From mahdi_meng at yahoo.com Sun Jul 1 18:23:06 2012 From: mahdi_meng at yahoo.com (m m) Date: Sun, 1 Jul 2012 09:23:06 -0700 (PDT) Subject: [FieldTrip] FW: Hi Friend! Message-ID: <1341159786.76669.androidMobile@web122403.mail.ne1.yahoo.com>

I guess your job search is going well. I just wanted to tell you to a new job opp in locality.
We have had several of our members take this opp and I have heard lots of perfect success stories.

The local paper has an article featuring one of our clients, Kelly Richards. It will also you all you all the important information you need to get started.
The link is http://specialoffers.com.br/angerabandoned/Daniel_Alien5/?a=198461&s=dprocessing and I think the story will be featured on the home-page until tomorrow.

TTYL!

-------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Sun Jul 1 22:15:56 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Sun, 01 Jul 2012 13:15:56 -0700 Subject: [FieldTrip] calculating correlation Message-ID: <4FF0AFFC.1040500@berkeley.edu> Hi FTers, I'd like to do two sorts of correlation calculations, and was wondering if there's any easy way to do this within FieldTrip. 1) I'd like to calculate the correlation between performance over trials and power within a specific frequency over trials. So I have the performance measure per trial, and my chan*freq measure after freqanalysis. So for each channel I have a series of power values (trials) and I have a series of performance measures (per trial), and now like to know (first within, and then over subjects) which channel's frequency power follows (correlates) with the performance. From the walkthrough I understand I can give in these performance measures through the design (cfg.design=[0.10.20.30.40.50.40.30.10.2];cfg.ivar=1;), but which method to use for ft_freqstatistics? I don't see statistics = 'correlation' or 'pearson' or 'spearman' in method = 'analytic. Also how to make the design to correlate over trials? 2) I'd like to calculate the correlation between the score on repeated questionnaire over participants with power within a frequency. So I have several power values per participant for each channel, and the repeated scores on the questionnaire for each participant. And now I'd like to calculate a value per channel reflecting the correlation over the repeats of the questionnaire and over participants. Any idea on FieldTrip settings? Both in general, is there a correlation statistics implemented, and more specifically for my question, how would I make the appropriate designs? Thanks so much! Ingrid -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 2 08:53:51 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 2 Jul 2012 08:53:51 +0200 Subject: [FieldTrip] calculating correlation In-Reply-To: <4FF0AFFC.1040500@berkeley.edu> References: <4FF0AFFC.1040500@berkeley.edu> Message-ID: <1AA66D8B-3685-4A8F-AED3-A1FF8C7A8D21@donders.ru.nl> Hi Ingrid, This calls for a statfun_corr or even a statfun_glm! It so happens that I have some of these sitting on my hard drive. As you know I am fond of beer, chocolate and co-authorships, so I am sure we can strike a deal. I have not yet had the opportunity to contribute these statfuns to FieldTrip, but now I sense a win-win-win situation: win 1 is for me (beer/chocolate/co-authorships/etc), win 2 is for you (you can compute your statistic of interest) and win 3 for the community (where you test the code, write documentation on the wiki etcetc). How does that sound for a plan? Cheers, JM On Jul 1, 2012, at 10:15 PM, Ingrid Nieuwenhuis wrote: > Hi FTers, > > I'd like to do two sorts of correlation calculations, and was wondering if there's any easy way to do this within FieldTrip. > > 1) I'd like to calculate the correlation between performance over trials and power within a specific frequency over trials. So I have the performance measure per trial, and my chan*freq measure after freqanalysis. So for each channel I have a series of power values (trials) and I have a series of performance measures (per trial), and now like to know (first within, and then over subjects) which channel's frequency power follows (correlates) with the performance. > > From the walkthrough I understand I can give in these performance measures through the design (cfg.design = [0.1 0.2 0.3 0.4 0.5 0.4 0.3 0.1 0.2]; cfg.ivar= 1;), but which method to use for ft_freqstatistics? I don't see statistics = 'correlation' or 'pearson' or 'spearman' in method = 'analytic. Also how to make the design to correlate over trials? > > 2) I'd like to calculate the correlation between the score on repeated questionnaire over participants with power within a frequency. So I have several power values per participant for each channel, and the repeated scores on the questionnaire for each participant. And now I'd like to calculate a value per channel reflecting the correlation over the repeats of the questionnaire and over participants. > > Any idea on FieldTrip settings? Both in general, is there a correlation statistics implemented, and more specifically for my question, how would I make the appropriate designs? > > Thanks so much! > Ingrid > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > _______________________________________________ > 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 johanna.zumer at donders.ru.nl Mon Jul 2 11:54:11 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Mon, 2 Jul 2012 11:54:11 +0200 Subject: [FieldTrip] Source localization using DICS for EEG data from combined MEG/EEG recordings In-Reply-To: References: Message-ID: Dear Marcel, I might have seen a similar error before when the number of channels in 'elec' do not match the number of channels in 'freq'. Could that be the cause? Also, does it matter that you are setting cfg.grad=elec, rather than cfg.elec=elec? To debug, it might be best to first call leadfield=ft_prepare_leadfield() to ensure that is computed correctly, and then set that output to cfg.grid.leadfield=leadfield, in your call to ft_sourceanalysis. cheers, Johanna 2012/6/26 Marcel Heers > Dear all, > > I am trying to perform source localization in the frequency domain > from EEG data using DICS. The data were recorded combined with MEG > (Neuromag data format). The volume conductor is a 3 shell realistic > head model created with bemcp. > When running DICS with the following settings > > cfg = []; > cfg.method = 'dics'; > cfg.grad = elec; > cfg.frequency = 14; > cfg.vol = vol_eeg; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = 5; > source = ft_sourceanalysis(cfg, freq); > > > I am am getting the following error message: > > ??? Error using ==> svd > Input to SVD must not contain NaN or Inf. > > Error in ==> beamformer_dics>pinv at 568 > [U,S,V] = svd(A,0); > > Error in ==> beamformer_dics at 314 > filt = pinv(lf' * invCf * lf) * lf' * invCf; % > Gross eqn. 3, use > PINV/SVD to cover rank deficient leadfield > > Error in ==> ft_sourceanalysis at 584 > dip(i) = beamformer_dics(grid, sens, vol, [], > squeeze(Cf(i,:,:)), optarg{:}); > > > and I am not sure what might be the cause. > > Maybe anyone can help me! Thank you in advance! > > Marcel > _______________________________________________ > 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 Don.Rojas at ucdenver.edu Mon Jul 2 14:34:31 2012 From: Don.Rojas at ucdenver.edu (Rojas, Don) Date: Mon, 2 Jul 2012 06:34:31 -0600 Subject: [FieldTrip] Source localization using DICS for EEG data from combined MEG/EEG recordings In-Reply-To: References: Message-ID: <9FCD53FD-5A0E-48F8-87B2-08717F732CC9@ucdenver.edu> Marcel, Also, you might check your volume conductor. I've seen a similar error when there were NaNs in the surface normals. Don Sent from my iPad On Jul 2, 2012, at 4:12 AM, "Johanna Zumer" > wrote: Dear Marcel, I might have seen a similar error before when the number of channels in 'elec' do not match the number of channels in 'freq'. Could that be the cause? Also, does it matter that you are setting cfg.grad=elec, rather than cfg.elec=elec? To debug, it might be best to first call leadfield=ft_prepare_leadfield() to ensure that is computed correctly, and then set that output to cfg.grid.leadfield=leadfield, in your call to ft_sourceanalysis. cheers, Johanna 2012/6/26 Marcel Heers > Dear all, I am trying to perform source localization in the frequency domain from EEG data using DICS. The data were recorded combined with MEG (Neuromag data format). The volume conductor is a 3 shell realistic head model created with bemcp. When running DICS with the following settings cfg = []; cfg.method = 'dics'; cfg.grad = elec; cfg.frequency = 14; cfg.vol = vol_eeg; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = 5; source = ft_sourceanalysis(cfg, freq); I am am getting the following error message: ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> beamformer_dics>pinv at 568 [U,S,V] = svd(A,0); Error in ==> beamformer_dics at 314 filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ==> ft_sourceanalysis at 584 dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); and I am not sure what might be the cause. Maybe anyone can help me! Thank you in advance! Marcel _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornabel at googlemail.com Mon Jul 2 14:52:58 2012 From: cornabel at googlemail.com (Cornelius Abel) Date: Mon, 2 Jul 2012 14:52:58 +0200 Subject: [FieldTrip] reverse source interpolate? In-Reply-To: <36BAC777-CD99-4F3E-95D1-A133F5CC2372@donders.ru.nl> References: <4FEB2620.3050505@googlemail.com> <36BAC777-CD99-4F3E-95D1-A133F5CC2372@donders.ru.nl> Message-ID: Hi mailing list, I'm still struggling with the conversion of coordinates between source and interpolated source space. For example, if i have the position of a single grid point how do i get the corresponding voxel in the interpolated source structure. Or the other way around, how to get the grid point which corresponds to a voxel (e.g the max voxel) in the interpolated source structure. I think this should be a common problem when working with virtual electrodes, shouldn't it? To make things easier i put together a example with the data from the source tutorial where i tried to calculated the grid pos of the max voxel in the interpolated source. clear all; load sourcePost_nocon; % source structure from tutorial mri = ft_read_mri('Subject01.mri'); % mri of subject01 from tutorial sourceNAI = sourcePost_nocon; sourceNAI.avg.pow = sourcePost_nocon.avg.pow ./ sourcePost_nocon.avg.noise; sourceNAI=rmfield(sourceNAI,'freq'); % had to remove that to let cfg = []; cfg.downsample = 2; cfg.parameter = 'avg.pow'; sourceNAIInt = ft_sourceinterpolate(cfg, sourceNAI , mri); % Find position of max activity [dum, maxindx] = max(sourceNAIInt.avg.pow(:)); [xi, yi, zi] = ind2sub(sourceNAIInt.dim, maxindx); posInt=[xi, yi, zi]; % Plot interpolated source with position of max activity cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'avg.pow'; cfg.locationcoordinates = 'voxel'; cfg.location = posInt; % location of max activity is marked correctly. figure; ft_sourceplot(cfg,sourceNAIInt); % Transform coordinate back to uninterpolated source??? dpos = warp_apply(inv(mri.transform), posInt, 'homogeneous'); % Plot uninterpolated source with position aquired from interpolated source cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'avg.pow'; cfg.locationcoordinates = 'voxel'; cfg.location = dpos; % unfortunately this coordinate is obviously wrong!!! WHY? figure; ft_sourceplot(cfg,sourceNAI); Unfortunately the solution of Jan Mathijs did not work, nor did mine :( Any ideas??? Cornelius 2012/6/28 jan-mathijs schoffelen > Hi Cornelius, > > Probably you should use: cfg.locationcoordinates to be 'head'. > > Best, > > JM > > On Jun 28, 2012, at 11:19 AM, Cornelius Abel wrote: > > Hi jan mathijs, hello mailing list, > > thanks for your answer. I think i got your idea with finding the minimum > in this squared differences. This should the work with positions of any > scaling, right? > However it gives me strange results when trying to get voxel indices in > the "raw" source using voxel indices aquired from interpolated source. > But even using the ctf coordinates in mm doesn't work. > > Here is a short script showing what i did, i also attached the necessary > mat files. > > greetings, Cornelius > > > clear all; > load testdata.mat; > > % Interpolate source on anatomy > cfg = []; > cfg.parameter = 'avg.itc'; > cfg.interpmethod = 'linear'; > sourceInt = ft_sourceinterpolate(cfg, source,mri); > > % Find position of max voxel in interpolated source > [maxval, maxindx] = max(sourceInt.avg.itc(:)); > [x,y,z]=ind2sub(size(sourceInt.avg.itc),maxindx); > pos=[x y z]; > > % plot this position in interpolated source > figure; > cfg = []; > cfg.method = 'ortho'; > cfg.funparameter = 'avg.itc'; > cfg.locationcoordinates = 'voxel'; > cfg.location = pos; > ft_sourceplot(cfg, sourceInt); > > % Calculate respective position in 'raw' source struct > dpos = source.pos - repmat(pos, size(source.pos,1),1); > [m,ind] = min(sum(dpos.^2,2)); > spos=source.pos(ind,:); > > % Plot position in 'raw' source. > % This gives not the position of max activity!!! > figure; > cfg = []; > cfg.method = 'ortho'; > cfg.funparameter = 'avg.itc'; > cfg.locationcoordinates = 'voxel'; > cfg.location = spos; > ft_sourceplot(cfg, source); > > > > 2012/6/27 jan-mathijs schoffelen > >> Hi Cornelius, >> >> There is no need to 'uninterpolate' because the coordinates are already >> expressed in the correct coordinate system. What you probably want is to >> find the index to the voxel in the original source-structure closest to >> your 'hotspot' in the interpolated image. >> This can be achieved by something like this: >> >> write down the coordinates of your favourite position in the interpolated >> image (in world coordinates, here I assume that you are still in MEG >> coordinate system and have not normalized to MNI space), call this pos >> >> pos = pos./10 (from mm to cm) >> >> dpos = source.pos - repmat(pos, size(source.pos,1),1); >> [m,ind] = min(sum(dpos.^2,2)); >> >> source is the original source structure. >> ind is the index you are looking for. >> >> If you have interpolate to the MNI-template grid you need to replace the >> source.pos with the set of grid positions from your template grid (i.e. >> expressed in MNI coordinates). >> >> >> Cheers, >> >> JM >> >> >> On Jun 27, 2012, at 5:26 PM, cornelius abel wrote: >> >> Hello, >> >> does anybody know how to get the uninterpolated source position giving >> the coordinates aquired after interpolation with an anatomy. >> In principle i want to get an individual source time course at the >> position i picked from the interpolated grand average source plot. Therfore >> i need the corresponding filter and its position in the source structure. >> >> I tried to get the position by applying the inverse transformation matrix >> of the used anatomy like: >> pos_before_interpolation=warp_apply(inv(anatomy.transform), >> position_after_interpolation); >> >> but that did not give usefull results :( >> >> Any ideas how it could be done? >> >> Greetings, Cornelius >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 drivolta81 at gmail.com Mon Jul 2 17:04:08 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Mon, 2 Jul 2012 17:04:08 +0200 Subject: [FieldTrip] Job advertisement: Research associate at the University of Glasgow Message-ID: *Research Associate, Institute of Neuroscience and Psychology, University of Glasgow* The Institute of Neuroscience and Psychology, University of Glasgow, has a vacancy for a Research Associate post for 3 years. The position contributes to a project entitled “Neural synchrony in neuropsychiatry and brain development”. Specifically, the job requires the analysis of existing MEG-data sets, data-acquisition and implementation of novel analytic tools, contributing to the design and programming of MEG experiments. *Responsibilities:* 1. To analyse MEG-data using complex time-frequency and source-localization techniques. 2. To assist in the supervision of data-acquisition and analysis-protocols. 3. To establish links with the MEG-expertise in the Institute and with international groups working in the field. 4. To recruit experimental subjects and to run the agreed behavioural and MEG-experiments, dealing with all aspects of testing the participants and storing data. 5. To perform statistical analyses of the experiments and to produce experimental reports describing these results. 6. To establish an expert reputation and track record in field/discipline. 7. Write up papers and identify high impact national and international journals for publication. 8. To contribute to the identification of potential funding sources and to assist in the securing of funding from external bodies to support future research. 9. To contribute fully to the planning and supervision of undergraduate students and postgraduate (PhD) students through day to day mentoring and longer term in planning research objectives. *Requirements:* 1. Ph.D or equivalent. 2. Extensive and up-to-date practical and theoretical knowledge in MEG or EEG. 3. Excellent knowledge of experimental statistics. 4. Excellent knowledge of source-localization techniques. 5. Excellent knowledge of Matlab and experimental control software. * * * * *Salary Range*** £31,948 - £35,938** * * *More Information:* 1. The position is available now (July 2012) 2. To apply, visit the University of Glasgow staff jobs website: * http://www.gla.ac.uk/about/jobs/* . Search for position 002148 3. For further info please contact: Dr. Peter Uhlhaas, peter.uhlhaas at brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Mon Jul 2 18:20:13 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Mon, 2 Jul 2012 18:20:13 +0200 Subject: [FieldTrip] Info about the power-line noise Message-ID: Dear fieldtrippers, I recently run into the attached figures (S01 files). It seems a failure of the power-line noise filter. I used the following settings quite succesfully for other subjects: cfg.dftfilter = 'yes'; cfg.padding = 10; An example of good figures are the "KAT" files. These data come from a visual task where people see moving concentrical gratings. Each trial has a different length that range between around 0.5 until 3 seconds. Would the bandstop filter be the only possible solution here? Thanks, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: S01_TFR1_high.png Type: image/png Size: 12615 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: S01_power_.png Type: image/png Size: 13211 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: KAT_TFR1_low.png Type: image/png Size: 11199 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: KAT_power_spectra1_high.png Type: image/png Size: 13236 bytes Desc: not available URL: From inieuwenhuis at berkeley.edu Mon Jul 2 18:38:37 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 02 Jul 2012 09:38:37 -0700 Subject: [FieldTrip] calculating correlation In-Reply-To: <1AA66D8B-3685-4A8F-AED3-A1FF8C7A8D21@donders.ru.nl> References: <4FF0AFFC.1040500@berkeley.edu> <1AA66D8B-3685-4A8F-AED3-A1FF8C7A8D21@donders.ru.nl> Message-ID: <4FF1CE8D.5020305@berkeley.edu> Hi JM! haha, sounds good, I'll contact you :) Cheers, Ingrid On 7/1/2012 11:53 PM, jan-mathijs schoffelen wrote: > Hi Ingrid, > > This calls for a statfun_corr or even a statfun_glm! It so happens > that I have some of these sitting on my hard drive. As you know I am > fond of beer, chocolate and co-authorships, so I am sure we can strike > a deal. I have not yet had the opportunity to contribute these > statfuns to FieldTrip, but now I sense a win-win-win situation: win 1 > is for me (beer/chocolate/co-authorships/etc), win 2 is for you (you > can compute your statistic of interest) and win 3 for the community > (where you test the code, write documentation on the wiki etcetc). How > does that sound for a plan? > > Cheers, > > JM > > On Jul 1, 2012, at 10:15 PM, Ingrid Nieuwenhuis wrote: > >> Hi FTers, >> >> I'd like to do two sorts of correlation calculations, and was >> wondering if there's any easy way to do this within FieldTrip. >> >> 1) I'd like to calculate the correlation between performance over >> trials and power within a specific frequency over trials. So I have >> the performance measure per trial, and my chan*freq measure after >> freqanalysis. So for each channel I have a series of power values >> (trials) and I have a series of performance measures (per trial), and >> now like to know (first within, and then over subjects) which >> channel's frequency power follows (correlates) with the performance. >> >> From the walkthrough >> I understand >> I can give in these performance measures through the design >> (cfg.design=[0.10.20.30.40.50.40.30.10.2];cfg.ivar=1;), but which >> method to use for ft_freqstatistics? I don't see statistics = >> 'correlation' or 'pearson' or 'spearman' in method = 'analytic. Also >> how to make the design to correlate over trials? >> >> 2) I'd like to calculate the correlation between the score on >> repeated questionnaire over participants with power within a >> frequency. So I have several power values per participant for each >> channel, and the repeated scores on the questionnaire for each >> participant. And now I'd like to calculate a value per channel >> reflecting the correlation over the repeats of the questionnaire and >> over participants. >> >> Any idea on FieldTrip settings? Both in general, is there a >> correlation statistics implemented, and more specifically for my >> question, how would I make the appropriate designs? >> >> Thanks so much! >> Ingrid >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> _______________________________________________ >> 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 -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Mon Jul 2 19:39:16 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Mon, 2 Jul 2012 18:39:16 +0100 Subject: [FieldTrip] calculating correlation In-Reply-To: <4FF0AFFC.1040500@berkeley.edu> References: <4FF0AFFC.1040500@berkeley.edu> Message-ID: Hi Ingrid, You're trying to test two very different things. 1) power-behavior correlation over trials, and differences between subjects are just unexplained variance. 2) power-behavior correlation across subjects. For 2) problem, I don't have anything to add to what Jan-Mathijs said. Correlation/GLM is very easy outside Fieldtrip but I hope Jan-Mathijs will include the GLM functions, it sounds very cool. For your "repeated questionnaires", I'd use a summary score (difference score for example) and do a simple correlation. For 1) problem, you could do a 2-level analysis, like SPM does for fMRI data: 1- you do correlation at the single-subject level, 2- you do a t-test on the slope (or your GLM column of interest), to test if it's different from zero. I don't know of Fieldtrip tools for this but I don't like this approach too much, because you lose quite some power and you don't model the trial-level noise. I've had some success using linear mixed-effects models for these types of research questions. There is the package lme4 in R which is very powerful. The only pain is to export data from Matlab and read them in R. You can get t-values from the linear mixed-effects models for each electrode/time point/freq point (unless you average over some dimension). Then you can use the cluster-level correction as implemented in Fieldtrip by flipping the sign of the t-statistics. There is some learning to do to use linear mixed-effects models but there are very flexible. Let me know if you need help with that. You can bribe me with the same things Jan-Mathijs likes... Hope this helps, 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 Sun, Jul 1, 2012 at 9:15 PM, Ingrid Nieuwenhuis wrote: > Hi FTers, > > I'd like to do two sorts of correlation calculations, and was wondering if > there's any easy way to do this within FieldTrip. > > 1) I'd like to calculate the correlation between performance over trials and > power within a specific frequency over trials. So I have the performance > measure per trial, and my chan*freq measure after freqanalysis. So for each > channel I have a series of power values (trials) and I have a series of > performance measures (per trial), and now like to know (first within, and > then over subjects) which channel's frequency power follows (correlates) > with the performance. > > From the walkthrough I understand I can give in these performance measures > through the design (cfg.design = [0.1 0.2 0.3 0.4 0.5 0.4 0.3 0.1 0.2]; > cfg.ivar= 1;), but which method to use for ft_freqstatistics? I don't see > statistics = 'correlation' or 'pearson' or 'spearman' in method = 'analytic. > Also how to make the design to correlate over trials? > > 2) I'd like to calculate the correlation between the score on repeated > questionnaire over participants with power within a frequency. So I have > several power values per participant for each channel, and the repeated > scores on the questionnaire for each participant. And now I'd like to > calculate a value per channel reflecting the correlation over the repeats of > the questionnaire and over participants. > > Any idea on FieldTrip settings? Both in general, is there a correlation > statistics implemented, and more specifically for my question, how would I > make the appropriate designs? > > Thanks so much! > Ingrid > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From inieuwenhuis at berkeley.edu Mon Jul 2 19:58:04 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 02 Jul 2012 10:58:04 -0700 Subject: [FieldTrip] calculating correlation In-Reply-To: References: <4FF0AFFC.1040500@berkeley.edu> Message-ID: <4FF1E12C.7010004@berkeley.edu> Hi Gio! Guys, where are the good old times of unconditional sharing between scientists for the greater good? ;) Must be the economy... Anyways, thanks! I'm just starting to learn R actually, I'll check out the lme4. Might be useful to include some FieldTrip to R functionality. I'll get in touch when I need help :) Cheers, Ingrid On 7/2/2012 10:39 AM, Gio Piantoni wrote: > Hi Ingrid, > > You're trying to test two very different things. > 1) power-behavior correlation over trials, and differences between > subjects are just unexplained variance. > 2) power-behavior correlation across subjects. > > For 2) problem, I don't have anything to add to what Jan-Mathijs said. > Correlation/GLM is very easy outside Fieldtrip but I hope Jan-Mathijs > will include the GLM functions, it sounds very cool. For your > "repeated questionnaires", I'd use a summary score (difference score > for example) and do a simple correlation. > > For 1) problem, you could do a 2-level analysis, like SPM does for > fMRI data: 1- you do correlation at the single-subject level, 2- you > do a t-test on the slope (or your GLM column of interest), to test if > it's different from zero. I don't know of Fieldtrip tools for this but > I don't like this approach too much, because you lose quite some power > and you don't model the trial-level noise. > I've had some success using linear mixed-effects models for these > types of research questions. There is the package lme4 in R which is > very powerful. The only pain is to export data from Matlab and read > them in R. You can get t-values from the linear mixed-effects models > for each electrode/time point/freq point (unless you average over some > dimension). Then you can use the cluster-level correction as > implemented in Fieldtrip by flipping the sign of the t-statistics. > There is some learning to do to use linear mixed-effects models but > there are very flexible. > Let me know if you need help with that. You can bribe me with the same > things Jan-Mathijs likes... > > Hope this helps, > > Gio > -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From johanna.zumer at donders.ru.nl Mon Jul 2 22:07:08 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Mon, 2 Jul 2012 22:07:08 +0200 Subject: [FieldTrip] Beamformer: different length of baseline and post baseline interval In-Reply-To: <1659120385.1619.1340961051346.JavaMail.root@zimbra> References: <1376177301.1612.1340961039830.JavaMail.root@zimbra> <1659120385.1619.1340961051346.JavaMail.root@zimbra> Message-ID: Dear Anna, Ideally for the common filter, you want the same amount of data T(s) per condition, where T = N x tw (and N is number of trials and tw is timewindow length). In your case, if the baselines for each conditions can be combined into one general baseline, and if you happen to have 100 trials per condition, then T_baseline = 3 x 100 x 0.5s = 150s. If you then use 1.5s length post-baseline, then T_each_condition = 100 x 1.5s = 150s, so you now have equal T for each condition for the common filter. However, in order to have an equal effect of tapers and edge-effects on the different conditions, you should use equal time window lengths in freqanalysis. Thus it would be better to split your post-baseline data into 3 segments of 500ms each before calling ft_freqanalysis, which again gives T = 100 x 0.5 x 3 = 150s. Cheers, Johanna 2012/6/29 Anna Wilsch > > Dear Fieldtrippers, > > I'm trying to beamform my MEG data by building a common filter including > three conditions and a baseline for each condition. The baseline intervals > have a duration of 500 ms. I was wondering if it is ok if the post-baseline > data are longer than that (1000 - 2000 ms). Does it have any negative > impact on the cross-spectral-density matrix and/or the common filter? Would > that still be a valid operation to do or is it necessary that baseline and > post baseline data have the same length? > Thank you for your comments. > > Cheers, > Anna > > > Anna Wilsch, Dipl.-Psych. > Auditory Cognition Research Group > Max Planck Institute for Human Cognitive and Brain Sciences > Stephanstr. 1a - Leipzig, Germany > (p) +49 (0)341 9940 2641 > (e) wilsch at cbs.mpg.de > > _______________________________________________ > 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 stan.vanpelt at fcdonders.ru.nl Tue Jul 3 09:17:47 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Tue, 3 Jul 2012 09:17:47 +0200 (CEST) Subject: [FieldTrip] Info about the power-line noise In-Reply-To: Message-ID: <997455910.845940.1341299867043.JavaMail.root@sculptor.zimbra.ru.nl> Hi Davide, Nice data (aside from what is indeed probably line noise). I see four approaches you could take, but not sure if it helps. You could just be unlucky with a very fluctuating line noise in this recording (see http://fieldtrip.fcdonders.nl/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter). The options I see: - Check if there is actually a datapadding up to 10 s. With already preprocessed data (e.g., after 3rd order gradiometer correction), it is not directly possible to data pad for subsequent dft-filtering. It happened to me not so long ago, that's why I ask. I made a workaround by first creating trials of 10s length, then do the dft-filetering, and after that cut the actual trials out. - If not already done, apply 3rd-order gradiometer correction first (ft_denoise_synthetic, or in the CTF DataEditor) - Use a bandstop-filter instead of the dft - Source-project the data. With my data that usually also gets rid of most line noise (I use LCMV to reconstruct a virtual sensor time course) Hope that helps. Stan ----- Oorspronkelijk bericht ----- > Van: "Davide Rivolta" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Maandag 2 juli 2012 18:20:13 > Onderwerp: [FieldTrip] Info about the power-line noise > Dear fieldtrippers, > I recently run into the attached figures (S01 files). It seems a > failure of the power-line noise filter. > I used the following settings quite succesfully for other subjects: > cfg.dftfilter = 'yes'; > cfg.padding = 10; > An example of good figures are the "KAT" files. > These data come from a visual task where people see moving > concentrical gratings. Each trial has a different length that range > between around 0.5 until 3 seconds. > Would the bandstop filter be the only possible solution here? > Thanks, > Davide > _______________________________________________ > 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 ivano_triggiani at yahoo.it Tue Jul 3 17:42:37 2012 From: ivano_triggiani at yahoo.it (Ivano Triggiani) Date: Tue, 3 Jul 2012 16:42:37 +0100 (BST) Subject: [FieldTrip] band pass and segmentation In-Reply-To: References: Message-ID: <1341330157.2152.YahooMailNeo@web28705.mail.ir2.yahoo.com> Hi all, I tried to use a simple cfg.bpfilter (0.1 - 40) for an EEG that I divide into 2 secs époques and giving a look it seems that at the board of every window the signal is reduced (just like following a parabolic trend). Is this a problem of the brutal segmentation (respect to a good windowing) or there's something else? Ivano -------------- next part -------------- An HTML attachment was scrubbed... URL: From andreas.wutz-1 at unitn.it Tue Jul 3 23:44:09 2012 From: andreas.wutz-1 at unitn.it (Wutz, Andreas) Date: Tue, 3 Jul 2012 23:44:09 +0200 Subject: [FieldTrip] Structure of 4D-Fourierspectrum with Multi-Taper Message-ID: Dear all, in requesting from a ft_freqanalysis with output ='fourier' and 2 multitapers, I figured out that in the 4D matrix in the field 'fourierspctrm' the first dimension refers to the number of tapers that are calculated (Number of trials -times- number of tapers). My question refers to the organization of this dimension. Are in the example with 2 tapers the two tapers from the same trial next to each other? Or do we have first, the outputs from the first taper for all the trials and then, all the trials for the 2nd taper? I would like to calculate the circular mean of the phase angles across trials and therefore would need to combine the outputs of the two tapers per trial. Is there already some fieldtrip function to do this? How should it be done? Thank you very much. Best Andreas Andreas Wutz PhD Student CIMeC - Center for Mind/Brain Sciences Università degli studi di Trento From jan.schoffelen at donders.ru.nl Wed Jul 4 09:19:30 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 4 Jul 2012 09:19:30 +0200 Subject: [FieldTrip] Structure of 4D-Fourierspectrum with Multi-Taper References: Message-ID: <6C2FF2A6-B080-424C-A01F-048215D181CD@donders.ru.nl> Hi Andreas, The tapers per trial are grouped together, i.e. it is according to the first scenario you sketch. Note that averaging fourier-coefficients across tapers is not correct, because each of the tapers induces a non-trivial phase shift. Phase differences however can be averaged across tapers, but for this you need a reference signal. Best, Jan-Mathijs On Jul 3, 2012, at 11:44 PM, Wutz, Andreas wrote: > Dear all, > > in requesting from a ft_freqanalysis with output ='fourier' and 2 multitapers, I figured out that in the 4D matrix in the field 'fourierspctrm' the first dimension refers to the number of tapers that are calculated (Number of trials -times- number of tapers). My question refers to the organization of this dimension. Are in the example with 2 tapers the two tapers from the same trial next to each other? Or do we have first, the outputs from the first taper for all the trials and then, all the trials for the 2nd taper? I would like to calculate the circular mean of the phase angles across trials and therefore would need to combine the outputs of the two tapers per trial. Is there already some fieldtrip function to do this? How should it be done? > > Thank you very much. > Best > Andreas > > Andreas Wutz > PhD Student > CIMeC - Center for Mind/Brain Sciences > Università degli studi di Trento > _______________________________________________ > 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 jm.horschig at donders.ru.nl Wed Jul 4 15:35:52 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 04 Jul 2012 15:35:52 +0200 Subject: [FieldTrip] Questions