There are now multiple approaches and tools available for doing this. The aim of the proposed workshop is to elucidate practical approaches for studying brain connectivity using MEG. This will be done by a set of presentations in which basics of connectivity and source space analysis are introduced. Then follows presentations by various toolbox developers. The toolbox presenters will be asked to 1) outline conceptually the types of connectivity approaches their toolboxes allow for and 2) describe how it practically can be done. Finally we will discuss how various connectivity measures can be tested using standardized data sets. Target audience: The workshop is targeted towards the advanced clinical or cognitive MEG user with an interest in embracing state-of-the-art methods for functional connectivity. Please see the satellite website for more details. You may register here. The registration deadline is June 30, 2012. Please note that there is a small (~10 euro) fee to cover costs, which you may pay at the door. For any further questions, you may send an email to the organizers at: biomag.network.practical at gmail.com We look forward to seeing you on August 25, 2012! Best regards, Ole Jensen, Sarang Dalal, and Johanna Zumer -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko.ikkai at gmail.com Mon Apr 2 21:18:19 2012 From: akiko.ikkai at gmail.com (Akiko Ikkai) Date: Mon, 2 Apr 2012 15:18:19 -0400 Subject: [FieldTrip] beamformer results smaller than brain In-Reply-To: References: Message-ID: Thanks, Arjen and Gio, I played around with cfg.inwardshift during ft_sourceanalysis, and adjusting it to somewhere between .25 and .5 gives decent results (it was originally set to 1), i.e. good coverage with no shrinkage. I'm actually a little confused about why one might need cfg.inwardshift parameter... Assuming the segmentation into different tissue types goes correctly, is it best to set the inwardshift parameters as close to 0 as possible (or not specify), since we'd want to put dipoles ranging the whole volume of the brain? Thanks! Akiko On Thu, Mar 29, 2012 at 5:13 AM, Gio Piantoni wrote: > Hi Akiko, > > Your headmodel looks pretty good and your beamformer plot seems to > cover most of the gray matter. > > However, it's good to check the location of your dipoles in respect to > your headmodel. For example, you can plot the .pos field of your > leadfield. Something like: > > ft_plot_mesh(bnd(3), 'facealpha', .5) > hold on > plot3(lead.pos(:,1), lead.pos(:,2), lead.pos(:,3), '.') > > It might well be that your grid is too coarse and some dipoles just > happen to be over the edge of the brain. Remember that your > "beamformer_result.png" is just an interpolation of the values of this > dipole grid. > > You can either try to make your grid more refined (but remember that > your computation time will significantly increase). Or you can > manipulate the way dipoles are considered inside or outside the brain > with "inwardshift" for ft_prepare_leadfield (although I'd advise > against using a negative value as some dipoles might really end up > outside of your brain mesh, with some numerical instabilities). > Another option (the easiest) is to nudge your grid by, say, a few > millimeters, so that the parietal dipoles will be just inside the > brain mesh. > > HTH, > > Gio > > -- > Giovanni Piantoni, MSc > Dept. Sleep & Cognition > Netherlands Institute for Neuroscience > Meibergdreef 47 > 1105 BA Amsterdam (NL) > > +31 20 5665492 > gio at gpiantoni.com > www.gpiantoni.com > > On Thu, Mar 29, 2012 at 00:22, Akiko Ikkai wrote: > > Hi Fieldtrip users, > > > > I'm hoping that someone could give me advice on segmentation and > beamformer > > on EEG data. I have EEG data set based on 128 channel cap. Thanks to the > > help I got in mid-Feb, I'm now able to create a decent > > segmentation (seg_results image attached) and volume conduction model. > > However, when I run beamformer based on these models, resulting > beamforming > > image is often smaller than the brain (beamformer_result attached). > > Particularly posterior parietal and occipital map is NaN. > > > > I have tried going back to segmentation and expanded brain by > using imdilate > > after ft_volumesegment such as: > > > > newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original > brain > > tissue from segmentation > > > > seg2.brain = newbrain; > > > > seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6; > > > > and run ft_prepare_mesh_new on seg2. Of course, I have to make sure > there is > > no intersect between different tissue types, so using imdilate has > > limitation. > > > > Could someone explain why this shrinkage might be happening, and how I > could > > fix it? > > > > Thanks in advance! Akiko > > > > -- > > Akiko Ikkai, Ph.D. > > Postdoctoral Fellow > > Department of Psychological and Brain Sciences > > Johns Hopkins University > > Ames Hall, 3400 N. Charles St. > > Baltimore, MD 21218 > > > > > > > > _______________________________________________ > > 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 > -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.vandenieuwenhuijzen at fcdonders.ru.nl Wed Apr 4 10:16:43 2012 From: m.vandenieuwenhuijzen at fcdonders.ru.nl (Marieke van de Nieuwenhuijzen) Date: Wed, 4 Apr 2012 10:16:43 +0200 (CEST) Subject: [FieldTrip] sudden errors in ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot In-Reply-To: <279226386.170300.1333525161466.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <1735698454.171384.1333527403632.JavaMail.root@draco.zimbra.ru.nl> Dear all, I have a problem with my beamforming script. The functions ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot all crash with the same main error, namely ??? Reference to non-existent field 'nChans'. Error in ==> ft_senstype at 188 elseif isheader && input.nChans==1 && ~isempty(regexp(input.label{1}, '^csc')) Error in ==> ft_convert_units at 56 if ft_senstype(obj, 'meg') Error in ==> ft_prepare_sourcemodel at 604 %(or of course ft_volumereslice, ft_volumesegment or ft_sourceplot, depending on the function) mri = ft_convert_units(mri); The only difference is that ft_volumereslice has the additional error layer Error in ==> ft_checkdata at 402 data = ft_convert_units(data); The code I am using is: cfg =[]; cfg.mri= subject.MRI; cfg.grid.warpmni = 'yes'; cfg.grid.resolution = 10; %resolution = 10 mm grid = ft_prepare_sourcemodel(cfg); mri = ft_read_mri(cfg.mri); mri.coordsys='ctf'; mri=ft_volumereslice([],mri); cfg = []; cfg.coordsys = 'ctf'; segmentedmri = ft_volumesegment(cfg, mri); mri.brainmask = segmentedmri.gray+segmentedmri.white+segmentedmri.csf; cfg = []; cfg.funparameter = 'brainmask'; figure; ft_sourceplot(cfg, mri); The curious thing is that this exact same code worked without any errors last week, but this week I am getting those errors. I am using the latest version of fieldtrip, and run ft_defaults before starting the script (although it also crashed when I didn't do that; I only started running ft_defaults when I got these errors). The fact that all errors seem to stem from the same error in ft_senstype, that this code has worked without any problems until last week, and that ft_senstype has been updated last Friday makes me suspect some bug during that update, but I am not sure about that. Does anyone have an idea as to what might be the problem here? Best, Marieke From r.oostenveld at donders.ru.nl Wed Apr 4 12:53:03 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 4 Apr 2012 12:53:03 +0200 Subject: [FieldTrip] sudden errors in ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot In-Reply-To: <1735698454.171384.1333527403632.JavaMail.root@draco.zimbra.ru.nl> References: <1735698454.171384.1333527403632.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <3B2F1399-1110-4339-A6EA-13DE99B083E6@donders.ru.nl> Dear Marieke The recently introduced bug has been tracked down and fixed. See http://bugzilla.fcdonders.nl/show_bug.cgi?id=1405 Sorry for the inconvenience. Robert On 4 Apr 2012, at 10:16, Marieke van de Nieuwenhuijzen wrote: > Dear all, > > I have a problem with my beamforming script. The functions ft_prepare_sourcemodel, ft_volumereslice, ft_volumesegment and ft_sourceplot all crash with the same main error, namely > > ??? Reference to non-existent field 'nChans'. > > Error in ==> ft_senstype at 188 > elseif isheader && input.nChans==1 && ~isempty(regexp(input.label{1}, '^csc')) > > Error in ==> ft_convert_units at 56 > if ft_senstype(obj, 'meg') > > Error in ==> ft_prepare_sourcemodel at 604 %(or of course ft_volumereslice, ft_volumesegment or ft_sourceplot, depending on the function) > mri = ft_convert_units(mri); > > The only difference is that ft_volumereslice has the additional error layer > > Error in ==> ft_checkdata at 402 > data = ft_convert_units(data); > > The code I am using is: > > cfg =[]; > cfg.mri= subject.MRI; > cfg.grid.warpmni = 'yes'; > cfg.grid.resolution = 10; %resolution = 10 mm > grid = ft_prepare_sourcemodel(cfg); > > mri = ft_read_mri(cfg.mri); > mri.coordsys='ctf'; > mri=ft_volumereslice([],mri); > > cfg = []; > cfg.coordsys = 'ctf'; > segmentedmri = ft_volumesegment(cfg, mri); > > mri.brainmask = segmentedmri.gray+segmentedmri.white+segmentedmri.csf; > cfg = []; > cfg.funparameter = 'brainmask'; > figure; > ft_sourceplot(cfg, mri); > > The curious thing is that this exact same code worked without any errors last week, but this week I am getting those errors. > > I am using the latest version of fieldtrip, and run ft_defaults before starting the script (although it also crashed when I didn't do that; I only started running ft_defaults when I got these errors). > > The fact that all errors seem to stem from the same error in ft_senstype, that this code has worked without any problems until last week, and that ft_senstype has been updated last Friday makes me suspect some bug during that update, but I am not sure about that. > > Does anyone have an idea as to what might be the problem here? > > Best, > Marieke > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.oostenveld at donders.ru.nl Wed Apr 4 12:56:09 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 4 Apr 2012 12:56:09 +0200 Subject: [FieldTrip] SPM-DCM course at the BIOMAG in Paris References: Message-ID: <60FE20C9-66C1-4682-B896-313A7E38E883@donders.ru.nl> Dear FieldTrip users Jean Daunizeau and Jeremie Mattout are organizing a DCM educational course at the BIOMAG conference in Paris in August. The registration for the course has just opened. Please see the attached flyer for further details best regards, Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Announcement_DCMcourse2012.pdf Type: application/pdf Size: 204397 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Fri Apr 6 20:05:56 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Fri, 6 Apr 2012 12:05:56 -0600 Subject: [FieldTrip] Removing channels from processed data Message-ID: Dear FieldTrippers, I'm using fieldtrip-20120405. I'm trying to remove a "bad" channel from a subject's processed data (output of ft_timelockanalysis and ft_freqanalysis). I've found the function ft_selectdata (which runs ft_selectdata_new), but when I define my cfg to remove the bad channel (cfg.channels={'all','-E59'}) and use the function, it also removes the dimord field which subsequent ft_* functions need (e.g., ft_multiplotER, ft_timelockgrandaverage). I could manually remove the channel, but I was hoping for a ft_* function that would modify the label field automatically. Manually replacing the channel with NaNs does not seem to be a solution because when I use ft_singleplotER to plot data from a ROI (i.e., multiple channels in a region) that includes this now-all-NaNs channel, nothing gets plotted (meaning a mean, and not a nanmean, function gets used to average over the ROI), so I fear the same thing will happen with other functions (e.g., ft_timelockstatistics). I also know I can use ft_rejectvisual early on in my processing, but I don't want to re-process my data (and I'm not currently using FT for artifact detection). So my question is: what's the best FieldTrip function-based way to remove a channel? Thanks, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Apr 6 20:50:11 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 6 Apr 2012 20:50:11 +0200 Subject: [FieldTrip] Removing channels from processed data In-Reply-To: References: Message-ID: <87CFA1EE-23A1-40B4-AF30-F96F63838BE7@donders.ru.nl> Dear Matt, It seems you have stumbled on some code that is still a bit under development, and apparently not really stable. ft_selectdata should be able to do the trick for you, but I suspect a bug in ft_selectdata_new, so I'd try ft_selectdata_old instead. To achieve this, you need to do something like this: selchan = ft_channelselection({'all' '-E59'}, data.label); data = ft_selectdata(data, 'channel', selchan); % notice the function's input now with key-value pairs, rather than a cfg. We hope to find some time to improve the ft_selectdata_new soon. For the time being, could you file a bug on this issue on our bugzilla website? (www.bugzilla.fcdonders.nl) Cheers, JM On Apr 6, 2012, at 8:05 PM, Matt Mollison wrote: > Dear FieldTrippers, > > I'm using fieldtrip-20120405. I'm trying to remove a "bad" channel from a subject's processed data (output of ft_timelockanalysis and ft_freqanalysis). I've found the function ft_selectdata (which runs ft_selectdata_new), but when I define my cfg to remove the bad channel (cfg.channels={'all','-E59'}) and use the function, it also removes the dimord field which subsequent ft_* functions need (e.g., ft_multiplotER, ft_timelockgrandaverage). > > I could manually remove the channel, but I was hoping for a ft_* function that would modify the label field automatically. Manually replacing the channel with NaNs does not seem to be a solution because when I use ft_singleplotER to plot data from a ROI (i.e., multiple channels in a region) that includes this now-all-NaNs channel, nothing gets plotted (meaning a mean, and not a nanmean, function gets used to average over the ROI), so I fear the same thing will happen with other functions (e.g., ft_timelockstatistics). I also know I can use ft_rejectvisual early on in my processing, but I don't want to re-process my data (and I'm not currently using FT for artifact detection). > > So my question is: what's the best FieldTrip function-based way to remove a channel? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Fri Apr 6 21:34:56 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Fri, 6 Apr 2012 13:34:56 -0600 Subject: [FieldTrip] Removing channels from processed data In-Reply-To: <87CFA1EE-23A1-40B4-AF30-F96F63838BE7@donders.ru.nl> References: <87CFA1EE-23A1-40B4-AF30-F96F63838BE7@donders.ru.nl> Message-ID: Thanks, JM. That seems to solve it. Bug submitted: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1409 Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Fri, Apr 6, 2012 at 12:50 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Matt, > > It seems you have stumbled on some code that is still a bit under > development, and apparently not really stable. > > ft_selectdata should be able to do the trick for you, but I suspect a bug > in ft_selectdata_new, so I'd try ft_selectdata_old instead. > > To achieve this, you need to do something like this: > > selchan = ft_channelselection({'all' '-E59'}, data.label); > data = ft_selectdata(data, 'channel', selchan); % notice the function's > input now with key-value pairs, rather than a cfg. > > We hope to find some time to improve the ft_selectdata_new soon. For the > time being, could you file a bug on this issue on our bugzilla website? ( > www.bugzilla.fcdonders.nl) > > Cheers, > > JM > > > On Apr 6, 2012, at 8:05 PM, Matt Mollison wrote: > > Dear FieldTrippers, > > I'm using fieldtrip-20120405. I'm trying to remove a "bad" channel from a > subject's processed data (output of ft_timelockanalysis and > ft_freqanalysis). I've found the function ft_selectdata (which runs > ft_selectdata_new), but when I define my cfg to remove the bad channel > (cfg.channels={'all','-E59'}) and use the function, it also removes the > dimord field which subsequent ft_* functions need (e.g., ft_multiplotER, > ft_timelockgrandaverage). > > I could manually remove the channel, but I was hoping for a ft_* function > that would modify the label field automatically. Manually replacing the > channel with NaNs does not seem to be a solution because when I use > ft_singleplotER to plot data from a ROI (i.e., multiple channels in a > region) that includes this now-all-NaNs channel, nothing gets plotted > (meaning a mean, and not a nanmean, function gets used to average over the > ROI), so I fear the same thing will happen with other functions (e.g., > ft_timelockstatistics). I also know I can use ft_rejectvisual early on in > my processing, but I don't want to re-process my data (and I'm not > currently using FT for artifact detection). > > So my question is: what's the best FieldTrip function-based way to remove > a channel? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > 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 dashiel.munding at gmail.com Sun Apr 8 20:52:40 2012 From: dashiel.munding at gmail.com (Dashiel Munding) Date: Sun, 8 Apr 2012 20:52:40 +0200 Subject: [FieldTrip] Problem reading trials into ft_rejectvisual Message-ID: Hello all, I'm trying to figure out a way of reading only selected trials into analysis without running through ft_rejectvisual every time. I have a list of trials that I have already rejected, and the documentation (http://fieldtrip.fcdonders.nl/reference/ft_rejectvisual) says that I should be able to use cfg.trials as a 1xN vector to put in a list of those trials that I want to use : cfg.trials = 'all' or a selection given as a 1xN vector (default = 'all') I've tried various formats for this vector (I'm new to both MATLAB and fieldtrip, so this might be a simple solve) but I can't get a positive result. I know I can save out the variable and read it in again at a later date, but this seems like a very inefficient way of doing it if all I need is a list of numbers, instead of a 1.5gb .m file... Has anyone come across/solved this problem? Can anyone provide me with an example of the syntax fieldtrip is expecting? I've tried: cfg.trials = {'all' '-56', '-151', '-232', '-53'}; cfg.trials = {'1','2','3','4','5','6','7','8','9','10','46'}; cfg.trials = {1,2,3,4,5,6,7,8,9,10,46}; and some other efforts to no avail! Thanks in advance, and sorry for naivety! Dashiel From dashiel.munding at gmail.com Sun Apr 8 20:56:22 2012 From: dashiel.munding at gmail.com (Dashiel Munding) Date: Sun, 8 Apr 2012 20:56:22 +0200 Subject: [FieldTrip] Problem reading trials into ft_rejectvisual In-Reply-To: References: Message-ID: Thought an example of the error message I'm getting might be useful in diagnosing the problem. I would delve further but I'm not an experienced MATLAB user, so I don't think my investigation would be very fruitful! --- Error using subsindex Function 'subsindex' is not defined for values of class 'cell'. Error in selfromraw (line 11) data.trial = data.trial(selrpt); Error in ft_selectdata_old (line 544) data = selfromraw(data, 'rpt', selrpt); Error in ft_selectdata (line 45) [varargout{1:nargout}] = ft_selectdata_old(varargin{:}); Error in ft_rejectvisual (line 196) data = ft_selectdata(data, 'rpt', cfg.trials); On 8 April 2012 20:52, Dashiel Munding wrote: > Hello all, > > I'm trying to figure out a way of reading only selected trials into > analysis without running through ft_rejectvisual every time. I have a > list of trials that I have already rejected, and the documentation > (http://fieldtrip.fcdonders.nl/reference/ft_rejectvisual) says that I > should be able to use cfg.trials as a 1xN vector to put in a list of > those trials that I want to use : > > cfg.trials      = 'all' or a selection given as a 1xN vector (default = 'all') > > I've tried various formats for this vector (I'm new to both MATLAB and > fieldtrip, so this might be a simple solve) but I can't get a positive > result. I know I can save out the variable and read it in again at a > later date, but this seems like a very inefficient way of doing it if > all I need is a list of numbers, instead of a 1.5gb .m file... > > Has anyone come across/solved this problem? Can anyone provide me with > an example of the syntax fieldtrip is expecting? > > I've tried: > > cfg.trials = {'all' '-56', '-151', '-232', '-53'}; > > cfg.trials = {'1','2','3','4','5','6','7','8','9','10','46'}; > > cfg.trials = {1,2,3,4,5,6,7,8,9,10,46}; > > and some other efforts to no avail! > > Thanks in advance, and sorry for naivety! > > Dashiel From matt.mollison at gmail.com Sun Apr 8 21:17:31 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Sun, 8 Apr 2012 13:17:31 -0600 Subject: [FieldTrip] Problem reading trials into ft_rejectvisual In-Reply-To: References: Message-ID: Dashiel, You're using curly braces {} for trial indexing; this creates a cell array, which you don't want. Try using brackets [] to form a vector: cfg.trials = [1,2,3,4,5,6,7,8,9,10,46]; Check out http://www.mathworks.com/help/techdoc/ref/specialcharacters.htmlfor more matlab character syntax. Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Sun, Apr 8, 2012 at 12:56 PM, Dashiel Munding wrote: > Thought an example of the error message I'm getting might be useful in > diagnosing the problem. I would delve further but I'm not an > experienced MATLAB user, so I don't think my investigation would be > very fruitful! > > --- > > Error using subsindex > Function 'subsindex' is not defined for values of class 'cell'. > > Error in selfromraw (line 11) > data.trial = data.trial(selrpt); > > Error in ft_selectdata_old (line 544) > data = selfromraw(data, 'rpt', selrpt); > > Error in ft_selectdata (line 45) > [varargout{1:nargout}] = ft_selectdata_old(varargin{:}); > > Error in ft_rejectvisual (line 196) > data = ft_selectdata(data, 'rpt', cfg.trials); > > On 8 April 2012 20:52, Dashiel Munding wrote: > > Hello all, > > > > I'm trying to figure out a way of reading only selected trials into > > analysis without running through ft_rejectvisual every time. I have a > > list of trials that I have already rejected, and the documentation > > (http://fieldtrip.fcdonders.nl/reference/ft_rejectvisual) says that I > > should be able to use cfg.trials as a 1xN vector to put in a list of > > those trials that I want to use : > > > > cfg.trials = 'all' or a selection given as a 1xN vector (default = > 'all') > > > > I've tried various formats for this vector (I'm new to both MATLAB and > > fieldtrip, so this might be a simple solve) but I can't get a positive > > result. I know I can save out the variable and read it in again at a > > later date, but this seems like a very inefficient way of doing it if > > all I need is a list of numbers, instead of a 1.5gb .m file... > > > > Has anyone come across/solved this problem? Can anyone provide me with > > an example of the syntax fieldtrip is expecting? > > > > I've tried: > > > > cfg.trials = {'all' '-56', '-151', '-232', '-53'}; > > > > cfg.trials = {'1','2','3','4','5','6','7','8','9','10','46'}; > > > > cfg.trials = {1,2,3,4,5,6,7,8,9,10,46}; > > > > and some other efforts to no avail! > > > > Thanks in advance, and sorry for naivety! > > > > Dashiel > > _______________________________________________ > 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 jarang.hahm at gmail.com Tue Apr 10 11:40:03 2012 From: jarang.hahm at gmail.com (Jarang Hahm) Date: Tue, 10 Apr 2012 18:40:03 +0900 Subject: [FieldTrip] =?utf-8?q?=5BFieldTrip=E2=80=8B=5D_Data_handling_afte?= =?utf-8?q?r_excluding_single_sensors_=28Neuromag=29?= Message-ID: Hi all, We are using Neuromag 306 sensors VectorView system. And only gradiometer sensors (204 sensors) are used for analysis. In the artifact rejection, I excluded four bad sensors, not as a pair, among 204 sensors. After time-frequency analysis, I got lost when combine the sensors. How can I deal with the data with a single sensor in part? Should I reject the sensor as a pair? Or, combine the signals only for the paired sensors? I want you to suggest the proper way to handle the data of one sensor in a pair. Thank you in advance, Jarang Hahm -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Tue Apr 10 13:16:47 2012 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Tue, 10 Apr 2012 13:16:47 +0200 Subject: [FieldTrip] =?utf-8?q?=5BFieldTrip=E2=80=8B=5D_Data_handling_afte?= =?utf-8?q?r_excluding_single_sensors_=28Neuromag=29?