on High pass and Dft filtering In-Reply-To: References: Message-ID: <4FF446B8.8040600@donders.ru.nl> HI Philipp, > The issue with the continuous data is the following: I tried using > cfg = []; > cfg.channel = {'EEG'}; > cfg.datafile = dataset; > cfg.headerfile = dataset; > cfg.dataset = dataset; > > cfg.continuous = 'yes'; > > (cfg.padding = 10;) > cfg.dftfilter = 'yes'; > > filteredContinuousData = ft_preprocessing(cfg); > > but looking at averaged timelocked data for the subject, the data looks > identical to the result I get using no filter at all, i.e., contaminated by > strong line noise. Including padding makes no difference either, therefore > the brackets. I tested this with my own data as well with as synthetic signal. The line noise is reduced by a factor of ~8 (I looked at the Fourier spectrum of the filtered and the unfiltered signal).The problem you encounter is either caused by nonstationarity of the 50Hz component (i.e. a drift in power, see FAQ), or maybe your acquisition system is misspecifying the sampling frequency a bit - Robert says this might happen, see: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1571 In any case, it might help for you if you specify cfg.dftfreq = [49.6:0.2:50.4 100 150] or similar (depends on your padding parameter). That might help to filter a bit 'better' (but maybe a bandstop filter works better here). Best, Jörn -- 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 frsantos at fpce.up.pt Wed Jul 4 18:35:36 2012 From: frsantos at fpce.up.pt (Fernando Ricardo Santos) Date: Wed, 4 Jul 2012 16:35:36 +0000 Subject: [FieldTrip] Introductory EEG/ERP Summer School in Porto, Portugal Message-ID: <2BAB036A9BAEA44984A131DFCE446108722337EB@SRVMBX02.fpceup.psi.up.pt> Dear FieldTrip users, The Laboratory of Neuropsychopsysiology (University of Porto, Portugal) is organizing "I CAN – 1st Cognitive and Affective Neurophysiology Summer School: Acquisition, processing and analysis of EEG signal" -- September 3-8, 2012. This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. The course will cover an introduction to the EEG and ERP techniques, acquisition of electrophysiological data of brain activity, signal processing, and statistical analysis of the data. All the modules will have a practical hands-on component and all lectures will be held in English. Scientific Coordination: -Professor João Marques-Teixeira Course tutors: -Fernando Ferreira-Santos -Pedro R. Almeida Venue and dates: Faculty of Psychology and Educational Sciences of the University of Porto (Portugal), from the 3rd to the 8th of September of 2012. For additional information on the Summer School please follow the link: http://www.fpce.up.pt/labpsi/summerschool/ Thank you and best wishes to all, -- Fernando Ferreira-Santos Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Dr. Manuel Pereira da Silva 4200-392 Porto (Portugal) Tel. +351 226079700 (ext. 301) Email: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From omidabbasi2000 at gmail.com Thu Jul 5 14:06:23 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Thu, 5 Jul 2012 16:36:23 +0430 Subject: [FieldTrip] help to apply field trip (topography plotting) In-Reply-To: References: Message-ID: Dear Developer At first, I thank you for useful source code. This is Omid. I'm a student that work on biological signal processing. I want to use your source code for plotting data topography of brain. I downloaded your code from this link ( http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but i can't use it in my project, because i have 19 signals from 19 sites on the brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your code in my project with different channel and data? It would grateful for me if you could help me to apply your code in my project. Best Regards Omid -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Fri Jul 6 12:59:05 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Fri, 6 Jul 2012 12:59:05 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? Message-ID: Dear list members, I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. Any help with this issue is greatly aprreciated! Cheers, Ulrich From johanna.zumer at donders.ru.nl Fri Jul 6 14:36:04 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Fri, 6 Jul 2012 14:36:04 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: Message-ID: Dear Ulrich, Only if the leadfields are the same, can you use the common filter. If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. Cheers, Johanna 2012/7/6 Pomper, Ulrich > Dear list members, > I want to compare source data between two different groups (patients and > controls). Each patient has an age and gender-matched control. > Is it correct to compute a common filter for each pair of subjects? The > TF-topographies do look different within each pair, so I would assume that > the sources are somewhat different. However, as I'm going to statistically > compare the two groups it would be nice to have common filters, as > otherwise any finding could be due to different filters as opposed to > different sources. > > Any help with this issue is greatly aprreciated! > Cheers, Ulrich > _______________________________________________ > 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 Ulrich.Pomper at charite.de Fri Jul 6 15:21:23 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Fri, 6 Jul 2012 15:21:23 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: , Message-ID: Dear Johanna, thanks for your quick reply! To clarify things: This is an EEG study, using a standard MNI-based headmodel for all subjects. I have a between subjects factor group (patients, controls) and a within subjects factor condition (A, B). Also, I can use a within subject contrast (active versus baseline) for the source analysis. Currently, I use one common filter for baseline and active data as well as both conditions for each subject. So I end up using one common filter per subject. My question I whether it would be more correct to additionally pool the data from matched subjects into one single filter. Thus resulting in one common filter per pair. Cheers, Ulrich ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer [johanna.zumer at donders.ru.nl] Sent: Friday, July 06, 2012 2:36 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Common beamforming filters for different groups? Dear Ulrich, Only if the leadfields are the same, can you use the common filter. If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. Cheers, Johanna 2012/7/6 Pomper, Ulrich > Dear list members, I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. Any help with this issue is greatly aprreciated! Cheers, Ulrich _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus From kmanning at robarts.ca Fri Jul 6 18:59:20 2012 From: kmanning at robarts.ca (Kathryn Manning) Date: Fri, 6 Jul 2012 12:59:20 -0400 Subject: [FieldTrip] Connectivity analysis Message-ID: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> Dear FieldTrip list members, I am comparing the connectivity patterns in the brain measured using fMRI and electrophysiological recordings. I am trying to correlate the LFP signals as a function of time, using a sliding window analysis. I'm able to generate plots using ft_connectivityplot but this is as a function of frequency. From what I can tell the 'mtmconvol' method generates data with a time aspect in it's dimord, but are there any functions available in fieldtrip in order to calculate the correlation as a function of time? Any help would be greatly appreciated, thank you so much. Kathryn From Don.Rojas at ucdenver.edu Fri Jul 6 19:02:41 2012 From: Don.Rojas at ucdenver.edu (Rojas, Don) Date: Fri, 6 Jul 2012 11:02:41 -0600 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: , Message-ID: Ulrich, It does not make sense to me to have a common filter per pair of subjects, only between conditions within a subject (which you say you are currently doing). Since, as Johanna suggested, you are using a standard brain and standard electrode locations, rather than individual ones, you can have a common leadfield matrix for all subjects. However, I don't think you can have a common beamformer filter, since that is computed for each subject based on the covariance or cross spectral density matrix, which would be unique to each subject. Therefore, the beamformer filter, which uses both the covariance and the leadfield, would be unique for each individual. You can save time simply by having a common leadfield matrix. Best, Don ----------------------- Don Rojas, Ph.D. Associate Professor of Psychiatry U. of Colorado Denver Anschutz Medical Campus Director, UCD Magnetoencephalography Lab 13001 E. 17th Pl F546 Aurora, CO 80045 303-724-4994 On Jul 6, 2012, at 7:21 AM, Pomper, Ulrich wrote: > Dear Johanna, > thanks for your quick reply! > > To clarify things: This is an EEG study, using a standard MNI-based headmodel for all subjects. > > I have a between subjects factor group (patients, controls) and a within subjects factor condition (A, B). Also, I can use a within subject contrast (active versus baseline) for the source analysis. > > Currently, I use one common filter for baseline and active data as well as both conditions for each subject. So I end up using one common filter per subject. > > My question I whether it would be more correct to additionally pool the data from matched subjects into one single filter. Thus resulting in one common filter per pair. > > > Cheers, Ulrich > > > > > > > > > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer [johanna.zumer at donders.ru.nl] > Sent: Friday, July 06, 2012 2:36 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Common beamforming filters for different groups? > > Dear Ulrich, > > Only if the leadfields are the same, can you use the common filter. > > If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. > > If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. > > Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? > > Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. > > Cheers, > Johanna > > > 2012/7/6 Pomper, Ulrich > > Dear list members, > I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. > Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. > > Any help with this issue is greatly aprreciated! > Cheers, Ulrich > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg > > Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From politzerahless at gmail.com Sat Jul 7 02:46:14 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Sat, 7 Jul 2012 08:46:14 +0800 Subject: [FieldTrip] help to apply field trip (topography plotting) Message-ID: Hi Omid, Welcome to Fieldtrip. You can find a lot of information about how to use Fieldtrip at http://fieldtrip.fcdonders.nl/walkthrough and http://fieldtrip.fcdonders.nl/tutorial. In your case, you need to get your data imported into Fieldtrip's format in MATLAB ( http://fieldtrip.fcdonders.nl/tutorial/preprocessing), as well as your channel layout (http://fieldtrip.fcdonders.nl/tutorial/layout) before proceeding to plotting. Good luck, Steve > Message: 1 > Date: Thu, 5 Jul 2012 16:36:23 +0430 > From: omid abbasi > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] help to apply field trip (topography plotting) > Message-ID: > < > CAPc_m1utoA_ZqC8_0q44hz5FX3yMfWP-gfke5Mes9_sEUOuyrA at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Developer > > At first, I thank you for useful source code. > > This is Omid. I'm a student that work on biological signal processing. I > want to use your source code for plotting data topography of brain. I > downloaded your code from this link ( > http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but i > can't use it in my project, because i have 19 signals from 19 sites on the > brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your > code in my project with different channel and data? > > It would grateful for me if you could help me to apply your code in my > project. > > Best Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From skelly2 at ccny.cuny.edu Sat Jul 7 07:00:40 2012 From: skelly2 at ccny.cuny.edu (skelly2 at ccny.cuny.edu) Date: Sat, 7 Jul 2012 01:00:40 -0400 (EDT) Subject: [FieldTrip] Postdoc position in systems neuroscience, City College of New York Message-ID: <201207070500.028516@pelican.admin.ccny.cuny.edu> Postdoctoral position in systems neuroscience, City College of New York A postdoctoral "Endeavor Scientist" position funded by the Child Mind Institute (CMI) is available starting this Fall in the lab of Simon Kelly at the City College of New York. The endeavor scientist will work on basic and clinical projects mainly using human electroencephalogram (EEG) recordings, under the joint supervision of Simon Kelly (http://bme.ccny.cuny.edu/people/faculty/skelly) of the Department of Biomedical Engineering, CCNY and Michael Milham (http://www.childmind.org/en/directory/clinicians/mmilham) of CMI. The position will involve analysis of data obtained from clinical and non-clinical populations at the Child Mind Institute and its collaborators, in addition to conducting basic studies of perception and cognition in the Kelly lab, particularly focusing on decision making and attention. A major goal will be to develop novel paradigms and data analysis approaches that allow neural signals to be linked with well-defined perceptual/cognitive computations, and to deploy these paradigms and approaches to studies at CMI. Clinical studies will be mainly in child and adolescent populations associated with clinically significant anxiety, attentional dysfunction, emotional dysregulation and learning impairments. Any innovative tools developed in the course of this position will be made publicly available. Applicants must have a Ph.D. in neuroscience or related field, including neural/biomedical engineering, applied mathematics and computer science. The candidate must have strong analytic/quantitative skills, be proficient in programming (especially Matlab), and have experience in psychophysics and EEG recording and analysis. Experience with fMRI is a strong plus, as some projects may involve a multimodal EEG/fMRI approach. The ideal candidate will be reliable, highly motivated, and will be equally productive when working independently or cooperatively. Applicants should send a curriculum vitae, contact information for three references, and a cover letter with a brief description of past research accomplishments as well as future research interests and career goals to Simon Kelly at skelly2 at ccny.cuny.edu. From jan.schoffelen at donders.ru.nl Sat Jul 7 20:01:23 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Sat, 7 Jul 2012 20:01:23 +0200 Subject: [FieldTrip] Connectivity analysis In-Reply-To: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> References: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> Message-ID: Hi Kathryn, I believe that ft_connectivityanalysis is capable of dealing with frequency domain data that contain a time dimension. I assume here that you would like to compute coherence, rather than correlation. Last time I checked, ft_connectivityanalysis could not compute an ordinary correlation coefficient. Best wishes, Jan-Mathijs On Jul 6, 2012, at 6:59 PM, Kathryn Manning wrote: > Dear FieldTrip list members, > > I am comparing the connectivity patterns in the brain measured using fMRI and electrophysiological recordings. I am trying to correlate the LFP signals as a function of time, using a sliding window analysis. I'm able to generate plots using ft_connectivityplot but this is as a function of frequency. From what I can tell the 'mtmconvol' method generates data with a time aspect in it's dimord, but are there any functions available in fieldtrip in order to calculate the correlation as a function of time? > > Any help would be greatly appreciated, thank you so much. > > Kathryn > _______________________________________________ > 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 bertram0611 at pku.edu.cn Sun Jul 8 09:50:20 2012 From: bertram0611 at pku.edu.cn (=?utf-8?B?6JSh5p6X?=) Date: Sun, 8 Jul 2012 15:50:20 +0800 (CST) Subject: [FieldTrip] =?gbk?q?How_to_import_*=2Ecnt_datafile_from_NeuroScan?= =?gbk?q?=3F?= Message-ID: <283648358.226.1341733820039.JavaMail.root@bj-mail07.pku.edu.cn> Dear FieldTrip list members, I wanna analyse the *.cnt datafile from NeuroScan. But I don't know how to do that. Because there are not detailed scripts. In my exp, the trigger code is 14. I don't what is eventvalue that equals trigger code? My EEG was recorded from 62 Ag/AgCl electrodes mounted in an elastic cap (Quick-Cap, NeuroScan Inc.,Herndon, Virginia, USA). Recordings were referenced to the left mastoid, but rereferenced to linked mastoids offline. The horizontal and vertical electrooculogram was also monitored. Electrode impedances were kept below 5 kO. The EEG and electrooculogram were amplified with a band-pass from DC to 70Hz and the sample rate was 500 Hz.The epoch interval was 1200ms, ranging from 200ms before the onset of the critical word to 1000 ms after it.I used a 100-ms poststimulus baseline for the critical words. can you give an example that analysing *.cnt data. my script and problems as follows: cfg = [] cfg.datafile = 's01.cnt' cfg.headerfile = 's01.cnt' cfg.channel = 'all' cfg.eventvalue = '14' raw = ft_definetrial(cfg); Warning: no trialfun was specified, using trialfun_general > In ft_definetrial at 123 evaluating trialfunction 'trialfun_general' ??? Reference to non-existent field 'trialdef'. Error in ==> trialfun_general at 29 if isfield(cfg.trialdef, 'eventvalue') && isempty(cfg.trialdef.eventvalue ), cfg.trialdef = rmfield(cfg.trialdef, 'eventvalue' ); end Error in ==> ft_definetrial at 175 [trl, event] = feval(cfg.trialfun, cfg); best regards -- Lin Cai Department of Psychology, Peking University, Beijing 100871, P.R.China From politzerahless at gmail.com Sun Jul 8 12:32:02 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Sun, 8 Jul 2012 18:32:02 +0800 Subject: [FieldTrip] How to import *.cnt datafile from NeuroScan? Message-ID: Hello Lin, In your code you need to specify an event type. To find out what the event type is, you can run ft_definetrial() with cfg.trialdef.eventtype='?', and it will tell you what event types are present in the file (see my sample below): addpath 'C:\Program Files\MATLAB\R2010a\toolbox\fieldtrip-20120512'; cd 'C:\Users\SJPA\Documents\MATLAB'; cfg = []; cfg.dataset = 'myneuroscanfile.cnt'; cfg.trialdef.eventtype = '?' cfg = ft_definetrial(cfg); After that, you can use that event type, along with cfg.dataset and cfg.trialdef.eventvalue, to define trials and import the data; see my example below (this code will take a continuous file but it will epoch it while importing, so you will end up with epoched data; also note, as far as I know, you don't need to specify cfg.headerfile) addpath 'C:\Program Files\MATLAB\R2010a\toolbox\fieldtrip-20120512'; cd 'C:\Users\SJPA\Documents\MATLAB'; cfg = []; cfg.dataset = 'myneuroscanfile.cnt'; cfg.trialdef.eventtype = 'trial'; cfg.trialdef.eventvalue = [4 5 6 7]; cfg = ft_definetrial(cfg); cfg.channel = []; cfg.continuous = 'yes'; data = ft_preprocessing(cfg); I noticed your e-mail signature says you are at Peking University; I am actually also at the psychology department in PKU and will be here until July 17th, if you need assistance feel free to contact me! Best, Steve Politzer-Ahles > > Message: 2 > Date: Sun, 8 Jul 2012 15:50:20 +0800 (CST) > From: ?? > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] How to import *.cnt datafile from NeuroScan? > Message-ID: > <283648358.226.1341733820039.JavaMail.root at bj-mail07.pku.edu.cn> > Content-Type: text/plain; charset=utf-8 > > Dear FieldTrip list members, > > I wanna analyse the *.cnt datafile from NeuroScan. But I don't know how to > do that. Because there are not detailed scripts. In my exp, the trigger > code is 14. I don't what is eventvalue that equals trigger code? My EEG was > recorded from 62 Ag/AgCl electrodes mounted in an elastic cap (Quick-Cap, > NeuroScan Inc.,Herndon, Virginia, USA). Recordings were referenced to the > left mastoid, but rereferenced to linked mastoids offline. The horizontal > and vertical electrooculogram was also monitored. Electrode impedances were > kept below 5 kO. The EEG and electrooculogram were amplified with a > band-pass from DC to 70Hz and the sample rate was 500 Hz.The epoch interval > was 1200ms, ranging from 200ms before the onset of the critical word to > 1000 ms after it.I used a 100-ms poststimulus baseline for the critical > words. > can you give an example that analysing *.cnt data. > my script and problems as follows: > cfg = [] > cfg.datafile = 's01.cnt' > cfg.headerfile = 's01.cnt' > cfg.channel = 'all' > cfg.eventvalue = '14' > raw = ft_definetrial(cfg); > Warning: no trialfun was specified, using trialfun_general > > In ft_definetrial at 123 > evaluating trialfunction 'trialfun_general' > ??? Reference to non-existent field 'trialdef'. > > Error in ==> trialfun_general at 29 > if isfield(cfg.trialdef, 'eventvalue') && isempty(cfg.trialdef.eventvalue > ), > cfg.trialdef = rmfield(cfg.trialdef, 'eventvalue' ); end > > Error in ==> ft_definetrial at 175 > [trl, event] = feval(cfg.trialfun, cfg); > best regards > > -- > Lin Cai > Department of Psychology, Peking University, Beijing 100871, P.R.China > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 20, Issue 12 > ***************************************** > -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From omidabbasi2000 at gmail.com Sun Jul 8 13:28:31 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Sun, 8 Jul 2012 15:58:31 +0430 Subject: [FieldTrip] help to apply field trip (topography plotting) In-Reply-To: References: Message-ID: Dear Steve Thank you very much for your good guidance. I review these links and if i have any question i will ask you again. Best Regards Omid On Sat, Jul 7, 2012 at 5:16 AM, Stephen Politzer-Ahles < politzerahless at gmail.com> wrote: > Hi Omid, > > Welcome to Fieldtrip. You can find a lot of information about how to use > Fieldtrip at http://fieldtrip.fcdonders.nl/walkthrough and > http://fieldtrip.fcdonders.nl/tutorial. In your case, you need to get > your data imported into Fieldtrip's format in MATLAB ( > http://fieldtrip.fcdonders.nl/tutorial/preprocessing), as well as your > channel layout (http://fieldtrip.fcdonders.nl/tutorial/layout) before > proceeding to plotting. > > Good luck, > Steve > > >> Message: 1 >> Date: Thu, 5 Jul 2012 16:36:23 +0430 >> From: omid abbasi >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] help to apply field trip (topography plotting) >> Message-ID: >> < >> CAPc_m1utoA_ZqC8_0q44hz5FX3yMfWP-gfke5Mes9_sEUOuyrA at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear Developer >> >> At first, I thank you for useful source code. >> >> This is Omid. I'm a student that work on biological signal processing. I >> want to use your source code for plotting data topography of brain. I >> downloaded your code from this link ( >> http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but >> i >> can't use it in my project, because i have 19 signals from 19 sites on the >> brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your >> code in my project with different channel and data? >> >> It would grateful for me if you could help me to apply your code in my >> project. >> >> Best Regards >> > > _______________________________________________ > 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 omidabbasi2000 at gmail.com Mon Jul 9 07:06:35 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Mon, 9 Jul 2012 09:36:35 +0430 Subject: [FieldTrip] Bipolar montage Message-ID: Dear Member lists I have .txt file of monopolar montage of EEG (EEG1020, 19 channel). How can i have bipolar montage of it? What's the relationship between bipolar montage and monopolar montage? Best Regards Omid -------------- next part -------------- An HTML attachment was scrubbed... URL: From ith at deakin.edu.au Mon Jul 9 09:26:03 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Mon, 9 Jul 2012 07:26:03 +0000 Subject: [FieldTrip] plotting dipoles on an anatomical mri Message-ID: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> Dear fieldTrip users, I am doing a dipole fit with the ft_dipolefitting function and I can plot and visualize the results with ft_plot_dipole, further I also want to compare the results with a beamformer results so, I tried plotting the ft_dipolefitting results with ft_sourceplot. I cannot yet very well understand how ft_sourceplot works, I understand that the dipole should be assigned with some value but cannot figure out how to do this. Can someone please give me some help in doing this? Following is the code I am using, where should I modify? cfg = []; cfg.location = dip_fitted.dip.pos; cfg.method='ortho'; ft_sourceplot(cfg,mri) where mri is the standard_mri.mat . I work in the MNI coordinates and my locations are in mm's. Thank you very much in advance. Kind regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr [Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 29155 bytes Desc: image001.jpg URL: From r.oostenveld at donders.ru.nl Mon Jul 9 09:40:56 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 9 Jul 2012 09:40:56 +0200 Subject: [FieldTrip] Bipolar montage In-Reply-To: References: Message-ID: <4E3F9B02-6C6D-4EA0-BADF-85A33B005C2D@donders.ru.nl> Dear Omid The option cfg.montage in ft_preprocessing allows you to convert your data between a monopolar to a bipolar montage. See the help of ft_preprocessing and the help of ft_apply_montage (which is the lower-level function that does the actual work). best regards, Robert On 9 Jul 2012, at 7:06, omid abbasi wrote: > Dear Member lists > > I have .txt file of monopolar montage of EEG (EEG1020, 19 channel). How can i have bipolar montage of it? What's the relationship between bipolar montage and monopolar montage? > > Best Regards > Omid > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Ulrich.Pomper at charite.de Mon Jul 9 09:51:56 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Mon, 9 Jul 2012 09:51:56 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: , , Message-ID: Thanks Don for you help! Best, Ulrich ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Rojas, Don [Don.Rojas at ucdenver.edu] Sent: Friday, July 06, 2012 7:02 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Common beamforming filters for different groups? Ulrich, It does not make sense to me to have a common filter per pair of subjects, only between conditions within a subject (which you say you are currently doing). Since, as Johanna suggested, you are using a standard brain and standard electrode locations, rather than individual ones, you can have a common leadfield matrix for all subjects. However, I don't think you can have a common beamformer filter, since that is computed for each subject based on the covariance or cross spectral density matrix, which would be unique to each subject. Therefore, the beamformer filter, which uses both the covariance and the leadfield, would be unique for each individual. You can save time simply by having a common leadfield matrix. Best, Don ----------------------- Don Rojas, Ph.D. Associate Professor of Psychiatry U. of Colorado Denver Anschutz Medical Campus Director, UCD Magnetoencephalography Lab 13001 E. 17th Pl F546 Aurora, CO 80045 303-724-4994 On Jul 6, 2012, at 7:21 AM, Pomper, Ulrich wrote: > Dear Johanna, > thanks for your quick reply! > > To clarify things: This is an EEG study, using a standard MNI-based headmodel for all subjects. > > I have a between subjects factor group (patients, controls) and a within subjects factor condition (A, B). Also, I can use a within subject contrast (active versus baseline) for the source analysis. > > Currently, I use one common filter for baseline and active data as well as both conditions for each subject. So I end up using one common filter per subject. > > My question I whether it would be more correct to additionally pool the data from matched subjects into one single filter. Thus resulting in one common filter per pair. > > > Cheers, Ulrich > > > > > > > > > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer [johanna.zumer at donders.ru.nl] > Sent: Friday, July 06, 2012 2:36 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Common beamforming filters for different groups? > > Dear Ulrich, > > Only if the leadfields are the same, can you use the common filter. > > If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. > > If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. > > Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? > > Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. > > Cheers, > Johanna > > > 2012/7/6 Pomper, Ulrich > > Dear list members, > I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. > Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. > > Any help with this issue is greatly aprreciated! > Cheers, Ulrich > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg > > Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus > > _______________________________________________ > 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 -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus From r.oostenveld at donders.ru.nl Mon Jul 9 10:02:16 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 9 Jul 2012 10:02:16 +0200 Subject: [FieldTrip] plotting dipoles on an anatomical mri In-Reply-To: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> References: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> Message-ID: Dear Imali The ft_sourceplot function was not designed to plot 3D data in combination with dipoles. If you use method=ortho, you can get the 3 intersections in the 3D volume at the location of the dipole. For the best control over the details of the plot, which you need for your specific application of combining dipoles and volumetric data, I suggest that you look at the ft_plot_slice function. If you do three ft_plot_slice calls for the three orientations (x,y,z) at the location of the dipole and combine that with ft_plot_dipole, you will probably visualize the 3D relation between the two types of data the clearest. Note that ft_plot_slice plots any slice in 3D, so you should use the 3D rotate option of the MATLAB figure. best regards, Robert On 9 Jul 2012, at 9:26, IMALI THANUJA HETTIARACHCHI wrote: > Dear fieldTrip users, > > I am doing a dipole fit with the ft_dipolefitting function and I can plot and visualize the results with ft_plot_dipole, further I also want to compare the results with a beamformer results so, I tried plotting the ft_dipolefitting results with ft_sourceplot. I cannot yet very well understand how ft_sourceplot works, I understand that the dipole should be assigned with some value but cannot figure out how to do this. > > Can someone please give me some help in doing this? Following is the code I am using, where should I modify? > > cfg = []; > cfg.location = dip_fitted.dip.pos; > cfg.method='ortho'; > ft_sourceplot(cfg,mri) > > where mri is the standard_mri.mat . I work in the MNI coordinates and my locations are in mm’s. > > > Thank you very much in advance. > > Kind regards > Imali > > Imali Thanuja Hettiarachchi > PhD Candidate > Centre for Intelligent Systems research > Deakin University, Geelong 3217, Australia. > Email: ith at deakin.edu.au > www.deakin.edu.au/cisr > > > > > > > _______________________________________________ > 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 omidabbasi2000 at gmail.com Mon Jul 9 10:35:45 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Mon, 9 Jul 2012 13:05:45 +0430 Subject: [FieldTrip] Bipolar montage In-Reply-To: <4E3F9B02-6C6D-4EA0-BADF-85A33B005C2D@donders.ru.nl> References: <4E3F9B02-6C6D-4EA0-BADF-85A33B005C2D@donders.ru.nl> Message-ID: Dear Robert Thank you for your fast answer I'll check it. Best Regards Omis On Mon, Jul 9, 2012 at 12:10 PM, Robert Oostenveld < r.oostenveld at donders.ru.nl> wrote: > Dear Omid > > The option cfg.montage in ft_preprocessing allows you to convert your data > between a monopolar to a bipolar montage. See the help of ft_preprocessing > and the help of ft_apply_montage (which is the lower-level function that > does the actual work). > > best regards, > Robert > > > On 9 Jul 2012, at 7:06, omid abbasi wrote: > > > Dear Member lists > > > > I have .txt file of monopolar montage of EEG (EEG1020, 19 channel). How > can i have bipolar montage of it? What's the relationship between bipolar > montage and monopolar montage? > > > > Best Regards > > Omid > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 9 11:48:18 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 09 Jul 2012 11:48:18 +0200 Subject: [FieldTrip] band pass and segmentation In-Reply-To: <1341330157.2152.YahooMailNeo@web28705.mail.ir2.yahoo.com> References: <1341330157.2152.YahooMailNeo@web28705.mail.ir2.yahoo.com> Message-ID: <4FFAA8E2.70100@donders.ru.nl> Hi Ivano, I don't understand your request exactly, could you attach an example figure and explain your issue by using that? Then I (or someone else) might be able to help you out. Best, Jörn On 7/3/2012 5:42 PM, Ivano Triggiani wrote: > Hi all, > > I tried to use a simple cfg.bpfilter (0.1 - 40) for an EEG that I > divide into 2 secs époques and giving a look it seems that at the > board of every window the signal is reduced (just like following a > parabolic trend). Is this a problem of the brutal segmentation > (respect to a good windowing) or there's something else? > > Ivano > > > > _______________________________________________ > 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 Mon Jul 9 12:17:33 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 09 Jul 2012 12:17:33 +0200 Subject: [FieldTrip] Fwd: Re: band pass and segmentation In-Reply-To: <1341828068.24326.YahooMailNeo@web28706.mail.ir2.yahoo.com> References: <1341828068.24326.YahooMailNeo@web28706.mail.ir2.yahoo.com> Message-ID: <4FFAAFBD.4080107@donders.ru.nl> Dear Ivano, I am forwarding your message and my reply to the discussion list again, so that others might benefit or add information. What you see looks to me pretty much like a filter artifact, which is common to occur at the edges of your signal. In order to reduce these, you can think of changing the order of your filter or, more ideal in my opinion, use filterpadding. You can either let FieldTrip do that by specifying cfg.padding or by defining your trials in a wider range (e.g. add 1s pre and post time of interest) and then only plot the time of interest, with the knowledge that the 1s padding before and after is corrupted by filter artifacts. Best, Jörn -------- Original Message -------- Subject: Re: [FieldTrip] band pass and segmentation Date: Mon, 9 Jul 2012 11:01:08 +0100 (BST) From: Ivano Triggiani Reply-To: Ivano Triggiani To: "Jörn M. Horschig" Hi Jorn, in attach an example. you can see in the third slide on the right the channel that "goes down". Thanks, Ivano ------------------------------------------------------------------------ "No man can wear one face to himself and another to the multitude, without finally getting bewildered as to which one is true." Nathaniel Hawthorne ------------------------------------------------------------------------ *Da:* ""Jörn M. Horschig"" *A:* Ivano Triggiani ; FieldTrip discussion list *Inviato:* Lunedì 9 Luglio 2012 11:48 *Oggetto:* Re: [FieldTrip] band pass and segmentation Hi Ivano, I don't understand your request exactly, could you attach an example figure and explain your issue by using that? Then I (or someone else) might be able to help you out. Best, Jörn On 7/3/2012 5:42 PM, Ivano Triggiani wrote: > Hi all, > > I tried to use a simple cfg.bpfilter (0.1 - 40) for an EEG that I > divide into 2 secs époques and giving a look it seems that at the > board of every window the signal is reduced (just like following a > parabolic trend). Is this a problem of the brutal segmentation > (respect to a good windowing) or there's something else? > > Ivano > > > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: Fieldtrip_EEG.ppt Type: application/vnd.ms-powerpoint Size: 169984 bytes Desc: not available URL: From vitoria.piai at gmail.com Mon Jul 9 15:18:47 2012 From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=) Date: Mon, 09 Jul 2012 15:18:47 +0200 Subject: [FieldTrip] plot functions and illustrator: set(gcf, 'interpreter', 'zbuffer') Message-ID: <4FFADA37.5070004@gmail.com> Hi, On the FT page, Roemer said that using set(gcf,'interpreter','zbuffer') may resolve problems when exporting from matlab as .eps and opening in Illustrator. That works fine for sensor-level data, for example TFRs with ft_singleplotTFR. But it doesn't work when, for example, using ft_sourceplot (I've akes around and I don't seem to be the only one having this problem). But ok, so far so good, I can get around it. But now I have an analysis I ran with LCMV for which I wanted to plot the results. Interestingly, if I use ft_singleplotTFR in this case, I cannot fix the bug with set(gcf,'interpreter','zbuffer'). It seems to behave like when using ft_sourceplot, instead of behaving as ft_singleplot when plotting sensor-level data. Has anyone dealt with this bug before? I mean, not being able to fix it with set(gcf,'interpreter','zbuffer')? Thanx a lot, Vitoria -- ** Please consider the environment - do you really need to print? ** From kmanning at robarts.ca Mon Jul 9 15:19:16 2012 From: kmanning at robarts.ca (Kathryn Manning) Date: Mon, 9 Jul 2012 09:19:16 -0400 Subject: [FieldTrip] Connectivity analysis In-Reply-To: References: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> Message-ID: <9EC69CEB-0315-4823-B241-71ED4649B9D5@robarts.ca> Thanks for your help! Best wishes, Kathryn On 2012-07-07, at 2:01 PM, jan-mathijs schoffelen wrote: Hi Kathryn, I believe that ft_connectivityanalysis is capable of dealing with frequency domain data that contain a time dimension. I assume here that you would like to compute coherence, rather than correlation. Last time I checked, ft_connectivityanalysis could not compute an ordinary correlation coefficient. Best wishes, Jan-Mathijs On Jul 6, 2012, at 6:59 PM, Kathryn Manning wrote: Dear FieldTrip list members, I am comparing the connectivity patterns in the brain measured using fMRI and electrophysiological recordings. I am trying to correlate the LFP signals as a function of time, using a sliding window analysis. I'm able to generate plots using ft_connectivityplot but this is as a function of frequency. From what I can tell the 'mtmconvol' method generates data with a time aspect in it's dimord, but are there any functions available in fieldtrip in order to calculate the correlation as a function of time? Any help would be greatly appreciated, thank you so much. Kathryn _______________________________________________ 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 stephen.whitmarsh at gmail.com Mon Jul 9 15:45:03 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Mon, 9 Jul 2012 15:45:03 +0200 Subject: [FieldTrip] plot functions and illustrator: set(gcf, 'interpreter', 'zbuffer') In-Reply-To: <4FFADA37.5070004@gmail.com> References: <4FFADA37.5070004@gmail.com> Message-ID: Hi Vitoria, Not really answering your questions, but from my experience I wouldn't export vector graphics of source data - just too many vectors. Instead why not export to high resolution (e.g. '-r600') png instead? I know my computer can certainly deal with those with less memory problems, I don't need to do anything vector-like on those images that I can't do on a bitmap. Cheers! Stephen p.s. same goes for fine-grained TFR's On 9 July 2012 15:18, Vitória Magalhães Piai wrote: > Hi, > > On the FT page, Roemer said that using set(gcf,'interpreter','**zbuffer') > may resolve problems when exporting from matlab as .eps and opening in > Illustrator. > > That works fine for sensor-level data, for example TFRs with > ft_singleplotTFR. But it doesn't work when, for example, using > ft_sourceplot (I've akes around and I don't seem to be the only one having > this problem). But ok, so far so good, I can get around it. > > But now I have an analysis I ran with LCMV for which I wanted to plot the > results. Interestingly, if I use ft_singleplotTFR in this case, I cannot > fix the bug with set(gcf,'interpreter','**zbuffer'). It seems to behave > like when using ft_sourceplot, instead of behaving as ft_singleplot when > plotting sensor-level data. > > Has anyone dealt with this bug before? I mean, not being able to fix it > with set(gcf,'interpreter','**zbuffer')? > > Thanx a lot, Vitoria > > > -- > ** Please consider the environment - do you really need to print? ** > > ______________________________**_________________ > 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 styll at med.ovgu.de Mon Jul 9 15:51:41 2012 From: styll at med.ovgu.de (styll at med.ovgu.de) Date: Mon, 9 Jul 2012 15:51:41 +0200 Subject: [FieldTrip] Problems with ft_app​ endata - merging dat​ asets​ Message-ID: <2854bfbc1930cfbba485e0aeb7488e16.squirrel@neuro2.med.uni-magdeburg.de> Hello, I probably have a problem with the use of ft_appendata. I want to merge 4 MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, etc.) of the same subject after I defined my trials of interest and preprocessed the 4 datasets individually. If I use ft_databrowser for a look into every single dataset, all trials (10 in each run/dataset) seems to be OK with the correct sequence: defined prestim time range, trigger and poststim time range. If I check the merged dataset I can go through all of the 40 trials, but there is no sequence like: prestim time range, trigger and poststim-time. Here is my pipeline for the first steps: %%%% run1 cfg.dataset=' \train01_64\run1\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run1'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_1 = ft_preprocessing(cfg) %%%% run2 cfg.dataset=' \train01_64\run2\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run2'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_2 = ft_preprocessing(cfg) the same for run3 and run4 %%%% merging the data cfg=[]; merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, prepro_run_4) Do I miss something or is there in error in my pipeline or in my strategy Best regards Sascha From styll at med.ovgu.de Mon Jul 9 15:56:52 2012 From: styll at med.ovgu.de (styll at med.ovgu.de) Date: Mon, 9 Jul 2012 15:56:52 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> Message-ID: <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> Hello, I probably have a problem with the use of ft_appendata. I want to merge 4 MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, etc.) of the same subject after I defined my trials of interest and preprocessed the 4 datasets individually. If I use ft_databrowser for a look into every single dataset, all trials (10 in each run/dataset) seems to be OK with the correct sequence: defined prestim time range, trigger and poststim time range. If I check the merged dataset I can go through all of the 40 trials, but there is no sequence like: prestim time range, trigger and poststim-time. Here is my pipeline for the first steps: %%%% run1 cfg.dataset=' \train01_64\run1\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run1'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_1 = ft_preprocessing(cfg) %%%% run2 cfg.dataset=' \train01_64\run2\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run2'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_2 = ft_preprocessing(cfg) the same for run3 and run4 %%%% merging the data cfg=[]; merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, prepro_run_4) Do I miss something or is there in error in my pipeline or in my strategy Best regards Sascha From dporada at uos.de Mon Jul 9 18:29:37 2012 From: dporada at uos.de (Porada Danja) Date: Mon, 9 Jul 2012 18:29:37 +0200 Subject: [FieldTrip] explained variance by ICA components Message-ID: <113D5DB2-88D7-4632-9F41-3DA2F409CF4B@uos.de> Hi, I computed an ICA on my MEG data. When I plot the components with the databrowser they are sorted according to variance in the data they accounted for. Or am I wrong? Where are those values saved? I want to know for each component how much variance it explains. Best, Danja From marco.rotonda at gmail.com Mon Jul 9 20:15:34 2012 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Mon, 9 Jul 2012 20:15:34 +0200 Subject: [FieldTrip] LARS and LASSO for connectivity Message-ID: Dear FieldTrip experts, I wasn't so happy to choose some ROIs with a priori knowledge in a GC analysis. So I searched a bit and I've found this wonderful solution which take care of all the voxels: http://www.ncbi.nlm.nih.gov/pubmed/21439388 Full-brain auto-regressive modeling (FARM) using fMRI Since there is already ft_mvaranalysis and ft_connectivityanalysis do you think that is possible to integrate the FARM approach into those functions? Regards, Marco From marco.rotonda at gmail.com Mon Jul 9 21:25:34 2012 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Mon, 9 Jul 2012 21:25:34 +0200 Subject: [FieldTrip] LARS and LASSO for connectivity Message-ID: Dear FieldTrip experts, I wasn't so happy to choose only some ROIs in a GC analysis. So I searched a bit and I've found this wonderful solution which take care of all the voxels: http://www.ncbi.nlm.nih.gov/pubmed/21439388 Full-brain auto-regressive modeling (FARM) using fMRI Since there are already ft_mvaranalysis and ft_connectivityanalysis, do you think that is possible to integrate the FARM approach into those functions? Regards, Marco From ith at deakin.edu.au Tue Jul 10 05:42:55 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Tue, 10 Jul 2012 03:42:55 +0000 Subject: [FieldTrip] plotting dipoles on an anatomical mri In-Reply-To: References: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> Message-ID: <5A1787011651BC42A4D41856DBC2E0603E047A96@mbox-f-3.du.deakin.edu.au> Dear Robert, Thank you very much for the very quick reply and the explaining. I am a bit struggling in the exact usage of ft_slice_plot function. I was trying to dig up on an example usage but was unable to find any. What does exactly in the use ft_plot_slice(dat, ...) , dat argument stands for? Can you please explain me on how to plot a 2D slice using the function? Thank you very much again. Regards Imali From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Robert Oostenveld Sent: Monday, 9 July 2012 6:02 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] plotting dipoles on an anatomical mri Dear Imali The ft_sourceplot function was not designed to plot 3D data in combination with dipoles. If you use method=ortho, you can get the 3 intersections in the 3D volume at the location of the dipole. For the best control over the details of the plot, which you need for your specific application of combining dipoles and volumetric data, I suggest that you look at the ft_plot_slice function. If you do three ft_plot_slice calls for the three orientations (x,y,z) at the location of the dipole and combine that with ft_plot_dipole, you will probably visualize the 3D relation between the two types of data the clearest. Note that ft_plot_slice plots any slice in 3D, so you should use the 3D rotate option of the MATLAB figure. best regards, Robert On 9 Jul 2012, at 9:26, IMALI THANUJA HETTIARACHCHI wrote: Dear fieldTrip users, I am doing a dipole fit with the ft_dipolefitting function and I can plot and visualize the results with ft_plot_dipole, further I also want to compare the results with a beamformer results so, I tried plotting the ft_dipolefitting results with ft_sourceplot. I cannot yet very well understand how ft_sourceplot works, I understand that the dipole should be assigned with some value but cannot figure out how to do this. Can someone please give me some help in doing this? Following is the code I am using, where should I modify? cfg = []; cfg.location = dip_fitted.dip.pos; cfg.method='ortho'; ft_sourceplot(cfg,mri) where mri is the standard_mri.mat . I work in the MNI coordinates and my locations are in mm's. Thank you very much in advance. Kind regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr _______________________________________________ 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 biomag.network.practical at gmail.com Tue Jul 10 09:21:37 2012 From: biomag.network.practical at gmail.com (Biomag Networks Satellite 25 Aug 2012) Date: Tue, 10 Jul 2012 09:21:37 +0200 Subject: [FieldTrip] Biomag Satellite Announcement: Open for Registration In-Reply-To: References: Message-ID: Dear Biomag community, A final reminder that you can still sign up for this Biomag Satellite Workshop on Practical Considerations for Network Analysis, until the end of this week (July 13 final deadline)! Please see link and details below. Best regards, Ole Jensen, Sarang Dalal, and Johanna Zumer On Mon, Apr 2, 2012 at 4:44 PM, Biomag Networks Satellite 25 Aug 2012 < biomag.network.practical at gmail.com> wrote: > 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 ith at deakin.edu.au Tue Jul 10 10:05:51 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Tue, 10 Jul 2012 08:05:51 +0000 Subject: [FieldTrip] Beamformer results for simulated data Message-ID: <5A1787011651BC42A4D41856DBC2E0603E047B22@mbox-f-3.du.deakin.edu.au> Dear fieldTrip Users, I am trying to run a dipole fit with the nonlinear grid search and a beamformer scan on a simulated data set, to compare the results. My simulated dipole is at the MNI coordinates [32.8 -85.8 28]. It is shown in red in DIP_1.jpg. The ft_dipolefitting results for the simulated dipole is in green in DIP_1.jpg. When I do the lcmv beamformer scan on the same simulated data and plot them I get results as in POW_1.jpg for avg.pow parameter and NAI_1.jpg for avg.nai parameter. Following is the code I use for the above purpose; cfg = []; cfg.vol = curry_vol; cfg.elec = sens; cfg.grid=template_grid; cfg.method = 'lcmv'; cfg.lambda='5%'; cfg.projectnoise='yes'; source = ft_sourceanalysis(cfg, timelock); load standard_mri.mat mri = ft_volumereslice([], mri); %% Figure POW_1.jpg % Aligning the measure of power increase with the structural MRI of subject cfg=[]; cfg.downsample=2; cfg.parameter='avg.pow'; source_int=ft_sourceinterpolate(cfg,source,mri); % Plot the interpolated data cfg=[]; cfg.method='slice'; cfg.funparameter='avg.pow'; figure,ft_sourceplot(cfg,source_int) %% Figure NAI_1.jpg % compute the neural activity index, i.e. projected power divided by % projected noise sourceNAI=source; sourceNAI.avg.nai=source.avg.pow./source.avg.noise; %neural activity index calculation cfg=[]; cfg.downsample=2; cfg.parameter='avg.nai'; sourceNAI_int=ft_sourceinterpolate(cfg,sourceNAI,mri); cfg = []; cfg.method = 'slice'; cfg.funparameter = 'avg.nai'; cfg.maskparameter=cfg.funparameter; figure ,ft_sourceplot(cfg, sourceNAI_int); Can you please direct me to what I am doing wrong or missing in my code to get sensible beamformer scan results. When I read the source_int.avg.pow and sourceNAI_int.avg.nai most of the values are NaN's. Many amny thanks in advance. Regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr [Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 29155 bytes Desc: image001.jpg URL: From jm.horschig at donders.ru.nl Tue Jul 10 12:20:35 2012 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 10 Jul 2012 12:20:35 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> Message-ID: <4FFC01F3.8010103@donders.ru.nl> Dear Sascha, What you do is perfectly fine, but what you want is not possible in FieldTrip (yet?). FieldTrip is designed such that triggers (and all other events) are stored with respect to sample number from the beginning of the recording, i.e. datafile on disk. However, when you merge datasets, FieldTrip cannot infer to what dataset a specific sample number belongs - in your case it could be coming from 4 different datasets - and thus dismisses this information completely. So, what you would need to as a workaround is to save the events with respect to your trials of interest (and dataset), and after merging, create a fake sampleinfo and event structure. Then, you would need to create events with samples respective to the fake sampleinfo. This is a somewhat tedious work, and only a hack to get what you want, but it's the only way so far :) But be aware that this work might result in a lot of nasty errors if you are not careful enough. If you do not know what I mean, feel free to send me a mail and I can try my best to explain what I mean with a short example script. Best, Jörn On 7/9/2012 3:56 PM, styll at med.ovgu.de wrote: > Hello, > > I probably have a problem with the use of ft_appendata. I want to merge 4 > MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, > etc.) of the same subject after I defined my trials of interest and > preprocessed the 4 datasets individually. If I use ft_databrowser for a > look into every single dataset, all trials (10 in each run/dataset) seems > to be OK with the correct sequence: defined prestim time range, trigger > and poststim time range. If I check the merged dataset I can go through > all of the 40 trials, but there is no sequence like: prestim time range, > trigger and poststim-time. Here is my pipeline for the first steps: > > %%%% run1 > cfg.dataset='…\train01_64\run1\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run1'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_1 = ft_preprocessing(cfg) > > %%%% run2 > cfg.dataset='…\train01_64\run2\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run2'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_2 = ft_preprocessing(cfg) > > the same for run3 and run4 > > %%%% merging the data > > cfg=[]; > merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, > prepro_run_4) > > Do I miss something or is there in error in my pipeline or in my strategy… > > Best regards > > Sascha > > > _______________________________________________ > 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 jm.horschig at donders.ru.nl Tue Jul 10 12:49:48 2012 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 10 Jul 2012 12:49:48 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> Message-ID: <4FFC08CC.2050302@donders.ru.nl> Hi Sascha, I just got reminded (thx Yuka-san) that you could use a ctf command to combine CTF datasets (of course, only if you got data from a CTF system): newCombinedDs [options] This program takes two or more datasets that have exactly the same collection parameters and combines them to make one dataset. Best, Jörn On 7/9/2012 3:56 PM, styll at med.ovgu.de wrote: > Hello, > > I probably have a problem with the use of ft_appendata. I want to merge 4 > MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, > etc.) of the same subject after I defined my trials of interest and > preprocessed the 4 datasets individually. If I use ft_databrowser for a > look into every single dataset, all trials (10 in each run/dataset) seems > to be OK with the correct sequence: defined prestim time range, trigger > and poststim time range. If I check the merged dataset I can go through > all of the 40 trials, but there is no sequence like: prestim time range, > trigger and poststim-time. Here is my pipeline for the first steps: > > %%%% run1 > cfg.dataset='…\train01_64\run1\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run1'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_1 = ft_preprocessing(cfg) > > %%%% run2 > cfg.dataset='…\train01_64\run2\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run2'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_2 = ft_preprocessing(cfg) > > the same for run3 and run4 > > %%%% merging the data > > cfg=[]; > merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, > prepro_run_4) > > Do I miss something or is there in error in my pipeline or in my strategy… > > Best regards > > Sascha > > > _______________________________________________ > 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 elilife at gmail.com Tue Jul 10 16:57:25 2012 From: elilife at gmail.com (Eliana Garcia) Date: Tue, 10 Jul 2012 16:57:25 +0200 Subject: [FieldTrip] problems with speed of processing Message-ID: Hello Dear Fieldtrip Community, I am having now problems with processing my data. I am analyzing a quite big data set with 400 trials that are composed by 10 sec (re-sampled at 150Hz). I am doing first a demean, then planar gradient transformation, time-frequency analysis using multitapers and then combine the planar gradient again. For the first subject always runs normally, but for the second one matlab gets really slow. I am taking care in deleting the variables that I create with big amount of data after I don't need them any more, so I am using just one big file that is being safe at the end (average time-frequency across trials) for each of the subjects. Every time matlab starts to analyze a new subject I am using clear all (with exceptions like directory and name of subject) but stills with every new subject it gets slower and slower. Do you have any advises to make the analysis faster? Sometimes is too slow and the computer normally crashes after 3 subjects. Thank you very much for the attention. Best, -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Tue Jul 10 18:01:30 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Tue, 10 Jul 2012 18:01:30 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: Dear Eliana, You could try creating a function that does all this preprocessing and then writes the output to file. If you then call this function in a (subject) loop you are sure that Matlab will free up the memory it used for that function. Perhaps it helps, Stephen On 10 July 2012 16:57, Eliana Garcia wrote: > Hello Dear Fieldtrip Community, > > I am having now problems with processing my data. I am analyzing a quite > big data set with 400 trials that are composed by 10 sec (re-sampled at > 150Hz). I am doing first a demean, then planar gradient transformation, > time-frequency analysis using multitapers and then combine the planar > gradient again. For the first subject always runs normally, but for the > second one matlab gets really slow. I am taking care in deleting the > variables that I create with big amount of data after I don't need them any > more, so I am using just one big file that is being safe at the end > (average time-frequency across trials) for each of the subjects. Every time > matlab starts to analyze a new subject I am using clear all (with > exceptions like directory and name of subject) but stills with every new > subject it gets slower and slower. > > Do you have any advises to make the analysis faster? Sometimes is too slow > and the computer normally crashes after 3 subjects. > > Thank you very much for the attention. > > Best, > > -- > Eliana García Cossio > Applied Neurotechnology Lab. > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > _______________________________________________ > 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 elilife at gmail.com Tue Jul 10 18:40:23 2012 From: elilife at gmail.com (Eliana Garcia) Date: Tue, 10 Jul 2012 18:40:23 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: Dear Stephen, Thanks for the suggestion. I have already one function that is doing all the preprocessing and saving as well. But this seams not to solve the issue. Thanks, Eliana On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh < stephen.whitmarsh at gmail.com> wrote: > Dear Eliana, > > You could try creating a function that does all this preprocessing and > then writes the output to file. > If you then call this function in a (subject) loop you are sure that > Matlab will free up the memory it used for that function. > > Perhaps it helps, > > Stephen > > On 10 July 2012 16:57, Eliana Garcia wrote: > >> Hello Dear Fieldtrip Community, >> >> I am having now problems with processing my data. I am analyzing a quite >> big data set with 400 trials that are composed by 10 sec (re-sampled at >> 150Hz). I am doing first a demean, then planar gradient transformation, >> time-frequency analysis using multitapers and then combine the planar >> gradient again. For the first subject always runs normally, but for the >> second one matlab gets really slow. I am taking care in deleting the >> variables that I create with big amount of data after I don't need them any >> more, so I am using just one big file that is being safe at the end >> (average time-frequency across trials) for each of the subjects. Every time >> matlab starts to analyze a new subject I am using clear all (with >> exceptions like directory and name of subject) but stills with every new >> subject it gets slower and slower. >> >> Do you have any advises to make the analysis faster? Sometimes is too >> slow and the computer normally crashes after 3 subjects. >> >> Thank you very much for the attention. >> >> Best, >> >> -- >> Eliana García Cossio >> Applied Neurotechnology Lab. >> Graduate School of Neural and Behavioural Science - Max Planck Research >> School >> Institute of Medical Psychology and Behavioural Neurobiology >> Universität Tübingen >> (+0049) 01 577-8587604 >> Otfried-Müller-Str. 47, 72076 >> Tübingen- Germany >> >> >> _______________________________________________ >> 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 > -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdeiss at ucsd.edu Tue Jul 10 20:49:49 2012 From: sdeiss at ucsd.edu (Steve Deiss) Date: Tue, 10 Jul 2012 11:49:49 -0700 Subject: [FieldTrip] read_biosig_header.m Message-ID: <4FFC794D.40508@ucsd.edu> The fieldtrip version we have calls function 'read_biosig_header' which calls 'sopen' with the following sequence. biosig = sopen(filename,'r'); For some reason it loses the digital triggers on channel 1 in our data after issuing the following warning: "Reading data file header... WARNING SOPEN(EDF): Physical Max/Min values of EDF data are not necessarily defining the dynamic range. Hence, OVERFLOWDETECTION might not work correctly. See also EEG2HIST and read http://dx.doi.org/10.1016/S1388-2457(99)00172-8 (A. Schlgl et al. Quality Control ... Clin. Neurophysiol. 1999, Dec; 110(12): 2165 - 2170). A copy is available here, too: http://www.dpmi.tugraz.at/schloegl/publications/neurophys1999_2165.pdf " If we let EEGLAB read the data, its function 'pop_biosig' calls 'sopen' with biosig = sopen(filename,'r',0,'OVERFLOWDETECTION:OFF'); The data read in here includes the triggers so that we can go on to epoch and process the data. We are not yet ready to upgrade to the very latest fieldtrip. So I would like to know if there is an easy way to determine if the latest version of fieldtrip changed anything in the way sopen is called from read_biosig_header? If it matches what EEGLAB does here, we can match that as a temporary fix. I'll try to download and unpack it to see, but if this is a known problem, fixed or not, I'd appreciate any tips. Thanks Steve From rn77 at sussex.ac.uk Wed Jul 11 05:25:36 2012 From: rn77 at sussex.ac.uk (Roshan Nair) Date: Wed, 11 Jul 2012 04:25:36 +0100 Subject: [FieldTrip] Importing '.mat' data in to fieldtrip Message-ID: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> Hi, I have MEG/EEG data in '.mat' format(Biomag 2012 data analysis dataset). The data is already epoched. It was straightforward to convert it in to the required fieldtrip structure - {label, fsample, trial, time} and run ft_databrowser on it. No problems so far. However, I feel I might be going wrong with the following:- 1. The trials include data for STI(stimulus) channels(I believe its an Elekta Neuromag Vectorview 306 system)? Is there a 'fieldtrip' way to represent this. Is this what 'data.trialinfo' is for? If so, how should I populate the trialinfo field. 2. The dataset comes with a file called 'design' with one entry(an integer) per trial. This is the category of the stimulus(living/non-living)presented to the subject for each trial. This is the output my classifier will be trained on. I'm assuming fieldtrip has some standard way of including this. I noticed, the multivariate analysis mentions a parameter called 'design'. Sorry, if thats confusing, but, I'm new to fieldtrip and MEG data. Thanks! Roshan From styll at med.ovgu.de Wed Jul 11 09:42:25 2012 From: styll at med.ovgu.de (styll at med.ovgu.de) Date: Wed, 11 Jul 2012 09:42:25 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <4FFC01F3.8010103@donders.ru.nl> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> <4FFC01F3.8010103@donders.ru.nl> Message-ID: <7436cf587bad96dc9ce7f72f058391fc.squirrel@neuro2.med.uni-magdeburg.de> Hi Jörn, thank you for useful information. I will try to set up the workaround that you mentioned in your mail. In the case of problems I contact you by mail :0) Best regards Sascha > Dear Sascha, > > What you do is perfectly fine, but what you want is not possible in > FieldTrip (yet?). FieldTrip is designed such that triggers (and all > other events) are stored with respect to sample number from the > beginning of the recording, i.e. datafile on disk. However, when you > merge datasets, FieldTrip cannot infer to what dataset a specific sample > number belongs - in your case it could be coming from 4 different > datasets - and thus dismisses this information completely. > > So, what you would need to as a workaround is to save the events with > respect to your trials of interest (and dataset), and after merging, > create a fake sampleinfo and event structure. Then, you would need to > create events with samples respective to the fake sampleinfo. This is a > somewhat tedious work, and only a hack to get what you want, but it's > the only way so far :) But be aware that this work might result in a lot > of nasty errors if you are not careful enough. > > If you do not know what I mean, feel free to send me a mail and I can > try my best to explain what I mean with a short example script. > > Best, > Jörn > > On 7/9/2012 3:56 PM, styll at med.ovgu.de wrote: >> Hello, >> >> I probably have a problem with the use of ft_appendata. I want to merge >> 4 >> MEG datasets (i.e. 4 runs, all the same number of channels, sampling >> rate, >> etc.) of the same subject after I defined my trials of interest and >> preprocessed the 4 datasets individually. If I use ft_databrowser for a >> look into every single dataset, all trials (10 in each run/dataset) >> seems >> to be OK with the correct sequence: defined prestim time range, trigger >> and poststim time range. If I check the merged dataset I can go through >> all of the 40 trials, but there is no sequence like: prestim time range, >> trigger and poststim-time. Here is my pipeline for the first steps: >> >> %%%% run1 >> cfg.dataset=' \train01_64\run1\c,rfDC'; >> cfg.trialdef.prestim=1; %%% in sec >> cfg.trialdef.poststim=5; %%% in sec >> cfg.trialfun = 'traildef_train01_all_pics_run1'; >> data_run1 = ft_definetrial(cfg) >> >> cfg.channel = {'MEG'}; >> cfg.dftfilter='yes'; >> prepro_run_1 = ft_preprocessing(cfg) >> >> %%%% run2 >> cfg.dataset=' \train01_64\run2\c,rfDC'; >> cfg.trialdef.prestim=1; %%% in sec >> cfg.trialdef.poststim=5; %%% in sec >> cfg.trialfun = 'traildef_train01_all_pics_run2'; >> data_run1 = ft_definetrial(cfg) >> >> cfg.channel = {'MEG'}; >> cfg.dftfilter='yes'; >> prepro_run_2 = ft_preprocessing(cfg) >> >> the same for run3 and run4 >> >> %%%% merging the data >> >> cfg=[]; >> merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, >> prepro_run_3, >> prepro_run_4) >> >> Do I miss something or is there in error in my pipeline or in my >> strategy >> >> Best regards >> >> Sascha >> >> >> _______________________________________________ >> 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 Wed Jul 11 10:20:58 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 11 Jul 2012 10:20:58 +0200 Subject: [FieldTrip] read_biosig_header.m In-Reply-To: <4FFC794D.40508@ucsd.edu> References: <4FFC794D.40508@ucsd.edu> Message-ID: <4FFD376A.8050206@donders.ru.nl> Dear Steve, Although I cannot help you directly and do not know about the specific error you got, you can find all code changes on http://code.google.com/p/fieldtrip/ For the biosig file you are referring to, please look here: http://code.google.com/p/fieldtrip/source/diff?path=/trunk/fileio/private/read_biosig_header.m&format=side&r=5429 (but as you can see, nothing changed there) Hope someone else can help out (Robert is on vacation right now, so maybe someone else can help) Best, Jörn On 7/10/2012 8:49 PM, Steve Deiss wrote: > The fieldtrip version we have calls function 'read_biosig_header' > which calls 'sopen' with the following sequence. > biosig = sopen(filename,'r'); > For some reason it loses the digital triggers on channel 1 in our data > after issuing the following warning: > > "Reading data file header... > WARNING SOPEN(EDF): Physical Max/Min values of EDF data are not > necessarily defining the dynamic range. > Hence, OVERFLOWDETECTION might not work correctly. See also > EEG2HIST and read > http://dx.doi.org/10.1016/S1388-2457(99)00172-8 (A. Schlgl et al. > Quality Control ... Clin. Neurophysiol. 