= In-Reply-To: References: Message-ID: Dear Jarang, I think there are two options: 1.) You exclude as a pair, as combining the two orthogonal sensors you want to capture the different directions of the magnetic field. 2.) Or you look at the horizontal and vertical gradiometers separately. The following script should allow you to extract the two different sensor types channel = ft_channelselection('MEG*2',data.label); index = match_str(data.label,channel); gradH_F = data; gradH_F.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); gradH_S = data; gradH_S.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); channel = ft_channelselection('MEG*3',data.label); index = match_str(data.label,channel); gradV_F = data; gradV_F.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); gradV_S = data; gradV_S.powspctrm(:,1:102,:,:) = data.powspctrm(:,index,:,:); data is a grand mean time frequency matrix with keep individuals = yes. I hope that helps. Best, Stephan El 10/04/2012, a las 11:40, Jarang Hahm escribió: > Hi all, > > > We are using Neuromag 306 sensors VectorView system. > And only gradiometer sensors (204 sensors) are used for analysis. > > > > In the artifact rejection, I excluded four bad sensors, not as a pair, among 204 sensors. > > After time-frequency analysis, I got lost when combine the sensors. > > > > How can I deal with the data with a single sensor in part? > > Should I reject the sensor as a pair? Or, combine the signals only for the paired sensors? > > > I want you to suggest the proper way to handle the data of one sensor in a pair. > > > > > Thank you in advance, > > > > Jarang Hahm > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Tue Apr 10 21:58:18 2012 From: lihqih at gmail.com (qi li) Date: Tue, 10 Apr 2012 15:58:18 -0400 Subject: [FieldTrip] ft_multiplotER Message-ID: Hi there, I tried to plot with the instruction in the tutorial. cfg=[];cfg.layout='ctf275'; ft_multiplotER(cfg,data) and get the following message 'reading layout from file ctf275.lay Error using ft_prepare_layout>readlay (line 668) could not open layout file: ctf275.lay' Any hints to solve the issue would be highly appreciated! From eelke.spaak at donders.ru.nl Wed Apr 11 08:02:11 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 11 Apr 2012 08:02:11 +0200 Subject: [FieldTrip] ft_multiplotER In-Reply-To: References: Message-ID: Hi qi, Could you try: cfg.layout = 'CTF275.lay'; so, uppercase letters 'CTF' and include the extension. That should work (at least, if the data you are trying to plot is from a CTF 275 system, which I assume it is). Best, Eelke On 10 April 2012 21:58, qi li wrote: > Hi there, > > I tried to plot with the instruction in the tutorial. > > cfg=[];cfg.layout='ctf275'; > ft_multiplotER(cfg,data) > and get the following message > > 'reading layout from file ctf275.lay > Error using ft_prepare_layout>readlay (line 668) > could not open layout file: ctf275.lay' > > Any hints to solve the issue would be highly appreciated! > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lihqih at gmail.com Wed Apr 11 22:13:23 2012 From: lihqih at gmail.com (qi li) Date: Wed, 11 Apr 2012 16:13:23 -0400 Subject: [FieldTrip] question on the coordinate Message-ID: Hi there, Our MRI data was already alined to Talariach coordinate. Let me call it mri. I aligned the MRI coordinate to MEG by ft_volumerealign and produce a variable called mri_other. mri_other=ft_volumerealign(cfg,mri); Now I reslice by mrirs=ft_volumereslice(cfg,mri_other) and do segmentation by cfg.coordsys='ctf; seg=ft_volumesegment(cfg,mrirs); I found mrirs.transform is not equal to mri_other.transform. Is this correct? I think re-slicing and segmentation should not change the transformation matrix. The last question is since our mri data was already aligned to Talariach, do we need to realign segmented? Thank you all! Qi From explena at gmail.com Thu Apr 12 10:57:44 2012 From: explena at gmail.com (Shen-Mou Hsu) Date: Thu, 12 Apr 2012 16:57:44 +0800 Subject: [FieldTrip] [problem] zero plv Message-ID: Dear Users, I try to calculate the phase locking values following the tutorial and encounter a problem. First, I ran freqanalysis as follows: cfg = []; cfg.channel = 'EEG'; cfg.method = 'mtmfft'; cfg.foi = 8:1:120; cfg.keeptrials = 'yes'; cfg.ouput = 'fourier'; cfg.tapsmofrq = 2; Phase= ft_freqanalysis(cfg, data); I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) Then, I ran connectivity analysis as follows cfg = []; cfg.method = 'plv'; PLV = ft_connectivityanalysis(cfg, Phase); Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: [0x113 double] I wondered if there is anything wrong with the previous steps. Many thanks! Shen-Mou Hsu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Apr 12 11:37:04 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 12 Apr 2012 11:37:04 +0200 Subject: [FieldTrip] [problem] zero plv In-Reply-To: References: Message-ID: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> Hi Shen-Mou, There's a typo in the cfg that you supply to ft_freqanalysis -> cfg.ouput should read cfg.output BW, JM On Apr 12, 2012, at 10:57 AM, Shen-Mou Hsu wrote: > Dear Users, > > I try to calculate the phase locking values following the tutorial and encounter a problem. > > First, I ran freqanalysis as follows: > cfg = []; > cfg.channel = 'EEG'; > cfg.method = 'mtmfft'; > cfg.foi = 8:1:120; > cfg.keeptrials = 'yes'; > cfg.ouput = 'fourier'; > cfg.tapsmofrq = 2; > Phase= ft_freqanalysis(cfg, data); > > I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) > > Then, I ran connectivity analysis as follows > cfg = []; > cfg.method = 'plv'; > PLV = ft_connectivityanalysis(cfg, Phase); > > Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: [0x113 double] > > I wondered if there is anything wrong with the previous steps. Many thanks! > > Shen-Mou Hsu > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From explena at gmail.com Thu Apr 12 12:15:40 2012 From: explena at gmail.com (Shen-Mou Hsu) Date: Thu, 12 Apr 2012 18:15:40 +0800 Subject: [FieldTrip] [problem] zero plv In-Reply-To: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> References: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> Message-ID: Hi JM, Apologize for such a stupid mistake. However, I have amended the typo and the results are the same. Both cumsumcnt and cumtapcnt returned constant values, 1101 (timepoints) and 3, respectively. I am indebted to your kindness in this matter. Shen-Mou On Thu, Apr 12, 2012 at 5:37 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Shen-Mou, > > There's a typo in the cfg that you supply to ft_freqanalysis -> cfg.ouput > should read cfg.output > > BW, > > JM > > On Apr 12, 2012, at 10:57 AM, Shen-Mou Hsu wrote: > > Dear Users, > > I try to calculate the phase locking values following the tutorial and > encounter a problem. > > First, I ran freqanalysis as follows: > cfg = []; > cfg.channel = 'EEG'; > cfg.method = 'mtmfft'; > cfg.foi = 8:1:120; > cfg.keeptrials = 'yes'; > cfg.ouput = 'fourier'; > cfg.tapsmofrq = 2; > Phase= ft_freqanalysis(cfg, data); > > I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are > constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) > > Then, I ran connectivity analysis as follows > cfg = []; > cfg.method = 'plv'; > PLV = ft_connectivityanalysis(cfg, Phase); > > Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: > [0x113 double] > > I wondered if there is anything wrong with the previous steps. Many thanks! > > Shen-Mou Hsu > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > > _______________________________________________ > 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 explena at gmail.com Thu Apr 12 12:57:18 2012 From: explena at gmail.com (Shen-Mou Hsu) Date: Thu, 12 Apr 2012 18:57:18 +0800 Subject: [FieldTrip] [problem] zero plv In-Reply-To: References: <633A1721-DC81-48D2-A9A5-E595BF226A8B@donders.ru.nl> Message-ID: Dear JM, After correcting the typo you pointed out, I do get the plv. Many thanks indeed! Shen-Mou On Thu, Apr 12, 2012 at 6:15 PM, Shen-Mou Hsu wrote: > Hi JM, > > Apologize for such a stupid mistake. However, I have amended the typo and > the results are the same. Both cumsumcnt and cumtapcnt returned constant > values, 1101 (timepoints) and 3, respectively. I am indebted to your > kindness in this matter. > > Shen-Mou > > > On Thu, Apr 12, 2012 at 5:37 PM, jan-mathijs schoffelen < > jan.schoffelen at donders.ru.nl> wrote: > >> Hi Shen-Mou, >> >> There's a typo in the cfg that you supply to ft_freqanalysis -> cfg.ouput >> should read cfg.output >> >> BW, >> >> JM >> >> On Apr 12, 2012, at 10:57 AM, Shen-Mou Hsu wrote: >> >> Dear Users, >> >> I try to calculate the phase locking values following the tutorial and >> encounter a problem. >> >> First, I ran freqanalysis as follows: >> cfg = []; >> cfg.channel = 'EEG'; >> cfg.method = 'mtmfft'; >> cfg.foi = 8:1:120; >> cfg.keeptrials = 'yes'; >> cfg.ouput = 'fourier'; >> cfg.tapsmofrq = 2; >> Phase= ft_freqanalysis(cfg, data); >> >> I noticed that the values in both Phase.cumsumcnt and Phase.cumtapcnt are >> constant values (BTW, what the meaning of cumsumcnt and cumtapcnt) >> >> Then, I ran connectivity analysis as follows >> cfg = []; >> cfg.method = 'plv'; >> PLV = ft_connectivityanalysis(cfg, Phase); >> >> Here, I got empty matrices in both labelcmb: {0x2 cell} and plvspctrm: >> [0x113 double] >> >> I wondered if there is anything wrong with the previous steps. Many >> thanks! >> >> Shen-Mou Hsu >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> >> _______________________________________________ >> 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 fredericroux at hotmail.de Thu Apr 12 19:01:49 2012 From: fredericroux at hotmail.de (Frederic Roux) Date: Thu, 12 Apr 2012 19:01:49 +0200 Subject: [FieldTrip] randomization vs permutation using ft_sourceanalysis Message-ID: Dear all, I would like to compute first level statistics of resting state source activity during eyes open and eyes closed to be able to compare this contrast across a group of subjects with different ages. I noticed that ft_sourceanalysis offers the possibility to contrast two conditions using cfg.randomization or cfg.permutation. The help documentation mentions that these options are required if one wants to contrast two conditions and apparently they do something different since they are mutually exclusive (one can not call ft_sourcenalysis with both). However, it is not clear to me how both options differ and how the data structure that is being returned can be used with ft_sourcestatistics. Any help would be as always highly appreciated. Best, Fred -- Frédéric Roux, PhD student Department of Neurophysiology Max Planck Institute for Brain Research D-60529 Frankfurt am Main Frederic.Roux at brain.mpg.de +49(0)69630183225 -------------- next part -------------- An HTML attachment was scrubbed... URL: From candida at nmr.mgh.harvard.edu Thu Apr 12 19:21:38 2012 From: candida at nmr.mgh.harvard.edu (Candida Jane Maria Ustine) Date: Thu, 12 Apr 2012 13:21:38 -0400 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data Message-ID: Hello All, I have just started reading about fieldtrip and I am learning a lot of exciting things. I have MEG data using the neuromag system and I wanted to run the Independent Component Analysis on the .fif files to remove the EOG and ECG artifact from them. I see that the documentation provided in the website( http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts) has resources to handle CTF datasets, and I was wondering if anyone has looked into the option of using the .fif files directly. Or is there a way to convert the *.fif files to the CTF format as there is an MNE utility to do the reverse mne_ctf2fif? Thanks much for your time and help! Best, Candida -- Candida Jane Maria Ustine Martinos Center for Biomedical Imaging MGH Kuperberg Lab The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From politzerahless at gmail.com Thu Apr 12 20:34:54 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Thu, 12 Apr 2012 13:34:54 -0500 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact Message-ID: Hi Candida, Welcome to FieldTrip. It seems you can import Neuromag data directly into FieldTrip: see http://fieldtrip.fcdonders.nl/getting_started/neuromag . Once the data are read into FieldTrip you can just save them as MATLAB files and you should be able to treat them the same as data from any other source once they're in FieldTrip's format. Best, Steve Politzer-Ahles On Thu, Apr 12, 2012 at 12:22 PM, wrote: > > Message: 4 > Date: Thu, 12 Apr 2012 13:21:38 -0400 > From: Candida Jane Maria Ustine > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact > on Neuromag(*.fif) data > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello All, > > I have just started reading about fieldtrip and I am learning a lot of > exciting things. > > I have MEG data using the neuromag system and I wanted to run the > Independent Component Analysis on the .fif files to remove the EOG and ECG > artifact from them. I see that the documentation provided in the website( > > http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts > ) > has resources to handle CTF datasets, and I was wondering if anyone has > looked into the option of using the .fif files directly. > Or is there a way to convert the *.fif files to the CTF format as there is > an MNE utility to do the reverse mne_ctf2fif? > > Thanks much for your time and help! > > Best, > Candida > > > > -- > Candida Jane Maria Ustine > Martinos Center for Biomedical Imaging > MGH > Kuperberg Lab > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Partners Compliance > HelpLine at http://www.partners.org/complianceline . If the e-mail was > sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120412/f79ae1c8/attachment.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 17, Issue 11 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rapela at ucsd.edu Thu Apr 12 21:41:54 2012 From: rapela at ucsd.edu (Joaquin Rapela) Date: Thu, 12 Apr 2012 12:41:54 -0700 Subject: [FieldTrip] Postdoctoral position in motor control Message-ID: <20120412194154.GA17424@dreaming.ucsd.edu> Please contact Prof. Della-Maggiore (vdellamaggiore at fmed.uba.ar) if you are interested in the following postdoctoral position in the lively city of Buenos Aires, Argentina. Cordially, Joaquin The Physiology of Action Lab (www.physiologyofactionlab.info) is looking for a candidate to fill a postdoctoral position in the Department of Physiology of the University of Buenos Aires, Argentina. The Labortory focuses on Human Behavioral Neuroscience, particularly in the area of motor control. We use Transcranial Magnetic Stimulation, Magnetic Resonance Imaging, EEG and psychophysics to study the neural mechanisms at the basis of different aspects of motor control. These include motor resonance and action understanding during action observation, online motor control and motor learning. Plastic changes induced by learning and stroke are also main interests of the lab. We are looking for a Ph.D. with a background in Neuroscience and, preferably, with experience in one ore more of the techniques used in the lab, and data analysis. Candidates with knowledge of Matlab would have priority. The postdoc is funded by a fellowship from the National Agency for the Promotion of Science and Technology (Argentina). Interested candidates could contact Dr. Valeria Della Maggiore at vdellamaggiore at fmed.uba.ar with a CV, a letter of interest and one or two references (email). Many thanks -- Valeria Della-Maggiore, Ph. D Department of Physiology, School of Medicine University of Buenos Aires Paraguay 2155, Capital Federal Buenos Aires, C1121ABG Argentina phone 54 11 5 950 9500 (2132) http://www.physiologyofactionlab.info ------------------------------------------------------------ being wild and disciplined at the same time.... -- Joaquin Rapela, PhD Swartz Center for Computational Neuroscience University of California San Diego 9500 Gilman Drive, San Diego, CA 92093-0559 tel: (858) 822-7536 fax: (858) 822-7556 http://sccn.ucsd.edu/~rapela ---------------------------------- the gods do not grant men all their gifts at once Nestor in The Iliad From alexandre.gramfort at inria.fr Fri Apr 13 08:50:39 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 13 Apr 2012 08:50:39 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: Message-ID: hi Candida, you should be able to import your fif files into fieldtrip but be careful when applying ICA on neuromag data as channels have different types and you have signals with 2 orders of magnitude difference between gradiometers and magnetometers. I am curious to know if fieldtrip handles this properly? and if so how. Also can Fieldtrip write data back into fif files keeping intact all the measurement info? thanks Alex -- Alexandre Gramfort, PhD alexandre.gramfort at inria.fr INRIA Parietal Project Team, NeuroSpin CEA Saclay Bat. 145, PC 156 91191 Gif-sur-Yvette, France http://alexandre.gramfort.net On Thu, Apr 12, 2012 at 7:21 PM, Candida Jane Maria Ustine wrote: > Hello All, > > I have just started reading about fieldtrip and I am learning a lot of > exciting things. > > I have MEG data using the neuromag system and I wanted to run the > Independent Component Analysis on the .fif files to remove the EOG and ECG > artifact from them. I see that the documentation provided in the > website(http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts) > has resources to handle CTF datasets, and I was wondering if anyone has > looked into the option of using the .fif files directly. > Or is there a way to convert the *.fif files to the CTF format as there is > an MNE utility to do the reverse mne_ctf2fif? > > Thanks much for your time and help! > > Best, > Candida > > > > -- > Candida Jane Maria Ustine > Martinos Center for Biomedical Imaging > MGH > Kuperberg Lab > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Partners Compliance > HelpLine at http://www.partners.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact the > sender and properly dispose of the e-mail. > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From jan.schoffelen at donders.ru.nl Fri Apr 13 09:01:40 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 Apr 2012 09:01:40 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: Message-ID: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> Hi Alex, > I am curious to know if fieldtrip handles this properly? and if so how. It depends a bit on the exact algorithm that is used, but for example the runica implementation (we use the EEGlab code for this) performs a whitening of the data prior to the decomposition. This would address the difference in magnitude issue, wouldn't it? > Also can Fieldtrip write data back into fif files keeping intact > all the measurement info? Not really; I have some code of Lauri's (which is not yet in FT), which can write epoched data to a fif-file. However, most of the measurement info is lost along the way. Also, since we're not fif-experts, it's not trivial for us to find out how the measurement info should be formatted. Of course it is possible to reverse engineer this from the mne-code, but this is heavily geared towards elekta hardware. Yet, I could imagine that this functionality could be valuable, because it would enable two-way traffic of data between FT and MNE-suite. Do you happen to have any code that writes meaningful measurement info? Best, Jan-Mathijs > > thanks > > Alex > -- > Alexandre Gramfort, PhD > alexandre.gramfort at inria.fr > INRIA Parietal Project Team, NeuroSpin CEA Saclay > Bat. 145, PC 156 > 91191 Gif-sur-Yvette, France > http://alexandre.gramfort.net > > On Thu, Apr 12, 2012 at 7:21 PM, Candida Jane Maria Ustine > wrote: >> Hello All, >> >> I have just started reading about fieldtrip and I am learning a lot of >> exciting things. >> >> I have MEG data using the neuromag system and I wanted to run the >> Independent Component Analysis on the .fif files to remove the EOG and ECG >> artifact from them. I see that the documentation provided in the >> website(http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts) >> has resources to handle CTF datasets, and I was wondering if anyone has >> looked into the option of using the .fif files directly. >> Or is there a way to convert the *.fif files to the CTF format as there is >> an MNE utility to do the reverse mne_ctf2fif? >> >> Thanks much for your time and help! >> >> Best, >> Candida >> >> >> >> -- >> Candida Jane Maria Ustine >> Martinos Center for Biomedical Imaging >> MGH >> Kuperberg Lab >> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Partners Compliance >> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent >> to you in error but does not contain patient information, please contact the >> sender and properly dispose of the e-mail. >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Fri Apr 13 09:22:53 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 13 Apr 2012 09:22:53 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> References: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> Message-ID: hi Jan-Mathijs, thanks for the quick answer. > It depends a bit on the exact algorithm that is used, but for example the > runica implementation (we use the EEGlab code for this) performs a whitening > of the data prior to the decomposition. This would address the difference in > magnitude issue, wouldn't it? it does yes. My question is then how do you compute the withering matrix? > Also can Fieldtrip write data back into fif files keeping intact > all the measurement info? > > Not really; I have some code of Lauri's (which is not yet in FT), which can > write epoched data to a fif-file. However, most of the measurement info is > lost along the way. that's what I feared. > Also, since we're not fif-experts, it's not trivial for > us to find out how the measurement info should be formatted. Of course it is > possible to reverse engineer this from the mne-code, but this is heavily > geared towards elekta hardware. Yet, I could imagine that this functionality > could be valuable, because it would enable two-way traffic of data between > FT and MNE-suite. that would be very valuable indeed. > Do you happen to have any code that writes meaningful > measurement info? not in one function or at least not in matlab. one should have a fiff_write_meas_info.m that does the opposite to: https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_read_meas_info.m part of the answer is in: https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_write_evoked.m a python example is in : https://github.com/mne-tools/mne-python/blob/master/mne/fiff/meas_info.py#L235 but I agree you need a fairly good understanding of the fif format… we might have to sit down together to do this. Alex From Andrew.Dykstra at med.uni-heidelberg.de Fri Apr 13 09:51:01 2012 From: Andrew.Dykstra at med.uni-heidelberg.de (Andrew R. Dykstra) Date: Fri, 13 Apr 2012 09:51:01 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data Message-ID: Hi Candida, An alternative to using fieldtrip would be EEGLAB (I believe Fieldtrip using the code there anyway). I was able to run ICA on my combined EEG/Neuromag-122 data using a combination of the MNE MATLAB toolbox (specifically, fiff_setup_read_raw & fiff_read_raw_segment) and EEGLAB's import from MATLAB matrix functionality. More work would be required to retain the sensor locations and resulting component topographies. Then, along the lines of Alex's concerns, you could run the decomposition separately for each sensor type (Mags/Grads/EEG). This may be unnecessary if the runica algorithm handles this properly (assuming you have imported the sensor types along with the time series data into EEGLAB). After subtracting out the artifact components, you could then replace the appropriate entires of your original data matrix and use fiff_write_raw_segment (from the nightly build of the MNE suite). Hope this helps, Andy -- Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov -------------- next part -------------- An HTML attachment was scrubbed... URL: From grion at sissa.it Fri Apr 13 11:14:08 2012 From: grion at sissa.it (Natalia Grion) Date: Fri, 13 Apr 2012 11:14:08 +0200 Subject: [FieldTrip] PLV definition and implementation Message-ID: <20120413111408.Horde.eLHMRh8V4mxPh_5gqW4WfWA@webmail.sissa.it> Dear Fieldtripers, I would like to know how you define and implement 'plv' (phase locking value) in the fieldtrip. I do not see any documentation on this issue of reference paper and I'm confused by the fact that this definition was used by Lachaux (1999) and fieldtrip is taking the cross-spectrum and doing