1999, Dec; 110(12): 2165 - 2170). > A copy is available here, too: > http://www.dpmi.tugraz.at/schloegl/publications/neurophys1999_2165.pdf " > > If we let EEGLAB read the data, its function 'pop_biosig' calls > 'sopen' with > biosig = sopen(filename,'r',0,'OVERFLOWDETECTION:OFF'); > The data read in here includes the triggers so that we can go on to > epoch and process the data. > > We are not yet ready to upgrade to the very latest fieldtrip. So I > would like to know if there is an easy way to > determine if the latest version of fieldtrip changed anything in the > way sopen is called from read_biosig_header? > If it matches what EEGLAB does here, we can match that as a temporary > fix. > > I'll try to download and unpack it to see, but if this is a known > problem, fixed or not, I'd appreciate any tips. > > Thanks > Steve > _______________________________________________ > 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 jm.horschig at donders.ru.nl Wed Jul 11 10:30:58 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 11 Jul 2012 10:30:58 +0200 Subject: [FieldTrip] Importing '.mat' data in to fieldtrip In-Reply-To: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> References: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> Message-ID: <4FFD39C2.8030205@donders.ru.nl> Dear Roshan, 0) Welcome to FieldTrip ;) 1) FieldTrip usuaully reads in the stimulus channel and refers to the triggers as events. See also here: http://fieldtrip.fcdonders.nl/faq/what_is_the_relation_between_events_such_as_triggers_and_trials trialinfo can be used for that when you have segmented trials. Actually, there is no obligation how trialinfo should look like, you can put whatever information in that you want. I got stimulus trigger, stimulus offset sample, response sample, response trigger and some additional flags in there, so everything that facilitates in sorting trials according to some criteria. To find out what data you have, you can try to use ft_senstype 2) you might want to look at the Donders Machine Learning Toolbox, which is under external/dmlt. For the design, I assume it's an ordinary design matrix, so maybe you want to read the walkthrough and these tutorials: http://fieldtrip.fcdonders.nl/walkthrough?s[]=design#statistics http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock?s[]=design http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq?s[]=design Good luck with the data and have fun with FieldTrip. Best, Jörn On 7/11/2012 5:25 AM, Roshan Nair wrote: > Hi, > > I have MEG/EEG data in '.mat' format(Biomag 2012 data analysis dataset). > The data is already epoched. It was straightforward to convert it in to the > required fieldtrip structure - {label, fsample, trial, time} and run > ft_databrowser on it. No problems so far. > > However, I feel I might be going wrong with the following:- > 1. The trials include data for STI(stimulus) channels(I believe its an > Elekta Neuromag Vectorview 306 system)? Is there a 'fieldtrip' way to > represent this. Is this what 'data.trialinfo' is for? If so, how should I > populate the trialinfo field. > 2. The dataset comes with a file called 'design' with one entry(an > integer) per trial. This is the category of the > stimulus(living/non-living)presented to the subject for each trial. This is > the output my classifier will be trained on. I'm assuming fieldtrip has > some standard way of including this. I noticed, the multivariate analysis > mentions a parameter called 'design'. > > Sorry, if thats confusing, but, I'm new to fieldtrip and MEG data. > > Thanks! > > Roshan > _______________________________________________ > 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 Michael.Stephan at esi-frankfurt.de Wed Jul 11 11:40:17 2012 From: Michael.Stephan at esi-frankfurt.de (Michael Stephan) Date: Wed, 11 Jul 2012 11:40:17 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: <4FFD4A01.6090807@esi-frankfurt.de> Dear Eliana, if your data sets vary in size you should sort them according to size and then process them starting with the largest data set. -- Michael Stephan Ernst Strüngmann Institute for Neuroscience in Cooperation with Max Planck Society Deutschordenstraße 46 D-60528 Frankfurt am Main eMail: Michael.Stephan at esi-frankfurt.de > Hello Dear Fieldtrip Community, > > I am having now problems with processing my data. I am analyzing a quite > big data set with 400 trials that are composed by 10 sec (re-sampled at > 150Hz). I am doing first a demean, then planar gradient transformation, > time-frequency analysis using multitapers and then combine the planar > gradient again. For the first subject always runs normally, but for the > second one matlab gets really slow. I am taking care in deleting the > variables that I create with big amount of data after I don't need them > any more, so I am using just one big file that is being safe at the end > (average time-frequency across trials) for each of the subjects. Every > time matlab starts to analyze a new subject I am using clear all (with > exceptions like directory and name of subject) but stills with every new > subject it gets slower and slower. > > Do you have any advises to make the analysis faster? Sometimes is too > slow and the computer normally crashes after 3 subjects. > > Thank you very much for the attention. > > Best, > > -- > Eliana García Cossio > Applied Neurotechnology Lab. > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From irina.simanova at mpi.nl Wed Jul 11 17:20:41 2012 From: irina.simanova at mpi.nl (Irina Simanova) Date: Wed, 11 Jul 2012 17:20:41 +0200 Subject: [FieldTrip] freqstatistics ivar and uvar In-Reply-To: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> References: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> Message-ID: <30D34709-7D37-4A58-9072-CBF708A78052@mpi.nl> Dear all, I have a very basic question on freqstatistics. I want to compare the TFR's in 3 experimental conditions over 12 subjects. I run the freqstatistics with cfg.method = 'depsamplesF'. cfg.uvar = 1 cfg.ivar = 2 cfg.design = [1:12 1:12 1:12; ones(1,12) 2*ones(1,12) 3*ones(1,12)] I am confused with the the following lines that FT prints out: repeated measurement in variable 1 over 12 levels number of repeated measurements in each level is 3 3 3 3 3 3 3 3 3 3 3 3 I assume it is correct, since it's exactly the same output as I get with the tutorial within-subjects statistics example. But why is not it the other way around? There are 3 levels of the independent variable, and the number of samples in each level is 12? Thank you! Best, Irina Here is the code: cfg = []; cfg.latency = [0 1.5]; cfg.channel = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesF'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.tail = 1; cfg.clustertail = 1; cfg.alpha = 0.05; cfg.numrandomization = 100; cfg.neighbours = neighbours; cfg.parameter = 'powspctrm'; cfg.design = design; cfg.uvar = 1; cfg.ivar = 2; [stat] = ft_freqstatistics(cfg, TFRgrand_1, TFRgrand_2, TFRgrand_3); computing statistic over the frequency range [3.962 39.937] computing statistic over the time range [0.000 1.500] selection powspctrm along dimension 2 selection powspctrm along dimension 3 selection powspctrm along dimension 4 using "ft_statistics_montecarlo" for the statistical testing using "statfun_depsamplesF" for the single-sample statistics constructing randomized design total number of measurements = 36 total number of variables = 2 number of independent variables = 1 number of unit variables = 1 number of within-cell variables = 0 number of control variables = 0 using a permutation resampling approach repeated measurement in variable 1 over 12 levels number of repeated measurements in each level is 3 3 3 3 3 3 3 3 3 3 3 3 computing a parametric threshold for clustering computing statistic From Bill.Budd at newcastle.edu.au Thu Jul 12 01:33:38 2012 From: Bill.Budd at newcastle.edu.au (Bill Budd) Date: Thu, 12 Jul 2012 09:33:38 +1000 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Hi Eliana I see something similar when using SPM8 to process data. I’ve heard that this might be because SPM8 uses fieldtrip functions to import my continuous EEG files (Biosemi/bdf) and these functions may not release memory in matlab after closing. When looping my preprocessing functions over multiple subjects I have the exactly same problem in SPM that you see in fieldtrip. This may not be causing your problem (or mine) but wondered if the processing your refer to also involves importing raw MEG data? The PCs I’m using have plenty of RAM/disk space (Win7/matlab 2011b). Be great to find a solution to this as it slows done processing multi subject data significantly! Cheers -Bill From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eliana Garcia Sent: Wednesday, 11 July 2012 2:40 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] problems with speed of processing Dear Stephen, Thanks for the suggestion. I have already one function that is doing all the preprocessing and saving as well. But this seams not to solve the issue. Thanks, Eliana On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh wrote: Dear Eliana, You could try creating a function that does all this preprocessing and then writes the output to file. If you then call this function in a (subject) loop you are sure that Matlab will free up the memory it used for that function. Perhaps it helps, Stephen On 10 July 2012 16:57, Eliana Garcia wrote: Hello Dear Fieldtrip Community, I am having now problems with processing my data. I am analyzing a quite big data set with 400 trials that are composed by 10 sec (re-sampled at 150Hz). I am doing first a demean, then planar gradient transformation, time-frequency analysis using multitapers and then combine the planar gradient again. For the first subject always runs normally, but for the second one matlab gets really slow. I am taking care in deleting the variables that I create with big amount of data after I don't need them any more, so I am using just one big file that is being safe at the end (average time-frequency across trials) for each of the subjects. Every time matlab starts to analyze a new subject I am using clear all (with exceptions like directory and name of subject) but stills with every new subject it gets slower and slower. Do you have any advises to make the analysis faster? Sometimes is too slow and the computer normally crashes after 3 subjects. Thank you very much for the attention. Best, -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany _______________________________________________ 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 -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Jul 12 08:17:48 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 12 Jul 2012 08:17:48 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> References: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Message-ID: Hi, Please, note that "clear all" clears variables, but does not free up memory, especially for files read from disk. You can check the memory usage with the command "top" in Linux command line. You'll see that nothing changes even if you use "clear all". I agree with Stephen that you need to write smaller functions for each subjects. Something like: for i = 1:numel(subj) do_analysis(subj) end Where "do_analysis.m" is a function you wrote to do all the analysis. In this way, Matlab takes care of memory management by itself (it frees the memory once the function has been executed). A more elaborate solution is to use the "qsub" functions included in fieldtrip. Try this: addpath /path/to/fieldtrip/qsub fname = 'do_analysis'; subj = {1, 2, 3, 4, 5}; qsubcellfun(fname, x1, 'memreq', 1024^3, 'timreq', 60*60, 'backend', 'local'); This will start a new Matlab session (and use a new Matlab license) and it will close it when the function has been executed. There should be no memory leaks at all. See "help qsubcellfun" for more info. Remember to use 'backend' 'local' unless you have access to Oracle Grid Engine or Torque. Hope this helps. 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, Jul 12, 2012 at 1:33 AM, Bill Budd wrote: > Hi Eliana > > > > I see something similar when using SPM8 to process data. I’ve heard that > this might be because SPM8 uses fieldtrip functions to import my continuous > EEG files (Biosemi/bdf) and these functions may not release memory in matlab > after closing. When looping my preprocessing functions over multiple > subjects I have the exactly same problem in SPM that you see in fieldtrip. > This may not be causing your problem (or mine) but wondered if the > processing your refer to also involves importing raw MEG data? > > > > The PCs I’m using have plenty of RAM/disk space (Win7/matlab 2011b). > > > > Be great to find a solution to this as it slows done processing multi > subject data significantly! > > > > Cheers > > > > -Bill > > > > > > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eliana Garcia > Sent: Wednesday, 11 July 2012 2:40 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] problems with speed of processing > > > > Dear Stephen, > > > > Thanks for the suggestion. I have already one function that is doing all the > preprocessing and saving as well. But this seams not to solve the issue. > > > > Thanks, > > Eliana > > > > On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh > wrote: > > Dear Eliana, > > > > You could try creating a function that does all this preprocessing and then > writes the output to file. > > If you then call this function in a (subject) loop you are sure that Matlab > will free up the memory it used for that function. > > > > Perhaps it helps, > > > > Stephen > > > > On 10 July 2012 16:57, Eliana Garcia wrote: > > Hello Dear Fieldtrip Community, > > > > I am having now problems with processing my data. I am analyzing a quite big > data set with 400 trials that are composed by 10 sec (re-sampled at 150Hz). > I am doing first a demean, then planar gradient transformation, > time-frequency analysis using multitapers and then combine the planar > gradient again. For the first subject always runs normally, but for the > second one matlab gets really slow. I am taking care in deleting the > variables that I create with big amount of data after I don't need them any > more, so I am using just one big file that is being safe at the end (average > time-frequency across trials) for each of the subjects. Every time matlab > starts to analyze a new subject I am using clear all (with exceptions like > directory and name of subject) but stills with every new subject it gets > slower and slower. > > > > Do you have any advises to make the analysis faster? Sometimes is too slow > and the computer normally crashes after 3 subjects. > > > > Thank you very much for the attention. > > > > Best, > > > > -- > > Eliana García Cossio > Applied Neurotechnology Lab. > > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > > > > _______________________________________________ > 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 > > > > > > -- > > Eliana García Cossio > Applied Neurotechnology Lab. > > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From d.oudebos at gmail.com Thu Jul 12 11:15:07 2012 From: d.oudebos at gmail.com (Danny Plass-Oude Bos) Date: Thu, 12 Jul 2012 11:15:07 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? Message-ID: Hi Fieldtrippers, I am using the stand-alone fieldtripbuffer emotiv2ft, in combination with python for signal analysis. As far as I understand, you can only use one Emotiv EPOC with this implementation. I'd like to use multiple epocs at the some time, and preferably on the same computer. Does anybody know if this is possible somehow with emotiv2ft? Or does anybody has other experience / ideas on this problem? Kind regards, Danny. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elilife at gmail.com Thu Jul 12 12:00:02 2012 From: elilife at gmail.com (Eliana Garcia) Date: Thu, 12 Jul 2012 12:00:02 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Message-ID: Thank you all for this interesting advices. I am not using Fieldtrip in this case to read the raw data (for this I am using a function from BCI2000), just for signal processing. The qsubcellfun function is new for me. I will implement it, this will solve the problem of memory as Giovanni mentioned. Thanks again, Eliana On Thu, Jul 12, 2012 at 8:17 AM, Gio Piantoni wrote: > Hi, > > Please, note that "clear all" clears variables, but does not free up > memory, especially for files read from disk. You can check the memory > usage with the command "top" in Linux command line. You'll see that > nothing changes even if you use "clear all". > I agree with Stephen that you need to write smaller functions for each > subjects. Something like: > > for i = 1:numel(subj) > do_analysis(subj) > end > Where "do_analysis.m" is a function you wrote to do all the analysis. > In this way, Matlab takes care of memory management by itself (it > frees the memory once the function has been executed). > > A more elaborate solution is to use the "qsub" functions included in > fieldtrip. Try this: > addpath /path/to/fieldtrip/qsub > fname = 'do_analysis'; > subj = {1, 2, 3, 4, 5}; > qsubcellfun(fname, x1, 'memreq', 1024^3, 'timreq', 60*60, 'backend', > 'local'); > > This will start a new Matlab session (and use a new Matlab license) > and it will close it when the function has been executed. There should > be no memory leaks at all. See "help qsubcellfun" for more info. > Remember to use 'backend' 'local' unless you have access to Oracle > Grid Engine or Torque. > > Hope this helps. > 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, Jul 12, 2012 at 1:33 AM, Bill Budd > wrote: > > Hi Eliana > > > > > > > > I see something similar when using SPM8 to process data. I’ve heard that > > this might be because SPM8 uses fieldtrip functions to import my > continuous > > EEG files (Biosemi/bdf) and these functions may not release memory in > matlab > > after closing. When looping my preprocessing functions over multiple > > subjects I have the exactly same problem in SPM that you see in > fieldtrip. > > This may not be causing your problem (or mine) but wondered if the > > processing your refer to also involves importing raw MEG data? > > > > > > > > The PCs I’m using have plenty of RAM/disk space (Win7/matlab 2011b). > > > > > > > > Be great to find a solution to this as it slows done processing multi > > subject data significantly! > > > > > > > > Cheers > > > > > > > > -Bill > > > > > > > > > > > > From: fieldtrip-bounces at science.ru.nl > > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eliana Garcia > > Sent: Wednesday, 11 July 2012 2:40 AM > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] problems with speed of processing > > > > > > > > Dear Stephen, > > > > > > > > Thanks for the suggestion. I have already one function that is doing all > the > > preprocessing and saving as well. But this seams not to solve the issue. > > > > > > > > Thanks, > > > > Eliana > > > > > > > > On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh > > wrote: > > > > Dear Eliana, > > > > > > > > You could try creating a function that does all this preprocessing and > then > > writes the output to file. > > > > If you then call this function in a (subject) loop you are sure that > Matlab > > will free up the memory it used for that function. > > > > > > > > Perhaps it helps, > > > > > > > > Stephen > > > > > > > > On 10 July 2012 16:57, Eliana Garcia wrote: > > > > Hello Dear Fieldtrip Community, > > > > > > > > I am having now problems with processing my data. I am analyzing a quite > big > > data set with 400 trials that are composed by 10 sec (re-sampled at > 150Hz). > > I am doing first a demean, then planar gradient transformation, > > time-frequency analysis using multitapers and then combine the planar > > gradient again. For the first subject always runs normally, but for the > > second one matlab gets really slow. I am taking care in deleting the > > variables that I create with big amount of data after I don't need them > any > > more, so I am using just one big file that is being safe at the end > (average > > time-frequency across trials) for each of the subjects. Every time matlab > > starts to analyze a new subject I am using clear all (with exceptions > like > > directory and name of subject) but stills with every new subject it gets > > slower and slower. > > > > > > > > Do you have any advises to make the analysis faster? Sometimes is too > slow > > and the computer normally crashes after 3 subjects. > > > > > > > > Thank you very much for the attention. > > > > > > > > Best, > > > > > > > > -- > > > > Eliana García Cossio > > Applied Neurotechnology Lab. > > > > Graduate School of Neural and Behavioural Science - Max Planck Research > > School > > Institute of Medical Psychology and Behavioural Neurobiology > > Universität Tübingen > > > > (+0049) 01 577-8587604 > > Otfried-Müller-Str. 47, 72076 > > Tübingen- Germany > > > > > > > > > > > > _______________________________________________ > > 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 > > > > > > > > > > > > -- > > > > Eliana García Cossio > > Applied Neurotechnology Lab. > > > > Graduate School of Neural and Behavioural Science - Max Planck Research > > School > > Institute of Medical Psychology and Behavioural Neurobiology > > Universität Tübingen > > > > (+0049) 01 577-8587604 > > Otfried-Müller-Str. 47, 72076 > > Tübingen- Germany > > > > > > > > > > _______________________________________________ > > 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 > -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabian.tomaschek at uni-tuebingen.de Thu Jul 12 15:25:11 2012 From: fabian.tomaschek at uni-tuebingen.de (=?iso-8859-1?Q?Fabian_Tomaschek_-_Universit=E4t_T=FCbingen?=) Date: Thu, 12 Jul 2012 15:25:11 +0200 Subject: [FieldTrip] Problems with "ft_megplanar" and fourier spectra. In-Reply-To: References: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Message-ID: <001501cd6031$c3f352e0$4bd9f8a0$@tomaschek@uni-tuebingen.de> Hi All, I’m currently performing a timefrequency analyis and its statistics as described on "http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis?s[]=wavelet&s[ ]=analysis" and "http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq". I got to the point where I should do "ft_megplanar" with my data. However, an error saying "'freq data should contain Fourier spectra'" occurs. Looking into the function, I saw that it requires a field called "fourierspctrm". However, I do not know where to get that field. Nor does "http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq" say anything about fourier spectra. Do you know any help? Thanks a lot. Fabian Es grüßt aus Tübingen Fabian Tomaschek -------------------------------------------------- -------------------------------------------------- Mobil: 0178 6312772 Institute: 07071 29-87529 Dept of Neurology University of Tuebingen Hoppe-Seyler-Str. 3 D-72076 Tuebingen -------------------------------------------------- -------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdeiss at ucsd.edu Thu Jul 12 19:01:14 2012 From: sdeiss at ucsd.edu (Steve Deiss) Date: Thu, 12 Jul 2012 10:01:14 -0700 Subject: [FieldTrip] read_biosig_header.m In-Reply-To: <4FFD376A.8050206@donders.ru.nl> References: <4FFC794D.40508@ucsd.edu> <4FFD376A.8050206@donders.ru.nl> Message-ID: <4FFF02DA.1090802@ucsd.edu> Thanks for this note. Changing the call in read_biosig_header and read_biosig_data does make the problem go away, ie., the digital trigger channel is not zeroed. I do not know what other side effects there could be. So I am a little wary. Steve On 07/11/12 01:20, "Jörn M. Horschig" wrote: > Dear Steve, > > Although I cannot help you directly and do not know about the specific > error you got, you can find all code changes on > http://code.google.com/p/fieldtrip/ > > For the biosig file you are referring to, please look here: > http://code.google.com/p/fieldtrip/source/diff?path=/trunk/fileio/private/read_biosig_header.m&format=side&r=5429 > > (but as you can see, nothing changed there) > > Hope someone else can help out (Robert is on vacation right now, so > maybe someone else can help) > > Best, > Jörn > > On 7/10/2012 8:49 PM, Steve Deiss wrote: >> The fieldtrip version we have calls function 'read_biosig_header' >> which calls 'sopen' with the following sequence. >> biosig = sopen(filename,'r'); >> For some reason it loses the digital triggers on channel 1 in our >> data after issuing the following warning: >> >> "Reading data file header... >> WARNING SOPEN(EDF): Physical Max/Min values of EDF data are not >> necessarily defining the dynamic range. >> Hence, OVERFLOWDETECTION might not work correctly. See also >> EEG2HIST and read >> http://dx.doi.org/10.1016/S1388-2457(99)00172-8 (A. Schlgl et al. >> Quality Control ... Clin. Neurophysiol. 1999, Dec; 110(12): 2165 - >> 2170). >> A copy is available here, too: >> http://www.dpmi.tugraz.at/schloegl/publications/neurophys1999_2165.pdf " >> >> If we let EEGLAB read the data, its function 'pop_biosig' calls >> 'sopen' with >> biosig = sopen(filename,'r',0,'OVERFLOWDETECTION:OFF'); >> The data read in here includes the triggers so that we can go on to >> epoch and process the data. >> >> We are not yet ready to upgrade to the very latest fieldtrip. So I >> would like to know if there is an easy way to >> determine if the latest version of fieldtrip changed anything in the >> way sopen is called from read_biosig_header? >> If it matches what EEGLAB does here, we can match that as a temporary >> fix. >> >> I'll try to download and unpack it to see, but if this is a known >> problem, fixed or not, I'd appreciate any tips. >> >> Thanks >> Steve >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Steve Deiss, M.Sc. MMIL Lab (Dale and Halgren), UCSD, La Jolla, CA, USA Neuroimaging Research Associate 858-246-1194 From b.reuderink at donders.ru.nl Fri Jul 13 07:48:52 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 13 Jul 2012 07:48:52 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? In-Reply-To: References: Message-ID: Hi Danny, How do you want to use multiple Emotivs? Do you want to stream them to one buffer in a synchronized manner, do you want your application to access two buffers, one for each Emotiv? The latter is more feasible I think, and could be implemented using two computers. I think one of the main issues would be connecting a FieldTrip buffer to a specific Emotiv headset if multiple receiver dongles are present on one computer. Best, Boris On Thu, Jul 12, 2012 at 11:15 AM, Danny Plass-Oude Bos wrote: > Hi Fieldtrippers, > > I am using the stand-alone fieldtripbuffer emotiv2ft, in combination with > python for signal analysis. > As far as I understand, you can only use one Emotiv EPOC with this > implementation. I'd like to use multiple epocs at the some time, and > preferably on the same computer. > Does anybody know if this is possible somehow with emotiv2ft? Or does > anybody has other experience / ideas on this problem? > > Kind regards, > > Danny. > > _______________________________________________ > 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 d.oudebos at gmail.com Fri Jul 13 09:39:58 2012 From: d.oudebos at gmail.com (Danny Plass-Oude Bos) Date: Fri, 13 Jul 2012 09:39:58 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? In-Reply-To: References: Message-ID: Hi Boris :) For me it doesn't matter if it is one buffer or multiple, as long as I can get the data, and know from which head set it is -- I'm not sure if the current buffer supports that kind of thing? The reason why I'd prefer not to have one computer for each head set, is because I'd like to use 8 head sets... Emotiv's own software can deal with multiple head sets. You can start up multiple control panels, and select which device it should listen to. So far, I have not been able to discover how to do a similar thing from the Emotiv SDK, however -- I guess that is also what you people would need to know to get the buffer working for multiple sets? Best, Danny. 2012/7/13 Boris Reuderink > Hi Danny, > > How do you want to use multiple Emotivs? Do you want to stream them to > one buffer in a synchronized manner, do you want your application to > access two buffers, one for each Emotiv? The latter is more feasible I > think, and could be implemented using two computers. > > I think one of the main issues would be connecting a FieldTrip buffer > to a specific Emotiv headset if multiple receiver dongles are present > on one computer. > > Best, > > Boris > > On Thu, Jul 12, 2012 at 11:15 AM, Danny Plass-Oude Bos > wrote: > > Hi Fieldtrippers, > > > > I am using the stand-alone fieldtripbuffer emotiv2ft, in combination with > > python for signal analysis. > > As far as I understand, you can only use one Emotiv EPOC with this > > implementation. I'd like to use multiple epocs at the some time, and > > preferably on the same computer. > > Does anybody know if this is possible somehow with emotiv2ft? Or does > > anybody has other experience / ideas on this problem? > > > > Kind regards, > > > > Danny. > > > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Fri Jul 13 12:20:38 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 13 Jul 2012 12:20:38 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? In-Reply-To: References: Message-ID: Whoa, 8 :). Okay. I was thinking of starting an emotiv2ft per headset somehow, but with 8 headsets that gets tedious and error-prone. Let's discuss a more principled solution in person. On Fri, Jul 13, 2012 at 9:39 AM, Danny Plass-Oude Bos wrote: > Hi Boris :) > > For me it doesn't matter if it is one buffer or multiple, as long as I can > get the data, and know from which head set it is -- I'm not sure if the > current buffer supports that kind of thing? > The reason why I'd prefer not to have one computer for each head set, is > because I'd like to use 8 head sets... > > Emotiv's own software can deal with multiple head sets. You can start up > multiple control panels, and select which device it should listen to. > So far, I have not been able to discover how to do a similar thing from the > Emotiv SDK, however -- I guess that is also what you people would need to > know to get the buffer working for multiple sets? > > Best, > > Danny. > > > > 2012/7/13 Boris Reuderink >> >> Hi Danny, >> >> How do you want to use multiple Emotivs? Do you want to stream them to >> one buffer in a synchronized manner, do you want your application to >> access two buffers, one for each Emotiv? The latter is more feasible I >> think, and could be implemented using two computers. >> >> I think one of the main issues would be connecting a FieldTrip buffer >> to a specific Emotiv headset if multiple receiver dongles are present >> on one computer. >> >> Best, >> >> Boris >> >> On Thu, Jul 12, 2012 at 11:15 AM, Danny Plass-Oude Bos >> wrote: >> > Hi Fieldtrippers, >> > >> > I am using the stand-alone fieldtripbuffer emotiv2ft, in combination >> > with >> > python for signal analysis. >> > As far as I understand, you can only use one Emotiv EPOC with this >> > implementation. I'd like to use multiple epocs at the some time, and >> > preferably on the same computer. >> > Does anybody know if this is possible somehow with emotiv2ft? Or does >> > anybody has other experience / ideas on this problem? >> > >> > Kind regards, >> > >> > Danny. >> > >> > _______________________________________________ >> > 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 > > > > _______________________________________________ > 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 vitoria.piai at gmail.com Fri Jul 13 15:07:10 2012 From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=) Date: Fri, 13 Jul 2012 15:07:10 +0200 Subject: [FieldTrip] timelockgrandaverage on planar gradients Message-ID: <50001D7E.9010609@gmail.com> Dear all, Until some weeks ago, I used to proceed with the following steps to compute ERFs: % For each subject dat = ft_preprocessing(cfgp, input); dat = ft_timelockanalysis(cfgtl, dat); cfg.method = 'template'; cfg.neighbours = ft_prepare_neighbours(cfg, dat); cfg.planarmethod = 'sincos'; cond = ft_megplanar(cfg, dat) cplanar{suj} = ft_combineplanar([], cond); ga = ft_timelockgrandaverage([], cplanar{:}); I excluded some channels for some subjects. I re-ran this script and now I'm left only with the channels that are common to all subjects. (I'm using the DCCN internal fieldtrip version). But I'm pretty sure it used to work until some time ago such that in the GA, I had all the planar gradients still. I understand where it comes from, coz I get the warning that gradiometer info is being discarded coz it cannot be averaged. I've found a previous post that came close (but still not there yet): http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003471.html But I'm not being able to understand the explanation in the tutorial about how to proceed: "Before calculating the grand average the data of each subject can be realigned to standard sensor positions with *ft_megrealign *", but then it's unclear to me what cfg.template should be when using ft_megrealign. So I tried (suggested by JM from another previous post) /"Alternatively, you could construct a gradiometer structure which //contains a meaningful average of the coil positions and orientations." / I made a grad in which grad.chanpos was an average of my participants [302x3]. I tried cfg.template = grad; cfg.template = grad.chanpos; cfg.template = grad.chanori; but I'm probably doing something wrong coz it didn't work still. In all three cases, the error is in ft_megrealign at 174 "cell contents reference from a non-cell array object". So I guess my questions are: - what should the template be? What am I doing wrong? - do I need to make a grad structure myself with all the averages or will the template do, once I get it right? Thanx loads, Vitória -- ** Please consider the environment - do you really need to print? ** -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Mon Jul 16 12:20:57 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Mon, 16 Jul 2012 12:20:57 +0200 Subject: [FieldTrip] Improvements in FieldTrip's real-time processing Message-ID: Dear FieldTrippers, I would like to bring to you attention that we have reorganzed and improved FieldTrip's programs for acquisition and real-time signal processing. The most important change for users is the new directory structure. For each platform, we now have a directory containing all the executables for that platform*: - realtime/bin/win32 for Windows, - realtime/bin/glnxa64 for Linux (64 bit), - realtime/bin/maci64 for OS-X (64 bit). To get started with real-time processing, you can take a look at the examples (http://fieldtrip.fcdonders.nl/development/realtime#example_scripts) and the background information (http://fieldtrip.fcdonders.nl/development/realtime) on the FieldTrip wiki. Besides restructuring the file layout, we have fixed a number of bugs, most notable being: - bug #1525 duplicated samples with low-latency settings [1], - bug #933 freezing buffer server due to deadlock in threading [2], - bug #1246 incorrect reading of configuration scripts [3], - bug #1020 memory problem in event handling [4]. We strongly recommend to download a fresh release of FieldTrip (http://fieldtrip.fcdonders.nl/download), and use the files from this new version. Best regards, Boris Reuderink [1] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1525 [2] http://bugzilla.fcdonders.nl/show_bug.cgi?id=933 [3] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1246 [4] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1020 * Please note that for now, the neuromag files are still in realtime/src/acquisition/neuromag/bin . -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From profabdo at gmail.com Mon Jul 16 13:33:20 2012 From: profabdo at gmail.com (Prof. Abdalla Mohamed) Date: Mon, 16 Jul 2012 13:33:20 +0200 Subject: [FieldTrip] Improvements in FieldTrip's real-time processing In-Reply-To: References: Message-ID: Dear Sir, I am not able to download fresh release FieldTrip and I got error of invalid e-mail address. Please may help me. Thanking you,we remain. Prof. Abdalla Mohamed, Systems & Biomedical Engineering Dept., Cairo University, Egypt. On Mon, Jul 16, 2012 at 12:20 PM, Boris Reuderink wrote: > Dear FieldTrippers, > > I would like to bring to you attention that we have reorganzed and > improved FieldTrip's programs for acquisition and real-time signal > processing. > > The most important change for users is the new directory structure. > For each platform, we now have a directory containing all the > executables for that platform*: > - realtime/bin/win32 for Windows, > - realtime/bin/glnxa64 for Linux (64 bit), > - realtime/bin/maci64 for OS-X (64 bit). > > To get started with real-time processing, you can take a look at the > examples ( > http://fieldtrip.fcdonders.nl/development/realtime#example_scripts) > and the background information > (http://fieldtrip.fcdonders.nl/development/realtime) on the FieldTrip > wiki. > > Besides restructuring the file layout, we have fixed a number of bugs, > most notable being: > - bug #1525 duplicated samples with low-latency settings [1], > - bug #933 freezing buffer server due to deadlock in threading [2], > - bug #1246 incorrect reading of configuration scripts [3], > - bug #1020 memory problem in event handling [4]. > > We strongly recommend to download a fresh release of FieldTrip > (http://fieldtrip.fcdonders.nl/download), and use the files from this > new version. > > Best regards, > > Boris Reuderink > > [1] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1525 > [2] http://bugzilla.fcdonders.nl/show_bug.cgi?id=933 > [3] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1246 > [4] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1020 > > > * Please note that for now, the neuromag files are still in > realtime/src/acquisition/neuromag/bin . > > -- > twitter.com/#!/breuderink | > github.com/breuderink | borisreuderink.nl > _______________________________________________ > 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 b.reuderink at donders.ru.nl Mon Jul 16 15:01:15 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Mon, 16 Jul 2012 15:01:15 +0200 Subject: [FieldTrip] Improvements in FieldTrip's real-time processing In-Reply-To: References: Message-ID: Dear Prof. Abdalla Mohamed, I just tried to download FieldTrip, and supplied a fake email address from http://10minutemail.com/ (as suggested on http://fieldtrip.fcdonders.nl/download.php), and I can download FieldTrip just fine. Perhaps you could try with a fake email adress as well? Best regards, Boris Reuderink On Mon, Jul 16, 2012 at 1:33 PM, Prof. Abdalla Mohamed wrote: > Dear Sir, > I am not able to download fresh release FieldTrip and I got error of invalid > e-mail address. > Please may help me. > Thanking you,we remain. > Prof. Abdalla Mohamed, > Systems & Biomedical Engineering Dept., > Cairo University, Egypt. > > On Mon, Jul 16, 2012 at 12:20 PM, Boris Reuderink > wrote: >> >> Dear FieldTrippers, >> >> I would like to bring to you attention that we have reorganzed and >> improved FieldTrip's programs for acquisition and real-time signal >> processing. >> >> The most important change for users is the new directory structure. >> For each platform, we now have a directory containing all the >> executables for that platform*: >> - realtime/bin/win32 for Windows, >> - realtime/bin/glnxa64 for Linux (64 bit), >> - realtime/bin/maci64 for OS-X (64 bit). >> >> To get started with real-time processing, you can take a look at the >> examples >> (http://fieldtrip.fcdonders.nl/development/realtime#example_scripts) >> and the background information >> (http://fieldtrip.fcdonders.nl/development/realtime) on the FieldTrip >> wiki. >> >> Besides restructuring the file layout, we have fixed a number of bugs, >> most notable being: >> - bug #1525 duplicated samples with low-latency settings [1], >> - bug #933 freezing buffer server due to deadlock in threading [2], >> - bug #1246 incorrect reading of configuration scripts [3], >> - bug #1020 memory problem in event handling [4]. >> >> We strongly recommend to download a fresh release of FieldTrip >> (http://fieldtrip.fcdonders.nl/download), and use the files from this >> new version. >> >> Best regards, >> >> Boris Reuderink >> >> [1] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1525 >> [2] http://bugzilla.fcdonders.nl/show_bug.cgi?id=933 >> [3] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1246 >> [4] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1020 >> >> >> * Please note that for now, the neuromag files are still in >> realtime/src/acquisition/neuromag/bin . >> >> -- >> twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl >> >> _______________________________________________ >> 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 -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From m.vandenieuwenhuijzen at fcdonders.ru.nl Mon Jul 16 19:03:57 2012 From: m.vandenieuwenhuijzen at fcdonders.ru.nl (Marieke van de Nieuwenhuijzen) Date: Mon, 16 Jul 2012 19:03:57 +0200 (CEST) Subject: [FieldTrip] graphical problem with ft_sourceplot In-Reply-To: <668686231.1061677.1342456205553.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <805894218.1061785.1342458237893.JavaMail.root@draco.zimbra.ru.nl> Dear all, I am trying to use ft_sourceplot to plot modelvalues ranging from negative to positive. The blobs of interest are the ones close to both the positive and negative extremes, so I want to mask the values surrounding zero. However, I can't seem to mask these values properly. The code I'm using is: cfg = []; cfg.method = 'slice'; cfg.funparameter = 'model'; cfg.maskparameter = cfg.funparameter cfg.colorlim = 'maxabs'; cfg.opacitymap = 'vdown' cfg.opacitylim = 'maxabs'; figure; ft_sourceplot(cfg,sourceInterpolated); Although this code masks the values around zero, it only plots the underlying MRI scan partially. It looks like only those voxels of the MRI scan that contain gridpoints which are located inside the brain according to grid_singleshell.inside are plotted in the underlying MRI. In fact, this is exactly how I would expect the functional overlay to behave (which it does), but not the underlying MRI scan. If I set cfg.opavitymap to 'rampup' I don't get this graphical glitch, i.e. the anatomical MRI scan is plotted completely. However, as this doesn't mask the zero values, using this setting is not an option for me. I am aware of the artefacts that can occur when using opacity. However, setting the renderer to zbuffer doesn't solve the problem at all. In fact, if I do this the anatomical scan isn't plotted at all, and the zero values are not masked. If I specify cfg.method as 'ortho' instead of 'slice', the resulting plot looks good (the complete anatomical MRI is plotted and the values around zero are masked), apart from some green line pieces surrounding the brain. Setting the renderer to zbuffer here does seem to get rid of those lines, but ignores the masking of the values around zero. Does any of you perhaps know how to get rid of the glitch (if it is indeed a glitch) when using the aforementioned code? Best, Marieke From hgould at memphis.edu Tue Jul 17 14:36:26 2012 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 17 Jul 2012 12:36:26 +0000 Subject: [FieldTrip] mexw files Message-ID: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com> I have just found fieldtrip and have started to work on the tutorial. I am trying to read the data for subject 1 in the tutorial and recieve the following error: cfg1 = ft_definetrial(cfg1); Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20120715\private\warning_once at 75 In ft_defaults at 91 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > In ft_defaults at 99 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > In ft_defaults at 99 In ft_definetrial at 111 ??? Invalid MEX-file 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); I have checked and the .mexw32 file is there What am I doing wrong? Herb Gould -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Tue Jul 17 15:04:26 2012 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Tue, 17 Jul 2012 15:04:26 +0200 (CEST) Subject: [FieldTrip] mexw files In-Reply-To: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com> Message-ID: <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> Hi Herbert, It seems you have multiple versions of SPM on your path, which may confuse FieldTrip. Could you try inserting the commands below in the matlab command window, before inserting the tutorial code? Best regards, Arjen restoredefaultpath addpath C:\FieldTrip\fieldtrip-20120715 ft_defaults ----- Oorspronkelijk bericht ----- > Van: "Herbert J Gould (hgould)" > Aan: fieldtrip at science.ru.nl > Verzonden: Dinsdag 17 juli 2012 14:36:26 > Onderwerp: [FieldTrip] mexw files > I have just found fieldtrip and have started to work on the tutorial. > I am trying to read the data for subject 1 in the tutorial and recieve > the following error: >   > cfg1         = ft_definetrial(cfg1); > Warning: multiple versions of SPM on your path will confuse FieldTrip > > In fieldtrip-20120715\private\warning_once at 75 >   In ft_defaults at 91 >   In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > > In ft_defaults at 99 >   In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > > In ft_defaults at 99 >   In ft_definetrial at 111 > ??? Invalid MEX-file > 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified > procedure could not be found. > . > Error in ==> ft_checkconfig at 71 > renamed         = ft_getopt(varargin, 'renamed'); > Error in ==> ft_definetrial at 116 > cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); >   > I have checked and the .mexw32 file is there What am I doing wrong? >   > Herb Gould > _______________________________________________ > 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 hgould at memphis.edu Tue Jul 17 15:22:47 2012 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 17 Jul 2012 13:22:47 +0000 Subject: [FieldTrip] mexw files In-Reply-To: <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> References: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com>, <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com> Dear Arjen, Thank you that took care of the SPM issue but it still leaves the .mexw32 issue. However it now is looking for the file in a different location >> restoredefaultpath >> addpath c:\FieldTrip\fieldtrip-20120715 >> ft_defaults ??? Invalid MEX-file 'c:\FieldTrip\fieldtrip-20120715\utilities\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); Error in ==> tutorial1 at 8 cfg1 = ft_definetrial(cfg1); >> Herb Gould ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, July 17, 2012 8:04 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] mexw files Hi Herbert, It seems you have multiple versions of SPM on your path, which may confuse FieldTrip. Could you try inserting the commands below in the matlab command window, before inserting the tutorial code? Best regards, Arjen restoredefaultpath addpath C:\FieldTrip\fieldtrip-20120715 ft_defaults ________________________________ Van: "Herbert J Gould (hgould)" Aan: fieldtrip at science.ru.nl Verzonden: Dinsdag 17 juli 2012 14:36:26 Onderwerp: [FieldTrip] mexw files I have just found fieldtrip and have started to work on the tutorial. I am trying to read the data for subject 1 in the tutorial and recieve the following error: cfg1 = ft_definetrial(cfg1); Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20120715\private\warning_once at 75 In ft_defaults at 91 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > In ft_defaults at 99 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > In ft_defaults at 99 In ft_definetrial at 111 ??? Invalid MEX-file 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); I have checked and the .mexw32 file is there What am I doing wrong? Herb Gould _______________________________________________ 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 jm.horschig at donders.ru.nl Tue Jul 17 15:47:43 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 17 Jul 2012 15:47:43 +0200 Subject: [FieldTrip] mexw files In-Reply-To: <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com> References: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com>, <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com> Message-ID: <50056CFF.7080103@donders.ru.nl> Dear Herb, it seems like the mex-file you are using is corrupt. Either it is from a corrupt download (in which case you'd need to download fieldtrip once more) or there is, or there is some other incompatibility between your windows/matlab combination that we have not encountered. Could you try downloading FieldTrip again and see whether the error persists? If it does persist, you could go to the src/ directory and type 'mex ft_getopt.c' to re-mex the file (in Matlab). Then copy the mexw32 file from that folder to utilities/. This is not an optimal solution, because you will probably encounter similar issues with other mexw32 files. If that works for you, it would be nice if you sent me (or someone else from the dev team) the file so that we can check whether the file is indeed different. Either way, please let us know whether (and if so how) you can resolve the problem. Best, Jörn On 7/17/2012 3:22 PM, Herbert J Gould (hgould) wrote: > > Dear Arjen, > > Thank you that took care of the SPM issue but it still leaves the > .mexw32 issue. However it now is looking for the file in a different > location > > >> restoredefaultpath > >> addpath c:\FieldTrip\fieldtrip-20120715 > >> ft_defaults > ??? Invalid MEX-file > 'c:\FieldTrip\fieldtrip-20120715\utilities\ft_getopt.mexw32': The > specified procedure could not be found. > > . > > Error in ==> ft_checkconfig at 71 > renamed = ft_getopt(varargin, 'renamed'); > > Error in ==> ft_definetrial at 116 > cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); > > Error in ==> tutorial1 at 8 > cfg1 = ft_definetrial(cfg1); > > >> > > Herb Gould > ------------------------------------------------------------------------ > *From:* fieldtrip-bounces at science.ru.nl > [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. > [a.stolk at fcdonders.ru.nl] > *Sent:* Tuesday, July 17, 2012 8:04 AM > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] mexw files > > Hi Herbert, > > It seems you have multiple versions of SPM on your path, which may > confuse FieldTrip. Could you try inserting the commands below in the > matlab command window, before inserting the tutorial code? > > Best regards, > > Arjen > > restoredefaultpath > > addpath C:\FieldTrip\fieldtrip-20120715 > > ft_defaults > > ------------------------------------------------------------------------ > > *Van: *"Herbert J Gould (hgould)" > *Aan: *fieldtrip at science.ru.nl > *Verzonden: *Dinsdag 17 juli 2012 14:36:26 > *Onderwerp: *[FieldTrip] mexw files > > I have just found fieldtrip and have started to work on the > tutorial. I am trying to read the data for subject 1 in the > tutorial and recieve the following error: > > cfg1 = ft_definetrial(cfg1); > Warning: multiple versions of SPM on your path will confuse FieldTrip > > In fieldtrip-20120715\private\warning_once at 75 > In ft_defaults at 91 > In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > > In ft_defaults at 99 > In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > > In ft_defaults at 99 > In ft_definetrial at 111 > ??? Invalid MEX-file > 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The > specified procedure could not be found. > > . > > Error in ==> ft_checkconfig at 71 > renamed = ft_getopt(varargin, 'renamed'); > > Error in ==> ft_definetrial at 116 > cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); > > I have checked and the .mexw32 file is there What am I doing wrong? > > Herb Gould > > > _______________________________________________ > 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 sguillor at ucla.edu Tue Jul 17 20:18:24 2012 From: sguillor at ucla.edu (S Guillory) Date: Tue, 17 Jul 2012 14:18:24 -0400 Subject: [FieldTrip] errors with ft_definetrial Message-ID: Hello, I'm trying to timelock to a specific event in an epoch and I'm having some difficulty setting it up in matlab. When not specifying an event, i.e. using '?', it identifies two types of events 'trial' and 'trigger' as well as the values. The problem I'm having is that there are two different triggers per trial and I am interested in only one of them, however when I specify cfg.trialdef.eventtype = 'trigger' and the cfg.trialdef.eventvalue = 'triggername', I get an error that no trials were defined. Is there a way to isolate the specific trigger without having to code a trial function. Thank you in advance for your time. -Sylvia -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Tue Jul 17 21:39:06 2012 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Tue, 17 Jul 2012 21:39:06 +0200 (CEST) Subject: [FieldTrip] errors with ft_definetrial In-Reply-To: Message-ID: <1895003729.997389.1342553946159.JavaMail.root@sculptor.zimbra.ru.nl> Hi Sylvia, What values exactly do you get for the 'trial' and 'trigger' event types? If, for instance, you have the values 1 and 2 (e.g. for conditions 1 and 2 respectively) for the 'trigger' event type, you can specifically read condition 1 by using: cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 1;  and more generally cfg.trialdef.prestim = 1; % one second before trigger with value 1 cfg.trialdef.poststim = 2; % two seconds after trigger with value 1 Hope this solves your problem? Arjen ----- Oorspronkelijk bericht ----- > Van: "S Guillory" > Aan: fieldtrip at donders.ru.nl > Verzonden: Dinsdag 17 juli 2012 20:18:24 > Onderwerp: [FieldTrip] errors with ft_definetrial > Hello, >  I'm trying to timelock to a specific event in an epoch and I'm > having some difficulty setting it up in matlab. When not specifying an > event, i.e. using '?', it identifies two types of events 'trial' > and 'trigger' as well as the values. The problem I'm having is that > there are two different triggers per trial and I am interested in only > one of them, however when I specify cfg.trialdef.eventtype = 'trigger' > and the cfg.trialdef.eventvalue = 'triggername', I get an error that > no trials were defined. Is there a way to isolate the specific > trigger without having to code a trial function. Thank you in advance > for your time. >  -Sylvia > _______________________________________________ > 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 hgould at memphis.edu Tue Jul 17 22:39:03 2012 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 17 Jul 2012 20:39:03 +0000 Subject: [FieldTrip] mexw files In-Reply-To: <50056CFF.7080103@donders.ru.nl> References: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com>, <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com>, <50056CFF.7080103@donders.ru.nl> Message-ID: <5306C43FAB1DB14992CDDF2D7EDB981B13A824BB@CH1PRD0410MB356.namprd04.prod.outlook.com> Dear Jorn, I downloaded the 20120716 version of Fieldtrip and the same problem occurred. Next I did the mex of ft_getopt.c and transfered it to Utilities. Still no joy as the same problem occured again. I am working on an older laptop running xp with an old 7.1 version of Matlab. I will be back in my lab next week where I can try it out on better equipment and newer software. Herb ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of "Jörn M. Horschig" [jm.horschig at donders.ru.nl] Sent: Tuesday, July 17, 2012 8:47 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] mexw files Dear Herb, it seems like the mex-file you are using is corrupt. Either it is from a corrupt download (in which case you'd need to download fieldtrip once more) or there is, or there is some other incompatibility between your windows/matlab combination that we have not encountered. Could you try downloading FieldTrip again and see whether the error persists? If it does persist, you could go to the src/ directory and type 'mex ft_getopt.c' to re-mex the file (in Matlab). Then copy the mexw32 file from that folder to utilities/. This is not an optimal solution, because you will probably encounter similar issues with other mexw32 files. If that works for you, it would be nice if you sent me (or someone else from the dev team) the file so that we can check whether the file is indeed different. Either way, please let us know whether (and if so how) you can resolve the problem. Best, Jörn On 7/17/2012 3:22 PM, Herbert J Gould (hgould) wrote: Dear Arjen, Thank you that took care of the SPM issue but it still leaves the .mexw32 issue. However it now is looking for the file in a different location >> restoredefaultpath >> addpath c:\FieldTrip\fieldtrip-20120715 >> ft_defaults ??? Invalid MEX-file 'c:\FieldTrip\fieldtrip-20120715\utilities\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); Error in ==> tutorial1 at 8 cfg1 = ft_definetrial(cfg1); >> Herb Gould ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, July 17, 2012 8:04 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] mexw files Hi Herbert, It seems you have multiple versions of SPM on your path, which may confuse FieldTrip. Could you try inserting the commands below in the matlab command window, before inserting the tutorial code? Best regards, Arjen restoredefaultpath addpath C:\FieldTrip\fieldtrip-20120715 ft_defaults ________________________________ Van: "Herbert J Gould (hgould)" Aan: fieldtrip at science.ru.nl Verzonden: Dinsdag 17 juli 2012 14:36:26 Onderwerp: [FieldTrip] mexw files I have just found fieldtrip and have started to work on the tutorial. I am trying to read the data for subject 1 in the tutorial and recieve the following error: cfg1 = ft_definetrial(cfg1); Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20120715\private\warning_once at 75 In ft_defaults at 91 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > In ft_defaults at 99 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > In ft_defaults at 99 In ft_definetrial at 111 ??? Invalid MEX-file 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); I have checked and the .mexw32 file is there What am I doing wrong? Herb Gould _______________________________________________ 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 ith at deakin.edu.au Thu Jul 19 06:44:38 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Thu, 19 Jul 2012 04:44:38 +0000 Subject: [FieldTrip] Question regarding ft_connectivitysimulation Message-ID: <5A1787011651BC42A4D41856DBC2E0603E048720@mbox-f-3.du.deakin.edu.au> Dear fieldTrippers, I am trying to generate some simulated signals from a known connectivity structure with ft_connectivitysimulation, and secondly to assign these signals to known dipole locations when using in ft_dipolesimulation. Is there any way I can assign a frequency to the signals in ft_connectivityanalysis, so that I can assign different known frequency signals for dipoles? Any help is really appreciated. Thank you very much. Kind regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr [Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 29155 bytes Desc: image001.jpg URL: From e.maris at psych.ru.nl Fri Jul 20 00:30:26 2012 From: e.maris at psych.ru.nl (Eric Maris) Date: Fri, 20 Jul 2012 00:30:26 +0200 (CEST) Subject: [FieldTrip] PhD position "Mechanisms of top-down control in the accumulation of sensory evidence" Message-ID: <02d301cd65fe$17ff7a90$47fe6fb0$@maris@psych.ru.nl> Dear Discussion List subscribers, I would to post an advertisement for a PhD position at the Donders Institute for Brain, Cognition and Behavior. Mechanisms of top-down control in the accumulation of sensory evidence Many studies have shown neurophysiological correlates of top-down factors in perception (e.g., attention and expectation) which are already active prior to the sampling of sensory evidence. One of the puzzling observations in this line of investigation is the rather weak relation between these anticipatory neurophysiological signals (typically, modulations of oscillatory activity) and perception (most importantly, accuracy). The overall objective of this project is to identify additional neurophysiological processes that explain behavioral accuracy and its modulation by attention. The main working hypothesis that guides us in this search is that one should not only investigate anticipatory neural activity but also the neural activity during the accumulation of sensory evidence. The objectives of this research project will be addressed in experiments in which extracranial neural signals are recorded using Magnetoencephalography (MEG). Within the Donders Institute (DI), you will belong to the research group Neurophysiology of Active Perception (PI Eric Maris). As this is a collaborative project within the DI, you will also be affiliated to the research groups Prediction & Attention (PI Floris de Lange) and Neuronal Oscillations (PI Ole Jensen). A successful candidate has a Master' s degree in a field at the interface of behavior and neurobiology (Cognitive Neuroscience, Neurobiology, Cognitive Science) and excellent analytic and quantitative skills. Programming skills (e.g., Matlab) are required, and it is an advantage if you have experience in running EEG or MEG experiments. Please include with your application: - a curriculum vitae, including academic qualifications, grades, a list of publications (if applicable), and the names and contact details of two referees; - a letter explaining your motivation, your interest in the project, and your competence in the research field;" Employment start date: 2012-10-15 Contract length: 4 years Contact Information: Dr. Eric Maris E-mail: e.maris at donders.ru.nl Website: http://www.nphyscog.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From dporada at uos.de Fri Jul 20 07:48:31 2012 From: dporada at uos.de (Porada Danja) Date: Fri, 20 Jul 2012 07:48:31 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds Message-ID: <0D507729-5866-4635-845A-E5C45F210830@uos.de> Hi, I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). Here is the problem: For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? And I have another question: Do I have to calculate the planar gradient before computing the grand average? Best, Danja From jm.horschig at donders.ru.nl Fri Jul 20 11:59:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 20 Jul 2012 11:59:37 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds In-Reply-To: <0D507729-5866-4635-845A-E5C45F210830@uos.de> References: <0D507729-5866-4635-845A-E5C45F210830@uos.de> Message-ID: <50092C09.7080109@donders.ru.nl> Hi Danja, you can could either compute the average yourself: /data.avg = squeeze(nanmean(data.trial, 1)); data.dimord = 'chan_time';/ Note that the covariance might be invalid here, not sure what ft_regressconfound does here. or call /data = ft_checkdata(data, 'datatype', 'raw')/ which converts the timelocked data back to raw data format, and you can call /ft_timelockanalysis /again with /cfg.keeptrials = 'no'/ (the latter would be my favourite) Regarding the planar gradient, I'd say no. Keep in mind that the planar gradient computation results in all values > 0, thus e.g. noise might not cancel out as efficiently and a simple t-test against with the classical null hypothesis becomes invalid. I don't do ERP analysis though, so if someone can provide a good reason for doing the transformation nonetheless, I might be convinced otherwise ;) Best, Jörn On 7/20/2012 7:48 AM, Porada Danja wrote: > Hi, > > I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). > > Here is the problem: > For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? > > > And I have another question: Do I have to calculate the planar gradient before computing the grand average? > > > Best, > Danja > _______________________________________________ > 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 dporada at uos.de Fri Jul 20 12:28:01 2012 From: dporada at uos.de (Porada Danja) Date: Fri, 20 Jul 2012 12:28:01 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds In-Reply-To: <800_1342766933_q6K6mqFs001171_0D507729-5866-4635-845A-E5C45F210830@uos.de> References: <800_1342766933_q6K6mqFs001171_0D507729-5866-4635-845A-E5C45F210830@uos.de> Message-ID: I just found out that I only have to use the field avg as input for ft_grandaverage... But I'm still wondering whether it is necessary to calculate the planar gradient before computing the grand average. Best, Danja Am 20.07.2012 um 07:48 schrieb Porada Danja: > Hi, > > I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). > > Here is the problem: > For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? > > > And I have another question: Do I have to calculate the planar gradient before computing the grand average? > > > Best, > Danja > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From stephen.whitmarsh at gmail.com Fri Jul 20 13:13:47 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 20 Jul 2012 13:13:47 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds In-Reply-To: References: <800_1342766933_q6K6mqFs001171_0D507729-5866-4635-845A-E5C45F210830@uos.de> Message-ID: Dear Danja, As Jorn said calculating the planar on ERF data creates some additional 'issues', mainly because the signal, as well as the noise, will always be positive (because of the pythagoras' square operation), and the noise will therefore be additive - i.e. it won't 'average out'. However, with similar amount of trials and other such caretaking comparisons between conditions it is in principle possible. As I see it there are two main reasons for going to planar: 1) more interpretable locations (of maximum amplitude difference): It relieves one from the neccecity to visually process the dipole pattern (positive and negative poles) as showing two sides of a single dipole with the source probably in between. 2) since you lose the orientation of the dipole in the planar transformation - an ideal anterior-posterior will give the same pattern as a left-right dipole when the maximum slope between the two poles lie on the same location - this can help you to average over subjects that might have different orientations but are located above similar regions. In addition the dipole pattern is in effect spatially smoothed (depending on how many neighbours you use), which might help your average as well. Cheers, Stephen On 20 July 2012 12:28, Porada Danja wrote: > I just found out that I only have to use the field avg as input for ft_grandaverage... > > But I'm still wondering whether it is necessary to calculate the planar gradient before computing the grand average. > > Best, > Danja > > Am 20.07.2012 um 07:48 schrieb Porada Danja: > >> Hi, >> >> I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). >> >> Here is the problem: >> For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? >> >> >> And I have another question: Do I have to calculate the planar gradient before computing the grand average? >> >> >> Best, >> Danja >> _______________________________________________ >> 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 sanchomoro at gmail.com Fri Jul 20 17:21:22 2012 From: sanchomoro at gmail.com (Sancho Moro) Date: Fri, 20 Jul 2012 17:21:22 +0200 Subject: [FieldTrip] Post-doctoral position in Multisensory integration/EEG Message-ID: *Post-doctoral position in Multisensory integration/EEG* * * Applications are invited for a full-time post-doctoral research position in the MULTISENSORY RESEARCH GROUP , led by Salvador Soto-Faraco, at the Pompeu Fabra University (Barcelona). The position is covered by a European Research Council grant on Multisensory Integration and Attention. *The project* addresses the interplay between multisensory integration processes and attention mechanisms. This research spans several functions (speech, temporal and spatial processing, in vision, audition and touch, and body representation) and research approaches (psychophysics, neuroimaging, and brain stimulation with TMS). *We seek* a person with solid experience who leads a research line focused on brain oscillatory dynamics. Involvement in some organizational and management aspects is expected. The candidate must (1) *have solid demonstrable experience (i.e., publications) in the field of oscillatory analysis using EEG and/or MEG*, (2) strong background in cognitive neuroscience, neuroscience, and/or cognitive psychology, and (3) scientific motivation about multisensory integration, perception and attention. *We offer* onsite ERP/EEG, TMS, and psychophysical testing facilities, neuronavigation system, a wide range of visual auditory and somatosensory stimulation equipment, and the use of fMRI and MEG recording facilities externally. The position will be funded and renewable on yearly basis for up to three years. Starting date: Feb 2013 or before. Salary: up to 36,000Eur/Year *How to apply* Applications should include: - a C.V. including a list of publications - the names of two referees who would willing to write letters of recommendation - a short cover letter describing research interests Check out www.mrg.upf.edu for info on the group. For informal enquiries about the position and applications, please contact Salvador Soto-Faraco at applications.MRGLab at gmail.com. Applications will be accepted until the position is filled. Please, mention that you are applying to the POSTDOCTORAL position in the email subject -- Salvador Soto Faraco ICREA Research Professor Dept. de Tecnologies de la Informació i les Comunicacions Universitat Pompeu Fabra C. Tanger, 122-140, room 55.108 Postal address: Roc Boronat 138 08018 Barcelona Spain Phone: +34 93.542.25.34 <%2B34%2093.542.25.34> Fax: +34 93..542.25.17 E-Mail: salvador.soto at icrea.cat http://www.mrg.upf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From xbai3 at uthsc.edu Sat Jul 21 01:28:49 2012 From: xbai3 at uthsc.edu (Bai, XiaoXiao) Date: Fri, 20 Jul 2012 23:28:49 +0000 Subject: [FieldTrip] About co-register the individual sudbject MRI and sensor locations Message-ID: <5D2CC5653262C14188174E20065A4C4EC8D457@hscmbx6.uthsc.tennessee.edu> Dear Sir/Madam, I am a new fieldtrip user and want to apply the beamformer method in Fieldtrip for the MEG data from 4D/BTI system. Now I can get a individual subject MRI in analysis/spm format from CURRY software. This is my code for create volume head model for the beamformer, mri_nom = ft_read_mri(mrifile); cfg = []; [segmentedmri] = ft_volumesegment(cfg, mri_nom); cfg = []; cfg.method = 'singleshell'; vol = ft_prepare_headmodel(cfg, segmentedmri); The vol and sensor locations were displayed and attached with here. How can I co-register the vol with sensors based on headshpe file (hs_file) for computing lead field for next step? Thanks a lot. Best regards, Xiaoxiao [X] [X] [X] Division of Clinical Neurosciences, Department of Pediatrics University of Tennessee Health Science Center, College of Medicine & Neuroscience Institute, LeBonheur Children's Hospital 777 Washington Avenue, P335 Memphis, TN 38105, USA Phone: 901-287-4612 Fax: 901-287-5325 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sensor and volume.png Type: image/x-png Size: 21343 bytes Desc: sensor and volume.png URL: From victor.veliks at gmail.com Sun Jul 22 22:28:07 2012 From: victor.veliks at gmail.com (viktor veliks) Date: Sun, 22 Jul 2012 23:28:07 +0300 Subject: [FieldTrip] Post-doctoral position in Multisensory integration/EEG In-Reply-To: References: Message-ID: Dear Salvador Soto-Faraco I would like to apply for the job you have published in FieldTrip list - post-doctoral research position in the MULTISENSORY RESEARCH GROUP. In attachment You may see my motivation letter with my skills, CV and list with 2 references. Sincerely, Dr.biol. Viktors Veliks On Fri, Jul 20, 2012 at 6:21 PM, Sancho Moro wrote: > Post-doctoral position in Multisensory integration/EEG > > > > Applications are invited for a full-time post-doctoral research position in > the MULTISENSORY RESEARCH GROUP, led by Salvador Soto-Faraco, at the Pompeu > Fabra University (Barcelona). The position is covered by a European Research > Council grant on Multisensory Integration and Attention. > > > > The project addresses the interplay between multisensory integration > processes and attention mechanisms. This research spans several functions > (speech, temporal and spatial processing, in vision, audition and touch, and > body representation) and research approaches (psychophysics, neuroimaging, > and brain stimulation with TMS). > > > > We seek a person with solid experience who leads a research line focused on > brain oscillatory dynamics. Involvement in some organizational and > management aspects is expected. The candidate must (1) have solid > demonstrable experience (i.e., publications) in the field of oscillatory > analysis using EEG and/or MEG, (2) strong background in cognitive > neuroscience, neuroscience, and/or cognitive psychology, and (3) scientific > motivation about multisensory integration, perception and attention. > > > > We offer onsite ERP/EEG, TMS, and psychophysical testing facilities, > neuronavigation system, a wide range of visual auditory and somatosensory > stimulation equipment, and the use of fMRI and MEG recording facilities > externally. The position will be funded and renewable on yearly basis for > up to three years. > > > > Starting date: Feb 2013 or before. > > Salary: up to 36,000Eur/Year > > > > How to apply > > Applications should include: > > - a C.V. including a list of publications > > - the names of two referees who would willing to write letters of > recommendation > > - a short cover letter describing research interests > > Check out www.mrg.upf.edu for info on the group. For informal enquiries > about the position and applications, please contact Salvador Soto-Faraco at > applications.MRGLab at gmail.com. Applications will be