some treatment (difficult to follow in the series of functions involved) to ignore amplitude consistency (I guess a different treatment from coherence 'coh' function). Could you clarify this to me or give me a reference paper? Thanks! Natalia From jan.schoffelen at donders.ru.nl Fri Apr 13 11:57:56 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 Apr 2012 11:57:56 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> Message-ID: <5DB5ADAB-2E6A-4B90-B8AD-69D7CF315BB4@donders.ru.nl> Hi Alex, > it does yes. My question is then how do you compute the withering matrix? That's the magic of EEGlab ;-). I did not look into the code but I would assume based on the estimate of the precision matrix. Do you think the magnitude problem will lead to numerical issues upon inversion of the covariance matrix? >> Also can Fieldtrip write data back into fif files keeping intact >> all the measurement info? >> >> Not really; I have some code of Lauri's (which is not yet in FT), which can >> write epoched data to a fif-file. However, most of the measurement info is >> lost along the way. > > that's what I feared. > >> Also, since we're not fif-experts, it's not trivial for >> us to find out how the measurement info should be formatted. Of course it is >> possible to reverse engineer this from the mne-code, but this is heavily >> geared towards elekta hardware. Yet, I could imagine that this functionality >> could be valuable, because it would enable two-way traffic of data between >> FT and MNE-suite. > > that would be very valuable indeed. > >> Do you happen to have any code that writes meaningful >> measurement info? > > not in one function or at least not in matlab. > > one should have a fiff_write_meas_info.m that does the opposite to: > > https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_read_meas_info.m > > part of the answer is in: > > https://github.com/mne-tools/mne-matlab/blob/master/matlab/fiff_write_evoked.m > > a python example is in : > > https://github.com/mne-tools/mne-python/blob/master/mne/fiff/meas_info.py#L235 > > but I agree you need a fairly good understanding of the fif format… > > we might have to sit down together to do this. I am afraid so. Well, I would certainly be up for it, because it would further strengthen both packages. Shall I come to you, or will you come to me ;-)? JM > Alex > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Fri Apr 13 12:08:10 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 13 Apr 2012 12:08:10 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: <5DB5ADAB-2E6A-4B90-B8AD-69D7CF315BB4@donders.ru.nl> References: <29636010-B832-42EF-9A14-A6FC1ED78509@donders.ru.nl> <5DB5ADAB-2E6A-4B90-B8AD-69D7CF315BB4@donders.ru.nl> Message-ID: hi JM, > That's the magic of EEGlab ;-). I did not look into the code but I would > assume based on the estimate of the precision matrix. Do you think the > magnitude problem will lead to numerical issues upon inversion of the > covariance matrix? probably not. > I am afraid so. Well, I would certainly be up for it, because it would > further strengthen both packages. Shall I come to you, or will you come to > me ;-)? Unless I come to you first, you'll come to me for Biomag in august I guess. Alex From Panagiotis.Tsiatsis at Tuebingen.MPG.de Fri Apr 13 19:00:14 2012 From: Panagiotis.Tsiatsis at Tuebingen.MPG.de (Panagiotis Tsiatsis) Date: Fri, 13 Apr 2012 19:00:14 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: References: Message-ID: <4F885B9E.6000307@Tuebingen.MPG.de> On 4/13/2012 8:50 AM, Alexandre Gramfort wrote: > but be careful when applying ICA on neuromag data as > channels have different types and you have signals > with 2 orders of magnitude difference between gradiometers > and magnetometers. > > I am curious to know if fieldtrip handles this properly? and if so how. Hi all, I am also working with CTF MEG data. What I ve been basically doing up to now was to split the datasets in two subsets: one containing only the MEGGRAD sensors (let s call it A) and another containing all the rest (let it be B). Then I would apply ICA only on the set containing the main MEG sensors, subtract the EOG-related components and re-construct the data without them (A'). Finally, I would merge A' with B. This works fine and the results that I am getting are convincing, the only problem is that of course the reference channels are still contaminated. I don t know if this would be a problem in subsequent analysis, ie source localization, maybe somebody who has more experience further down this road could comment on that. Best, Panagiotis -- Panagiotis S. Tsiatsis Max Planck Institute for Biological Cybernetics Cognitive NeuroImaging Group Tuebingen, Germany From cas243 at georgetown.edu Fri Apr 13 19:52:47 2012 From: cas243 at georgetown.edu (Clara A. Scholl) Date: Fri, 13 Apr 2012 13:52:47 -0400 Subject: [FieldTrip] dimensions for coherence Message-ID: Dear Fieldtrip users, I'm encountering a problem with calculating coherence between two time courses. I suspect I'm misunderstanding something very basic. When I calculate the coherence using data with multiple trials -- with dimensions rpttap_chan_freq, everything works fine (I get a coherence spectrum calculation that is averaged over the rpt dimension). However if I want to limit the calculation to data with dimensions chan_freq (i.e. find the coherence between the fourier spectra (containing both amplitude and phase info) of a single timecourse on two different channels (where those channels are specified using cfg.channelcmb)), I get an error. I've tried to do this two different ways. If I still use the rpttap_chan_freq data, I tried specifying cfg.trials=1 in the connectivity analysis input, and the error given is: ??? Index exceeds matrix dimensions. Error in ==> ft_connectivity_corr at 131 p1 = reshape(input(j,powindx(:,1),:,:,:), siz(2:end)); Error in ==> ft_connectivityanalysis at 471 [datout, varout, nrpt] = ft_connectivity_corr(data.(inparam), optarg{:}); ->>If I input frequency data with dimensions chan_freq into ft_connectivityanalysis (still only specifying cfg.method='coh' and the channel combinations I'm interested in with cfg.channelcmb) the output is: ??? Index exceeds matrix dimensions. Error in ==> ft_checkdata>fixcsd at 843 tmpdat1 = data.fourierspctrm(indx,cmbindx(:,1),:,:); Error in ==> ft_checkdata at 629 data = fixcsd(data, cmbrepresentation, channelcmb); Error in ==> univariate2bivariate at 37 data = ft_checkdata(data, 'cmbrepresentation', 'sparse', 'channelcmb', cmb); Error in ==> ft_connectivityanalysis at 320 [data, powindx, hasrpt] = univariate2bivariate(data, 'fourierspctrm', 'crsspctrm', dtype, 'cmb', cfg.channelcmb, 'keeprpt', normrpt); ->>Does the coherence calculation appear to require more than one (complex) value at each channel & frequency band of interest? Am I confused about what the rpttap dimension contains? My time window is narrow and my fft calculation only has 1 taper, is that a problem? Because the fourier calculation at each channel_frequency point contains both amplitude and phase information, wouldn't data with chan_freq dimensions be sufficient to calculate the cross spectral densities between the fourier transforms of two channels? Thanks for any guidance, Clara From jan.schoffelen at donders.ru.nl Fri Apr 13 20:28:31 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 Apr 2012 20:28:31 +0200 Subject: [FieldTrip] dimensions for coherence In-Reply-To: References: Message-ID: Hi Clara, Did you check the tutorial on the website? http://fieldtrip.fcdonders.nl/tutorial/connectivity The input data to ft_connectivityanalysis has some requirements. For coherence, you either need a freq-structure containing a 'fourierspctrm' field, or a 'crsspctrm' (+ 'powspctrm') field. The 'fourierspctrm' by definition should have a dimord of 'rpttap_chan_freq(_time', and the 'crsspctrm' may have lost the 'rpt' or 'rpttap' dimension. If your freq data looks different, you will not be able to compute coherence. Admittedly, the error messages you get are quite unspecific, but given the scarce information you are providing with respect to what exactly you have been doing, I can only give some general advice and point you to the documentation. Best, Jan-Mathijs On Apr 13, 2012, at 7:52 PM, Clara A. Scholl wrote: > Dear Fieldtrip users, > > I'm encountering a problem with calculating coherence between two time > courses. I suspect I'm misunderstanding something very basic. > > When I calculate the coherence using data with multiple trials -- with > dimensions rpttap_chan_freq, everything works fine (I get a coherence > spectrum calculation that is averaged over the rpt dimension). > However if I want to limit the calculation to data with dimensions > chan_freq (i.e. find the coherence between the fourier spectra > (containing both amplitude and phase info) of a single timecourse on > two different channels (where those channels are specified using > cfg.channelcmb)), I get an error. I've tried to do this two different > ways. If I still use the rpttap_chan_freq data, I tried specifying > cfg.trials=1 in the connectivity analysis input, and the error given > is: > ??? Index exceeds matrix dimensions. > > Error in ==> ft_connectivity_corr at 131 > p1 = reshape(input(j,powindx(:,1),:,:,:), siz(2:end)); > > Error in ==> ft_connectivityanalysis at 471 > [datout, varout, nrpt] = ft_connectivity_corr(data.(inparam), optarg{:}); > > > ->>If I input frequency data with dimensions chan_freq into > ft_connectivityanalysis (still only specifying cfg.method='coh' and > the channel combinations I'm interested in with cfg.channelcmb) the > output is: > > ??? Index exceeds matrix dimensions. > > Error in ==> ft_checkdata>fixcsd at 843 > tmpdat1 = data.fourierspctrm(indx,cmbindx(:,1),:,:); > > Error in ==> ft_checkdata at 629 > data = fixcsd(data, cmbrepresentation, channelcmb); > > Error in ==> univariate2bivariate at 37 > data = ft_checkdata(data, 'cmbrepresentation', 'sparse', > 'channelcmb', cmb); > > Error in ==> ft_connectivityanalysis at 320 > [data, powindx, hasrpt] = univariate2bivariate(data, > 'fourierspctrm', 'crsspctrm', dtype, 'cmb', cfg.channelcmb, 'keeprpt', > normrpt); > > > ->>Does the coherence calculation appear to require more than one > (complex) value at each channel & frequency band of interest? Am I > confused about what the rpttap dimension contains? My time window is > narrow and my fft calculation only has 1 taper, is that a problem? > Because the fourier calculation at each channel_frequency point > contains both amplitude and phase information, wouldn't data with > chan_freq dimensions be sufficient to calculate the cross spectral > densities between the fourier transforms of two channels? > > Thanks for any guidance, > Clara > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cas243 at georgetown.edu Fri Apr 13 21:01:34 2012 From: cas243 at georgetown.edu (Clara A. Scholl) Date: Fri, 13 Apr 2012 15:01:34 -0400 Subject: [FieldTrip] dimensions for coherence In-Reply-To: References: Message-ID: Thank you Jan-Mathijs! I was using the the coherence tutorial (http://fieldtrip.fcdonders.nl/tutorial/coherence) but after reading the connectivity tutorial I'm still confused. A more parsimonious way to phrase my question would be: Why do I get an error when my fourierspctrm with dimord rpttap_chan_freq has dimensions of 1 x 128 x 10 (the key being, just 1 rpttap value for each channel x frequency combination)? At each channel & frequency, fourierspctrum contains a complex value so the data structure contains the phase and amplitude information at each channel and frequency, which I think -- perhaps incorrectly -- should be sufficient to calculate the coherence. I'll paste below an example of the error I'm getting, beginning with the initial data structure through the ft_connectivityanalysis error. IF the initial data structure (called tmp in this example) has rpt size > 1, then I don't get the error. Thanks, Clara tmp = label: {128x1 cell} time: [0.3380 0.3400 0.3420 0.3440 0.3460 0.3480 0.3500 0.3520 0.3540 0.3560 0.3580 0.3600 0.3620 0.3640 0.3660 0.3680 0.3700 0.3720] cfg: [1x1 struct] trial: [1x128x18 double] sampleinfo: [1 18] dimord: 'rpt_chan_time' >> cfg=[]; cfg.output='fourier'; cfg.method='mtmfft'; cfg.tapsmofrq=28; cfg.channel={'all'}; freqm0=ft_freqanalysis(cfg, tmp) the input is timelock data with 128 channels and 18 timebins processing trials Warning: using only one taper for specified smoothing > In specest/private/warning_once at 75 In ft_specest_mtmfft at 96 In ft_freqanalysis at 519 processing trial 1/1 nfft: 18 samples, datalength: 18 samples, 1 tapers the call to "ft_freqanalysis" took 0 seconds and an estimated 0 MB freqm0 = label: {128x1 cell} dimord: 'rpttap_chan_freq' freq: [0 27.7778 55.5556 83.3333 111.1111 138.8889 166.6667 194.4444 222.2222 250.0000] fourierspctrm: [1x128x10 double] cumsumcnt: 18 cumtapcnt: 1 cfg: [1x1 struct] >> cfg=[]; cfg.method='coh'; cfg.channelcmb={'E34', 'E98'}; fdm0=ft_connectivityanalysis(cfg, freqm0) selection fourierspctrm along dimension 2 ??? Index exceeds matrix dimensions. Error in ==> ft_connectivity_corr at 131 p1 = reshape(input(j,powindx(:,1),:,:,:), siz(2:end)); Error in ==> ft_connectivityanalysis at 471 [datout, varout, nrpt] = ft_connectivity_corr(data.(inparam), optarg{:}); From alexandre.gramfort at inria.fr Sun Apr 15 14:34:44 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Sun, 15 Apr 2012 14:34:44 +0200 Subject: [FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data In-Reply-To: <4F885B9E.6000307@Tuebingen.MPG.de> References: <4F885B9E.6000307@Tuebingen.MPG.de> Message-ID: Dear Panagiotis, the only potential caveat I see for the inverse problem is that you reduce the rank of your data but using ICA. To take care of this you make sure that your inverse solver takes it into account via the whitening noise covariance matrix that should also be applied to the gain/leadfield matrix. Alex On Fri, Apr 13, 2012 at 7:00 PM, Panagiotis Tsiatsis wrote: > On 4/13/2012 8:50 AM, Alexandre Gramfort wrote: >> >> but be careful when applying ICA on neuromag data as >> channels have different types and you have signals >> with 2 orders of magnitude difference between gradiometers >> and magnetometers. >> >> I am curious to know if fieldtrip handles this properly? and if so how. > > Hi all, > > I am also working with CTF MEG data. What I ve been basically doing up to > now was to split the datasets in two subsets: one containing only the > MEGGRAD sensors (let s call it A)  and another containing all the rest (let > it be B). Then I would apply ICA only on the set containing the main MEG > sensors, subtract the EOG-related components and re-construct the data > without them (A'). Finally, I would merge A' with B. This works fine and the > results that I am getting are convincing, the only problem is that of course > the reference channels are still contaminated. I don t know if this would be > a problem in subsequent analysis, ie source localization, maybe somebody who > has more experience further down this road could comment on that. > > > Best, > Panagiotis > > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From B.Haendel at gmx.net Mon Apr 16 15:56:13 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Mon, 16 Apr 2012 15:56:13 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad Message-ID: <20120416135613.3220@gmx.net> Dear fieldtrip users, has anyone experience in using ft_denoise_synthetic? If I try to calculate 3rd order grads in the below specified way the data does not change with respect to the input data (which has no synthetic gradiometer applied). Is there some obvious misunderstanding on my side of how to use this function or is our environment truly noiseless :) Cheers, Barbara cfg=[]; cfg.gradient ='G3BR'; cfg.trials = 'all'; data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); >> data_3rdorder.grad.balance ans = G1BR: [1x1 struct] G2BR: [1x1 struct] G3BR: [1x1 struct] current: 'G3BR' previous: {'none'} >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) ans = 0 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From michael.wibral at web.de Mon Apr 16 16:46:27 2012 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 16 Apr 2012 16:46:27 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <20120416135613.3220@gmx.net> References: <20120416135613.3220@gmx.net> Message-ID: An HTML attachment was scrubbed... URL: From stan.vanpelt at fcdonders.ru.nl Mon Apr 16 16:59:25 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Mon, 16 Apr 2012 16:59:25 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: Message-ID: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> Hi Barbara, I can replicate your finding, but am unsure what is causing it. Maybe the difference/correction is lower than the Matlab or CTF precision? In any case, i f the 3rd order gradients were on, ft_denoise_synthetic would undo the G3BR-balancing, ergo it toggles. Best, Stan ----- Oorspronkelijk bericht ----- > Van: "Michael Wibral" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Maandag 16 april 2012 16:46:27 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hi Barbara, > are you certain that the original data do not have 3rd gradients > enabled? - looking at them once in dataEditor, switching to 3rd grads > and accidentally forgetting to unclick 'save parameters with dataset' > will make them have 3rd grads... > When I last used ft_denoise_synthetic it worked pretty much as > described (??). > Michael > Gesendet: Montag, 16. April 2012 um 15:56 Uhr > Von: "Barbara Haendel" > An: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] ft_denoise_synthetic 3rd order grad > Dear fieldtrip users, > has anyone experience in using ft_denoise_synthetic? If I try to > calculate 3rd order grads in the below specified way the data does not > change with respect to the input data (which has no synthetic > gradiometer applied). Is there some obvious misunderstanding on my > side of how to use this function or is our environment truly noiseless > :) > Cheers, > Barbara > cfg=[]; > cfg.gradient ='G3BR'; > cfg.trials = 'all'; > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > >> data_3rdorder.grad.balance > ans = > G1BR: [1x1 struct] > G2BR: [1x1 struct] > G3BR: [1x1 struct] > current: 'G3BR' > previous: {'none'} > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > ans = 0 > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 -- Stan van Pelt Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 10981 Fax: (+31) (0)24 36 10989 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Panagiotis.Tsiatsis at Tuebingen.MPG.de Mon Apr 16 17:53:56 2012 From: Panagiotis.Tsiatsis at Tuebingen.MPG.de (Panagiotis Tsiatsis) Date: Mon, 16 Apr 2012 17:53:56 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <4F8C4094.2020707@Tuebingen.MPG.de> Hello girls and guys, It is working for my CTF MEG data - the version that I have is v4692 2011-11-07. The other thing that might cause a problem could be ommiting the reference channels definition before the ft_ preprocessing command that gave you your "dataprepro" i.e maybe you might need something like this cfg = []; ... //various preprocessing parameters ... cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; dataprepro = ft_preprocessing(cfg); Hope you are lucky :) Best, Panagiotis On 4/16/2012 4:59 PM, Stan van Pelt wrote: > Hi Barbara, > > I can replicate your finding, but am unsure what is causing it. Maybe > the difference/correction is lower than the Matlab or CTF precision? > In any case, if the 3rd order gradients were on, ft_denoise_synthetic > would undo the G3BR-balancing, ergo it toggles. > > Best, > Stan > > > ------------------------------------------------------------------------ > > *Van: *"Michael Wibral" > *Aan: *"Email discussion list for the FieldTrip project" > > *Verzonden: *Maandag 16 april 2012 16:46:27 > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > Hi Barbara, > > are you certain that the original data do not have 3rd gradients > enabled? - looking at them once in dataEditor, switching to 3rd > grads and accidentally forgetting to unclick 'save parameters with > dataset' will make them have 3rd grads... > > When I last used ft_denoise_synthetic it worked pretty much as > described (??). > > Michael > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > *Von:* "Barbara Haendel" > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > Dear fieldtrip users, > > has anyone experience in using ft_denoise_synthetic? If I try to > calculate 3rd order grads in the below specified way the data does > not change with respect to the input data (which has no synthetic > gradiometer applied). Is there some obvious misunderstanding on my > side of how to use this function or is our environment truly > noiseless :) > > Cheers, > Barbara > > cfg=[]; > cfg.gradient ='G3BR'; > cfg.trials = 'all'; > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > >> data_3rdorder.grad.balance > > ans = > > G1BR: [1x1 struct] > G2BR: [1x1 struct] > G3BR: [1x1 struct] > current: 'G3BR' > previous: {'none'} > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > ans = 0 > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 > > > > > -- > Stan van Pelt > > Donders Institute for Brain, Cognition and Behaviour, Radboud > University Nijmegen > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > E-mail: stan.vanpelt at donders.ru.nl > Website: www.ru.nl/donders/ > Phone: (+31) (0)24 36 10981 > Fax: (+31) (0)24 36 10989 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Panagiotis S. Tsiatsis Max Planck Institute for Biological Cybernetics Cognitive NeuroImaging Group Tuebingen, Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Tue Apr 17 00:07:45 2012 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 17 Apr 2012 00:07:45 +0200 Subject: [FieldTrip] NeuroScan QuikCap64 Message-ID: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> Hi, I have recently started using a NeuroScan 64 Channel SynAmps2 System with a QuikCap. Does anyone know how to prepare a layout for this cap? From the Scan4.2. software, I only get x and y coordinates, but no z coordinates, and on the setup CD I can only find PDF files with the layout. Any suggestions are welcome. Thanks a lot, Julian ******************************************** Julian Keil International Laboratory for Brain Music and Sound Research (BRAMS) Pavillon 1430 Mont-Royal Université de Montréal Montréal, Québec Canada, H2V 4P3 julian.keil at uni-konstanz.de +1-514-343-6111-29653 www.brams.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Tue Apr 17 08:41:01 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Tue, 17 Apr 2012 09:41:01 +0300 Subject: [FieldTrip] Signal viewer + Biosemi Message-ID: Hello, I looked I the Signal viewer example in the following page: http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer I just want to know how could I view a signal coming directly from the biosemi device? (I think the following line should be changed: cfg.dataset = 'buffer://localhost:1972'; but I don't know what to put) Thanks for your help -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From diana.ibanescu at gmail.com Tue Apr 17 10:33:11 2012 From: diana.ibanescu at gmail.com (Diana Ibanescu) Date: Tue, 17 Apr 2012 10:33:11 +0200 Subject: [FieldTrip] Function ft_prepare_bemmodel deprecated... Message-ID: Hello, I am interested in an example how to compute an EEG leadfield with OpenMEEG in the Fieldtrip toolbox. I found a demo script here: http://fieldtrip.fcdonders.nl/example/testing_bem_created_leadfields When I call the function ft_prepare_bemmodel(cfg, vol) I receive the following warning: "Warning: FT_PREPARE_BEMMODEL is deprecated, please use FT_HEADMODEL_BEM_... with cfg.method = 'bem_bladeebla' instead." The function ft_headmodel_bem_openmeeg receive as parameter "geom" while ft_prepare_bemmodel receive other parameters: vol = ft_headmodel_openmeeg(geom, ...) Optional input arguments should be specified in key-value pairs and can include isolatedsource = string, 'yes' or 'no' hdmfile = string, filename with BEM headmodel conductivity = vector, conductivity of each compartment Are the 2 functions similar? Is there any demo updated after the function ft_prepare_bemmodel became deprecated? What function can I use instead? Thank you, Diana. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue Apr 17 11:35:17 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 17 Apr 2012 11:35:17 +0200 Subject: [FieldTrip] NeuroScan QuikCap64 In-Reply-To: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> References: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> Message-ID: Hi Julian, Have a look at our layout tutorial: http://fieldtrip.fcdonders.nl/tutorial/layout Starting from the PDF files (or bitmap (jpg/png) files based on them) you should be able to easily create a layout using ft_prepare_layout. Best, Eelke On 17 April 2012 00:07, Julian Keil wrote: > Hi, > > I have recently started using a NeuroScan 64 Channel SynAmps2 System with a > QuikCap. > Does anyone know how to prepare a layout for this cap? > From the Scan4.2. software, I only get x and y coordinates, but no z > coordinates, and on the setup CD I can only find PDF files with the layout. > > Any suggestions are welcome. > > Thanks a lot, > > Julian > > > > ******************************************** > Julian Keil > > International Laboratory for Brain > Music and Sound Research (BRAMS) > > Pavillon 1430 Mont-Royal > Université de Montréal > Montréal, Québec > Canada,  H2V 4P3 > > julian.keil at uni-konstanz.de > +1-514-343-6111-29653 > www.brams.org > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Tue Apr 17 12:57:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 17 Apr 2012 12:57:37 +0200 Subject: [FieldTrip] NeuroScan QuikCap64 In-Reply-To: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> References: <91E077A3-B0DA-4B58-B383-82158178116F@gmail.com> Message-ID: <4F8D4CA1.2050108@donders.ru.nl> Hi Julian, layout-files are in 2D, thus there is no need for a third dimenstion. You can use the x- and y-coordinates from your software package. If you got a third coordinate, you can try to build an elect-structure, see: http://fieldtrip.fcdonders.nl/faq/how_are_electrodes_magnetometers_or_gradiometers_described In case you got no third dimension, you can just set the z-coordinates to 0 for the elect-structure. It won't be 100% correct though, but the best you can do when only having a 2D layout at hand. You can also try one of the other layouts that we have that look similar, i.e. any layout that obeys the 1020-system (I am using easycapM11.lay, just try ft_prepare_layout while setting cfg.feedback='yes') Best, Jörn On 4/17/2012 12:07 AM, Julian Keil wrote: > Hi, > > I have recently started using a NeuroScan 64 Channel SynAmps2 System > with a QuikCap. > Does anyone know how to prepare a layout for this cap? > From the Scan4.2. software, I only get x and y coordinates, but no z > coordinates, and on the setup CD I can only find PDF files with the > layout. > > Any suggestions are welcome. > > Thanks a lot, > > Julian > > > > ********************************************** > *Julian Keil* > * > * > /International Laboratory for Brain/ > /Music and Sound Research (BRAMS)/ > > Pavillon 1430 Mont-Royal > Université de Montréal > Montréal, Québec > Canada, H2V 4P3 > > julian.keil at uni-konstanz.de > +1-514-343-6111-29653 > www.brams.org > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.severens at maartenskliniek.nl Tue Apr 17 14:51:41 2012 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Tue, 17 Apr 2012 14:51:41 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Hi Hamza You first need to start a buffer to read the data from de biosemi device, so start the biosemi2ft, see here http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. Then if you do not change the defaults you do not need to change the cfg.dataset field for the signal viewer. There is also a signal viewer based on c code (so no extra matlab session is necessary). You can find it here: fieldtrip/realtime/utilities/viewer Best, Marianne ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] Sent: Tuesday, April 17, 2012 8:41 AM To: Email discussion list for the FieldTrip project Subject: [FieldTrip] Signal viewer + Biosemi Hello, I looked I the Signal viewer example in the following page: http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer I just want to know how could I view a signal coming directly from the biosemi device? (I think the following line should be changed: cfg.dataset = 'buffer://localhost:1972'; but I don't know what to put) Thanks for your help -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3, 6574 NA Ubbergen (bij Nijmegen) Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From giulia.rizza at tiscali.it Tue Apr 17 15:04:23 2012 From: giulia.rizza at tiscali.it (Giulia Rizza) Date: Tue, 17 Apr 2012 15:04:23 +0200 (CEST) Subject: [FieldTrip] R: NeuroScan QuikCap64 Message-ID: <29197848.94691334667863183.JavaMail.defaultUser@defaultHost> Hi Julian I had the same problem some time ago and I found a list of the coordinates for all the channels in the download session of this link (then I followed the instructions in the FT tutorial): http://robertoostenveld. ruhosting.nl/index.php/electrode/#aes1994 Hope this helps Giulia >---- Messaggio originale---- >Da: julian.keil at gmail.com >Data: 17/04/2012 0.07 >A: "Email discussion list for the FieldTrip project" >Ogg: [FieldTrip] NeuroScan QuikCap64 > >Hi, > >I have recently started using a NeuroScan 64 Channel SynAmps2 System with a QuikCap. >Does anyone know how to prepare a layout for this cap? >From the Scan4.2. software, I only get x and y coordinates, but no z coordinates, and on the setup CD I can only find PDF files with the layout. > >Any suggestions are welcome. > >Thanks a lot, > >Julian > > > >******************************************** >Julian Keil > >International Laboratory for Brain >Music and Sound Research (BRAMS) > >Pavillon 1430 Mont-Royal >Université de Montréal >Montréal, Québec >Canada, H2V 4P3 > >julian.keil at uni-konstanz.de >+1-514-343-6111-29653 >www.brams.org > > > > > > >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru. nl/mailman/listinfo/fieldtrip Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più di uno spot in TV.Per ogni nuovo abbonato 30 € di premio per te e per lui! Un amico al mese e parli e navighisempre gratis: http://freelosophy.tiscali.it/ From julian.keil at gmail.com Tue Apr 17 15:21:16 2012 From: julian.keil at gmail.com (Julian Keil) Date: Tue, 17 Apr 2012 15:21:16 +0200 Subject: [FieldTrip] R: NeuroScan QuikCap64 In-Reply-To: <29197848.94691334667863183.JavaMail.defaultUser@defaultHost> References: <29197848.94691334667863183.JavaMail.defaultUser@defaultHost> Message-ID: <4A1B2E1E-A2CE-4381-AF8F-20EE9A83A7E7@gmail.com> Hi, thanks a lot you all! Out of laziness, I wanted to avoid doing the layout by hand from the image file :-) And thanks to Catarina, who sent me the 3D-Positions, I didn't have to. So if anyone ever runs into the same problem, here's a .mat-file with labels, positions (as provided by NeuroScan) and the created layout. Best, Julian ******************************************** Julian Keil International Laboratory for Brain Music and Sound Research (BRAMS) Pavillon 1430 Mont-Royal Université de Montréal Montréal, Québec Canada, H2V 4P3 julian.keil at uni-konstanz.de +1-514-343-6111-29653 www.brams.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NeuroScan64.mat Type: application/x-matlab-workspace Size: 4265 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at fcdonders.ru.nl Tue Apr 17 16:13:46 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Tue, 17 Apr 2012 16:13:46 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <4F8C4094.2020707@Tuebingen.MPG.de> Message-ID: <2082724711.41482.1334672026438.JavaMail.root@sculptor.zimbra.ru.nl> Hi Panagiotis, Good point, thanks. It works for me now. Best, Stan ----- Oorspronkelijk bericht ----- > Van: "Panagiotis Tsiatsis" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Maandag 16 april 2012 17:53:56 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hello girls and guys, > It is working for my CTF MEG data - the version that I have is v4692 > 2011-11-07. > The other thing that might cause a problem could be ommiting the > reference channels definition before the ft_ preprocessing command > that gave you your "dataprepro" > i.e maybe you might need something like this > cfg = []; > ... > //various preprocessing parameters > ... > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > dataprepro = ft_preprocessing(cfg); > Hope you are lucky :) > Best, > Panagiotis > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > Hi Barbara, > > I can replicate your finding, but am unsure what is causing it. > > Maybe > > the difference/correction is lower than the Matlab or CTF precision? > > In any case, if the 3rd order gradients were on, > > ft_denoise_synthetic > > would undo the G3BR-balancing, ergo it toggles. > > Best, > > Stan > > ----- Oorspronkelijk bericht ----- > > > Van: "Michael Wibral" > > > Aan: "Email discussion list for the FieldTrip project" > > > > > > Verzonden: Maandag 16 april 2012 16:46:27 > > > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Hi Barbara, > > > are you certain that the original data do not have 3rd gradients > > > enabled? - looking at them once in dataEditor, switching to 3rd > > > grads > > > and accidentally forgetting to unclick 'save parameters with > > > dataset' > > > will make them have 3rd grads... > > > When I last used ft_denoise_synthetic it worked pretty much as > > > described (??). > > > Michael > > > Gesendet: Montag, 16. April 2012 um 15:56 Uhr > > > Von: "Barbara Haendel" > > > An: fieldtrip at donders.ru.nl > > > Betreff: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Dear fieldtrip users, > > > has anyone experience in using ft_denoise_synthetic? If I try to > > > calculate 3rd order grads in the below specified way the data does > > > not > > > change with respect to the input data (which has no synthetic > > > gradiometer applied). Is there some obvious misunderstanding on my > > > side of how to use this function or is our environment truly > > > noiseless > > > :) > > > Cheers, > > > Barbara > > > cfg=[]; > > > cfg.gradient ='G3BR'; > > > cfg.trials = 'all'; > > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > >> data_3rdorder.grad.balance > > > ans = > > > G1BR: [1x1 struct] > > > G2BR: [1x1 struct] > > > G3BR: [1x1 struct] > > > current: 'G3BR' > > > previous: {'none'} > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > ans = 0 > > > -- > > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > > Jetzt informieren: > > > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > > _______________________________________________ > > > 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 > > -- > > Stan van Pelt > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > University Nijmegen > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > E-mail: stan.vanpelt at donders.ru.nl > > Website: www.ru.nl/donders/ > > Phone: (+31) (0)24 36 10981 > > Fax: (+31) (0)24 36 10989 > > _______________________________________________ > > fieldtrip mailing list fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Stan van Pelt Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 10981 Fax: (+31) (0)24 36 10989 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nathanweisz at mac.com Tue Apr 17 22:39:48 2012 From: nathanweisz at mac.com (Nathan Weisz) Date: Tue, 17 Apr 2012 22:39:48 +0200 Subject: [FieldTrip] postdoc positions @ CIMeC Message-ID: Dear all, not directly fieldtrip related ... I will be soon posting calls for postdoc positions at my new institution: http://www.unitn.it/cimec The postdoc positions will be within a new ERC-funded project (http://cordis.europa.eu/projects/rcn/103253_en.html), which will investigate the role of ongoing oscillatory activity patterns on perception. The studies conducted within this project will mainly use MEG and combined EEG / TMS. Apart from offline studies, relevant brain activity patterns will be used to control experiments in "realtime". I would be interested in getting in touch with postdocs or soon-to-be-postdocs who may be interested in working in such a project. The CIMeC offers access to state-of-the-art neuroimaging / -stimulation facilities along with an international and academically stimulating flair. Needless to say that it is located in a beautiful surrounding for the out-of-the-lab times (especially for mountain and water-sport lovers) and wine + food are not too bad as well. The salary is internationally competetive. Please pass this on to anyone you think might be interested. Best, Nathan -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Wed Apr 18 09:18:04 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 18 Apr 2012 10:18:04 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: Thank you Marianne I did not ask for just viewing the signal only, but to do realtime processing in general. Thanks again Hamza On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne < m.severens at maartenskliniek.nl> wrote: > Hi Hamza > > You first need to start a buffer to read the data from de biosemi device, > so start the biosemi2ft, see here > http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. > Then if you do not change the defaults you do not need to change the > cfg.dataset field for the signal viewer. > > There is also a signal viewer based on c code (so no extra matlab session > is necessary). You can find it here: fieldtrip/realtime/utilities/viewer > > Best, Marianne > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] > Sent: Tuesday, April 17, 2012 8:41 AM > To: Email discussion list for the FieldTrip project > Subject: [FieldTrip] Signal viewer + Biosemi > > Hello, > > I looked I the Signal viewer example in the following page: > http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer > > I just want to know how could I view a signal coming directly from the > biosemi device? > (I think the following line should be changed: > cfg.dataset = 'buffer://localhost:1972'; > but I don't know what to put) > > Thanks for your help > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is > geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking > van deze informatie is conform het Privacy reglement van de Sint > Maartenskliniek. De informatie is uitsluitend bestemd voor de > geadresseerde. Gebruik van deze informatie door anderen dan de > geadresseerde is, zonder voorafgaande schriftelijke toestemming van de > rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de > juiste en volledige overbrenging van de inhoud van een gezonden e-mail, > noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.vandenbroek at donders.ru.nl Wed Apr 18 10:04:34 2012 From: p.vandenbroek at donders.ru.nl (Philip van den Broek) Date: Wed, 18 Apr 2012 10:04:34 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> Hi Hamza, In that case you might be interested in BrainStream (for documentation, see website www.brainstream.nu), which also contains a section about how we connect to all fieldtrip supported devices. Might you be interested in BrainStream, the code can be downloaded from (http://code.google.com/p/brainstream/). Kind Regards Philip van den Broek Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour Centre for Cognition On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > Thank you Marianne > > I did not ask for just viewing the signal only, but to do realtime processing in general. > > Thanks again > > Hamza > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne wrote: > Hi Hamza > > You first need to start a buffer to read the data from de biosemi device, so start the biosemi2ft, see here http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. Then if you do not change the defaults you do not need to change the cfg.dataset field for the signal viewer. > > There is also a signal viewer based on c code (so no extra matlab session is necessary). You can find it here: fieldtrip/realtime/utilities/viewer > > Best, Marianne > ________________________________________ > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] > Sent: Tuesday, April 17, 2012 8:41 AM > To: Email discussion list for the FieldTrip project > Subject: [FieldTrip] Signal viewer + Biosemi > > Hello, > > I looked I the Signal viewer example in the following page: > http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer > > I just want to know how could I view a signal coming directly from the biosemi device? > (I think the following line should be changed: > cfg.dataset = 'buffer://localhost:1972'; > but I don't know what to put) > > Thanks for your help > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3, > 6574 NA Ubbergen (bij Nijmegen) > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 hamzaf at sabanciuniv.edu Wed Apr 18 10:52:16 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 18 Apr 2012 11:52:16 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> Message-ID: Thanks Philip I downloaded the BrainStream code but I did not work with it yet. But when you recommend me to use BrainStream is it because it contains things that fieldtrip functions cannot do or because it is just another alternative for making online experiments? I did not looked carefully at BrainStream webpage, but I feel that fieldtrip is more flexible regarding help and mailing. Regards Hamza On Wed, Apr 18, 2012 at 11:04 AM, Philip van den Broek < p.vandenbroek at donders.ru.nl> wrote: > Hi Hamza, > > In that case you might be interested in BrainStream (for documentation, > see website www.brainstream.nu), which also contains a section about how > we connect to all fieldtrip supported devices. Might you be interested in > BrainStream, the code can be downloaded from ( > http://code.google.com/p/brainstream/). > > Kind Regards > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > > Thank you Marianne > > I did not ask for just viewing the signal only, but to do realtime > processing in general. > > Thanks again > > Hamza > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne < > m.severens at maartenskliniek.nl> wrote: > >> Hi Hamza >> >> You first need to start a buffer to read the data from de biosemi device, >> so start the biosemi2ft, see here >> http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. >> Then if you do not change the defaults you do not need to change the >> cfg.dataset field for the signal viewer. >> >> There is also a signal viewer based on c code (so no extra matlab session >> is necessary). You can find it here: fieldtrip/realtime/utilities/viewer >> >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] >> On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >> Sent: Tuesday, April 17, 2012 8:41 AM >> To: Email discussion list for the FieldTrip project >> Subject: [FieldTrip] Signal viewer + Biosemi >> >> Hello, >> >> I looked I the Signal viewer example in the following page: >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >> >> I just want to know how could I view a signal coming directly from the >> biosemi device? >> (I think the following line should be changed: >> cfg.dataset = 'buffer://localhost:1972'; >> but I don't know what to put) >> >> Thanks for your help >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking >> van deze informatie is conform het Privacy reglement van de Sint >> Maartenskliniek. De informatie is uitsluitend bestemd voor de >> geadresseerde. Gebruik van deze informatie door anderen dan de >> geadresseerde is, zonder voorafgaande schriftelijke toestemming van de >> rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de >> juiste en volledige overbrenging van de inhoud van een gezonden e-mail, >> noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.vandenbroek at donders.ru.nl Wed Apr 18 12:10:54 2012 From: p.vandenbroek at donders.ru.nl (Philip van den Broek) Date: Wed, 18 Apr 2012 12:10:54 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> Message-ID: <2ADC0647-2CD2-4F84-8A1D-BAB78AB57E68@donders.ru.nl> Hi Hamza, > But when you recommend me to use BrainStream is it because it contains things that fieldtrip functions cannot do or because it is just another alternative for making online experiments? No, you should be able to do everything with fieldtrip. It is indeed another alternative for making online experiments with a different approach, which I thought might be of interest to you (or in general to anyone else involved in conducting real-time (BCI) experiments), but in the end off course that's something you can only decide. BrainStream is designed specifically for defining and executing real-time experiments and uses fieldtrips realtime buffer and hardware interfacing solutions (i.e., biosemi2ft, tmsi2ft etc.). It has all kind of built-in solutions for starting extra Matlab clients, automatic parallel execution, easy access to and switching between devices, information exchange, simulating from file or random data. In the design, you can use any Matlab code, including fieldtrip functions. However, you need to learn its specific way of defining experiments. Kind regards Philip > > Regards > > Hamza > > On Wed, Apr 18, 2012 at 11:04 AM, Philip van den Broek wrote: > Hi Hamza, > > In that case you might be interested in BrainStream (for documentation, see website www.brainstream.nu), which also contains a section about how we connect to all fieldtrip supported devices. Might you be interested in BrainStream, the code can be downloaded from (http://code.google.com/p/brainstream/). > > Kind Regards > > Philip van den Broek > Radboud University Nijmegen > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > > On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > >> Thank you Marianne >> >> I did not ask for just viewing the signal only, but to do realtime processing in general. >> >> Thanks again >> >> Hamza >> >> On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne wrote: >> Hi Hamza >> >> You first need to start a buffer to read the data from de biosemi device, so start the biosemi2ft, see here http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. Then if you do not change the defaults you do not need to change the cfg.dataset field for the signal viewer. >> >> There is also a signal viewer based on c code (so no extra matlab session is necessary). You can find it here: fieldtrip/realtime/utilities/viewer >> >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >> Sent: Tuesday, April 17, 2012 8:41 AM >> To: Email discussion list for the FieldTrip project >> Subject: [FieldTrip] Signal viewer + Biosemi >> >> Hello, >> >> I looked I the Signal viewer example in the following page: >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >> >> I just want to know how could I view a signal coming directly from the biosemi device? >> (I think the following line should be changed: >> cfg.dataset = 'buffer://localhost:1972'; >> but I don't know what to put) >> >> Thanks for your help >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> _______________________________________________ >> 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 > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 hamzaf at sabanciuniv.edu Wed Apr 18 16:30:55 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Wed, 18 Apr 2012 17:30:55 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: <2ADC0647-2CD2-4F84-8A1D-BAB78AB57E68@donders.ru.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> <0891EF20-48F6-4EBE-A983-B6DEE4090426@donders.ru.nl> <2ADC0647-2CD2-4F84-8A1D-BAB78AB57E68@donders.ru.nl> Message-ID: Thanks a lot Philip for the information. Regards Hamza On Wed, Apr 18, 2012 at 1:10 PM, Philip van den Broek < p.vandenbroek at donders.ru.nl> wrote: > Hi Hamza, > > But when you recommend me to use BrainStream is it because it contains > things that fieldtrip functions cannot do or because it is just another > alternative for making online experiments? > > No, you should be able to do everything with fieldtrip. It is indeed > another alternative for making online experiments with a different > approach, which I thought might be of interest to you (or in general to > anyone else involved in conducting real-time (BCI) experiments), but in the > end off course that's something you can only decide. > BrainStream is designed specifically for defining and executing real-time > experiments and uses fieldtrips realtime buffer and hardware interfacing > solutions (i.e., biosemi2ft, tmsi2ft etc.). It has all kind of built-in > solutions for starting extra Matlab clients, automatic parallel execution, > easy access to and switching between devices, information exchange, > simulating from file or random data. In the design, you can use any Matlab > code, including fieldtrip functions. However, you need to learn its > specific way of defining experiments. > > Kind regards > Philip > > > > Regards > > Hamza > > On Wed, Apr 18, 2012 at 11:04 AM, Philip van den Broek < > p.vandenbroek at donders.ru.nl> wrote: > >> Hi Hamza, >> >> In that case you might be interested in BrainStream (for documentation, >> see website www.brainstream.nu), which also contains a section about how >> we connect to all fieldtrip supported devices. Might you be interested in >> BrainStream, the code can be downloaded from ( >> http://code.google.com/p/brainstream/). >> >> Kind Regards >> >> Philip van den Broek >> Radboud University Nijmegen >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> >> On Apr 18, 2012, at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: >> >> Thank you Marianne >> >> I did not ask for just viewing the signal only, but to do realtime >> processing in general. >> >> Thanks again >> >> Hamza >> >> On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne < >> m.severens at maartenskliniek.nl> wrote: >> >>> Hi Hamza >>> >>> You first need to start a buffer to read the data from de biosemi >>> device, so start the biosemi2ft, see here >>> http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. >>> Then if you do not change the defaults you do not need to change the >>> cfg.dataset field for the signal viewer. >>> >>> There is also a signal viewer based on c code (so no extra matlab >>> session is necessary). You can find it here: >>> fieldtrip/realtime/utilities/viewer >>> >>> Best, Marianne >>> ________________________________________ >>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] >>> On Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >>> Sent: Tuesday, April 17, 2012 8:41 AM >>> To: Email discussion list for the FieldTrip project >>> Subject: [FieldTrip] Signal viewer + Biosemi >>> >>> Hello, >>> >>> I looked I the Signal viewer example in the following page: >>> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >>> >>> I just want to know how could I view a signal coming directly from the >>> biosemi device? >>> (I think the following line should be changed: >>> cfg.dataset = 'buffer://localhost:1972'; >>> but I don't know what to put) >>> >>> Thanks for your help >>> >>> >>> -- >>> Hamza Fawzi Altakroury >>> Graduate student - MA >>> Faculty of Engineering and Natural Sciences >>> Sabancı University >>> >>> Disclaimer >>> Vrijgave van de informatie verzonden met dit e-mail bericht is >>> geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking >>> van deze informatie is conform het Privacy reglement van de Sint >>> Maartenskliniek. De informatie is uitsluitend bestemd voor de >>> geadresseerde. Gebruik van deze informatie door anderen dan de >>> geadresseerde is, zonder voorafgaande schriftelijke toestemming van de >>> rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de >>> juiste en volledige overbrenging van de inhoud van een gezonden e-mail, >>> noch voor de ontvangst daarvan. >>> >>> Sint Maartenskliniek >>> Hengstdal 3, >>> 6574 NA Ubbergen (bij Nijmegen) >>> Telefoon 024-3659 911 >>> Telefax 024-3659 204 >>> KvK nummer 41055111 >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> _______________________________________________ >> 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 >> > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > _______________________________________________ > 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 > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at inria.fr Wed Apr 18 23:02:49 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Wed, 18 Apr 2012 23:02:49 +0200 Subject: [FieldTrip] Function ft_prepare_bemmodel deprecated... In-Reply-To: References: Message-ID: Hello diana, thanks for reporting the API change. I'll see if I can update the scripts: openmeeg_eeg_leadfield_example.m openmeeg_meg_leadfield_example.m feel free to give it a try if I am not too reactive... Alex On Tue, Apr 17, 2012 at 10:33 AM, Diana Ibanescu wrote: > Hello, > > I am interested in an example how to compute an EEG leadfield with OpenMEEG > in the Fieldtrip toolbox. I found a demo script here: > http://fieldtrip.fcdonders.nl/example/testing_bem_created_leadfields > When I call the function ft_prepare_bemmodel(cfg, vol) I receive the > following warning: > "Warning: FT_PREPARE_BEMMODEL is deprecated, please use FT_HEADMODEL_BEM_... > with cfg.method = 'bem_bladeebla' > instead." > The function ft_headmodel_bem_openmeeg receive as parameter "geom" while > ft_prepare_bemmodel receive other parameters: >  vol = ft_headmodel_openmeeg(geom, ...) > >   Optional input arguments should be specified in key-value pairs and can >   include >     isolatedsource   = string, 'yes' or 'no' >     hdmfile          = string, filename with BEM headmodel >     conductivity     = vector, conductivity of each compartment > > Are the 2 functions similar? Is there any demo updated after the function > ft_prepare_bemmodel became deprecated? What function can I use instead? > > Thank you, > Diana. > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From B.Haendel at gmx.net Thu Apr 19 08:59:39 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Thu, 19 Apr 2012 08:59:39 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <4F8C4094.2020707@Tuebingen.MPG.de> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de> Message-ID: <20120419065939.195940@gmx.net> Hey there, thanks a lot for the replies! Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. Thanks again, Barbara -------- Original-Nachricht -------- > Datum: Mon, 16 Apr 2012 17:53:56 +0200 > Von: Panagiotis Tsiatsis > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hello girls and guys, > > It is working for my CTF MEG data - the version that I have is v4692 > 2011-11-07. > > The other thing that might cause a problem could be ommiting the > reference channels definition before the ft_ preprocessing command that > gave you your "dataprepro" > > i.e maybe you might need something like this > > cfg = []; > > ... > //various preprocessing parameters > ... > > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > > dataprepro = ft_preprocessing(cfg); > > > Hope you are lucky :) > > Best, > Panagiotis > > > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > Hi Barbara, > > > > I can replicate your finding, but am unsure what is causing it. Maybe > > the difference/correction is lower than the Matlab or CTF precision? > > In any case, if the 3rd order gradients were on, ft_denoise_synthetic > > would undo the G3BR-balancing, ergo it toggles. > > > > Best, > > Stan > > > > > > ------------------------------------------------------------------------ > > > > *Van: *"Michael Wibral" > > *Aan: *"Email discussion list for the FieldTrip project" > > > > *Verzonden: *Maandag 16 april 2012 16:46:27 > > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Hi Barbara, > > > > are you certain that the original data do not have 3rd gradients > > enabled? - looking at them once in dataEditor, switching to 3rd > > grads and accidentally forgetting to unclick 'save parameters with > > dataset' will make them have 3rd grads... > > > > When I last used ft_denoise_synthetic it worked pretty much as > > described (??). > > > > Michael > > > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > > *Von:* "Barbara Haendel" > > *An:* fieldtrip at donders.ru.nl > > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Dear fieldtrip users, > > > > has anyone experience in using ft_denoise_synthetic? If I try to > > calculate 3rd order grads in the below specified way the data does > > not change with respect to the input data (which has no synthetic > > gradiometer applied). Is there some obvious misunderstanding on my > > side of how to use this function or is our environment truly > > noiseless :) > > > > Cheers, > > Barbara > > > > cfg=[]; > > cfg.gradient ='G3BR'; > > cfg.trials = 'all'; > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > > > > >> data_3rdorder.grad.balance > > > > ans = > > > > G1BR: [1x1 struct] > > G2BR: [1x1 struct] > > G3BR: [1x1 struct] > > current: 'G3BR' > > previous: {'none'} > > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > > ans = 0 > > > > -- > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > Jetzt informieren: > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > _______________________________________________ > > 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 > > > > > > > > > > -- > > Stan van Pelt > > > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > University Nijmegen > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > E-mail: stan.vanpelt at donders.ru.nl > > Website: www.ru.nl/donders/ > > Phone: (+31) (0)24 36 10981 > > Fax: (+31) (0)24 36 10989 > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From B.Haendel at gmx.net Thu Apr 19 08:59:39 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Thu, 19 Apr 2012 08:59:39 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <4F8C4094.2020707@Tuebingen.MPG.de> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de> Message-ID: <20120419065939.195940@gmx.net> Hey there, thanks a lot for the replies! Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. Thanks again, Barbara -------- Original-Nachricht -------- > Datum: Mon, 16 Apr 2012 17:53:56 +0200 > Von: Panagiotis Tsiatsis > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hello girls and guys, > > It is working for my CTF MEG data - the version that I have is v4692 > 2011-11-07. > > The other thing that might cause a problem could be ommiting the > reference channels definition before the ft_ preprocessing command that > gave you your "dataprepro" > > i.e maybe you might need something like this > > cfg = []; > > ... > //various preprocessing parameters > ... > > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > > dataprepro = ft_preprocessing(cfg); > > > Hope you are lucky :) > > Best, > Panagiotis > > > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > Hi Barbara, > > > > I can replicate your finding, but am unsure what is causing it. Maybe > > the difference/correction is lower than the Matlab or CTF precision? > > In any case, if the 3rd order gradients were on, ft_denoise_synthetic > > would undo the G3BR-balancing, ergo it toggles. > > > > Best, > > Stan > > > > > > ------------------------------------------------------------------------ > > > > *Van: *"Michael Wibral" > > *Aan: *"Email discussion list for the FieldTrip project" > > > > *Verzonden: *Maandag 16 april 2012 16:46:27 > > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Hi Barbara, > > > > are you certain that the original data do not have 3rd gradients > > enabled? - looking at them once in dataEditor, switching to 3rd > > grads and accidentally forgetting to unclick 'save parameters with > > dataset' will make them have 3rd grads... > > > > When I last used ft_denoise_synthetic it worked pretty much as > > described (??). > > > > Michael > > > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > > *Von:* "Barbara Haendel" > > *An:* fieldtrip at donders.ru.nl > > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > Dear fieldtrip users, > > > > has anyone experience in using ft_denoise_synthetic? If I try to > > calculate 3rd order grads in the below specified way the data does > > not change with respect to the input data (which has no synthetic > > gradiometer applied). Is there some obvious misunderstanding on my > > side of how to use this function or is our environment truly > > noiseless :) > > > > Cheers, > > Barbara > > > > cfg=[]; > > cfg.gradient ='G3BR'; > > cfg.trials = 'all'; > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > > > > >> data_3rdorder.grad.balance > > > > ans = > > > > G1BR: [1x1 struct] > > G2BR: [1x1 struct] > > G3BR: [1x1 struct] > > current: 'G3BR' > > previous: {'none'} > > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > > ans = 0 > > > > -- > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > Jetzt informieren: > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > _______________________________________________ > > 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 > > > > > > > > > > -- > > Stan van Pelt > > > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > University Nijmegen > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > E-mail: stan.vanpelt at donders.ru.nl > > Website: www.ru.nl/donders/ > > Phone: (+31) (0)24 36 10981 > > Fax: (+31) (0)24 36 10989 > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Panagiotis S. Tsiatsis > Max Planck Institute for Biological Cybernetics > Cognitive NeuroImaging Group > Tuebingen, Germany > -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a From jan.schoffelen at donders.ru.nl Thu Apr 19 10:02:43 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 19 Apr 2012 10:02:43 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <20120419065939.195940@gmx.net> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de> <20120419065939.195940@gmx.net> Message-ID: Hi Barbara, Good plan to adjust the code a bit in this respect. Could you please file a bug about this on our bugzilla list: bugzilla.fcdonders.nl Best wishes, Jan-Mathijs On Apr 19, 2012, at 8:59 AM, Barbara Haendel wrote: > > > Hey there, thanks a lot for the replies! > > Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. > > Thanks again, > Barbara > > > > > -------- Original-Nachricht -------- >> Datum: Mon, 16 Apr 2012 17:53:56 +0200 >> Von: Panagiotis Tsiatsis >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > >> Hello girls and guys, >> >> It is working for my CTF MEG data - the version that I have is v4692 >> 2011-11-07. >> >> The other thing that might cause a problem could be ommiting the >> reference channels definition before the ft_ preprocessing command that >> gave you your "dataprepro" >> >> i.e maybe you might need something like this >> >> cfg = []; >> >> ... >> //various preprocessing parameters >> ... >> >> cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; >> >> dataprepro = ft_preprocessing(cfg); >> >> >> Hope you are lucky :) >> >> Best, >> Panagiotis >> >> >> On 4/16/2012 4:59 PM, Stan van Pelt wrote: >>> Hi Barbara, >>> >>> I can replicate your finding, but am unsure what is causing it. Maybe >>> the difference/correction is lower than the Matlab or CTF precision? >>> In any case, if the 3rd order gradients were on, ft_denoise_synthetic >>> would undo the G3BR-balancing, ergo it toggles. >>> >>> Best, >>> Stan >>> >>> >>> ------------------------------------------------------------------------ >>> >>> *Van: *"Michael Wibral" >>> *Aan: *"Email discussion list for the FieldTrip project" >>> >>> *Verzonden: *Maandag 16 april 2012 16:46:27 >>> *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad >>> >>> Hi Barbara, >>> >>> are you certain that the original data do not have 3rd gradients >>> enabled? - looking at them once in dataEditor, switching to 3rd >>> grads and accidentally forgetting to unclick 'save parameters with >>> dataset' will make them have 3rd grads... >>> >>> When I last used ft_denoise_synthetic it worked pretty much as >>> described (??). >>> >>> Michael >>> >>> *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr >>> *Von:* "Barbara Haendel" >>> *An:* fieldtrip at donders.ru.nl >>> *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad >>> >>> Dear fieldtrip users, >>> >>> has anyone experience in using ft_denoise_synthetic? If I try to >>> calculate 3rd order grads in the below specified way the data does >>> not change with respect to the input data (which has no synthetic >>> gradiometer applied). Is there some obvious misunderstanding on my >>> side of how to use this function or is our environment truly >>> noiseless :) >>> >>> Cheers, >>> Barbara >>> >>> cfg=[]; >>> cfg.gradient ='G3BR'; >>> cfg.trials = 'all'; >>> data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); >>> >>> >>>>> data_3rdorder.grad.balance >>> >>> ans = >>> >>> G1BR: [1x1 struct] >>> G2BR: [1x1 struct] >>> G3BR: [1x1 struct] >>> current: 'G3BR' >>> previous: {'none'} >>> >>>>> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) >>> >>> ans = 0 >>> >>> -- >>> NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! >>> Jetzt informieren: >> http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a >>> _______________________________________________ >>> 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 >>> >>> >>> >>> >>> -- >>> Stan van Pelt >>> >>> Donders Institute for Brain, Cognition and Behaviour, Radboud >>> University Nijmegen >>> Kapittelweg 29, 6525 EN Nijmegen, Netherlands >>> E-mail: stan.vanpelt at donders.ru.nl >>> Website: www.ru.nl/donders/ >>> Phone: (+31) (0)24 36 10981 >>> Fax: (+31) (0)24 36 10989 >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Panagiotis S. Tsiatsis >> Max Planck Institute for Biological Cybernetics >> Cognitive NeuroImaging Group >> Tuebingen, Germany >> > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Thu Apr 19 10:24:57 2012 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 19 Apr 2012 10:24:57 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <20120419065939.195940@gmx.net> References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de>, <20120419065939.195940@gmx.net> Message-ID: An HTML attachment was scrubbed... URL: From B.Haendel at gmx.net Thu Apr 19 11:01:59 2012 From: B.Haendel at gmx.net (Barbara Haendel) Date: Thu, 19 Apr 2012 11:01:59 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: References: <95345142.24585.1334588365133.JavaMail.root@sculptor.zimbra.ru.nl> <4F8C4094.2020707@Tuebingen.MPG.de>, <20120419065939.195940@gmx.net> Message-ID: <20120419090159.195980@gmx.net> Hey Michael, I completely agree that there should be a warning especially because the specification in data.grad.balance.current is consequently wrong. As Jan-Mathijs suggested I filed a bug report to fieldtrip. Best, Barbara -------- Original-Nachricht -------- > Datum: Thu, 19 Apr 2012 10:24:57 +0200 (CEST) > Von: "Michael Wibral" > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de From b.reuderink at donders.ru.nl Thu Apr 19 12:48:03 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Thu, 19 Apr 2012 12:48:03 +0200 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: Dear Hamza, Could you perhaps elaborate on your question? I was also under the impression that you asked how to view the (real time) Biosemi signals --- which Marianne explained. What are you trying to achieve, what is your approach, and on what aspect are you asking for help? Best, Boris On Wed, Apr 18, 2012 at 9:18 AM, Hamza Fawzi Altakroury (Student) wrote: > Thank you Marianne > > I did not ask for just viewing the signal only, but to do realtime > processing in general. > > Thanks again > > Hamza > > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne > wrote: >> >> Hi Hamza >> >> You first need to start a buffer to read the data from de biosemi device, >> so start the biosemi2ft, see here >> http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. >> Then if you do not change the defaults you do not need to change the >> cfg.dataset field for the signal viewer. >> >> There is also a signal viewer based on c code (so no extra matlab session >> is necessary). You can find it here: fieldtrip/realtime/utilities/viewer >> >> Best, Marianne >> ________________________________________ >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On >> Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] >> Sent: Tuesday, April 17, 2012 8:41 AM >> To: Email discussion list for the FieldTrip project >> Subject: [FieldTrip] Signal viewer + Biosemi >> >> Hello, >> >> I looked I the Signal viewer example in the following page: >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer >> >> I just want to know how could I view a signal coming directly from the >> biosemi device? >> (I think the following line should be changed: >>  cfg.dataset        = 'buffer://localhost:1972'; >> but I don't know what to put) >> >> Thanks for your help >> >> >> -- >> Hamza Fawzi Altakroury >> Graduate student - MA >> Faculty of Engineering and Natural Sciences >> Sabancı University >> >> Disclaimer >> Vrijgave van de informatie verzonden met dit e-mail bericht is >> geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van >> deze informatie is conform het Privacy reglement van de Sint >> Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. >> Gebruik van deze informatie door anderen dan de geadresseerde is, zonder >> voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De >> Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging >> van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. >> >> Sint Maartenskliniek >> Hengstdal 3, >> 6574 NA Ubbergen (bij Nijmegen) >> Telefoon 024-3659 911 >> Telefax 024-3659 204 >> KvK nummer 41055111 >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From alexandre.gramfort at inria.fr Fri Apr 20 09:13:33 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Fri, 20 Apr 2012 09:13:33 +0200 Subject: [FieldTrip] Function ft_prepare_bemmodel deprecated... In-Reply-To: References: Message-ID: Hello Diana, I've just fixed on the svn the OpenMEEG demo scripts which had accidentally been broken. Once you update your version, you should now be able to run: openmeeg_eeg_leadfield_example.m  openmeeg_meg_leadfield_example.m which will confirm that OpenMEEG works as expected. Best, Alex On Wed, Apr 18, 2012 at 11:02 PM, Alexandre Gramfort wrote: > Hello diana, > > thanks for reporting the API change. > > I'll see if I can update the scripts: > > openmeeg_eeg_leadfield_example.m  openmeeg_meg_leadfield_example.m > > feel free to give it a try if I am not too reactive... > > Alex > > On Tue, Apr 17, 2012 at 10:33 AM, Diana Ibanescu > wrote: >> Hello, >> >> I am interested in an example how to compute an EEG leadfield with OpenMEEG >> in the Fieldtrip toolbox. I found a demo script here: >> http://fieldtrip.fcdonders.nl/example/testing_bem_created_leadfields >> When I call the function ft_prepare_bemmodel(cfg, vol) I receive the >> following warning: >> "Warning: FT_PREPARE_BEMMODEL is deprecated, please use FT_HEADMODEL_BEM_... >> with cfg.method = 'bem_bladeebla' >> instead." >> The function ft_headmodel_bem_openmeeg receive as parameter "geom" while >> ft_prepare_bemmodel receive other parameters: >>  vol = ft_headmodel_openmeeg(geom, ...) >> >>   Optional input arguments should be specified in key-value pairs and can >>   include >>     isolatedsource   = string, 'yes' or 'no' >>     hdmfile          = string, filename with BEM headmodel >>     conductivity     = vector, conductivity of each compartment >> >> Are the 2 functions similar? Is there any demo updated after the function >> ft_prepare_bemmodel became deprecated? What function can I use instead? >> >> Thank you, >> Diana. >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> From hamzaf at sabanciuniv.edu Sat Apr 21 09:28:57 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 21 Apr 2012 10:28:57 +0300 Subject: [FieldTrip] Signal viewer + Biosemi In-Reply-To: References: <70FC3ACFFB46314EBEAF9101EA45F50E0736485BEC@smkexch02.maartenskliniek.nl> Message-ID: Dear Boris Due to my misunderstanding I thought the realtime processing is done by reading the data from a gdf file that is created by the biosemi2ft function. Reading the signal viewer discription on your site made me understand the realtime processing and reading from a buffter. To read the data from the biosemi I thought I should change the address (cfg.dataset = 'buffer://localhost:1972';), but, thanks to Marianne, I could view the signals easily from biosemi by keeping the line as it is. The command lines that I typed are: In cmd: *biosemi2ft example.config.txt out - *In MatLab: *cfg = []; * *cfg.blocksize = 1; % seconds * *cfg.dataset = 'buffer://localhost:1972'; % where to read the data* Best, Hamza On Thu, Apr 19, 2012 at 1:48 PM, Boris Reuderink wrote: > Dear Hamza, > > Could you perhaps elaborate on your question? I was also under the > impression that you asked how to view the (real time) Biosemi signals > --- which Marianne explained. What are you trying to achieve, what is > your approach, and on what aspect are you asking for help? > > Best, > > Boris > > On Wed, Apr 18, 2012 at 9:18 AM, Hamza Fawzi Altakroury (Student) > wrote: > > Thank you Marianne > > > > I did not ask for just viewing the signal only, but to do realtime > > processing in general. > > > > Thanks again > > > > Hamza > > > > > > On Tue, Apr 17, 2012 at 3:51 PM, Severens, Marianne > > wrote: > >> > >> Hi Hamza > >> > >> You first need to start a buffer to read the data from de biosemi > device, > >> so start the biosemi2ft, see here > >> > http://fieldtrip.fcdonders.nl/development/realtime/biosemi?s[]=biosemi2ft. > >> Then if you do not change the defaults you do not need to change the > >> cfg.dataset field for the signal viewer. > >> > >> There is also a signal viewer based on c code (so no extra matlab > session > >> is necessary). You can find it here: fieldtrip/realtime/utilities/viewer > >> > >> Best, Marianne > >> ________________________________________ > >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > On > >> Behalf Of Hamza Fawzi Altakroury (Student) [hamzaf at sabanciuniv.edu] > >> Sent: Tuesday, April 17, 2012 8:41 AM > >> To: Email discussion list for the FieldTrip project > >> Subject: [FieldTrip] Signal viewer + Biosemi > >> > >> Hello, > >> > >> I looked I the Signal viewer example in the following page: > >> http://fieldtrip.fcdonders.nl/example/ft_realtime_signalviewer > >> > >> I just want to know how could I view a signal coming directly from the > >> biosemi device? > >> (I think the following line should be changed: > >> cfg.dataset = 'buffer://localhost:1972'; > >> but I don't know what to put) > >> > >> Thanks for your help > >> > >> > >> -- > >> Hamza Fawzi Altakroury > >> Graduate student - MA > >> Faculty of Engineering and Natural Sciences > >> Sabancı University > >> > >> Disclaimer > >> Vrijgave van de informatie verzonden met dit e-mail bericht is > >> geaccordeerd door de ontvanger en/of zijn behandelend arts. > Verstrekking van > >> deze informatie is conform het Privacy reglement van de Sint > >> Maartenskliniek. De informatie is uitsluitend bestemd voor de > geadresseerde. > >> Gebruik van deze informatie door anderen dan de geadresseerde is, zonder > >> voorafgaande schriftelijke toestemming van de rechthebbende , verboden. > De > >> Sint Maartenskliniek staat niet in voor de juiste en volledige > overbrenging > >> van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > >> > >> Sint Maartenskliniek > >> Hengstdal 3, > >> 6574 NA Ubbergen (bij Nijmegen) > >> Telefoon 024-3659 911 > >> Telefax 024-3659 204 > >> KvK nummer 41055111 > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > > > -- > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabancı University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > twitter.com/#!