accepted until the > position is filled. > > Please, mention that you are applying to the POSTDOCTORAL position in the > email subject > > > > > > -- > Salvador Soto Faraco > ICREA Research Professor > Dept. de Tecnologies de la Informació i les Comunicacions > Universitat Pompeu Fabra > C. Tanger, 122-140, room 55.108 > > Postal address: > Roc Boronat 138 > 08018 Barcelona > Spain > > > Phone: +34 93.542.25.34 > Fax: +34 93..542.25.17 > E-Mail: salvador.soto at icrea.cat > http://www.mrg.upf.edu > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From omidabbasi2000 at gmail.com Tue Jul 24 17:49:05 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Tue, 24 Jul 2012 20:19:05 +0430 Subject: [FieldTrip] help to apply field trip (topography plotting) In-Reply-To: References: Message-ID: Dear Steve I have a project in ERP analyzing. I provide a task for it. Any 2 sec, a square appear in the left side of screen or in the right side of screen. And subject have to look to other side of screen. I don't have any software to analyze it. I write some code for it but i think i haven't enough information about ERP analyzing. Some latency and amplitude like P300 and N100 is important for me. Do you have any information about ERP analyzing. I know i take your time with my basic question, but i think the only person that can help me is you. Thank you very much Best Regards On Sat, Jul 7, 2012 at 5:16 AM, Stephen Politzer-Ahles < politzerahless at gmail.com> wrote: > Hi Omid, > > Welcome to Fieldtrip. You can find a lot of information about how to use > Fieldtrip at http://fieldtrip.fcdonders.nl/walkthrough and > http://fieldtrip.fcdonders.nl/tutorial. In your case, you need to get > your data imported into Fieldtrip's format in MATLAB ( > http://fieldtrip.fcdonders.nl/tutorial/preprocessing), as well as your > channel layout (http://fieldtrip.fcdonders.nl/tutorial/layout) before > proceeding to plotting. > > Good luck, > Steve > > >> Message: 1 >> Date: Thu, 5 Jul 2012 16:36:23 +0430 >> From: omid abbasi >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] help to apply field trip (topography plotting) >> Message-ID: >> < >> CAPc_m1utoA_ZqC8_0q44hz5FX3yMfWP-gfke5Mes9_sEUOuyrA at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear Developer >> >> At first, I thank you for useful source code. >> >> This is Omid. I'm a student that work on biological signal processing. I >> want to use your source code for plotting data topography of brain. I >> downloaded your code from this link ( >> http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but >> i >> can't use it in my project, because i have 19 signals from 19 sites on the >> brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your >> code in my project with different channel and data? >> >> It would grateful for me if you could help me to apply your code in my >> project. >> >> Best Regards >> > > _______________________________________________ > 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 ajavitt at NKI.RFMH.ORG Thu Jul 19 17:05:37 2012 From: ajavitt at NKI.RFMH.ORG (Javitt, Aaron) Date: Thu, 19 Jul 2012 11:05:37 -0400 Subject: [FieldTrip] Automatic Artifact Rejection Message-ID: <2586A1048152BE4D861E64A98700AD420B374DBB@nki-mail.NKI.rfmh.org> I am attempting to use automatic artifact rejection based on uV threshold levels (ft_artifact_threshold). When I run ft_rejectartifact some of the datasets run just fine but on others, all the trials are rejected which then causes an error and the program crashes. Since I have a lot of files to analyze I didn't want to go through all of the files by hand, is there a way to know which datasets are going to have all of the trials rejected when ft_rejectartifact is called before I actually call it. -Aaron 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Wed Jul 25 23:43:59 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Wed, 25 Jul 2012 22:43:59 +0100 Subject: [FieldTrip] SPM M/EEG 2012 course lectures now available online In-Reply-To: References: Message-ID: Dear colleagues, Sorry for possible cross-posting. We are pleased to announce that video recordings and presentations from the May 2012 SPM for M/EEG Course at the Wellcome Trust Centre for Neuroimaging, are now freely available online at http://www.fil.ion.ucl.ac.uk/spm/course/video/#MEEG12 The new recordings complement the previously recorded set of lectures covering SPM for fMRI, PET and VBM. We hope that this resource will be useful for SPM M/EEG users as well as for the broader neuroimaging community. With best wishes, Vladimir Litvak Lecturer, Wellcome Trust Centre for Neuroimaging on behalf of SPM faculty From dargilboa at gmail.com Thu Jul 26 01:29:25 2012 From: dargilboa at gmail.com (Dar Gilboa) Date: Thu, 26 Jul 2012 02:29:25 +0300 Subject: [FieldTrip] Help with EEG ROI Timecourse Analysis Message-ID: Hello, I'm a new user of Fieldtrip, and I want to write a script that performs source reconstruction on an EEG data file (initially in TRC or EDF format) and extracts ROI timecourses based on the AAL parcellation (Tzourio-Mazoyer et al. 2002). I have matlab files with details of the parcellation, which assign an ROI number to each voxel in a matrix. I assume the parcellation can be inputted using ft_prepare_atlas. I was wondering if someone has done something similar to this so I don't have to start from scratch, or if anyone has some helpful advice. Thanks, Dar -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.weiss at klinikum.uni-tuebingen.de Thu Jul 26 06:41:10 2012 From: daniel.weiss at klinikum.uni-tuebingen.de (Klinik) Date: Thu, 26 Jul 2012 06:41:10 +0200 Subject: [FieldTrip] SPM M/EEG 2012 course lectures now available online In-Reply-To: References: Message-ID: ! Von meinem iPhone gesendet Am 25.07.2012 um 23:43 schrieb Vladimir Litvak : > Dear colleagues, > > Sorry for possible cross-posting. > > We are pleased to announce that video recordings and presentations > from the May 2012 SPM for M/EEG Course at the Wellcome Trust Centre > for Neuroimaging, are now freely available online at > > http://www.fil.ion.ucl.ac.uk/spm/course/video/#MEEG12 > > The new recordings complement the previously recorded set of lectures > covering SPM for fMRI, PET and VBM. We hope that this resource will be > useful for SPM M/EEG users as well as for the broader neuroimaging > community. > > With best wishes, > > Vladimir Litvak > Lecturer, Wellcome Trust Centre for Neuroimaging > on behalf of SPM faculty > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From marco.buiatti at gmail.com Thu Jul 26 12:36:39 2012 From: marco.buiatti at gmail.com (Marco Buiatti) Date: Thu, 26 Jul 2012 12:36:39 +0200 Subject: [FieldTrip] interactions between two factors In-Reply-To: References: Message-ID: Dear FieldTrippers, some time ago I have posted the message below concerning how to compute the statistical interaction between two factors in an EEG study with the FieldTrip cluster-based statistical analysis. Since I believe it is a problem of general interest, I was confident I would have received some replies, no matter how critics. But I had no reply and I am trying to guess why: - the problem is trivial, I should go back to my statistics books and solve it myself; - the problem is ill-posed, I should go back to my statistics books and reformulate it correctly; - the problem is tabou, no one dares commits to a solution because it could be a wrong one. - the problem is solved: I should read message number #. Thanks a lot for your feedback, Best, Marco On 25 May 2012 15:58, Marco Buiatti wrote: > Dear FieldTrippers, > > I am analysing an EEG study with 2x4 factors: one varies between 4 > parametrically varying levels (1 to 4), the second between two levels. > > I have three questions concerning the use of Fieldtrip cluster-based > non parametric statistical analysis in this case: > > 1) How to compute the interaction between the two factors. Let's start > from the simplest case of a 2x2 design, factors varying between values > A1 and A2 for the first factor, B1 and B2 for the second. Please tell > me if it is correct to compute the interaction by: > - computing the difference diffA=ERP(A1)-ERP(A2) separately in > condition B1 and B2, for every subject > - performing a within-subjects statistical analysis between diffA in > condition B1 and diffA in condition B2 (function > statfun_depsamplesT.m). > > 2) Now consider that factor A varies parametrically between values 1 > to 4. For the main effect of this factor, I have used the Fieldtrip > function statfun_depsamplesregrT.m and I'm satisfied with it. Is it > correct to compute the interaction by > - computing the regression > regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside > function statfun_depsamplesregrT.m) separately in condition B1 and B2, > for every subject > - performing a within-subjects statistical analysis between regrA in > condition B1 and regrA in condition B2 (function > statfun_depsamplesT.m)? > > 3) Since BEFORE looking at the data (this is to prevent Eric's > contestation...) I expect a dipolar topography for the regression > (data are in average reference), I would like to combine into a joint > cluster negative and positive clusters. I have tried by changing > statfun_depsamplesregrT.m by just taking the absolute value of the > regression, but I get weird results (a huge, non significant cluster). > Is it possible that since values are now all positive, I should use a > different statistical test at the single bin level? Any other > suggestions? > > Thanks in advance for your help, > > Marco > > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** -- Marco Buiatti, PhD CEA/DSV/I2BM / NeuroSpin INSERM U992 - Cognitive Neuroimaging Unit Bât 145 - Point Courrier 156 Gif sur Yvette F-91191 FRANCE Ph: +33(0)169.08.65.21 Fax: +33(0)169.08.79.73 E-mail: marco.buiatti at gmail.com http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti *********************************************** From lihqih at gmail.com Thu Jul 26 16:58:51 2012 From: lihqih at gmail.com (qi li) Date: Thu, 26 Jul 2012 10:58:51 -0400 Subject: [FieldTrip] lateral view plot Message-ID: Hi there, Can fieldtrip make the plot like brain lateral view or something like suma such that descriptive statistics can be mapped on? Thanks a lot! Qi From jm.horschig at donders.ru.nl Thu Jul 26 17:23:25 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 26 Jul 2012 17:23:25 +0200 Subject: [FieldTrip] lateral view plot In-Reply-To: References: Message-ID: <501160ED.4050307@donders.ru.nl> Hi Qi, you can see here what's possible: http://fieldtrip.fcdonders.nl/tutorial/plotting?s[]=source&s[]=plot#plotting_data_at_the_source_level or in the tutorial: http://fieldtrip.fcdonders.nl/tutorial/beamformer?#neural_activity_index http://fieldtrip.fcdonders.nl/tutorial/beamformer?#plotting_options see also ft_sourceplot: http://fieldtrip.fcdonders.nl/reference/ft_sourceplot You can use cfg.funparameter and cfg.maskparameter to specify what you want to plot. Have fun ;) Jörn On 7/26/2012 4:58 PM, qi li wrote: > Hi there, > > Can fieldtrip make the plot like brain lateral view or something like > suma such that descriptive statistics can be mapped on? Thanks a lot! > > Qi > _______________________________________________ > 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 arno at cerco.ups-tlse.fr Thu Jul 26 18:35:49 2012 From: arno at cerco.ups-tlse.fr (Arnaud Delorme) Date: Thu, 26 Jul 2012 09:35:49 -0700 Subject: [FieldTrip] interactions between two factors In-Reply-To: References: Message-ID: Dear Marco, I believe the first answer is the correct one. The problem is somewhat trivial but not implemented yet. The LIMO toolbox will let you perform 2-way statistics with cluster correction for multiple comparisons. Best, Arno On Jul 26, 2012, at 3:36 AM, Marco Buiatti wrote: > Dear FieldTrippers, > > some time ago I have posted the message below concerning how to > compute the statistical interaction between two factors in an EEG > study with the FieldTrip cluster-based statistical analysis. Since I > believe it is a problem of general interest, I was confident I would > have received some replies, no matter how critics. But I had no reply > and I am trying to guess why: > > - the problem is trivial, I should go back to my statistics books and > solve it myself; > - the problem is ill-posed, I should go back to my statistics books > and reformulate it correctly; > - the problem is tabou, no one dares commits to a solution because it > could be a wrong one. > - the problem is solved: I should read message number #. > > Thanks a lot for your feedback, > > Best, > > Marco > > On 25 May 2012 15:58, Marco Buiatti wrote: >> Dear FieldTrippers, >> >> I am analysing an EEG study with 2x4 factors: one varies between 4 >> parametrically varying levels (1 to 4), the second between two levels. >> >> I have three questions concerning the use of Fieldtrip cluster-based >> non parametric statistical analysis in this case: >> >> 1) How to compute the interaction between the two factors. Let's start >> from the simplest case of a 2x2 design, factors varying between values >> A1 and A2 for the first factor, B1 and B2 for the second. Please tell >> me if it is correct to compute the interaction by: >> - computing the difference diffA=ERP(A1)-ERP(A2) separately in >> condition B1 and B2, for every subject >> - performing a within-subjects statistical analysis between diffA in >> condition B1 and diffA in condition B2 (function >> statfun_depsamplesT.m). >> >> 2) Now consider that factor A varies parametrically between values 1 >> to 4. For the main effect of this factor, I have used the Fieldtrip >> function statfun_depsamplesregrT.m and I'm satisfied with it. Is it >> correct to compute the interaction by >> - computing the regression >> regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside >> function statfun_depsamplesregrT.m) separately in condition B1 and B2, >> for every subject >> - performing a within-subjects statistical analysis between regrA in >> condition B1 and regrA in condition B2 (function >> statfun_depsamplesT.m)? >> >> 3) Since BEFORE looking at the data (this is to prevent Eric's >> contestation...) I expect a dipolar topography for the regression >> (data are in average reference), I would like to combine into a joint >> cluster negative and positive clusters. I have tried by changing >> statfun_depsamplesregrT.m by just taking the absolute value of the >> regression, but I get weird results (a huge, non significant cluster). >> Is it possible that since values are now all positive, I should use a >> different statistical test at the single bin level? Any other >> suggestions? >> >> Thanks in advance for your help, >> >> Marco >> >> >> >> -- >> Marco Buiatti, PhD >> >> CEA/DSV/I2BM / NeuroSpin >> INSERM U992 - Cognitive Neuroimaging Unit >> Bât 145 - Point Courrier 156 >> Gif sur Yvette F-91191 FRANCE >> Ph: +33(0)169.08.65.21 >> Fax: +33(0)169.08.79.73 >> E-mail: marco.buiatti at gmail.com >> http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti >> >> *********************************************** > > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Arnaud Delorme, PhD Centre de Recherche Cerveau et Cognition - UMR 5549 Pavillon Baudot, Hopital Purpan, BP 25202 31052 Toulouse Cedex, France From arno at cerco.ups-tlse.fr Thu Jul 26 18:35:49 2012 From: arno at cerco.ups-tlse.fr (Arnaud Delorme) Date: Thu, 26 Jul 2012 09:35:49 -0700 Subject: [FieldTrip] interactions between two factors In-Reply-To: References: Message-ID: Dear Marco, I believe the first answer is the correct one. The problem is somewhat trivial but not implemented yet. The LIMO toolbox will let you perform 2-way statistics with cluster correction for multiple comparisons. Best, Arno On Jul 26, 2012, at 3:36 AM, Marco Buiatti wrote: > Dear FieldTrippers, > > some time ago I have posted the message below concerning how to > compute the statistical interaction between two factors in an EEG > study with the FieldTrip cluster-based statistical analysis. Since I > believe it is a problem of general interest, I was confident I would > have received some replies, no matter how critics. But I had no reply > and I am trying to guess why: > > - the problem is trivial, I should go back to my statistics books and > solve it myself; > - the problem is ill-posed, I should go back to my statistics books > and reformulate it correctly; > - the problem is tabou, no one dares commits to a solution because it > could be a wrong one. > - the problem is solved: I should read message number #. > > Thanks a lot for your feedback, > > Best, > > Marco > > On 25 May 2012 15:58, Marco Buiatti wrote: >> Dear FieldTrippers, >> >> I am analysing an EEG study with 2x4 factors: one varies between 4 >> parametrically varying levels (1 to 4), the second between two levels. >> >> I have three questions concerning the use of Fieldtrip cluster-based >> non parametric statistical analysis in this case: >> >> 1) How to compute the interaction between the two factors. Let's start >> from the simplest case of a 2x2 design, factors varying between values >> A1 and A2 for the first factor, B1 and B2 for the second. Please tell >> me if it is correct to compute the interaction by: >> - computing the difference diffA=ERP(A1)-ERP(A2) separately in >> condition B1 and B2, for every subject >> - performing a within-subjects statistical analysis between diffA in >> condition B1 and diffA in condition B2 (function >> statfun_depsamplesT.m). >> >> 2) Now consider that factor A varies parametrically between values 1 >> to 4. For the main effect of this factor, I have used the Fieldtrip >> function statfun_depsamplesregrT.m and I'm satisfied with it. Is it >> correct to compute the interaction by >> - computing the regression >> regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside >> function statfun_depsamplesregrT.m) separately in condition B1 and B2, >> for every subject >> - performing a within-subjects statistical analysis between regrA in >> condition B1 and regrA in condition B2 (function >> statfun_depsamplesT.m)? >> >> 3) Since BEFORE looking at the data (this is to prevent Eric's >> contestation...) I expect a dipolar topography for the regression >> (data are in average reference), I would like to combine into a joint >> cluster negative and positive clusters. I have tried by changing >> statfun_depsamplesregrT.m by just taking the absolute value of the >> regression, but I get weird results (a huge, non significant cluster). >> Is it possible that since values are now all positive, I should use a >> different statistical test at the single bin level? Any other >> suggestions? >> >> Thanks in advance for your help, >> >> Marco >> >> >> >> -- >> Marco Buiatti, PhD >> >> CEA/DSV/I2BM / NeuroSpin >> INSERM U992 - Cognitive Neuroimaging Unit >> Bât 145 - Point Courrier 156 >> Gif sur Yvette F-91191 FRANCE >> Ph: +33(0)169.08.65.21 >> Fax: +33(0)169.08.79.73 >> E-mail: marco.buiatti at gmail.com >> http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti >> >> *********************************************** > > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Arnaud Delorme, PhD Centre de Recherche Cerveau et Cognition - UMR 5549 Pavillon Baudot, Hopital Purpan, BP 25202 31052 Toulouse Cedex, France From politzerahless at gmail.com Fri Jul 27 16:25:07 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Fri, 27 Jul 2012 09:25:07 -0500 Subject: [FieldTrip] interactions between two factors Message-ID: Hello Marco, For how to test an interaction in a 2x2 design, see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-January/003447.html(and some additional information at http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003338.html, http://mailman.science.ru.nl/pipermail/fieldtrip/2011-September/004244.html, and Anderson & Braak 2003 in *Journal of Statistical Computation & Simulation*). I'm not sure about the other two issues you mentioned, though. Best, Steve Message: 1 > Date: Thu, 26 Jul 2012 12:36:39 +0200 > From: Marco Buiatti > To: fieldtrip at donders.ru.nl > Subject: Re: [FieldTrip] interactions between two factors > Message-ID: > < > CA+wnTO2TL7XtzsKX2QciqXZO9hVxGUZTPjXwoYtS54ztRc0KeQ at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear FieldTrippers, > > some time ago I have posted the message below concerning how to > compute the statistical interaction between two factors in an EEG > study with the FieldTrip cluster-based statistical analysis. Since I > believe it is a problem of general interest, I was confident I would > have received some replies, no matter how critics. But I had no reply > and I am trying to guess why: > > - the problem is trivial, I should go back to my statistics books and > solve it myself; > - the problem is ill-posed, I should go back to my statistics books > and reformulate it correctly; > - the problem is tabou, no one dares commits to a solution because it > could be a wrong one. > - the problem is solved: I should read message number #. > > Thanks a lot for your feedback, > > Best, > > Marco > > On 25 May 2012 15:58, Marco Buiatti wrote: > > Dear FieldTrippers, > > > > I am analysing an EEG study with 2x4 factors: one varies between 4 > > parametrically varying levels (1 to 4), the second between two levels. > > > > I have three questions concerning the use of Fieldtrip cluster-based > > non parametric statistical analysis in this case: > > > > 1) How to compute the interaction between the two factors. Let's start > > from the simplest case of a 2x2 design, factors varying between values > > A1 and A2 for the first factor, B1 and B2 for the second. Please tell > > me if it is correct to compute the interaction by: > > - computing the difference diffA=ERP(A1)-ERP(A2) separately in > > condition B1 and B2, for every subject > > - performing a within-subjects statistical analysis between diffA in > > condition B1 and diffA in condition B2 (function > > statfun_depsamplesT.m). > > > > 2) Now consider that factor A varies parametrically between values 1 > > to 4. For the main effect of this factor, I have used the Fieldtrip > > function statfun_depsamplesregrT.m and I'm satisfied with it. Is it > > correct to compute the interaction by > > - computing the regression > > regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside > > function statfun_depsamplesregrT.m) separately in condition B1 and B2, > > for every subject > > - performing a within-subjects statistical analysis between regrA in > > condition B1 and regrA in condition B2 (function > > statfun_depsamplesT.m)? > > > > 3) Since BEFORE looking at the data (this is to prevent Eric's > > contestation...) I expect a dipolar topography for the regression > > (data are in average reference), I would like to combine into a joint > > cluster negative and positive clusters. I have tried by changing > > statfun_depsamplesregrT.m by just taking the absolute value of the > > regression, but I get weird results (a huge, non significant cluster). > > Is it possible that since values are now all positive, I should use a > > different statistical test at the single bin level? Any other > > suggestions? > > > > Thanks in advance for your help, > > > > Marco > > > > > > > > -- > > Marco Buiatti, PhD > > > > CEA/DSV/I2BM / NeuroSpin > > INSERM U992 - Cognitive Neuroimaging Unit > > B?t 145 - Point Courrier 156 > > Gif sur Yvette F-91191 FRANCE > > Ph: +33(0)169.08.65.21 > > Fax: +33(0)169.08.79.73 > > E-mail: marco.buiatti at gmail.com > > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erdosttorun at gmail.com Sat Jul 28 22:47:21 2012 From: erdosttorun at gmail.com (erdost torun) Date: Sat, 28 Jul 2012 23:47:21 +0300 Subject: [FieldTrip] May I use fieldtrip on social science time series data? Message-ID: Hello everyone! I wonder whether I could use fieldtrip toolbox to do wavelet based causality analysis on Social science data, such as birth rates or malaria statistics. From the fieldtrip webpage, I understand that researches using fieldtrip mainly focus on MEG, EEG, and invasive electrophysiological data. Hence, I want to be sure that fieldtrip is suitable for other time series. Thank you in advance. All the best, Erdost From eelke.spaak at donders.ru.nl Mon Jul 30 13:21:46 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 30 Jul 2012 13:21:46 +0200 Subject: [FieldTrip] May I use fieldtrip on social science time series data? In-Reply-To: References: Message-ID: Hello Erdost, Indeed, FieldTrip is designed specifically for the analysis of electrophysiological neuroscientific data. However, I don't see a reason why you should not use it for analysing different time series as well, if you think this will be useful to you. Best, Eelke On 28 July 2012 22:47, erdost torun wrote: > Hello everyone! > > I wonder whether I could use fieldtrip toolbox to do wavelet based > causality analysis on Social science data, such as birth rates or > malaria statistics. From the fieldtrip webpage, I understand that > researches using fieldtrip mainly focus on MEG, EEG, and invasive > electrophysiological data. Hence, I want to be sure that fieldtrip is > suitable for other time series. Thank you in advance. > > All the best, > > Erdost > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Mon Jul 30 15:43:59 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 30 Jul 2012 15:43:59 +0200 Subject: [FieldTrip] May I use fieldtrip on social science time series data? In-Reply-To: References: Message-ID: <50168F9F.6060400@donders.ru.nl> Dear Erdost, I agree as well with Eelke. In particular, apart from some methods (e.g. source reconstruction), there is no explicit assumption made about the origin of the data. While the algorithms are per se suited for any type of data, the options might be specific for your data. So, e.g. be sure to not demean or detrend your data when preprocessing (check what the defaults are for each function!). If would be great to let us all know if you publish your results in a particular scientific journal. Best of luck&success, Jörn On 7/28/2012 10:47 PM, erdost torun wrote: > Hello everyone! > > I wonder whether I could use fieldtrip toolbox to do wavelet based > causality analysis on Social science data, such as birth rates or > malaria statistics. From the fieldtrip webpage, I understand that > researches using fieldtrip mainly focus on MEG, EEG, and invasive > electrophysiological data. Hence, I want to be sure that fieldtrip is > suitable for other time series. Thank you in advance. > > All the best, > > Erdost > _______________________________________________ > 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 polomacnenad at gmail.com Mon Jul 30 16:10:54 2012 From: polomacnenad at gmail.com (Nenad Polomac) Date: Mon, 30 Jul 2012 16:10:54 +0200 Subject: [FieldTrip] MEG-anatomical MRI image coregistration Message-ID: Hello, I am analyzing MEG CTF data. I want to do source localisation and I have two particular questions regarding the anatomical MRI images. 1. Is it allowed to use anatomical MRI images from a two different MRI devices in a one source localisation study? We already have routinely obtain anatomical images for some patients and those are obtained on the 1.5 Tesla MRI. And for other patients we will record anatomical MRI on 3 Tesla. So, what do you think can we use this data in the same source analysis study. 2. The anatomical MRI images from a few subject were not marked with the vitamin E during imaging for relevant skull points (nasion and ear canals). So, I think to mark them now in some imaging software. The MEG data were properly marked during acquisition for this skull points. What is your opinion about accuracy of software based marking. How big localisation error might be? Thank you in advance! Kind regards! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Mon Jul 30 16:48:33 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Mon, 30 Jul 2012 16:48:33 +0200 Subject: [FieldTrip] MEG-anatomical MRI image coregistration In-Reply-To: References: Message-ID: Dear Nenad, My 2 cents: 1) As long as you are convinced that both give appropriately accurate segmentations - something easily checked along the way by superimposing stripped brain,stull etc on the original scan - I don't see any reason against using them together in one study. Also, as you will probably not work on the high resolution of your T3 (i.e. 1mm isomorphic), but on downsampled grids for beamformer (i.e. 5 mm isomorphic), below the resolution of your 1.5T scans, differences in resolution should not confound your results on source level. Ofcourse in some specific cases in between- or within-group comparisons you could do a control analysis, e.g. using scan device as a covariate in your analysis, just to be sure, but I can think of only some very specific situations where that could be the case. 2) The localisation error would be related to how close you think you can co-register [sic]. I would consider that addive uncertainty above the localisation errors you'll unavoidably already have with your recording (movement) and source reconstruction (i.e. point-spread of the beamformer and such). I don't know what you mean exactly with 'software-based marking'. If you know where your MEG coils where in respect to anatomical landmarks, you can intelligently 'guess' where they are on the anatomical and just put them there by hand (nasion would be pretty close, ears probably put them e.g. 1.5 cm anterior to ear canals). The added uncertainty will be the degree of uncertainty you have being able to do that, right? If with 'software-based marking' you mean the use of a polemus device than that would probably be better. In any case, being conservative i would say the by-eye-method would increase your uncertainly by another cm or 2, instead of about a cm when appropriately using vitamin markers. I have no data to back that claim up though. Good luck! Stephen On 30 July 2012 16:10, Nenad Polomac wrote: > Hello, > > I am analyzing MEG CTF data. I want to do source localisation and I have two > particular questions regarding the anatomical MRI images. > > 1. Is it allowed to use anatomical MRI images from a two different MRI > devices in a one source localisation study? We already have routinely obtain > anatomical images for some patients and those are obtained on the 1.5 Tesla > MRI. And for other patients we will record anatomical MRI on 3 Tesla. So, > what do you think can we use this data in the same source analysis study. > > 2. The anatomical MRI images from a few subject were not marked with the > vitamin E during imaging for relevant skull points (nasion and ear canals). > So, I think to mark them now in some imaging software. The MEG data were > properly marked during acquisition for this skull points. > What is your opinion about accuracy of software based marking. How big > localisation error might be? > > Thank you in advance! > > Kind regards! > > Nenad > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From nenga at gmx.net Mon Jul 30 18:29:38 2012 From: nenga at gmx.net (Carina Oehrn) Date: Mon, 30 Jul 2012 18:29:38 +0200 Subject: [FieldTrip] granger causality Message-ID: <20120730162938.56630@gmx.net> Hi there, I have got an iEEG dataset and would like to look at the directionality of interactions between two channels in two different conditions using granger causality. Hopefully somebody here can help me :-) 1.) I know that I can calculate the appropriate model order and window length with the bsmart toolbox. But from the documentation I somehow do not get the format of data I should use for this calculation. When I enter the time-frequency data (which I want to use to estimate granger causality) (size: 2 x 2 x freq x time points), it doesn't work. Any advise? I have a sampling rate of 1000. What sort of time window and maximal model order would make sense do you think? 2)I would like to keep the time domain analyzing my data. What do you think would be an appropriate sliding time window using the 'ft_mvaranalysis' function? And what does it mean exactly? By choosing the model order, I am already determining the maximal time lag between the two functions. Are the values then estimated for the whole time window? 3)What do you think about statistics? Would it makes sense to use the non-parametric cluster approach to shuffle within patients and do a group analysis that way? Thank you so much in advance! Best, Carina As a summary,I am doing following steps with field trip: cfg = []; cfg.dftfilter ='yes' prep_cond1{subj} = ft_preprocessing(cfg, data); cfg = []; cfg.order = 5; cfg.toolbox = 'bsmart'; cfg.t_ftimwin = 0.05 cfg.toi = -1:0.001:3.5; mdata_cond1{subj}= ft_mvaranalysis(cfg, prep_cond1{subj}); cfg = []; cfg.method = 'mvar'; cfg.foi = 4:100; cond1_freq{subj}= ft_freqanalysis_mvar(cfg,mdata_cond1{subj}); cfg = []; cfg.method = 'granger'; cond1_granger{subj} = ft_connectivityanalysis(cfg, cond1_freq{subj}); From erdosttorun at gmail.com Tue Jul 31 13:33:58 2012 From: erdosttorun at gmail.com (erdost torun) Date: Tue, 31 Jul 2012 14:33:58 +0300 Subject: [FieldTrip] May I use fieldtrip on social science time series data? Message-ID: Dear Eelke and Jorne, Thank you both for your intesest. I plan to implement Wavelet-based Granger Causality on Social Science data through Fieldtrip toolbox. Hope I can make it correctly. If I publish any paper on it, I will share the results with you. Thank you so much All the best, Erdost Torun Dokuz Eylul University Dept of International Business and Trade From stephen.whitmarsh at gmail.com Tue Jul 31 17:35:52 2012 From: stephen.whitmarsh at gmail.com (stephen whitmarsh) Date: Tue, 31 Jul 2012 15:35:52 +0000 (UTC) Subject: [FieldTrip] Invitation to connect on LinkedIn Message-ID: <1955016892.13426275.1343748952505.JavaMail.app@ela4-app0131.prod> LinkedIn ------------ FieldTrip, I'd like to add you to my professional network on LinkedIn. - stephen stephen whitmarsh aio at Radboud Netherlands Confirm that you know stephen whitmarsh: https://www.linkedin.com/e/-kyqm8y-h5b5fjjo-12/isd/8060512829/VSO4ebwG/?hs=false&tok=1jOyZbi12DKRk1 -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/-kyqm8y-h5b5fjjo-12/o2zr3wMN-KUziWnbF0JpKw1y-MN7WW_ZDEc0/goo/fieldtrip%40science%2Eru%2Enl/20061/I2717672971_1/?hs=false&tok=3aVU5rC6CDKRk1 (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Tue Jul 31 22:45:16 2012 From: lihqih at gmail.com (qi li) Date: Tue, 31 Jul 2012 16:45:16 -0400 Subject: [FieldTrip] sourceplot Message-ID: Hi, I am having trouble to call the ft_sourceplot after ft_sourceanalysis. After sourceanalysis I have a source struct ans = time: [1x399 double] pos: [8196x3 double] inside: [1x8196 double] outside: [1x0 double] method: 'average' avg: [1x1 struct] cfg: [1x1 struct] unit: 'cm' Avg field has the following structure ans = mom: {1x8196 cell} pow: [8196x399 double] I want to plot the pow in the brian, so I use cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'avg.pow'; cfg.maskparameter = cfg.funparameter; cfg.funcolorlim = [0.0 1.2]; cfg.opacitylim = [0.0 1.2]; cfg.opacitymap = 'rampup'; figure ft_sourceplot(cfg, source); but the message says 'Error using ft_checkdata (line 307) This function requires volume data as input. Error in ft_volumedownsample (line 58) source = ft_checkdata(source, 'datatype', 'volume', 'feedback', 'no'); Error in ft_sourceplot (line 290) data = ft_volumedownsample(tmpcfg, data);' What does volume data point to? Thanks! From mahdi_meng at yahoo.com Sun Jul 1 18:23:06 2012 From: mahdi_meng at yahoo.com (m m) Date: Sun, 1 Jul 2012 09:23:06 -0700 (PDT) Subject: [FieldTrip] FW: Hi Friend! Message-ID: <1341159786.76669.androidMobile@web122403.mail.ne1.yahoo.com>

I guess your job search is going well. I just wanted to tell you to a new job opp in locality.