/breuderink | > github.com/breuderink | borisreuderink.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at gmx.de Sun Apr 22 09:07:06 2012 From: paul_c at gmx.de (Paul Czienskowski) Date: Sun, 22 Apr 2012 09:07:06 +0200 Subject: [FieldTrip] Question concerning ft_headmodel_bem_openmeeg Message-ID: <4F93AE1A.50405@gmx.de> Dear all, I want to create headmodels with the ft_headmodel_bem_openmeeg function, and - for I formerly used the ft_prepare_bemmodel function - decided to delve into the new function first, to see how it works. Anyway, I stumbled upon something that puzzled me a bit. In line 96 to 106, the boundaries are rearranged to be inside first, which to my understanding means, that the first boundary in the array of boundaries will be the innermost one (i.e. the brain in my case) and the last boundary will be the outermost one (i.e. skin). Everything's fine hitherto. But from line 108 on, things become quite odd. Line 108 and 109 define the first compartment to be the skin and the last to be the source compartment. This is cross-checked again in line 127 to 129. To my understanding this is a contradiction and I would appreciate, if anybody could tell me if I got something completely wrong, or if the function does odd things. If the function is correct, there should at least be a comment explaining why this contradiction makes sense anyway. Best regards, Paul From matt.mollison at gmail.com Mon Apr 23 05:54:33 2012 From: matt.mollison at gmail.com (Matt Mollison) Date: Sun, 22 Apr 2012 21:54:33 -0600 Subject: [FieldTrip] Oscillatory power normalization Message-ID: Hi FieldTrippers, In almost all the papers I've read involving oscillatory power, some kind of transformation is done to the data due to the 1/f power spectrum effect (power decreases as frequency increases). I'm mostly looking at within-subjects experiments (every subject behaved in all conditions) comparing conditions across subjects, but it seems like normalizing the power spectrum should apply in any case (especially if any kind of parametric stats are done—right?). Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis to make these transformations (e.g., log10 normalization, dB normalization [EEGLab does this], vector length normalization, etc.; the only thing I see is in ft_sourcedescriptives, but I'm not doing source analyses), and it confuses me why this is the case. I can't find much discussion regarding the 1/f issue on the FT wiki or the mailing list. This seems like an important step that is missing from any frequency analysis workflow. Am I missing something (meaning I just don't see the option), am I misunderstanding something (meaning I'm incorrect in this assumption), or is this an issue that needs to be fixed? Thanks, Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon Apr 23 08:49:00 2012 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Mon, 23 Apr 2012 08:49:00 +0200 Subject: [FieldTrip] Oscillatory power normalization In-Reply-To: References: Message-ID: <6CC16DD9-C72B-4CA4-A7C9-D504BBCF9447@psi.ucm.es> Hi Matt, I think Fieltrip does not do these transformations. However you could do cfg.baselinetype = 'relative' (power post/power pre) and take the log10 and multiply by 10 (TF.powerspctrm). Then you should have dB. best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 23/04/2012, a las 05:54, Matt Mollison escribió: > Hi FieldTrippers, > > In almost all the papers I've read involving oscillatory power, some kind of transformation is done to the data due to the 1/f power spectrum effect (power decreases as frequency increases). I'm mostly looking at within-subjects experiments (every subject behaved in all conditions) comparing conditions across subjects, but it seems like normalizing the power spectrum should apply in any case (especially if any kind of parametric stats are done—right?). > > Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis to make these transformations (e.g., log10 normalization, dB normalization [EEGLab does this], vector length normalization, etc.; the only thing I see is in ft_sourcedescriptives, but I'm not doing source analyses), and it confuses me why this is the case. I can't find much discussion regarding the 1/f issue on the FT wiki or the mailing list. This seems like an important step that is missing from any frequency analysis workflow. Am I missing something (meaning I just don't see the option), am I misunderstanding something (meaning I'm incorrect in this assumption), or is this an issue that needs to be fixed? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > _______________________________________________ > 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 eelke.spaak at donders.ru.nl Mon Apr 23 11:54:42 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 23 Apr 2012 11:54:42 +0200 Subject: [FieldTrip] Oscillatory power normalization In-Reply-To: References: Message-ID: Hi Matt, When you are comparing power across conditions, it is not really necessary to apply an explicit correction for the dominant 1/f component of the raw spectrum. Since this 1/f component is present in both conditions, when you subtract power in one condition from power in another condition (or compute the ratio, or log-ratio, or relative change, or whatever), the 1/f will cancel out and you will only be left with whatever is due to your experimental manipulation. This is true because the contrast is done per frequency. (Note that comparing activity versus baseline is just a special case of looking at a contrast between conditions, so the same argument holds there.) The only time when an explicit correction for 1/f is useful, is when you want to look at raw power. The most dominant oscillatory features (visual alpha, visual contrast induced gamma...) will usually be evident in raw spectra without such a correction, by the way. Correcting for 1/f can be done in many ways, the most simple one is simply taking the logarithm of power, something like: freqCorrected = freqUncorrected; freqCorrected.powspctrm = log10(freqCorrected.powspctrm); Or you could take the first derivative in the time domain (equivalent to multiplying the spectrum with f, search for post by Robert on this on the FT list). Or you could take the log of both the frequency- and power axes, then fit a line, and subtract it, then transform back (10^corrected data). But, the main point is: in the vast majority of typical cognitive experiments, correcting for 1/f is not needed. Best, Eelke On 23 April 2012 05:54, Matt Mollison wrote: > Hi FieldTrippers, > > In almost all the papers I've read involving oscillatory power, some kind of > transformation is done to the data due to the 1/f power spectrum effect > (power decreases as frequency increases). I'm mostly looking at > within-subjects experiments (every subject behaved in all conditions) > comparing conditions across subjects, but it seems like normalizing the > power spectrum should apply in any case (especially if any kind of > parametric stats are done—right?). > > Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis > to make these transformations (e.g., log10 normalization, dB normalization > [EEGLab does this], vector length normalization, etc.; the only thing I see > is in ft_sourcedescriptives, but I'm not doing source analyses), and it > confuses me why this is the case. I can't find much discussion regarding the > 1/f issue on the FT wiki or the mailing list. This seems like an important > step that is missing from any frequency analysis workflow. Am I missing > something (meaning I just don't see the option), am I misunderstanding > something (meaning I'm incorrect in this assumption), or is this an issue > that needs to be fixed? > > Thanks, > Matt > > -- > Univ. of Colorado at Boulder > Dept. of Psychology and Neuroscience > matthew.mollison at colorado.edu > http://psych.colorado.edu/~mollison/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jdien07 at mac.com Tue Apr 24 08:41:20 2012 From: jdien07 at mac.com (Joseph Dien) Date: Tue, 24 Apr 2012 02:41:20 -0400 Subject: [FieldTrip] Oscillatory power normalization In-Reply-To: References: Message-ID: <454AC917-60FD-4CF6-BF21-242DF4B5B4D0@mac.com> I'm new to spectral analysis so take anything I say with a grain of salt: 1) If one intends on taking the average of a band (like 8-12Hz for alpha), seems like maybe helpful to correct for 1/f so the lower bands don't dominate? 2) Another issue is spectral density (correcting for frequency bin width for discrete Fourier). As far as I can tell, FieldTrip isn't doing this. Seems like it should be standard. Or at least it should say in the documentation whether it is being done. Am I wrong? Cheers! Joe On Apr 23, 2012, at 5:54 AM, Eelke Spaak wrote: > Hi Matt, > > When you are comparing power across conditions, it is not really > necessary to apply an explicit correction for the dominant 1/f > component of the raw spectrum. Since this 1/f component is present in > both conditions, when you subtract power in one condition from power > in another condition (or compute the ratio, or log-ratio, or relative > change, or whatever), the 1/f will cancel out and you will only be > left with whatever is due to your experimental manipulation. This is > true because the contrast is done per frequency. (Note that comparing > activity versus baseline is just a special case of looking at a > contrast between conditions, so the same argument holds there.) > > The only time when an explicit correction for 1/f is useful, is when > you want to look at raw power. The most dominant oscillatory features > (visual alpha, visual contrast induced gamma...) will usually be > evident in raw spectra without such a correction, by the way. > Correcting for 1/f can be done in many ways, the most simple one is > simply taking the logarithm of power, something like: > > freqCorrected = freqUncorrected; > freqCorrected.powspctrm = log10(freqCorrected.powspctrm); > > Or you could take the first derivative in the time domain (equivalent > to multiplying the spectrum with f, search for post by Robert on this > on the FT list). Or you could take the log of both the frequency- and > power axes, then fit a line, and subtract it, then transform back > (10^corrected data). > > But, the main point is: in the vast majority of typical cognitive > experiments, correcting for 1/f is not needed. > > Best, > Eelke > > On 23 April 2012 05:54, Matt Mollison wrote: >> Hi FieldTrippers, >> >> In almost all the papers I've read involving oscillatory power, some kind of >> transformation is done to the data due to the 1/f power spectrum effect >> (power decreases as frequency increases). I'm mostly looking at >> within-subjects experiments (every subject behaved in all conditions) >> comparing conditions across subjects, but it seems like normalizing the >> power spectrum should apply in any case (especially if any kind of >> parametric stats are done—right?). >> >> Anyway, it's not apparent to me how to use FT functions like ft_freqanalysis >> to make these transformations (e.g., log10 normalization, dB normalization >> [EEGLab does this], vector length normalization, etc.; the only thing I see >> is in ft_sourcedescriptives, but I'm not doing source analyses), and it >> confuses me why this is the case. I can't find much discussion regarding the >> 1/f issue on the FT wiki or the mailing list. This seems like an important >> step that is missing from any frequency analysis workflow. Am I missing >> something (meaning I just don't see the option), am I misunderstanding >> something (meaning I'm incorrect in this assumption), or is this an issue >> that needs to be fixed? >> >> Thanks, >> Matt >> >> -- >> Univ. of Colorado at Boulder >> Dept. of Psychology and Neuroscience >> matthew.mollison at colorado.edu >> http://psych.colorado.edu/~mollison/ >> >> _______________________________________________ >> 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 -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ From stan.vanpelt at fcdonders.ru.nl Tue Apr 24 10:14:54 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Tue, 24 Apr 2012 10:14:54 +0200 (CEST) Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: Message-ID: <506536226.7942.1335255294672.JavaMail.root@sculptor.zimbra.ru.nl> Hi all, A follow-up question on the implementation of 3rd-order gradiometer correction in FT: I am puzzling how one can do both 3-order grad. correction and dft-filtering properly using FT. the logical sequency would be to do ft_denoise_synthetic first, and subsequently dft-filtering using ft_preprocessing. However, in that case it is no longer possible to pad the data when calling ft_preprocessing, because it now processes trial-data (output from ft_denoise_synthetic), and doesn't read in the original dataset anymore. or am I mistaken here? I could see 3 alternatives, which seem to be more like (computationally) suboptimal workarounds: - Apply ft_denoise_synthetic on the entire dataset, then dft-filter the entire dataset, and then run ft_redefinetrial to cut the data into actual trials - Adjust the trial definition such that longer data segments are read in, equivalent to your padding size. Then apply ft_denoise_synthetic on these trials, then dft-filter them, and then run ft_redefinetrial to cut the data into actual trials - Doing the 3-rd order grad. correction first using the DataEditor, and then process it further using FT. Any thoughts? Best, Stan ----- Oorspronkelijk bericht ----- > Van: "Michael Wibral" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Donderdag 19 april 2012 10:24:57 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hey there, > sorry for not thinking about it any earlier, indeed I can confirm that > ft_denoise.. needs the reference channels to function properly. I > remember having to preprocess in a funny order in old ft versions, to > do artefcat rejection without the refs and denoising with the refs. > Personally, I think the code should check whether the refs are there > and otherwise throw an error. Since ft_denoise.. only concerns CTF > (and bti??) systems, where the refs have fixed names this could be > easily implemented, or am I mistaken? > Best, > Michael > Gesendet: Donnerstag, 19. April 2012 um 08:59 Uhr > Von: "Barbara Haendel" > An: "Email discussion list for the FieldTrip project" > , fieldtrip at donders.ru.nl > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > Hey there, thanks a lot for the replies! > Panagiotis hit the mark. Indeed the reference channels were excluded > in the first round of preprocessing. May be one could include a short > note on that in the ft_denoise m-file description since only including > relevant channels is the normal way to treat data in preprocessing. > Thanks again, > Barbara > -------- Original-Nachricht -------- > > Datum: Mon, 16 Apr 2012 17:53:56 +0200 > > Von: Panagiotis Tsiatsis > > An: Email discussion list for the FieldTrip project > > > > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > Hello girls and guys, > > > > It is working for my CTF MEG data - the version that I have is v4692 > > 2011-11-07. > > > > The other thing that might cause a problem could be ommiting the > > reference channels definition before the ft_ preprocessing command > > that > > gave you your "dataprepro" > > > > i.e maybe you might need something like this > > > > cfg = []; > > > > ... > > //various preprocessing parameters > > ... > > > > cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; > > > > dataprepro = ft_preprocessing(cfg); > > > > > > Hope you are lucky :) > > > > Best, > > Panagiotis > > > > > > On 4/16/2012 4:59 PM, Stan van Pelt wrote: > > > Hi Barbara, > > > > > > I can replicate your finding, but am unsure what is causing it. > > > Maybe > > > the difference/correction is lower than the Matlab or CTF > > > precision? > > > In any case, if the 3rd order gradients were on, > > > ft_denoise_synthetic > > > would undo the G3BR-balancing, ergo it toggles. > > > > > > Best, > > > Stan > > > > > > > > > ------------------------------------------------------------------------ > > > > > > *Van: *"Michael Wibral" > > > *Aan: *"Email discussion list for the FieldTrip project" > > > > > > *Verzonden: *Maandag 16 april 2012 16:46:27 > > > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > > > Hi Barbara, > > > > > > are you certain that the original data do not have 3rd gradients > > > enabled? - looking at them once in dataEditor, switching to 3rd > > > grads and accidentally forgetting to unclick 'save parameters with > > > dataset' will make them have 3rd grads... > > > > > > When I last used ft_denoise_synthetic it worked pretty much as > > > described (??). > > > > > > Michael > > > > > > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr > > > *Von:* "Barbara Haendel" > > > *An:* fieldtrip at donders.ru.nl > > > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad > > > > > > Dear fieldtrip users, > > > > > > has anyone experience in using ft_denoise_synthetic? If I try to > > > calculate 3rd order grads in the below specified way the data does > > > not change with respect to the input data (which has no synthetic > > > gradiometer applied). Is there some obvious misunderstanding on my > > > side of how to use this function or is our environment truly > > > noiseless :) > > > > > > Cheers, > > > Barbara > > > > > > cfg=[]; > > > cfg.gradient ='G3BR'; > > > cfg.trials = 'all'; > > > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); > > > > > > > > > >> data_3rdorder.grad.balance > > > > > > ans = > > > > > > G1BR: [1x1 struct] > > > G2BR: [1x1 struct] > > > G3BR: [1x1 struct] > > > current: 'G3BR' > > > previous: {'none'} > > > > > > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) > > > > > > ans = 0 > > > > > > -- > > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > > Jetzt informieren: > > http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > > _______________________________________________ > > > 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 > > > > > > > > > > > > > > > -- > > > Stan van Pelt > > > > > > Donders Institute for Brain, Cognition and Behaviour, Radboud > > > University Nijmegen > > > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > > > E-mail: stan.vanpelt at donders.ru.nl > > > Website: www.ru.nl/donders/ > > > Phone: (+31) (0)24 36 10981 > > > Fax: (+31) (0)24 36 10989 > > > > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > > Panagiotis S. Tsiatsis > > Max Planck Institute for Biological Cybernetics > > Cognitive NeuroImaging Group > > Tuebingen, Germany > > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 -- Stan van Pelt Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 10981 Fax: (+31) (0)24 36 10989 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue Apr 24 10:26:18 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 24 Apr 2012 10:26:18 +0200 Subject: [FieldTrip] ft_denoise_synthetic 3rd order grad In-Reply-To: <506536226.7942.1335255294672.JavaMail.root@sculptor.zimbra.ru.nl> References: <506536226.7942.1335255294672.