We have had several of our members take this opp and I have heard lots of perfect success stories.

The local paper has an article featuring one of our clients, Kelly Richards. It will also you all you all the important information you need to get started.
The link is http://specialoffers.com.br/angerabandoned/Daniel_Alien5/?a=198461&s=dprocessing and I think the story will be featured on the home-page until tomorrow.

TTYL!

-------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Sun Jul 1 22:15:56 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Sun, 01 Jul 2012 13:15:56 -0700 Subject: [FieldTrip] calculating correlation Message-ID: <4FF0AFFC.1040500@berkeley.edu> Hi FTers, I'd like to do two sorts of correlation calculations, and was wondering if there's any easy way to do this within FieldTrip. 1) I'd like to calculate the correlation between performance over trials and power within a specific frequency over trials. So I have the performance measure per trial, and my chan*freq measure after freqanalysis. So for each channel I have a series of power values (trials) and I have a series of performance measures (per trial), and now like to know (first within, and then over subjects) which channel's frequency power follows (correlates) with the performance. From the walkthrough I understand I can give in these performance measures through the design (cfg.design=[0.10.20.30.40.50.40.30.10.2];cfg.ivar=1;), but which method to use for ft_freqstatistics? I don't see statistics = 'correlation' or 'pearson' or 'spearman' in method = 'analytic. Also how to make the design to correlate over trials? 2) I'd like to calculate the correlation between the score on repeated questionnaire over participants with power within a frequency. So I have several power values per participant for each channel, and the repeated scores on the questionnaire for each participant. And now I'd like to calculate a value per channel reflecting the correlation over the repeats of the questionnaire and over participants. Any idea on FieldTrip settings? Both in general, is there a correlation statistics implemented, and more specifically for my question, how would I make the appropriate designs? Thanks so much! Ingrid -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 2 08:53:51 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 2 Jul 2012 08:53:51 +0200 Subject: [FieldTrip] calculating correlation In-Reply-To: <4FF0AFFC.1040500@berkeley.edu> References: <4FF0AFFC.1040500@berkeley.edu> Message-ID: <1AA66D8B-3685-4A8F-AED3-A1FF8C7A8D21@donders.ru.nl> Hi Ingrid, This calls for a statfun_corr or even a statfun_glm! It so happens that I have some of these sitting on my hard drive. As you know I am fond of beer, chocolate and co-authorships, so I am sure we can strike a deal. I have not yet had the opportunity to contribute these statfuns to FieldTrip, but now I sense a win-win-win situation: win 1 is for me (beer/chocolate/co-authorships/etc), win 2 is for you (you can compute your statistic of interest) and win 3 for the community (where you test the code, write documentation on the wiki etcetc). How does that sound for a plan? Cheers, JM On Jul 1, 2012, at 10:15 PM, Ingrid Nieuwenhuis wrote: > Hi FTers, > > I'd like to do two sorts of correlation calculations, and was wondering if there's any easy way to do this within FieldTrip. > > 1) I'd like to calculate the correlation between performance over trials and power within a specific frequency over trials. So I have the performance measure per trial, and my chan*freq measure after freqanalysis. So for each channel I have a series of power values (trials) and I have a series of performance measures (per trial), and now like to know (first within, and then over subjects) which channel's frequency power follows (correlates) with the performance. > > From the walkthrough I understand I can give in these performance measures through the design (cfg.design = [0.1 0.2 0.3 0.4 0.5 0.4 0.3 0.1 0.2]; cfg.ivar= 1;), but which method to use for ft_freqstatistics? I don't see statistics = 'correlation' or 'pearson' or 'spearman' in method = 'analytic. Also how to make the design to correlate over trials? > > 2) I'd like to calculate the correlation between the score on repeated questionnaire over participants with power within a frequency. So I have several power values per participant for each channel, and the repeated scores on the questionnaire for each participant. And now I'd like to calculate a value per channel reflecting the correlation over the repeats of the questionnaire and over participants. > > Any idea on FieldTrip settings? Both in general, is there a correlation statistics implemented, and more specifically for my question, how would I make the appropriate designs? > > Thanks so much! > Ingrid > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > _______________________________________________ > 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 johanna.zumer at donders.ru.nl Mon Jul 2 11:54:11 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Mon, 2 Jul 2012 11:54:11 +0200 Subject: [FieldTrip] Source localization using DICS for EEG data from combined MEG/EEG recordings In-Reply-To: References: Message-ID: Dear Marcel, I might have seen a similar error before when the number of channels in 'elec' do not match the number of channels in 'freq'. Could that be the cause? Also, does it matter that you are setting cfg.grad=elec, rather than cfg.elec=elec? To debug, it might be best to first call leadfield=ft_prepare_leadfield() to ensure that is computed correctly, and then set that output to cfg.grid.leadfield=leadfield, in your call to ft_sourceanalysis. cheers, Johanna 2012/6/26 Marcel Heers > Dear all, > > I am trying to perform source localization in the frequency domain > from EEG data using DICS. The data were recorded combined with MEG > (Neuromag data format). The volume conductor is a 3 shell realistic > head model created with bemcp. > When running DICS with the following settings > > cfg = []; > cfg.method = 'dics'; > cfg.grad = elec; > cfg.frequency = 14; > cfg.vol = vol_eeg; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = 5; > source = ft_sourceanalysis(cfg, freq); > > > I am am getting the following error message: > > ??? Error using ==> svd > Input to SVD must not contain NaN or Inf. > > Error in ==> beamformer_dics>pinv at 568 > [U,S,V] = svd(A,0); > > Error in ==> beamformer_dics at 314 > filt = pinv(lf' * invCf * lf) * lf' * invCf; % > Gross eqn. 3, use > PINV/SVD to cover rank deficient leadfield > > Error in ==> ft_sourceanalysis at 584 > dip(i) = beamformer_dics(grid, sens, vol, [], > squeeze(Cf(i,:,:)), optarg{:}); > > > and I am not sure what might be the cause. > > Maybe anyone can help me! Thank you in advance! > > Marcel > _______________________________________________ > 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 Don.Rojas at ucdenver.edu Mon Jul 2 14:34:31 2012 From: Don.Rojas at ucdenver.edu (Rojas, Don) Date: Mon, 2 Jul 2012 06:34:31 -0600 Subject: [FieldTrip] Source localization using DICS for EEG data from combined MEG/EEG recordings In-Reply-To: References: Message-ID: <9FCD53FD-5A0E-48F8-87B2-08717F732CC9@ucdenver.edu> Marcel, Also, you might check your volume conductor. I've seen a similar error when there were NaNs in the surface normals. Don Sent from my iPad On Jul 2, 2012, at 4:12 AM, "Johanna Zumer" > wrote: Dear Marcel, I might have seen a similar error before when the number of channels in 'elec' do not match the number of channels in 'freq'. Could that be the cause? Also, does it matter that you are setting cfg.grad=elec, rather than cfg.elec=elec? To debug, it might be best to first call leadfield=ft_prepare_leadfield() to ensure that is computed correctly, and then set that output to cfg.grid.leadfield=leadfield, in your call to ft_sourceanalysis. cheers, Johanna 2012/6/26 Marcel Heers > Dear all, I am trying to perform source localization in the frequency domain from EEG data using DICS. The data were recorded combined with MEG (Neuromag data format). The volume conductor is a 3 shell realistic head model created with bemcp. When running DICS with the following settings cfg = []; cfg.method = 'dics'; cfg.grad = elec; cfg.frequency = 14; cfg.vol = vol_eeg; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = 5; source = ft_sourceanalysis(cfg, freq); I am am getting the following error message: ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> beamformer_dics>pinv at 568 [U,S,V] = svd(A,0); Error in ==> beamformer_dics at 314 filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ==> ft_sourceanalysis at 584 dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); and I am not sure what might be the cause. Maybe anyone can help me! Thank you in advance! Marcel _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornabel at googlemail.com Mon Jul 2 14:52:58 2012 From: cornabel at googlemail.com (Cornelius Abel) Date: Mon, 2 Jul 2012 14:52:58 +0200 Subject: [FieldTrip] reverse source interpolate? In-Reply-To: <36BAC777-CD99-4F3E-95D1-A133F5CC2372@donders.ru.nl> References: <4FEB2620.3050505@googlemail.com> <36BAC777-CD99-4F3E-95D1-A133F5CC2372@donders.ru.nl> Message-ID: Hi mailing list, I'm still struggling with the conversion of coordinates between source and interpolated source space. For example, if i have the position of a single grid point how do i get the corresponding voxel in the interpolated source structure. Or the other way around, how to get the grid point which corresponds to a voxel (e.g the max voxel) in the interpolated source structure. I think this should be a common problem when working with virtual electrodes, shouldn't it? To make things easier i put together a example with the data from the source tutorial where i tried to calculated the grid pos of the max voxel in the interpolated source. clear all; load sourcePost_nocon; % source structure from tutorial mri = ft_read_mri('Subject01.mri'); % mri of subject01 from tutorial sourceNAI = sourcePost_nocon; sourceNAI.avg.pow = sourcePost_nocon.avg.pow ./ sourcePost_nocon.avg.noise; sourceNAI=rmfield(sourceNAI,'freq'); % had to remove that to let cfg = []; cfg.downsample = 2; cfg.parameter = 'avg.pow'; sourceNAIInt = ft_sourceinterpolate(cfg, sourceNAI , mri); % Find position of max activity [dum, maxindx] = max(sourceNAIInt.avg.pow(:)); [xi, yi, zi] = ind2sub(sourceNAIInt.dim, maxindx); posInt=[xi, yi, zi]; % Plot interpolated source with position of max activity cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'avg.pow'; cfg.locationcoordinates = 'voxel'; cfg.location = posInt; % location of max activity is marked correctly. figure; ft_sourceplot(cfg,sourceNAIInt); % Transform coordinate back to uninterpolated source??? dpos = warp_apply(inv(mri.transform), posInt, 'homogeneous'); % Plot uninterpolated source with position aquired from interpolated source cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'avg.pow'; cfg.locationcoordinates = 'voxel'; cfg.location = dpos; % unfortunately this coordinate is obviously wrong!!! WHY? figure; ft_sourceplot(cfg,sourceNAI); Unfortunately the solution of Jan Mathijs did not work, nor did mine :( Any ideas??? Cornelius 2012/6/28 jan-mathijs schoffelen > Hi Cornelius, > > Probably you should use: cfg.locationcoordinates to be 'head'. > > Best, > > JM > > On Jun 28, 2012, at 11:19 AM, Cornelius Abel wrote: > > Hi jan mathijs, hello mailing list, > > thanks for your answer. I think i got your idea with finding the minimum > in this squared differences. This should the work with positions of any > scaling, right? > However it gives me strange results when trying to get voxel indices in > the "raw" source using voxel indices aquired from interpolated source. > But even using the ctf coordinates in mm doesn't work. > > Here is a short script showing what i did, i also attached the necessary > mat files. > > greetings, Cornelius > > > clear all; > load testdata.mat; > > % Interpolate source on anatomy > cfg = []; > cfg.parameter = 'avg.itc'; > cfg.interpmethod = 'linear'; > sourceInt = ft_sourceinterpolate(cfg, source,mri); > > % Find position of max voxel in interpolated source > [maxval, maxindx] = max(sourceInt.avg.itc(:)); > [x,y,z]=ind2sub(size(sourceInt.avg.itc),maxindx); > pos=[x y z]; > > % plot this position in interpolated source > figure; > cfg = []; > cfg.method = 'ortho'; > cfg.funparameter = 'avg.itc'; > cfg.locationcoordinates = 'voxel'; > cfg.location = pos; > ft_sourceplot(cfg, sourceInt); > > % Calculate respective position in 'raw' source struct > dpos = source.pos - repmat(pos, size(source.pos,1),1); > [m,ind] = min(sum(dpos.^2,2)); > spos=source.pos(ind,:); > > % Plot position in 'raw' source. > % This gives not the position of max activity!!! > figure; > cfg = []; > cfg.method = 'ortho'; > cfg.funparameter = 'avg.itc'; > cfg.locationcoordinates = 'voxel'; > cfg.location = spos; > ft_sourceplot(cfg, source); > > > > 2012/6/27 jan-mathijs schoffelen > >> Hi Cornelius, >> >> There is no need to 'uninterpolate' because the coordinates are already >> expressed in the correct coordinate system. What you probably want is to >> find the index to the voxel in the original source-structure closest to >> your 'hotspot' in the interpolated image. >> This can be achieved by something like this: >> >> write down the coordinates of your favourite position in the interpolated >> image (in world coordinates, here I assume that you are still in MEG >> coordinate system and have not normalized to MNI space), call this pos >> >> pos = pos./10 (from mm to cm) >> >> dpos = source.pos - repmat(pos, size(source.pos,1),1); >> [m,ind] = min(sum(dpos.^2,2)); >> >> source is the original source structure. >> ind is the index you are looking for. >> >> If you have interpolate to the MNI-template grid you need to replace the >> source.pos with the set of grid positions from your template grid (i.e. >> expressed in MNI coordinates). >> >> >> Cheers, >> >> JM >> >> >> On Jun 27, 2012, at 5:26 PM, cornelius abel wrote: >> >> Hello, >> >> does anybody know how to get the uninterpolated source position giving >> the coordinates aquired after interpolation with an anatomy. >> In principle i want to get an individual source time course at the >> position i picked from the interpolated grand average source plot. Therfore >> i need the corresponding filter and its position in the source structure. >> >> I tried to get the position by applying the inverse transformation matrix >> of the used anatomy like: >> pos_before_interpolation=warp_apply(inv(anatomy.transform), >> position_after_interpolation); >> >> but that did not give usefull results :( >> >> Any ideas how it could be done? >> >> Greetings, Cornelius >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 drivolta81 at gmail.com Mon Jul 2 17:04:08 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Mon, 2 Jul 2012 17:04:08 +0200 Subject: [FieldTrip] Job advertisement: Research associate at the University of Glasgow Message-ID: *Research Associate, Institute of Neuroscience and Psychology, University of Glasgow* The Institute of Neuroscience and Psychology, University of Glasgow, has a vacancy for a Research Associate post for 3 years. The position contributes to a project entitled “Neural synchrony in neuropsychiatry and brain development”. Specifically, the job requires the analysis of existing MEG-data sets, data-acquisition and implementation of novel analytic tools, contributing to the design and programming of MEG experiments. *Responsibilities:* 1. To analyse MEG-data using complex time-frequency and source-localization techniques. 2. To assist in the supervision of data-acquisition and analysis-protocols. 3. To establish links with the MEG-expertise in the Institute and with international groups working in the field. 4. To recruit experimental subjects and to run the agreed behavioural and MEG-experiments, dealing with all aspects of testing the participants and storing data. 5. To perform statistical analyses of the experiments and to produce experimental reports describing these results. 6. To establish an expert reputation and track record in field/discipline. 7. Write up papers and identify high impact national and international journals for publication. 8. To contribute to the identification of potential funding sources and to assist in the securing of funding from external bodies to support future research. 9. To contribute fully to the planning and supervision of undergraduate students and postgraduate (PhD) students through day to day mentoring and longer term in planning research objectives. *Requirements:* 1. Ph.D or equivalent. 2. Extensive and up-to-date practical and theoretical knowledge in MEG or EEG. 3. Excellent knowledge of experimental statistics. 4. Excellent knowledge of source-localization techniques. 5. Excellent knowledge of Matlab and experimental control software. * * * * *Salary Range*** £31,948 - £35,938** * * *More Information:* 1. The position is available now (July 2012) 2. To apply, visit the University of Glasgow staff jobs website: * http://www.gla.ac.uk/about/jobs/* . Search for position 002148 3. For further info please contact: Dr. Peter Uhlhaas, peter.uhlhaas at brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Mon Jul 2 18:20:13 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Mon, 2 Jul 2012 18:20:13 +0200 Subject: [FieldTrip] Info about the power-line noise Message-ID: Dear fieldtrippers, I recently run into the attached figures (S01 files). It seems a failure of the power-line noise filter. I used the following settings quite succesfully for other subjects: cfg.dftfilter = 'yes'; cfg.padding = 10; An example of good figures are the "KAT" files. These data come from a visual task where people see moving concentrical gratings. Each trial has a different length that range between around 0.5 until 3 seconds. Would the bandstop filter be the only possible solution here? Thanks, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: S01_TFR1_high.png Type: image/png Size: 12615 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: S01_power_.png Type: image/png Size: 13211 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: KAT_TFR1_low.png Type: image/png Size: 11199 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: KAT_power_spectra1_high.png Type: image/png Size: 13236 bytes Desc: not available URL: From inieuwenhuis at berkeley.edu Mon Jul 2 18:38:37 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 02 Jul 2012 09:38:37 -0700 Subject: [FieldTrip] calculating correlation In-Reply-To: <1AA66D8B-3685-4A8F-AED3-A1FF8C7A8D21@donders.ru.nl> References: <4FF0AFFC.1040500@berkeley.edu> <1AA66D8B-3685-4A8F-AED3-A1FF8C7A8D21@donders.ru.nl> Message-ID: <4FF1CE8D.5020305@berkeley.edu> Hi JM! haha, sounds good, I'll contact you :) Cheers, Ingrid On 7/1/2012 11:53 PM, jan-mathijs schoffelen wrote: > Hi Ingrid, > > This calls for a statfun_corr or even a statfun_glm! It so happens > that I have some of these sitting on my hard drive. As you know I am > fond of beer, chocolate and co-authorships, so I am sure we can strike > a deal. I have not yet had the opportunity to contribute these > statfuns to FieldTrip, but now I sense a win-win-win situation: win 1 > is for me (beer/chocolate/co-authorships/etc), win 2 is for you (you > can compute your statistic of interest) and win 3 for the community > (where you test the code, write documentation on the wiki etcetc). How > does that sound for a plan? > > Cheers, > > JM > > On Jul 1, 2012, at 10:15 PM, Ingrid Nieuwenhuis wrote: > >> Hi FTers, >> >> I'd like to do two sorts of correlation calculations, and was >> wondering if there's any easy way to do this within FieldTrip. >> >> 1) I'd like to calculate the correlation between performance over >> trials and power within a specific frequency over trials. So I have >> the performance measure per trial, and my chan*freq measure after >> freqanalysis. So for each channel I have a series of power values >> (trials) and I have a series of performance measures (per trial), and >> now like to know (first within, and then over subjects) which >> channel's frequency power follows (correlates) with the performance. >> >> From the walkthrough >> I understand >> I can give in these performance measures through the design >> (cfg.design=[0.10.20.30.40.50.40.30.10.2];cfg.ivar=1;), but which >> method to use for ft_freqstatistics? I don't see statistics = >> 'correlation' or 'pearson' or 'spearman' in method = 'analytic. Also >> how to make the design to correlate over trials? >> >> 2) I'd like to calculate the correlation between the score on >> repeated questionnaire over participants with power within a >> frequency. So I have several power values per participant for each >> channel, and the repeated scores on the questionnaire for each >> participant. And now I'd like to calculate a value per channel >> reflecting the correlation over the repeats of the questionnaire and >> over participants. >> >> Any idea on FieldTrip settings? Both in general, is there a >> correlation statistics implemented, and more specifically for my >> question, how would I make the appropriate designs? >> >> Thanks so much! >> Ingrid >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> _______________________________________________ >> 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 -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Mon Jul 2 19:39:16 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Mon, 2 Jul 2012 18:39:16 +0100 Subject: [FieldTrip] calculating correlation In-Reply-To: <4FF0AFFC.1040500@berkeley.edu> References: <4FF0AFFC.1040500@berkeley.edu> Message-ID: Hi Ingrid, You're trying to test two very different things. 1) power-behavior correlation over trials, and differences between subjects are just unexplained variance. 2) power-behavior correlation across subjects. For 2) problem, I don't have anything to add to what Jan-Mathijs said. Correlation/GLM is very easy outside Fieldtrip but I hope Jan-Mathijs will include the GLM functions, it sounds very cool. For your "repeated questionnaires", I'd use a summary score (difference score for example) and do a simple correlation. For 1) problem, you could do a 2-level analysis, like SPM does for fMRI data: 1- you do correlation at the single-subject level, 2- you do a t-test on the slope (or your GLM column of interest), to test if it's different from zero. I don't know of Fieldtrip tools for this but I don't like this approach too much, because you lose quite some power and you don't model the trial-level noise. I've had some success using linear mixed-effects models for these types of research questions. There is the package lme4 in R which is very powerful. The only pain is to export data from Matlab and read them in R. You can get t-values from the linear mixed-effects models for each electrode/time point/freq point (unless you average over some dimension). Then you can use the cluster-level correction as implemented in Fieldtrip by flipping the sign of the t-statistics. There is some learning to do to use linear mixed-effects models but there are very flexible. Let me know if you need help with that. You can bribe me with the same things Jan-Mathijs likes... Hope this helps, 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 Sun, Jul 1, 2012 at 9:15 PM, Ingrid Nieuwenhuis wrote: > Hi FTers, > > I'd like to do two sorts of correlation calculations, and was wondering if > there's any easy way to do this within FieldTrip. > > 1) I'd like to calculate the correlation between performance over trials and > power within a specific frequency over trials. So I have the performance > measure per trial, and my chan*freq measure after freqanalysis. So for each > channel I have a series of power values (trials) and I have a series of > performance measures (per trial), and now like to know (first within, and > then over subjects) which channel's frequency power follows (correlates) > with the performance. > > From the walkthrough I understand I can give in these performance measures > through the design (cfg.design = [0.1 0.2 0.3 0.4 0.5 0.4 0.3 0.1 0.2]; > cfg.ivar= 1;), but which method to use for ft_freqstatistics? I don't see > statistics = 'correlation' or 'pearson' or 'spearman' in method = 'analytic. > Also how to make the design to correlate over trials? > > 2) I'd like to calculate the correlation between the score on repeated > questionnaire over participants with power within a frequency. So I have > several power values per participant for each channel, and the repeated > scores on the questionnaire for each participant. And now I'd like to > calculate a value per channel reflecting the correlation over the repeats of > the questionnaire and over participants. > > Any idea on FieldTrip settings? Both in general, is there a correlation > statistics implemented, and more specifically for my question, how would I > make the appropriate designs? > > Thanks so much! > Ingrid > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From inieuwenhuis at berkeley.edu Mon Jul 2 19:58:04 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 02 Jul 2012 10:58:04 -0700 Subject: [FieldTrip] calculating correlation In-Reply-To: References: <4FF0AFFC.1040500@berkeley.edu> Message-ID: <4FF1E12C.7010004@berkeley.edu> Hi Gio! Guys, where are the good old times of unconditional sharing between scientists for the greater good? ;) Must be the economy... Anyways, thanks! I'm just starting to learn R actually, I'll check out the lme4. Might be useful to include some FieldTrip to R functionality. I'll get in touch when I need help :) Cheers, Ingrid On 7/2/2012 10:39 AM, Gio Piantoni wrote: > Hi Ingrid, > > You're trying to test two very different things. > 1) power-behavior correlation over trials, and differences between > subjects are just unexplained variance. > 2) power-behavior correlation across subjects. > > For 2) problem, I don't have anything to add to what Jan-Mathijs said. > Correlation/GLM is very easy outside Fieldtrip but I hope Jan-Mathijs > will include the GLM functions, it sounds very cool. For your > "repeated questionnaires", I'd use a summary score (difference score > for example) and do a simple correlation. > > For 1) problem, you could do a 2-level analysis, like SPM does for > fMRI data: 1- you do correlation at the single-subject level, 2- you > do a t-test on the slope (or your GLM column of interest), to test if > it's different from zero. I don't know of Fieldtrip tools for this but > I don't like this approach too much, because you lose quite some power > and you don't model the trial-level noise. > I've had some success using linear mixed-effects models for these > types of research questions. There is the package lme4 in R which is > very powerful. The only pain is to export data from Matlab and read > them in R. You can get t-values from the linear mixed-effects models > for each electrode/time point/freq point (unless you average over some > dimension). Then you can use the cluster-level correction as > implemented in Fieldtrip by flipping the sign of the t-statistics. > There is some learning to do to use linear mixed-effects models but > there are very flexible. > Let me know if you need help with that. You can bribe me with the same > things Jan-Mathijs likes... > > Hope this helps, > > Gio > -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From johanna.zumer at donders.ru.nl Mon Jul 2 22:07:08 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Mon, 2 Jul 2012 22:07:08 +0200 Subject: [FieldTrip] Beamformer: different length of baseline and post baseline interval In-Reply-To: <1659120385.1619.1340961051346.JavaMail.root@zimbra> References: <1376177301.1612.1340961039830.JavaMail.root@zimbra> <1659120385.1619.1340961051346.JavaMail.root@zimbra> Message-ID: Dear Anna, Ideally for the common filter, you want the same amount of data T(s) per condition, where T = N x tw (and N is number of trials and tw is timewindow length). In your case, if the baselines for each conditions can be combined into one general baseline, and if you happen to have 100 trials per condition, then T_baseline = 3 x 100 x 0.5s = 150s. If you then use 1.5s length post-baseline, then T_each_condition = 100 x 1.5s = 150s, so you now have equal T for each condition for the common filter. However, in order to have an equal effect of tapers and edge-effects on the different conditions, you should use equal time window lengths in freqanalysis. Thus it would be better to split your post-baseline data into 3 segments of 500ms each before calling ft_freqanalysis, which again gives T = 100 x 0.5 x 3 = 150s. Cheers, Johanna 2012/6/29 Anna Wilsch > > Dear Fieldtrippers, > > I'm trying to beamform my MEG data by building a common filter including > three conditions and a baseline for each condition. The baseline intervals > have a duration of 500 ms. I was wondering if it is ok if the post-baseline > data are longer than that (1000 - 2000 ms). Does it have any negative > impact on the cross-spectral-density matrix and/or the common filter? Would > that still be a valid operation to do or is it necessary that baseline and > post baseline data have the same length? > Thank you for your comments. > > Cheers, > Anna > > > Anna Wilsch, Dipl.-Psych. > Auditory Cognition Research Group > Max Planck Institute for Human Cognitive and Brain Sciences > Stephanstr. 