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Hi Stan, To me, it seems all three options would be fine, and I actually don't think they are computationally suboptimal. I would probably go for option 2, and have done so with a similar problem in the past. This worked well for me. Best, Eelke On 24 April 2012 10:14, Stan van Pelt wrote: > Hi all, > > A follow-up question on the implementation of 3rd-order gradiometer > correction in FT: > > I am puzzling how one can do both 3-order grad. correction and dft-filtering > properly using FT. the logical sequency would be to do ft_denoise_synthetic > first, and subsequently dft-filtering using ft_preprocessing. However, in > that case it is no longer possible to pad the data when calling > ft_preprocessing, because it now processes trial-data (output from > ft_denoise_synthetic), and doesn't read in the original dataset anymore. or > am I mistaken here? > > I could see 3 alternatives, which seem to be more > like (computationally) suboptimal workarounds: > - Apply ft_denoise_synthetic on the entire dataset, then dft-filter the > entire dataset, and then run ft_redefinetrial to cut the data into actual > trials > - Adjust the trial definition such that longer data segments are read in, > equivalent to your padding size. Then apply ft_denoise_synthetic on these > trials, then dft-filter them, and then run ft_redefinetrial to cut the data > into actual trials > - Doing the 3-rd order grad. correction first using the DataEditor, and then > process it further using FT. > > Any thoughts? > > Best, Stan > > > ________________________________ > > Van: "Michael Wibral" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Donderdag 19 april 2012 10:24:57 > Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Hey there, > > sorry for not thinking about it any earlier, indeed I can confirm that > ft_denoise.. needs the reference channels to function properly. I remember > having to preprocess in a funny order in old ft versions, to do artefcat > rejection without the refs and denoising with the refs. > > Personally, I think the code should check whether the refs are there and > otherwise throw an error. Since ft_denoise.. only concerns CTF (and bti??) > systems, where the refs have fixed names this could be easily implemented, > or am I mistaken? > > Best, > Michael > Gesendet: Donnerstag, 19. April 2012 um 08:59 Uhr > Von: "Barbara Haendel" > An: "Email discussion list for the FieldTrip project" > , fieldtrip at donders.ru.nl > Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > > > Hey there, thanks a lot for the replies! > > Panagiotis hit the mark. Indeed the reference channels were excluded in the > first round of preprocessing. May be one could include a short note on that > in the ft_denoise m-file description since only including relevant channels > is the normal way to treat data in preprocessing. > > Thanks again, > Barbara > > > > > -------- Original-Nachricht -------- >> Datum: Mon, 16 Apr 2012 17:53:56 +0200 >> Von: Panagiotis Tsiatsis >> An: Email discussion list for the FieldTrip project >> >> Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad > >> Hello girls and guys, >> >> It is working for my CTF MEG data - the version that I have is v4692 >> 2011-11-07. >> >> The other thing that might cause a problem could be ommiting the >> reference channels definition before the ft_ preprocessing command that >> gave you your "dataprepro" >> >> i.e maybe you might need something like this >> >> cfg = []; >> >> ... >> //various preprocessing parameters >> ... >> >> cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'}; >> >> dataprepro = ft_preprocessing(cfg); >> >> >> Hope you are lucky :) >> >> Best, >> Panagiotis >> >> >> On 4/16/2012 4:59 PM, Stan van Pelt wrote: >> > Hi Barbara, >> > >> > I can replicate your finding, but am unsure what is causing it. Maybe >> > the difference/correction is lower than the Matlab or CTF precision? >> > In any case, if the 3rd order gradients were on, ft_denoise_synthetic >> > would undo the G3BR-balancing, ergo it toggles. >> > >> > Best, >> > Stan >> > >> > >> > ------------------------------------------------------------------------ >> > >> > *Van: *"Michael Wibral" >> > *Aan: *"Email discussion list for the FieldTrip project" >> > >> > *Verzonden: *Maandag 16 april 2012 16:46:27 >> > *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad >> > >> > Hi Barbara, >> > >> > are you certain that the original data do not have 3rd gradients >> > enabled? - looking at them once in dataEditor, switching to 3rd >> > grads and accidentally forgetting to unclick 'save parameters with >> > dataset' will make them have 3rd grads... >> > >> > When I last used ft_denoise_synthetic it worked pretty much as >> > described (??). >> > >> > Michael >> > >> > *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr >> > *Von:* "Barbara Haendel" >> > *An:* fieldtrip at donders.ru.nl >> > *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad >> > >> > Dear fieldtrip users, >> > >> > has anyone experience in using ft_denoise_synthetic? If I try to >> > calculate 3rd order grads in the below specified way the data does >> > not change with respect to the input data (which has no synthetic >> > gradiometer applied). Is there some obvious misunderstanding on my >> > side of how to use this function or is our environment truly >> > noiseless :) >> > >> > Cheers, >> > Barbara >> > >> > cfg=[]; >> > cfg.gradient ='G3BR'; >> > cfg.trials = 'all'; >> > data_3rdorder = ft_denoise_synthetic(cfg, dataprepro); >> > >> > >> > >> data_3rdorder.grad.balance >> > >> > ans = >> > >> > G1BR: [1x1 struct] >> > G2BR: [1x1 struct] >> > G3BR: [1x1 struct] >> > current: 'G3BR' >> > previous: {'none'} >> > >> > >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:)) >> > >> > ans = 0 >> > >> > -- >> > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! >> > Jetzt informieren: >> http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a >> > _______________________________________________ >> > 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 >> > >> > >> > >> > >> > -- >> > Stan van Pelt >> > >> > Donders Institute for Brain, Cognition and Behaviour, Radboud >> > University Nijmegen >> > Kapittelweg 29, 6525 EN Nijmegen, Netherlands >> > E-mail: stan.vanpelt at donders.ru.nl >> > Website: www.ru.nl/donders/ >> > Phone: (+31) (0)24 36 10981 >> > Fax: (+31) (0)24 36 10989 >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Panagiotis S. Tsiatsis >> Max Planck Institute for Biological Cybernetics >> Cognitive NeuroImaging Group >> Tuebingen, Germany >> > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > _______________________________________________ > 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 > > > > > -- > Stan van Pelt > > Donders Institute for Brain, Cognition and Behaviour, Radboud University > Nijmegen > Kapittelweg 29, 6525 EN Nijmegen, Netherlands > E-mail:  stan.vanpelt at donders.ru.nl > Website: www.ru.nl/donders/ > Phone:  (+31) (0)24 36 10981 > Fax:    (+31) (0)24 36 10989 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From alexandre.gramfort at inria.fr Wed Apr 25 09:07:07 2012 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Wed, 25 Apr 2012 09:07:07 +0200 Subject: [FieldTrip] Question concerning ft_headmodel_bem_openmeeg In-Reply-To: <4F93AE1A.50405@gmx.de> References: <4F93AE1A.50405@gmx.de> Message-ID: Hi Paul, I've not looked into the new functions yet and I am not sure it has been ever tested for openmeeg (robert, cristiano?). I'd stick to the old functions for urgent matters. Feel free to send me a patch if you end up fixing problems with the new ones. I'll review the changes ASAP. Best, Alex On Sun, Apr 22, 2012 at 9:07 AM, Paul Czienskowski wrote: > Dear all, > > I want to create headmodels with the ft_headmodel_bem_openmeeg function, and > - for I formerly used the ft_prepare_bemmodel function - decided to delve > into the new function first, to see how it works. Anyway, I stumbled upon > something that puzzled me a bit. In line 96 to 106, the boundaries are > rearranged to be inside first, which to my understanding means, that the > first boundary in the array of boundaries will be the innermost one (i.e. > the brain in my case) and the last boundary will be the outermost one (i.e. > skin). Everything's fine hitherto. But from line 108 on, things become quite > odd. Line 108 and 109 define the first compartment to be the skin and the > last to be the source compartment. This is cross-checked again in line 127 > to 129. To my understanding this is a contradiction and I would appreciate, > if anybody could tell me if I got something completely wrong, or if the > function does odd things. If the function is correct, there should at least > be a comment explaining why this contradiction makes sense anyway. > > Best regards, > Paul > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > From v.poghosyan at humanbraindynamics.com Wed Apr 25 13:29:25 2012 From: v.poghosyan at humanbraindynamics.com (Vahe Poghosyan) Date: Wed, 25 Apr 2012 14:29:25 +0300 Subject: [FieldTrip] General questions In-Reply-To: References: <4F93AE1A.50405@gmx.de> Message-ID: <00ec01cd22d6$ad53fa00$07fbee00$@poghosyan@humanbraindynamics.com> Dear fieldtrip users and developer, I am new to fieldtrip. I think it's an excellent toolbox (thanks to the developers), but have few general questions: 1. I understand that fieldtrip is a data analysis toolbox, however the results of the analysis need to be visualized. I find the fieldtrip visualization functions, especially of the source analysis results (e.g. ft_sourceplot, ft_sourceinterpolate, ft_sourcemovie) inadequate. My question is how do you usually visualize the results of the source analysis? Do you write your own matlab functions, including font-ends to fieldtrip plotting functions or you use other freely/commercially available tools that can import fieldtrip structures or you are satisfied with what is provided in the fieldtrip toolbox? 2. It seems that the documentation provided on the fieldtrip website is not very up-to-date and the descriptions of many configuration options in the *.m files are not documented. At the moment to understand all the available configuration options, and what different functions are doing and how they are implemented, I am debugging them step-by-step. Short of debugging or every time asking questions in this list, is there another way of getting information about all the available configuration options for different fieldtrip functions and their implementation details? 3. I found some functions in the fieldtrip's SVN (trunc) version (on googlecode), which are not available in the daily releases on the ftp server (e.g. ft_surfacecheck). Is it safe to use those functions (I understand that the toolbox is released under GPL)? 4. Are the measurement units used throughout fieldtrip functions basic SI (International System of Units) units? More specifically, what are the units of the inputs to ft_dipolesimulation (cfg.dip.signal, cfg.dip.amplitude)? Are they A*m or nA*m or something else? What are the units of the output from the minimumnormestimate? A/m? Thanks in advance Vahe Poghosyan, Ph.D. Senior Scientist Lab. for Human Brain Dynamics AAI Scientific Cultural Services Ltd. http://aaiscs.com/LHBD/ From jpnv2006 at gmail.com Wed Apr 25 16:39:05 2012 From: jpnv2006 at gmail.com (Juan Pablo Neira) Date: Wed, 25 Apr 2012 16:39:05 +0200 Subject: [FieldTrip] Individual MRI - Atlas Message-ID: Hello, I would like to know if it is possible to use the ft_sourceplot function with an individual MRI (coordsys: ctf) and an Atlas A tried to use one atlas from the Faq "aal_MNI_V4.img". After ft_prepare_atlas the coordinate system was coord:mni. When I used the ft_sourceplot function (ortho method), there were some warnings about labels not found and points outside the atlas, but I always clicked in inside my MRI. Should I have my MRI and the atlas in the same coordinate system (mni)? Regards, Juan Pablo Neira Vesga From yuvharpaz at gmail.com Wed Apr 25 20:13:10 2012 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Wed, 25 Apr 2012 21:13:10 +0300 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: References: Message-ID: Hi there I had left to right error with this atlas in sourceplot. download the newer .nii version. http://fmri.wfubmc.edu/software/PickAtlas yuval On 25 April 2012 17:39, Juan Pablo Neira wrote: > Hello, > > I would like to know if it is possible to use the ft_sourceplot > function with an individual MRI (coordsys: ctf) and an Atlas > > A tried to use one atlas from the Faq "aal_MNI_V4.img". After > ft_prepare_atlas the coordinate system was coord:mni. > > When I used the ft_sourceplot function (ortho method), there were some > warnings about labels not found and points outside the atlas, but I > always clicked in inside my MRI. Should I have my MRI and the atlas > in the same coordinate system (mni)? > > Regards, > > Juan Pablo Neira Vesga > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Thu Apr 26 00:04:12 2012 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Wed, 25 Apr 2012 22:04:12 +0000 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <7270aa3bcbfd9.4f574cba@mail.uh.edu> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>, <7270aa3bcbfd9.4f574cba@mail.uh.edu> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> Hi I encounted the same problem with ft_databrowser: ************* fetching artifacts... Error using ft_fetch_data (line 57) data does not contain a consistent trial definition, fetching data is not possible Error in ft_databrowser>redraw_cb (line 1159) art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); Error in ft_databrowser (line 535) redraw_cb(h); **************** The same data works OK with [data] = ft_rejectvisual(cfg, data) I have: MacOS 10.6.8 MATLAB 7.13.0.564 (R2011b) Matlab re-installation did not help in my case. I would be grateful for any tips. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] Sent: Wednesday, March 07, 2012 6:55 PM To: Email discussion list for the FieldTrip project Cc: fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] Error -> ft_databrowser Hi Michael, I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution. But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution. Mehmet ----- Original Message ----- From: "Epstein, Michael" Date: Wednesday, March 7, 2012 11:29 am Subject: Re: [FieldTrip] Error -> ft_databrowser To: fieldtrip at donders.ru.nl > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list. > > -Michael > > > ________________________________ > Dear Fieldtrippers, > > > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? > > > fieldtrip version 20120130, matlab version R2010a, operating system windows 7. > > > Thanks in advance for any suggestions. > > > > ??? Error using ==> ft_fetch_data at 57 > data does not contain a consistent trial definition, fetching data is not > possible > > > Error in ==> ft_databrowser>redraw_cb at 1159 > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); > > > Error in ==> ft_databrowser at 535 > redraw_cb(h); > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > _______________________________________________ > 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 r.vandermeij at donders.ru.nl Thu Apr 26 10:13:18 2012 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Thu, 26 Apr 2012 10:13:18 +0200 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org> <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> Message-ID: Hi Elena, >From the looks of it you are using an old version of FieldTrip. Could you download the latest version and see if the problem persists? Best, Roemer On Thu, Apr 26, 2012 at 12:04 AM, Elena Orekhova wrote: > Hi > I encounted the same problem with ft_databrowser: > > ************* > fetching artifacts... Error using ft_fetch_data (line 57) > > data does not contain a consistent trial definition, fetching data is not > possible > > Error in ft_databrowser>redraw_cb (line 1159) > > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > Error in ft_databrowser (line 535) > redraw_cb(h); > **************** > > The same data works OK with > [data] = ft_rejectvisual(cfg, data) > > I have: > MacOS 10.6.8 > MATLAB 7.13.0.564 (R2011b) > > Matlab re-installation did not help in my case. > I would be grateful for any tips. > > Elena > ------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] > *Sent:* Wednesday, March 07, 2012 6:55 PM > > *To:* Email discussion list for the FieldTrip project > *Cc:* fieldtrip at donders.ru.nl > *Subject:* Re: [FieldTrip] Error -> ft_databrowser > > Hi Michael, > > > I have posted the question actually but I didn't hear any suggestions > about it. The same error was posted yesterday by someone else. > > > just to repeat what i have replied in the other post, i tried many things > to solve it (changed the code, run the databrowser code line by line, > updated fieldtrip version at etc.), but none of them solved the problem. I > started getting the error after I tried using parallel processing scripts > in matlab. But as i said, i have no basis to say that this caused the > problem. So basically, i do not know any scientific solution. > > > But an old school method solved the problem in my case. Simply i > uninstalled and re-installed matlab. Never got the error again. You may > want to try this. I have no other solution. > > > Mehmet > > > > > > ----- Original Message ----- > From: "Epstein, Michael" > Date: Wednesday, March 7, 2012 11:29 am > Subject: Re: [FieldTrip] Error -> ft_databrowser > To: fieldtrip at donders.ru.nl > > > Hi - I am actually encountering the same error with databrowser, > and was wondering if you ever came up with a solution to this problem - or > if anyone else has a solution - I didn't find a response on the mailing > list. > > > > > > -Michael > > > > > > > > > > ------------------------------ > > > Dear Fieldtrippers, > > > > > > > > > I am encountering a strange error while i try to use ft_databrowser. > The error code is as below. I have never seen this error earlier. I used > ft_databrowser many times and its only last 2 days that i am getting the > error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and > used the newer version but still the same error. Strangely, i dont get this > error when i tried with other computers (same matlab version (R2010a), same > operating system (windows 7) on both computers. Has anyone got this error > before? what may cause this error? > > > > > > > > > fieldtrip version 20120130, matlab version R2010a, operating system > windows 7. > > > > > > > > > Thanks in advance for any suggestions. > > > > > > > > > > > > ??? Error using ==> ft_fetch_data at 57 > > > data does not contain a consistent trial definition, fetching data is > not > > > possible > > > > > > > > > Error in ==> ft_databrowser>redraw_cb at 1159 > > > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > > > > > > > > Error in ==> ft_databrowser at 535 > > > redraw_cb(h); > > > > > ------------------------------ > > Conserve Resources. Print only when necessary. > > > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended > recipient. It may contain confidential information which is legally > privilegedor otherwise protected by law. If you received this e-mail in > error or from someone who is not authorized to send it to you, you are > strictly prohibited from reviewing, using, disseminating, distributing or > copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN > E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your > cooperation. > > > _______________________________________________ > > 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 > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Apr 26 10:19:56 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 26 Apr 2012 10:19:56 +0200 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>, <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> Message-ID: <4F99052C.1010508@donders.ru.nl> Hi Elena, most likely your data has trials with overlapping sample points. Unfortunately, the databrowser does not support this, or to be more specific ft_fetch_data does not support this. The reason for this is that a specific segment in time is defined twice in your data, and it is not clear what segment it is you would like to look at (due to filter artifacts and other preprocessing steps, the data will most likely have different values for the same sample points). For non-continuous data (already preprocessed data), it should be able to implement this nonetheless, but that's on our todo list. The best way for now is to call ft_redefinetrial and cut out the overlapping segments. You could also hack your way around this by removing data.sampleinfo. FieldTrip will then make up arbitrary, meaningless sample numbers. Keep in mind that we do not recommend this though. There is no way that the reconstructed sample numbers can be traced back to your original data! (well... if your programming skills are reasonable enough, it is possible, but that requires some further hacking, and a lot of effort). Best, Jörn On 4/26/2012 12:04 AM, Elena Orekhova wrote: > Hi > I encounted the same problem with ft_databrowser: > > ************* > fetching artifacts... Error using ft_fetch_data (line 57) > data does not contain a consistent trial definition, fetching data is not > possible > > Error in ft_databrowser>redraw_cb (line 1159) > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > Error in ft_databrowser (line 535) > redraw_cb(h); > **************** > > The same data works OK with > [data] = ft_rejectvisual(cfg, data) > > I have: > MacOS 10.6.8 > MATLAB 7.13.0.564 (R2011b) > > Matlab re-installation did not help in my case. > I would be grateful for any tips. > > Elena > ------------------------------------------------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl > [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun > [mcoskun at mail.uh.edu] > *Sent:* Wednesday, March 07, 2012 6:55 PM > *To:* Email discussion list for the FieldTrip project > *Cc:* fieldtrip at donders.ru.nl > *Subject:* Re: [FieldTrip] Error -> ft_databrowser > > Hi Michael, > > > I have posted the question actually but I didn't hear any suggestions > about it. The same error was posted yesterday by someone else. > > > just to repeat what i have replied in the other post, i tried many > things to solve it (changed the code, run the databrowser code line by > line, updated fieldtrip version at etc.), but none of them solved the > problem. I started getting the error after I tried using parallel > processing scripts in matlab. But as i said, i have no basis to say > that this caused the problem. So basically, i do not know any > scientific solution. > > > But an old school method solved the problem in my case. Simply i > uninstalled and re-installed matlab. Never got the error again. You > may want to try this. I have no other solution. > > > Mehmet > > > > > > ----- Original Message ----- > From: "Epstein, Michael" > Date: Wednesday, March 7, 2012 11:29 am > Subject: Re: [FieldTrip] Error -> ft_databrowser > To: fieldtrip at donders.ru.nl > > > Hi - I am actually encountering the same error with databrowser, and > was wondering if you ever came up with a solution to this problem - or > if anyone else has a solution - I didn't find a response on the > mailing list. > > > > > > -Michael > > > > > > > > > > > ------------------------------------------------------------------------ > > > Dear Fieldtrippers, > > > > > > > > > I am encountering a strange error while i try to use ft_databrowser. > The error code is as below. I have never seen this error earlier. I > used ft_databrowser many times and its only last 2 days that i am > getting the error. I downloaded a newer version of fieldtrip > (fieldtrip-20120130) and used the newer version but still the same > error. Strangely, i dont get this error when i tried with other > computers (same matlab version (R2010a), same operating system > (windows 7) on both computers. Has anyone got this error before? what > may cause this error? > > > > > > > > > fieldtrip version 20120130, matlab version R2010a, operating system > windows 7. > > > > > > > > > Thanks in advance for any suggestions. > > > > > > > > > > > > ??? Error using ==> ft_fetch_data at 57 > > > data does not contain a consistent trial definition, fetching data is not > > > possible > > > > > > > > > Error in ==> ft_databrowser>redraw_cb at 1159 > > > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', > endsample); > > > > > > > > > Error in ==> ft_databrowser at 535 > > > redraw_cb(h); > > > > > > ------------------------------------------------------------------------ > > Conserve Resources. Print only when necessary. > > > > IMPORTANT NOTICE: This e-mail is meant only for the use of the > intended recipient. It may contain confidential information which is > legally privilegedor otherwise protected by law. If you received this > e-mail in error or from someone who is not authorized to send it to > you, you are strictly prohibited from reviewing, using, disseminating, > distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF > THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. > Thank you for your cooperation. > > > _______________________________________________ > > 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 -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Apr 26 10:47:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 26 Apr 2012 10:47:37 +0200 Subject: [FieldTrip] General questions In-Reply-To: <00ec01cd22d6$ad53fa00$07fbee00$@poghosyan@humanbraindynamics.com> References: <4F93AE1A.50405@gmx.de> <00ec01cd22d6$ad53fa00$07fbee00$@poghosyan@humanbraindynamics.com> Message-ID: <4F990BA9.5030709@donders.ru.nl> Dear Vahe, thanks for your elaborate feedback. Of course, we are working hard to make FieldTrip more intuitive and user-friendly. We are quite aware that there are lot of things which are suboptimal, some of them that you also pointed out. Here's my comments on your points: > 1. I understand that fieldtrip is a data analysis toolbox, however the > results of the analysis need to be visualized. I find the fieldtrip > visualization functions, especially of the source analysis results (e.g. > ft_sourceplot, ft_sourceinterpolate, ft_sourcemovie) inadequate. > My question is how do you usually visualize the results of the source > analysis? Do you write your own matlab functions, including font-ends to > fieldtrip plotting functions or you use other freely/commercially available > tools that can import fieldtrip structures or you are satisfied with what is > provided in the fieldtrip toolbox? What exactly do you find inadequate? The way the plots look like or the way you need to call the functions? I have to admit that plotting results in sourcespace is more complex than plotting in sensor space. This is simply because there are so many more options and parameters. The intention of FT is not to provide the user with an easy-to-click GUI which hides important options, but to require the user to think him-/herself about important options like downsampling, interpolation options, normalization, etc. (to answer your question on my behalf: I am satisfied, once I found out how to plot - which took some time). > 2. It seems that the documentation provided on the fieldtrip website is not > very up-to-date and the descriptions of many configuration options in the > *.m files are not documented. At the moment to understand all the available > configuration options, and what different functions are doing and how they > are implemented, I am debugging them step-by-step. > Short of debugging or every time asking questions in this list, is there > another way of getting information about all the available configuration > options for different fieldtrip functions and their implementation details? Yes, there is an overview other than what the help is showing: http://fieldtrip.fcdonders.nl/reference/index For a function overview: http://fieldtrip.fcdonders.nl/reference The function and configuration reference of the FieldTrip wiki is literally a collection of all the helps. Note that for some functions, there are undocumented functions (which has a reason), they are mostly hidden and explained in the comments below the help. We (will) try to make the naming consistent throughout FieldTrip, so that, once acquainted with the naming scheme, the cfg options should be self-explanatory. Can you point to a particular example where the cfg-options are not documented adequately? This is for us sometimes a bit hard to figure out, because we know FT already quite well and thus need to rely on feedback of new users. But if you have any questions how a certain function works, or about the algorithm behind, feel free to just write a mail to this list - that's what it is there for ;) > 3. I found some functions in the fieldtrip's SVN (trunc) version (on > googlecode), which are not available in the daily releases on the ftp server > (e.g. ft_surfacecheck). > Is it safe to use those functions (I understand that the toolbox is released > under GPL)? Sorry, I don't know as I have neither written nor used these functions. > 4. Are the measurement units used throughout fieldtrip functions basic SI > (International System of Units) units? More specifically, what are the units > of the inputs to ft_dipolesimulation (cfg.dip.signal, cfg.dip.amplitude)? > Are they A*m or nA*m or something else? What are the units of the output > from the minimumnormestimate? A/m? I also cannot be of much help here, but as far as I know unit declaration are a consistent problem throughout FieldTrip, and currently we are working on restructuring the code and making this clearer. I would be tempted to say that the unit is a 'what-you-put-in-comes-out', i.e. if your data is measured in nA and the distance measured in cm, then the unit will be nA*cm. But, I don't know exactly. You can try to search the FieldTrip wiki for 'units' or any related search term, but I am afraid that most pages will be rather a collection of To-Dos for/from one of us. Maybe mire helpful might be this to search in the mailinglist for old posts on units (I couldn't find any, sorry)" http://fieldtrip.fcdonders.nl/discussion_list I hope Robert or Jan-Mathijs (currently on vacation) can give you more elaborate feedback on the last two question of yours. Best, Jörn > > > Thanks in advance > > Vahe Poghosyan, Ph.D. > Senior Scientist > Lab. for Human Brain Dynamics > AAI Scientific Cultural Services Ltd. > http://aaiscs.com/LHBD/ > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From Elena.Orekhova at neuro.gu.se Thu Apr 26 11:20:05 2012 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Thu, 26 Apr 2012 09:20:05 +0000 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org> <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se>, Message-ID: <32CC77C0C8A7AD4B9410934642608E1F25391E36@exchccr1.neuro.gu.se> Indeed it works OK for the latest version. Thank you! Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Roemer van der Meij [r.vandermeij at donders.ru.nl] Sent: Thursday, April 26, 2012 10:13 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] Error -> ft_databrowser Hi Elena, >From the looks of it you are using an old version of FieldTrip. Could you download the latest version and see if the problem persists? Best, Roemer On Thu, Apr 26, 2012 at 12:04 AM, Elena Orekhova > wrote: Hi I encounted the same problem with ft_databrowser: ************* fetching artifacts... Error using ft_fetch_data (line 57) data does not contain a consistent trial definition, fetching data is not possible Error in ft_databrowser>redraw_cb (line 1159) art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); Error in ft_databrowser (line 535) redraw_cb(h); **************** The same data works OK with [data] = ft_rejectvisual(cfg, data) I have: MacOS 10.6.8 MATLAB 7.13.0.564 (R2011b) Matlab re-installation did not help in my case. I would be grateful for any tips. Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] Sent: Wednesday, March 07, 2012 6:55 PM To: Email discussion list for the FieldTrip project Cc: fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] Error -> ft_databrowser Hi Michael, I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution. But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution. Mehmet ----- Original Message ----- From: "Epstein, Michael" > Date: Wednesday, March 7, 2012 11:29 am Subject: Re: [FieldTrip] Error -> ft_databrowser To: fieldtrip at donders.ru.nl > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list. > > -Michael > > > ________________________________ > Dear Fieldtrippers, > > > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? > > > fieldtrip version 20120130, matlab version R2010a, operating system windows 7. > > > Thanks in advance for any suggestions. > > > > ??? Error using ==> ft_fetch_data at 57 > data does not contain a consistent trial definition, fetching data is not > possible > > > Error in ==> ft_databrowser>redraw_cb at 1159 > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample); > > > Error in ==> ft_databrowser at 535 > redraw_cb(h); > ________________________________ > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > _______________________________________________ > 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 -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From bibi.raquel at gmail.com Thu Apr 26 14:30:14 2012 From: bibi.raquel at gmail.com (Raquel Bibi) Date: Thu, 26 Apr 2012 08:30:14 -0400 Subject: [FieldTrip] Error -> ft_databrowser In-Reply-To: <4F99052C.1010508@donders.ru.nl> References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org> <7270aa3bcbfd9.4f574cba@mail.uh.edu> <32CC77C0C8A7AD4B9410934642608E1F25391DE8@exchccr1.neuro.gu.se> <4F99052C.1010508@donders.ru.nl> Message-ID: <6FA6AC40-1549-475F-93C3-80681B6BDAF5@gmail.com> Another way of knowing sample information is to include it again in the trl definition of your trial function so that the 4th ( any column after the first three) column reads event(i).sample. The information will always be available in the trialinfo field of the data. Regards, Raquel Sent from my iPhone On Apr 26, 2012, at 4:19 AM, "Jörn M. Horschig" wrote: > Hi Elena, > > most likely your data has trials with overlapping sample points. Unfortunately, the databrowser does not support this, or to be more specific ft_fetch_data does not support this. The reason for this is that a specific segment in time is defined twice in your data, and it is not clear what segment it is you would like to look at (due to filter artifacts and other preprocessing steps, the data will most likely have different values for the same sample points). For non-continuous data (already preprocessed data), it should be able to implement this nonetheless, but that's on our todo list. The best way for now is to call ft_redefinetrial and cut out the overlapping segments. > > You could also hack your way around this by removing data.sampleinfo. FieldTrip will then make up arbitrary, meaningless sample numbers. Keep in mind that we do not recommend this though. There is no way that the reconstructed sample numbers can be traced back to your original data! (well... if your programming skills are reasonable enough, it is possible, but that requires some further hacking, and a lot of effort). > > Best, > Jörn > > On 4/26/2012 12:04 AM, Elena Orekhova wrote: >> >> Hi >> I encounted the same problem with ft_databrowser: >> >> ************* >> fetching artifacts... Error using ft_fetch_data (line 57) >> data does not contain a consistent trial definition, fetching data is not >> possible >> >> Error in ft_databrowser>redraw_cb (line 1159) >> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', >> endsample); >> >> Error in ft_databrowser (line 535) >> redraw_cb(h); >> **************** >> >> The same data works OK with >> [data] = ft_rejectvisual(cfg, data) >> >> I have: >> MacOS 10.6.8 >> MATLAB 7.13.0.564 (R2011b) >> >> Matlab re-installation did not help in my case. >> I would be grateful for any tips. >> >> Elena >> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Mehmet-Akif Coskun [mcoskun at mail.uh.edu] >> Sent: Wednesday, March 07, 2012 6:55 PM >> To: Email discussion list for the FieldTrip project >> Cc: fieldtrip at donders.ru.nl >> Subject: Re: [FieldTrip] Error -> ft_databrowser >> >> Hi Michael, >> >> >> I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. >> >> >> just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution. >> >> >> But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution. >> >> >> Mehmet >> >> >> >> >> >> ----- Original Message ----- >> From: "Epstein, Michael" >> Date: Wednesday, March 7, 2012 11:29 am >> Subject: Re: [FieldTrip] Error -> ft_databrowser >> To: fieldtrip at donders.ru.nl >> >> > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list. >> > >> > -Michael >> > >> > >> > >> > Dear Fieldtrippers, >> > >> > >> > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error? >> > >> > >> > fieldtrip version 20120130, matlab version R2010a, operating system windows 7. >> > > > _______________________________________________ > 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 r.oostenveld at donders.ru.nl Thu Apr 26 23:35:31 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 26 Apr 2012 23:35:31 +0200 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: References: Message-ID: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> Hi Juan You should indeed have the data and the atlas in the same coordinate system (e.g. MNI). They don't need to have the same resolution. best Robert On 25 Apr 2012, at 16:39, Juan Pablo Neira wrote: > Hello, > > I would like to know if it is possible to use the ft_sourceplot > function with an individual MRI (coordsys: ctf) and an Atlas > > A tried to use one atlas from the Faq "aal_MNI_V4.img". After > ft_prepare_atlas the coordinate system was coord:mni. > > When I used the ft_sourceplot function (ortho method), there were some > warnings about labels not found and points outside the atlas, but I > always clicked in inside my MRI. Should I have my MRI and the atlas > in the same coordinate system (mni)? > > Regards, > > Juan Pablo Neira Vesga > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From anokhina at psychiatry.wustl.edu Thu Apr 26 23:38:05 2012 From: anokhina at psychiatry.wustl.edu (Anokhin, Andrey) Date: Thu, 26 Apr 2012 21:38:05 +0000 Subject: [FieldTrip] POSTDOC POSITION Message-ID: A postdoctoral training position is available in the Department of Psychiatry at Washington University School of Medicine. The successful candidate will participate in an interdisciplinary research program linking genetics, brain function, and behavior in order to understand the etiology of addiction and related characteristics such as impulsivity and reward dysregulation. We are seeking a psychophysiologist/neuroscientist/biomedical engineer with a strong background in the analysis of EEG, ERP, and/or fMRI data. This position is available within National Institute on Drug Abuse funded Institutional National Research Service Award to support multi-disciplinary training in drug abuse (including nicotine and tobacco dependence) research. The primary focus of this position will be on advanced analysis of brain electrophysiology and fMRI data obtained in large genetically informative samples (twins, genotyping data). The overall goal of his research is to investigate brain mechanisms mediating genetic influences on individual differences in self-regulation of behavior, including inhibitory control, performance monitoring, decision making, and reinforcement learning. The candidate will have opportunity to interact with multi-disciplinary faculty and obtain research training in different areas including statistical/quantitative, molecular and genetic epidemiologic, clinical and neuroscience aspects of research on substance use disorders. The position is available immediately, and applications will be accepted until the position is filled. Washington University in St. Louis is an Affirmative Action/Equal Opportunity Employer. To apply, please contact Andrey Anokhin (Andrey at wustl.edu). ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jpnv2006 at gmail.com Fri Apr 27 09:53:03 2012 From: jpnv2006 at gmail.com (Juan Pablo Neira) Date: Fri, 27 Apr 2012 09:53:03 +0200 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> References: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> Message-ID: Thank you for your help, But is there any possibility of not using an MNI (average) brain and take advantage of the atlas.? We are working with individual MRIs and we do not want to visualize results in the MNI brain. We could build an atlas, based on our MRI, with other toolbox. But now we would like to use this atlas in the ft_sourceplot and ft_volumelookup functions. Thanks in advance, Juan Pablo Neira On Thu, Apr 26, 2012 at 11:35 PM, Robert Oostenveld wrote: > Hi Juan > > You should indeed have the data and the atlas in the same coordinate system (e.g. MNI). They don't need to have the same resolution. > > best > Robert > > > On 25 Apr 2012, at 16:39, Juan Pablo Neira wrote: > >> Hello, >> >> I would like to know if it is possible to use the ft_sourceplot >> function with an individual MRI (coordsys: ctf) and an Atlas >> >> A tried to use one atlas from the Faq "aal_MNI_V4.img".  After >> ft_prepare_atlas the coordinate system was coord:mni. >> >> When I used the ft_sourceplot function (ortho method), there were some >> warnings about labels not found and points outside the atlas, but I >> always clicked in inside my MRI.  Should I have my MRI and the atlas >> in the same coordinate system (mni)? >> >> Regards, >> >> Juan Pablo Neira Vesga >> _______________________________________________ >> 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 Elena.Orekhova at neuro.gu.se Fri Apr 27 11:07:18 2012 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 27 Apr 2012 09:07:18 +0000 Subject: [FieldTrip] ft_volumereslice problem Message-ID: <32CC77C0C8A7AD4B9410934642608E1F25391F48@exchccr1.neuro.gu.se> Hi, I try to reslice MRI from [157 204 203] to [256 256 256] I do: cfg = []; cfg.dim = [256 256 256]; mri_resl = ft_volumereslice(cfg, mri); but I get the error (see below) I use latest FT version with Mac OS 10.6.8 and Matlab 7.13.0.564 (R2011b) Thanks in advance Elena ********************* the input is volume data with dimensions [157 204 203] reslicing from [157 204 203] to [256 256 256] the input is volume data with dimensions [157 204 203] the input is volume data with dimensions [256 256 256] 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 (line 467) ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num); Error in ft_sourceinterpolate (line 376) av( sel) = my_interpn(fv, ax(sel), ay(sel), az(sel), cfg.interpmethod, cfg.feedback); Error in ft_volumereslice (line 147) reslice = ft_sourceinterpolate(tmpcfg, mri, reslice); -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuvharpaz at gmail.com Fri Apr 27 18:02:35 2012 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Fri, 27 Apr 2012 19:02:35 +0300 Subject: [FieldTrip] Individual MRI - Atlas In-Reply-To: References: <81674723-B52D-4D3A-858B-9737E819E363@donders.ru.nl> Message-ID: Dear Juan Pablo Neira I think what has to be done in this case is first to transfer the MRI to MNI space following steps described here. http://fieldtrip.fcdonders.nl/development/minimum_norm_estimate_new?s[]=mri&s[]=mni then you use the transformation in reverse on the atlas so you end up with an MNI atlas reshaped according to the individual MRI. then you can set sourceplot to use the atlas and give you names of regions when using the plot (ortho mode) interactively. you can also generate masks to color regions etc. I haven't done it but it should be possible. Yuval On 27 April 2012 10:53, Juan Pablo Neira wrote: > Thank you for your help, > > But is there any possibility of not using an MNI (average) brain and > take advantage of the atlas.? We are working with individual MRIs and > we do not want to visualize results in the MNI brain. > > We could build an atlas, based on our MRI, with other toolbox. But > now we would like to use this atlas in the ft_sourceplot and > ft_volumelookup functions. > > Thanks in advance, > > Juan Pablo Neira > > On Thu, Apr 26, 2012 at 11:35 PM, Robert Oostenveld > wrote: > > Hi Juan > > > > You should indeed have the data and the atlas in the same coordinate > system (e.g. MNI). They don't need to have the same resolution. > > > > best > > Robert > > > > > > On 25 Apr 2012, at 16:39, Juan Pablo Neira wrote: > > > >> Hello, > >> > >> I would like to know if it is possible to use the ft_sourceplot > >> function with an individual MRI (coordsys: ctf) and an Atlas > >> > >> A tried to use one atlas from the Faq "aal_MNI_V4.img". After > >> ft_prepare_atlas the coordinate system was coord:mni. > >> > >> When I used the ft_sourceplot function (ortho method), there were some > >> warnings about labels not found and points outside the atlas, but I > >> always clicked in inside my MRI. Should I have my MRI and the atlas > >> in the same coordinate system (mni)? > >> > >> Regards, > >> > >> Juan Pablo Neira Vesga > >> _______________________________________________ > >> 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 > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.N.Maijers at student.ru.nl Sat Apr 28 16:01:25 2012 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Sat, 28 Apr 2012 16:01:25 +0200 Subject: [FieldTrip] Problem in ft_timelockstatistics() phase Message-ID: <20120428160125.521cf366@sander-H57M-USB3> Hi, I am trying to rework a small FieldTrip experiment I did last year (reproduction of larger experiment done by Irina Simanova). Calling ft_timelockstatistics() on two ERP data partitions results in an error: "Undefined function 'fieldnames' for input arguments of type 'cell'." I'm running FieldTrip under MATLAB R2011b 64-bit on Linux. I see a possible cause of the problem, in that these data we pre-analysed with ft_timelockanalysis() a year ago, or longer. I read them from parts of the data set I was supplied with. Maybe there have been breaking changes to this function in the meantime? The cfg struct that I pass as parameter seems in line with the current documentation, though. LOG: >> main() data_set_location = /media/SAMSUNG/0,data_set/EEG/0 MATLAB output_dir = /tmp/EEG Data set part file: timelock10_lp Data set part file: timelock11_lp CONTRAST [class 1, size = 220]: participant timelock10_lp on condition avg_anm_aud_lp [class 2, size = 224]: participant timelock10_lp on condition avg_tls_aud_lp cfg method: 'crossvalidate' latency: [0 0.7000] channel: {1x60 cell} nfolds: 5 mva: {2x1 cell} design: [444x1 double] class_1_data__struct avg: [62x501 double] var: [62x501 double] fsample: 500 time: [1x501 double] dof: [62x501 double] label: {62x1 cell} trial: [220x62x501 double] dimord: 'rpt_chan_time' cfg: [1x1 struct] class_2_data__struct avg: [62x501 double] var: [62x501 double] fsample: 500 time: [1x501 double] dof: [62x501 double] label: {62x1 cell} trial: [224x62x501 double] dimord: 'rpt_chan_time' cfg: [1x1 struct] selected 60 channels selected 351 time bins selected 1 frequency bins using "ft_statistics_crossvalidate" for the statistical testing fixing random number generator for reproducibility creating sample indices using 5-fold cross-validation validating fold 1 of 5 for 1 datasets validating fold 2 of 5 for 1 datasets validating fold 3 of 5 for 1 datasets validating fold 4 of 5 for 1 datasets validating fold 5 of 5 for 1 datasets Undefined function 'fieldnames' for input arguments of type 'cell'. Error in ft_statistics_crossvalidate (line 84) fn = fieldnames(stat.model{1}); Error in statistics_wrapper (line 298) [stat] = statmethod(cfg, dat, design); Error in ft_timelockstatistics (line 110) [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Error in main/modeling (line 203) stat = ft_timelockstatistics(cfg, class_1_datastruct, class_2_datastruct); Error in main/statistics (line 225) stat = modeling(data_set, method, obj_class_1_and_2); Error in main/ERP_experiment (line 374) stats = statistics(data_set, contrasts, method); Error in main (line 401) stats_x = ERP_experiment(data_set_location, 'RR', output_dir) Any suggestions would be welcom! Kind regards, Sander Maijers From hamzaf at sabanciuniv.edu Sat Apr 28 18:08:16 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 28 Apr 2012 19:08:16 +0300 Subject: [FieldTrip] Error in a given example Message-ID: Hello, While trying to understand the ft_deinetrial I tried the following example from the page ( http://fieldtrip.fcdonders.nl/tutorial/preprocessing) cfg = []; cfg.dataset = 'Subject01.ds'; cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for fully incongruent (FIC). cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 2; % in seconds cfg = ft_definetrial(cfg); I get the following error readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) reading the events from 'Subject01.ds\Subject01.res4' readCTFds: Data set error : size of meg4 file(s) 0 bytes (from dir command) 179071200 bytes (from res4 file) ??? Error using ==> ft_definetrial at 185 no trials were defined, see FT_DEFINETRIAL for help I wonder why? Best -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sat Apr 28 18:12:20 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sat, 28 Apr 2012 19:12:20 +0300 Subject: [FieldTrip] cfg.trialdef.eventtype Message-ID: Hello, I wonder what should be written after in this variable (cfg.trialdef.eventtype) ? and what is meant by '?' ? Best -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Apr 29 07:01:00 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 29 Apr 2012 08:01:00 +0300 Subject: [FieldTrip] Error in a given example In-Reply-To: References: Message-ID: Hello, I discovered the solution, I should but the full path of 'Subject01.ds'. I did not saw that in the tutorial but I found that in the previous messages. Best On Sat, Apr 28, 2012 at 7:08 PM, Hamza Fawzi Altakroury (Student) < hamzaf at sabanciuniv.edu> wrote: > Hello, > > While trying to understand the ft_deinetrial > > I tried the following example from the page ( > http://fieldtrip.fcdonders.nl/tutorial/preprocessing) > > cfg = []; > cfg.dataset = 'Subject01.ds'; > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for > fully incongruent (FIC). > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 2; % in seconds > cfg = ft_definetrial(cfg); > > I get the following error > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > reading the events from 'Subject01.ds\Subject01.res4' > > readCTFds: Data set error : size of meg4 file(s) > 0 bytes (from dir command) > 179071200 bytes (from res4 file) > > ??? Error using ==> ft_definetrial at 185 > no trials were defined, see FT_DEFINETRIAL for help > > > I wonder why? > > Best > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Sun Apr 29 07:07:55 2012 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Student)) Date: Sun, 29 Apr 2012 08:07:55 +0300 Subject: [FieldTrip] cfg.trialdef.eventtype In-Reply-To: References: Message-ID: Sorry in being rush in asking questions, I found the solution By typing '?' we get info about the file, one of them the eventtype. Hamza On Sat, Apr 28, 2012 at 7:12 PM, Hamza Fawzi Altakroury (Student) < hamzaf at sabanciuniv.edu> wrote: > Hello, > > I wonder what should be written after in this variable > (cfg.trialdef.eventtype) ? > and what is meant by '?' ? > > Best > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From vitoria.piai at gmail.com Sun Apr 29 15:19:16 2012 From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=) Date: Sun, 29 Apr 2012 15:19:16 +0200 Subject: [FieldTrip] error in ft_databrowser Message-ID: <4F9D3FD4.2050301@gmail.com> Hi there, I'm getting the following error when trying ft_databrowser on the output of ft_componentanalysis (ft_topoplotIC on the same dataset works fine): ??? Error using ==> keyvalcheck at 77 the input argument 'tag' is forbidden Error in ==> ft_plot_text at 44 keyvalcheck(varargin, 'optional', {'hpos', 'vpos', 'width', 'height', 'hlim', 'vlim', 'Color', .... Error in ==> ft_databrowser>redraw_cb at 1346 ft_plot_text(labelx(laysel), labely(laysel), opt.hdr.label(chanindx(i)), 'tag', 'timecourse', 'HorizontalAlignment', 'right'); Error in ==> ft_databrowser at 548 redraw_cb(h); I'm using the ft_databrowser version updated on the 25th of April. Is this a bug? Thank you, Vitória -- ** Please consider the environment - do you really need to print? **