1a - Leipzig, Germany > (p) +49 (0)341 9940 2641 > (e) wilsch at cbs.mpg.de > > _______________________________________________ > 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 stan.vanpelt at fcdonders.ru.nl Tue Jul 3 09:17:47 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Tue, 3 Jul 2012 09:17:47 +0200 (CEST) Subject: [FieldTrip] Info about the power-line noise In-Reply-To: Message-ID: <997455910.845940.1341299867043.JavaMail.root@sculptor.zimbra.ru.nl> Hi Davide, Nice data (aside from what is indeed probably line noise). I see four approaches you could take, but not sure if it helps. You could just be unlucky with a very fluctuating line noise in this recording (see http://fieldtrip.fcdonders.nl/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter). The options I see: - Check if there is actually a datapadding up to 10 s. With already preprocessed data (e.g., after 3rd order gradiometer correction), it is not directly possible to data pad for subsequent dft-filtering. It happened to me not so long ago, that's why I ask. I made a workaround by first creating trials of 10s length, then do the dft-filetering, and after that cut the actual trials out. - If not already done, apply 3rd-order gradiometer correction first (ft_denoise_synthetic, or in the CTF DataEditor) - Use a bandstop-filter instead of the dft - Source-project the data. With my data that usually also gets rid of most line noise (I use LCMV to reconstruct a virtual sensor time course) Hope that helps. Stan ----- Oorspronkelijk bericht ----- > Van: "Davide Rivolta" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Maandag 2 juli 2012 18:20:13 > Onderwerp: [FieldTrip] Info about the power-line noise > Dear fieldtrippers, > I recently run into the attached figures (S01 files). It seems a > failure of the power-line noise filter. > I used the following settings quite succesfully for other subjects: > cfg.dftfilter = 'yes'; > cfg.padding = 10; > An example of good figures are the "KAT" files. > These data come from a visual task where people see moving > concentrical gratings. Each trial has a different length that range > between around 0.5 until 3 seconds. > Would the bandstop filter be the only possible solution here? > Thanks, > Davide > _______________________________________________ > 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 ivano_triggiani at yahoo.it Tue Jul 3 17:42:37 2012 From: ivano_triggiani at yahoo.it (Ivano Triggiani) Date: Tue, 3 Jul 2012 16:42:37 +0100 (BST) Subject: [FieldTrip] band pass and segmentation In-Reply-To: References: Message-ID: <1341330157.2152.YahooMailNeo@web28705.mail.ir2.yahoo.com> Hi all, I tried to use a simple cfg.bpfilter (0.1 - 40) for an EEG that I divide into 2 secs époques and giving a look it seems that at the board of every window the signal is reduced (just like following a parabolic trend). Is this a problem of the brutal segmentation (respect to a good windowing) or there's something else? Ivano -------------- next part -------------- An HTML attachment was scrubbed... URL: From andreas.wutz-1 at unitn.it Tue Jul 3 23:44:09 2012 From: andreas.wutz-1 at unitn.it (Wutz, Andreas) Date: Tue, 3 Jul 2012 23:44:09 +0200 Subject: [FieldTrip] Structure of 4D-Fourierspectrum with Multi-Taper Message-ID: Dear all, in requesting from a ft_freqanalysis with output ='fourier' and 2 multitapers, I figured out that in the 4D matrix in the field 'fourierspctrm' the first dimension refers to the number of tapers that are calculated (Number of trials -times- number of tapers). My question refers to the organization of this dimension. Are in the example with 2 tapers the two tapers from the same trial next to each other? Or do we have first, the outputs from the first taper for all the trials and then, all the trials for the 2nd taper? I would like to calculate the circular mean of the phase angles across trials and therefore would need to combine the outputs of the two tapers per trial. Is there already some fieldtrip function to do this? How should it be done? Thank you very much. Best Andreas Andreas Wutz PhD Student CIMeC - Center for Mind/Brain Sciences Università degli studi di Trento From jan.schoffelen at donders.ru.nl Wed Jul 4 09:19:30 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 4 Jul 2012 09:19:30 +0200 Subject: [FieldTrip] Structure of 4D-Fourierspectrum with Multi-Taper References: Message-ID: <6C2FF2A6-B080-424C-A01F-048215D181CD@donders.ru.nl> Hi Andreas, The tapers per trial are grouped together, i.e. it is according to the first scenario you sketch. Note that averaging fourier-coefficients across tapers is not correct, because each of the tapers induces a non-trivial phase shift. Phase differences however can be averaged across tapers, but for this you need a reference signal. Best, Jan-Mathijs On Jul 3, 2012, at 11:44 PM, Wutz, Andreas wrote: > Dear all, > > in requesting from a ft_freqanalysis with output ='fourier' and 2 multitapers, I figured out that in the 4D matrix in the field 'fourierspctrm' the first dimension refers to the number of tapers that are calculated (Number of trials -times- number of tapers). My question refers to the organization of this dimension. Are in the example with 2 tapers the two tapers from the same trial next to each other? Or do we have first, the outputs from the first taper for all the trials and then, all the trials for the 2nd taper? I would like to calculate the circular mean of the phase angles across trials and therefore would need to combine the outputs of the two tapers per trial. Is there already some fieldtrip function to do this? How should it be done? > > Thank you very much. > Best > Andreas > > Andreas Wutz > PhD Student > CIMeC - Center for Mind/Brain Sciences > Università degli studi di Trento > _______________________________________________ > 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 jm.horschig at donders.ru.nl Wed Jul 4 15:35:52 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 04 Jul 2012 15:35:52 +0200 Subject: [FieldTrip] Questions on High pass and Dft filtering In-Reply-To: References: Message-ID: <4FF446B8.8040600@donders.ru.nl> HI Philipp, > The issue with the continuous data is the following: I tried using > cfg = []; > cfg.channel = {'EEG'}; > cfg.datafile = dataset; > cfg.headerfile = dataset; > cfg.dataset = dataset; > > cfg.continuous = 'yes'; > > (cfg.padding = 10;) > cfg.dftfilter = 'yes'; > > filteredContinuousData = ft_preprocessing(cfg); > > but looking at averaged timelocked data for the subject, the data looks > identical to the result I get using no filter at all, i.e., contaminated by > strong line noise. Including padding makes no difference either, therefore > the brackets. I tested this with my own data as well with as synthetic signal. The line noise is reduced by a factor of ~8 (I looked at the Fourier spectrum of the filtered and the unfiltered signal).The problem you encounter is either caused by nonstationarity of the 50Hz component (i.e. a drift in power, see FAQ), or maybe your acquisition system is misspecifying the sampling frequency a bit - Robert says this might happen, see: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1571 In any case, it might help for you if you specify cfg.dftfreq = [49.6:0.2:50.4 100 150] or similar (depends on your padding parameter). That might help to filter a bit 'better' (but maybe a bandstop filter works better here). Best, Jörn -- 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 frsantos at fpce.up.pt Wed Jul 4 18:35:36 2012 From: frsantos at fpce.up.pt (Fernando Ricardo Santos) Date: Wed, 4 Jul 2012 16:35:36 +0000 Subject: [FieldTrip] Introductory EEG/ERP Summer School in Porto, Portugal Message-ID: <2BAB036A9BAEA44984A131DFCE446108722337EB@SRVMBX02.fpceup.psi.up.pt> Dear FieldTrip users, The Laboratory of Neuropsychopsysiology (University of Porto, Portugal) is organizing "I CAN – 1st Cognitive and Affective Neurophysiology Summer School: Acquisition, processing and analysis of EEG signal" -- September 3-8, 2012. This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. The course will cover an introduction to the EEG and ERP techniques, acquisition of electrophysiological data of brain activity, signal processing, and statistical analysis of the data. All the modules will have a practical hands-on component and all lectures will be held in English. Scientific Coordination: -Professor João Marques-Teixeira Course tutors: -Fernando Ferreira-Santos -Pedro R. Almeida Venue and dates: Faculty of Psychology and Educational Sciences of the University of Porto (Portugal), from the 3rd to the 8th of September of 2012. For additional information on the Summer School please follow the link: http://www.fpce.up.pt/labpsi/summerschool/ Thank you and best wishes to all, -- Fernando Ferreira-Santos Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Dr. Manuel Pereira da Silva 4200-392 Porto (Portugal) Tel. +351 226079700 (ext. 301) Email: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From omidabbasi2000 at gmail.com Thu Jul 5 14:06:23 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Thu, 5 Jul 2012 16:36:23 +0430 Subject: [FieldTrip] help to apply field trip (topography plotting) In-Reply-To: References: Message-ID: Dear Developer At first, I thank you for useful source code. This is Omid. I'm a student that work on biological signal processing. I want to use your source code for plotting data topography of brain. I downloaded your code from this link ( http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but i can't use it in my project, because i have 19 signals from 19 sites on the brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your code in my project with different channel and data? It would grateful for me if you could help me to apply your code in my project. Best Regards Omid -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Fri Jul 6 12:59:05 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Fri, 6 Jul 2012 12:59:05 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? Message-ID: Dear list members, I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. Any help with this issue is greatly aprreciated! Cheers, Ulrich From johanna.zumer at donders.ru.nl Fri Jul 6 14:36:04 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Fri, 6 Jul 2012 14:36:04 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: Message-ID: Dear Ulrich, Only if the leadfields are the same, can you use the common filter. If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. Cheers, Johanna 2012/7/6 Pomper, Ulrich > Dear list members, > I want to compare source data between two different groups (patients and > controls). Each patient has an age and gender-matched control. > Is it correct to compute a common filter for each pair of subjects? The > TF-topographies do look different within each pair, so I would assume that > the sources are somewhat different. However, as I'm going to statistically > compare the two groups it would be nice to have common filters, as > otherwise any finding could be due to different filters as opposed to > different sources. > > Any help with this issue is greatly aprreciated! > Cheers, Ulrich > _______________________________________________ > 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 Ulrich.Pomper at charite.de Fri Jul 6 15:21:23 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Fri, 6 Jul 2012 15:21:23 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: , Message-ID: Dear Johanna, thanks for your quick reply! To clarify things: This is an EEG study, using a standard MNI-based headmodel for all subjects. I have a between subjects factor group (patients, controls) and a within subjects factor condition (A, B). Also, I can use a within subject contrast (active versus baseline) for the source analysis. Currently, I use one common filter for baseline and active data as well as both conditions for each subject. So I end up using one common filter per subject. My question I whether it would be more correct to additionally pool the data from matched subjects into one single filter. Thus resulting in one common filter per pair. Cheers, Ulrich ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer [johanna.zumer at donders.ru.nl] Sent: Friday, July 06, 2012 2:36 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Common beamforming filters for different groups? Dear Ulrich, Only if the leadfields are the same, can you use the common filter. If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. Cheers, Johanna 2012/7/6 Pomper, Ulrich > Dear list members, I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. Any help with this issue is greatly aprreciated! Cheers, Ulrich _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus From kmanning at robarts.ca Fri Jul 6 18:59:20 2012 From: kmanning at robarts.ca (Kathryn Manning) Date: Fri, 6 Jul 2012 12:59:20 -0400 Subject: [FieldTrip] Connectivity analysis Message-ID: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> Dear FieldTrip list members, I am comparing the connectivity patterns in the brain measured using fMRI and electrophysiological recordings. I am trying to correlate the LFP signals as a function of time, using a sliding window analysis. I'm able to generate plots using ft_connectivityplot but this is as a function of frequency. From what I can tell the 'mtmconvol' method generates data with a time aspect in it's dimord, but are there any functions available in fieldtrip in order to calculate the correlation as a function of time? Any help would be greatly appreciated, thank you so much. Kathryn From Don.Rojas at ucdenver.edu Fri Jul 6 19:02:41 2012 From: Don.Rojas at ucdenver.edu (Rojas, Don) Date: Fri, 6 Jul 2012 11:02:41 -0600 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: , Message-ID: Ulrich, It does not make sense to me to have a common filter per pair of subjects, only between conditions within a subject (which you say you are currently doing). Since, as Johanna suggested, you are using a standard brain and standard electrode locations, rather than individual ones, you can have a common leadfield matrix for all subjects. However, I don't think you can have a common beamformer filter, since that is computed for each subject based on the covariance or cross spectral density matrix, which would be unique to each subject. Therefore, the beamformer filter, which uses both the covariance and the leadfield, would be unique for each individual. You can save time simply by having a common leadfield matrix. Best, Don ----------------------- Don Rojas, Ph.D. Associate Professor of Psychiatry U. of Colorado Denver Anschutz Medical Campus Director, UCD Magnetoencephalography Lab 13001 E. 17th Pl F546 Aurora, CO 80045 303-724-4994 On Jul 6, 2012, at 7:21 AM, Pomper, Ulrich wrote: > Dear Johanna, > thanks for your quick reply! > > To clarify things: This is an EEG study, using a standard MNI-based headmodel for all subjects. > > I have a between subjects factor group (patients, controls) and a within subjects factor condition (A, B). Also, I can use a within subject contrast (active versus baseline) for the source analysis. > > Currently, I use one common filter for baseline and active data as well as both conditions for each subject. So I end up using one common filter per subject. > > My question I whether it would be more correct to additionally pool the data from matched subjects into one single filter. Thus resulting in one common filter per pair. > > > Cheers, Ulrich > > > > > > > > > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer [johanna.zumer at donders.ru.nl] > Sent: Friday, July 06, 2012 2:36 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Common beamforming filters for different groups? > > Dear Ulrich, > > Only if the leadfields are the same, can you use the common filter. > > If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. > > If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. > > Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? > > Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. > > Cheers, > Johanna > > > 2012/7/6 Pomper, Ulrich > > Dear list members, > I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. > Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. > > Any help with this issue is greatly aprreciated! > Cheers, Ulrich > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg > > Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From politzerahless at gmail.com Sat Jul 7 02:46:14 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Sat, 7 Jul 2012 08:46:14 +0800 Subject: [FieldTrip] help to apply field trip (topography plotting) Message-ID: Hi Omid, Welcome to Fieldtrip. You can find a lot of information about how to use Fieldtrip at http://fieldtrip.fcdonders.nl/walkthrough and http://fieldtrip.fcdonders.nl/tutorial. In your case, you need to get your data imported into Fieldtrip's format in MATLAB ( http://fieldtrip.fcdonders.nl/tutorial/preprocessing), as well as your channel layout (http://fieldtrip.fcdonders.nl/tutorial/layout) before proceeding to plotting. Good luck, Steve > Message: 1 > Date: Thu, 5 Jul 2012 16:36:23 +0430 > From: omid abbasi > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] help to apply field trip (topography plotting) > Message-ID: > < > CAPc_m1utoA_ZqC8_0q44hz5FX3yMfWP-gfke5Mes9_sEUOuyrA at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Developer > > At first, I thank you for useful source code. > > This is Omid. I'm a student that work on biological signal processing. I > want to use your source code for plotting data topography of brain. I > downloaded your code from this link ( > http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but i > can't use it in my project, because i have 19 signals from 19 sites on the > brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your > code in my project with different channel and data? > > It would grateful for me if you could help me to apply your code in my > project. > > Best Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From skelly2 at ccny.cuny.edu Sat Jul 7 07:00:40 2012 From: skelly2 at ccny.cuny.edu (skelly2 at ccny.cuny.edu) Date: Sat, 7 Jul 2012 01:00:40 -0400 (EDT) Subject: [FieldTrip] Postdoc position in systems neuroscience, City College of New York Message-ID: <201207070500.028516@pelican.admin.ccny.cuny.edu> Postdoctoral position in systems neuroscience, City College of New York A postdoctoral "Endeavor Scientist" position funded by the Child Mind Institute (CMI) is available starting this Fall in the lab of Simon Kelly at the City College of New York. The endeavor scientist will work on basic and clinical projects mainly using human electroencephalogram (EEG) recordings, under the joint supervision of Simon Kelly (http://bme.ccny.cuny.edu/people/faculty/skelly) of the Department of Biomedical Engineering, CCNY and Michael Milham (http://www.childmind.org/en/directory/clinicians/mmilham) of CMI. The position will involve analysis of data obtained from clinical and non-clinical populations at the Child Mind Institute and its collaborators, in addition to conducting basic studies of perception and cognition in the Kelly lab, particularly focusing on decision making and attention. A major goal will be to develop novel paradigms and data analysis approaches that allow neural signals to be linked with well-defined perceptual/cognitive computations, and to deploy these paradigms and approaches to studies at CMI. Clinical studies will be mainly in child and adolescent populations associated with clinically significant anxiety, attentional dysfunction, emotional dysregulation and learning impairments. Any innovative tools developed in the course of this position will be made publicly available. Applicants must have a Ph.D. in neuroscience or related field, including neural/biomedical engineering, applied mathematics and computer science. The candidate must have strong analytic/quantitative skills, be proficient in programming (especially Matlab), and have experience in psychophysics and EEG recording and analysis. Experience with fMRI is a strong plus, as some projects may involve a multimodal EEG/fMRI approach. The ideal candidate will be reliable, highly motivated, and will be equally productive when working independently or cooperatively. Applicants should send a curriculum vitae, contact information for three references, and a cover letter with a brief description of past research accomplishments as well as future research interests and career goals to Simon Kelly at skelly2 at ccny.cuny.edu. From jan.schoffelen at donders.ru.nl Sat Jul 7 20:01:23 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Sat, 7 Jul 2012 20:01:23 +0200 Subject: [FieldTrip] Connectivity analysis In-Reply-To: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> References: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> Message-ID: Hi Kathryn, I believe that ft_connectivityanalysis is capable of dealing with frequency domain data that contain a time dimension. I assume here that you would like to compute coherence, rather than correlation. Last time I checked, ft_connectivityanalysis could not compute an ordinary correlation coefficient. Best wishes, Jan-Mathijs On Jul 6, 2012, at 6:59 PM, Kathryn Manning wrote: > Dear FieldTrip list members, > > I am comparing the connectivity patterns in the brain measured using fMRI and electrophysiological recordings. I am trying to correlate the LFP signals as a function of time, using a sliding window analysis. I'm able to generate plots using ft_connectivityplot but this is as a function of frequency. From what I can tell the 'mtmconvol' method generates data with a time aspect in it's dimord, but are there any functions available in fieldtrip in order to calculate the correlation as a function of time? > > Any help would be greatly appreciated, thank you so much. > > Kathryn > _______________________________________________ > 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 bertram0611 at pku.edu.cn Sun Jul 8 09:50:20 2012 From: bertram0611 at pku.edu.cn (=?utf-8?B?6JSh5p6X?=) Date: Sun, 8 Jul 2012 15:50:20 +0800 (CST) Subject: [FieldTrip] =?gbk?q?How_to_import_*=2Ecnt_datafile_from_NeuroScan?= =?gbk?q?=3F?= Message-ID: <283648358.226.1341733820039.JavaMail.root@bj-mail07.pku.edu.cn> Dear FieldTrip list members, I wanna analyse the *.cnt datafile from NeuroScan. But I don't know how to do that. Because there are not detailed scripts. In my exp, the trigger code is 14. I don't what is eventvalue that equals trigger code? My EEG was recorded from 62 Ag/AgCl electrodes mounted in an elastic cap (Quick-Cap, NeuroScan Inc.,Herndon, Virginia, USA). Recordings were referenced to the left mastoid, but rereferenced to linked mastoids offline. The horizontal and vertical electrooculogram was also monitored. Electrode impedances were kept below 5 kO. The EEG and electrooculogram were amplified with a band-pass from DC to 70Hz and the sample rate was 500 Hz.The epoch interval was 1200ms, ranging from 200ms before the onset of the critical word to 1000 ms after it.I used a 100-ms poststimulus baseline for the critical words. can you give an example that analysing *.cnt data. my script and problems as follows: cfg = [] cfg.datafile = 's01.cnt' cfg.headerfile = 's01.cnt' cfg.channel = 'all' cfg.eventvalue = '14' raw = ft_definetrial(cfg); Warning: no trialfun was specified, using trialfun_general > In ft_definetrial at 123 evaluating trialfunction 'trialfun_general' ??? Reference to non-existent field 'trialdef'. Error in ==> trialfun_general at 29 if isfield(cfg.trialdef, 'eventvalue') && isempty(cfg.trialdef.eventvalue ), cfg.trialdef = rmfield(cfg.trialdef, 'eventvalue' ); end Error in ==> ft_definetrial at 175 [trl, event] = feval(cfg.trialfun, cfg); best regards -- Lin Cai Department of Psychology, Peking University, Beijing 100871, P.R.China From politzerahless at gmail.com Sun Jul 8 12:32:02 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Sun, 8 Jul 2012 18:32:02 +0800 Subject: [FieldTrip] How to import *.cnt datafile from NeuroScan? Message-ID: Hello Lin, In your code you need to specify an event type. To find out what the event type is, you can run ft_definetrial() with cfg.trialdef.eventtype='?', and it will tell you what event types are present in the file (see my sample below): addpath 'C:\Program Files\MATLAB\R2010a\toolbox\fieldtrip-20120512'; cd 'C:\Users\SJPA\Documents\MATLAB'; cfg = []; cfg.dataset = 'myneuroscanfile.cnt'; cfg.trialdef.eventtype = '?' cfg = ft_definetrial(cfg); After that, you can use that event type, along with cfg.dataset and cfg.trialdef.eventvalue, to define trials and import the data; see my example below (this code will take a continuous file but it will epoch it while importing, so you will end up with epoched data; also note, as far as I know, you don't need to specify cfg.headerfile) addpath 'C:\Program Files\MATLAB\R2010a\toolbox\fieldtrip-20120512'; cd 'C:\Users\SJPA\Documents\MATLAB'; cfg = []; cfg.dataset = 'myneuroscanfile.cnt'; cfg.trialdef.eventtype = 'trial'; cfg.trialdef.eventvalue = [4 5 6 7]; cfg = ft_definetrial(cfg); cfg.channel = []; cfg.continuous = 'yes'; data = ft_preprocessing(cfg); I noticed your e-mail signature says you are at Peking University; I am actually also at the psychology department in PKU and will be here until July 17th, if you need assistance feel free to contact me! Best, Steve Politzer-Ahles > > Message: 2 > Date: Sun, 8 Jul 2012 15:50:20 +0800 (CST) > From: ?? > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] How to import *.cnt datafile from NeuroScan? > Message-ID: > <283648358.226.1341733820039.JavaMail.root at bj-mail07.pku.edu.cn> > Content-Type: text/plain; charset=utf-8 > > Dear FieldTrip list members, > > I wanna analyse the *.cnt datafile from NeuroScan. But I don't know how to > do that. Because there are not detailed scripts. In my exp, the trigger > code is 14. I don't what is eventvalue that equals trigger code? My EEG was > recorded from 62 Ag/AgCl electrodes mounted in an elastic cap (Quick-Cap, > NeuroScan Inc.,Herndon, Virginia, USA). Recordings were referenced to the > left mastoid, but rereferenced to linked mastoids offline. The horizontal > and vertical electrooculogram was also monitored. Electrode impedances were > kept below 5 kO. The EEG and electrooculogram were amplified with a > band-pass from DC to 70Hz and the sample rate was 500 Hz.The epoch interval > was 1200ms, ranging from 200ms before the onset of the critical word to > 1000 ms after it.I used a 100-ms poststimulus baseline for the critical > words. > can you give an example that analysing *.cnt data. > my script and problems as follows: > cfg = [] > cfg.datafile = 's01.cnt' > cfg.headerfile = 's01.cnt' > cfg.channel = 'all' > cfg.eventvalue = '14' > raw = ft_definetrial(cfg); > Warning: no trialfun was specified, using trialfun_general > > In ft_definetrial at 123 > evaluating trialfunction 'trialfun_general' > ??? Reference to non-existent field 'trialdef'. > > Error in ==> trialfun_general at 29 > if isfield(cfg.trialdef, 'eventvalue') && isempty(cfg.trialdef.eventvalue > ), > cfg.trialdef = rmfield(cfg.trialdef, 'eventvalue' ); end > > Error in ==> ft_definetrial at 175 > [trl, event] = feval(cfg.trialfun, cfg); > best regards > > -- > Lin Cai > Department of Psychology, Peking University, Beijing 100871, P.R.China > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 20, Issue 12 > ***************************************** > -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From omidabbasi2000 at gmail.com Sun Jul 8 13:28:31 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Sun, 8 Jul 2012 15:58:31 +0430 Subject: [FieldTrip] help to apply field trip (topography plotting) In-Reply-To: References: Message-ID: Dear Steve Thank you very much for your good guidance. I review these links and if i have any question i will ask you again. Best Regards Omid On Sat, Jul 7, 2012 at 5:16 AM, Stephen Politzer-Ahles < politzerahless at gmail.com> wrote: > Hi Omid, > > Welcome to Fieldtrip. You can find a lot of information about how to use > Fieldtrip at http://fieldtrip.fcdonders.nl/walkthrough and > http://fieldtrip.fcdonders.nl/tutorial. In your case, you need to get > your data imported into Fieldtrip's format in MATLAB ( > http://fieldtrip.fcdonders.nl/tutorial/preprocessing), as well as your > channel layout (http://fieldtrip.fcdonders.nl/tutorial/layout) before > proceeding to plotting. > > Good luck, > Steve > > >> Message: 1 >> Date: Thu, 5 Jul 2012 16:36:23 +0430 >> From: omid abbasi >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] help to apply field trip (topography plotting) >> Message-ID: >> < >> CAPc_m1utoA_ZqC8_0q44hz5FX3yMfWP-gfke5Mes9_sEUOuyrA at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear Developer >> >> At first, I thank you for useful source code. >> >> This is Omid. I'm a student that work on biological signal processing. I >> want to use your source code for plotting data topography of brain. I >> downloaded your code from this link ( >> http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but >> i >> can't use it in my project, because i have 19 signals from 19 sites on the >> brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your >> code in my project with different channel and data? >> >> It would grateful for me if you could help me to apply your code in my >> project. >> >> Best Regards >> > > _______________________________________________ > 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 omidabbasi2000 at gmail.com Mon Jul 9 07:06:35 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Mon, 9 Jul 2012 09:36:35 +0430 Subject: [FieldTrip] Bipolar montage Message-ID: Dear Member lists I have .txt file of monopolar montage of EEG (EEG1020, 19 channel). How can i have bipolar montage of it? What's the relationship between bipolar montage and monopolar montage? Best Regards Omid -------------- next part -------------- An HTML attachment was scrubbed... URL: From ith at deakin.edu.au Mon Jul 9 09:26:03 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Mon, 9 Jul 2012 07:26:03 +0000 Subject: [FieldTrip] plotting dipoles on an anatomical mri Message-ID: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> Dear fieldTrip users, I am doing a dipole fit with the ft_dipolefitting function and I can plot and visualize the results with ft_plot_dipole, further I also want to compare the results with a beamformer results so, I tried plotting the ft_dipolefitting results with ft_sourceplot. I cannot yet very well understand how ft_sourceplot works, I understand that the dipole should be assigned with some value but cannot figure out how to do this. Can someone please give me some help in doing this? Following is the code I am using, where should I modify? cfg = []; cfg.location = dip_fitted.dip.pos; cfg.method='ortho'; ft_sourceplot(cfg,mri) where mri is the standard_mri.mat . I work in the MNI coordinates and my locations are in mm's. Thank you very much in advance. Kind regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr [Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 29155 bytes Desc: image001.jpg URL: From r.oostenveld at donders.ru.nl Mon Jul 9 09:40:56 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 9 Jul 2012 09:40:56 +0200 Subject: [FieldTrip] Bipolar montage In-Reply-To: References: Message-ID: <4E3F9B02-6C6D-4EA0-BADF-85A33B005C2D@donders.ru.nl> Dear Omid The option cfg.montage in ft_preprocessing allows you to convert your data between a monopolar to a bipolar montage. See the help of ft_preprocessing and the help of ft_apply_montage (which is the lower-level function that does the actual work). best regards, Robert On 9 Jul 2012, at 7:06, omid abbasi wrote: > Dear Member lists > > I have .txt file of monopolar montage of EEG (EEG1020, 19 channel). How can i have bipolar montage of it? What's the relationship between bipolar montage and monopolar montage? > > Best Regards > Omid > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Ulrich.Pomper at charite.de Mon Jul 9 09:51:56 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Mon, 9 Jul 2012 09:51:56 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: , , Message-ID: Thanks Don for you help! Best, Ulrich ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Rojas, Don [Don.Rojas at ucdenver.edu] Sent: Friday, July 06, 2012 7:02 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Common beamforming filters for different groups? Ulrich, It does not make sense to me to have a common filter per pair of subjects, only between conditions within a subject (which you say you are currently doing). Since, as Johanna suggested, you are using a standard brain and standard electrode locations, rather than individual ones, you can have a common leadfield matrix for all subjects. However, I don't think you can have a common beamformer filter, since that is computed for each subject based on the covariance or cross spectral density matrix, which would be unique to each subject. Therefore, the beamformer filter, which uses both the covariance and the leadfield, would be unique for each individual. You can save time simply by having a common leadfield matrix. Best, Don ----------------------- Don Rojas, Ph.D. Associate Professor of Psychiatry U. of Colorado Denver Anschutz Medical Campus Director, UCD Magnetoencephalography Lab 13001 E. 17th Pl F546 Aurora, CO 80045 303-724-4994 On Jul 6, 2012, at 7:21 AM, Pomper, Ulrich wrote: > Dear Johanna, > thanks for your quick reply! > > To clarify things: This is an EEG study, using a standard MNI-based headmodel for all subjects. > > I have a between subjects factor group (patients, controls) and a within subjects factor condition (A, B). Also, I can use a within subject contrast (active versus baseline) for the source analysis. > > Currently, I use one common filter for baseline and active data as well as both conditions for each subject. So I end up using one common filter per subject. > > My question I whether it would be more correct to additionally pool the data from matched subjects into one single filter. Thus resulting in one common filter per pair. > > > Cheers, Ulrich > > > > > > > > > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer [johanna.zumer at donders.ru.nl] > Sent: Friday, July 06, 2012 2:36 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Common beamforming filters for different groups? > > Dear Ulrich, > > Only if the leadfields are the same, can you use the common filter. > > If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. > > If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. > > Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? > > Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. > > Cheers, > Johanna > > > 2012/7/6 Pomper, Ulrich > > Dear list members, > I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. > Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. > > Any help with this issue is greatly aprreciated! > Cheers, Ulrich > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg > > Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus > > _______________________________________________ > 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 -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus From r.oostenveld at donders.ru.nl Mon Jul 9 10:02:16 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 9 Jul 2012 10:02:16 +0200 Subject: [FieldTrip] plotting dipoles on an anatomical mri In-Reply-To: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> References: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> Message-ID: Dear Imali The ft_sourceplot function was not designed to plot 3D data in combination with dipoles. If you use method=ortho, you can get the 3 intersections in the 3D volume at the location of the dipole. For the best control over the details of the plot, which you need for your specific application of combining dipoles and volumetric data, I suggest that you look at the ft_plot_slice function. If you do three ft_plot_slice calls for the three orientations (x,y,z) at the location of the dipole and combine that with ft_plot_dipole, you will probably visualize the 3D relation between the two types of data the clearest. Note that ft_plot_slice plots any slice in 3D, so you should use the 3D rotate option of the MATLAB figure. best regards, Robert On 9 Jul 2012, at 9:26, IMALI THANUJA HETTIARACHCHI wrote: > Dear fieldTrip users, > > I am doing a dipole fit with the ft_dipolefitting function and I can plot and visualize the results with ft_plot_dipole, further I also want to compare the results with a beamformer results so, I tried plotting the ft_dipolefitting results with ft_sourceplot. I cannot yet very well understand how ft_sourceplot works, I understand that the dipole should be assigned with some value but cannot figure out how to do this. > > Can someone please give me some help in doing this? Following is the code I am using, where should I modify? > > cfg = []; > cfg.location = dip_fitted.dip.pos; > cfg.method='ortho'; > ft_sourceplot(cfg,mri) > > where mri is the standard_mri.mat . I work in the MNI coordinates and my locations are in mm’s. > > > Thank you very much in advance. > > Kind regards > Imali > > Imali Thanuja Hettiarachchi > PhD Candidate > Centre for Intelligent Systems research > Deakin University, Geelong 3217, Australia. > Email: ith at deakin.edu.au > www.deakin.edu.au/cisr > > > > > > > _______________________________________________ > 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 omidabbasi2000 at gmail.com Mon Jul 9 10:35:45 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Mon, 9 Jul 2012 13:05:45 +0430 Subject: [FieldTrip] Bipolar montage In-Reply-To: <4E3F9B02-6C6D-4EA0-BADF-85A33B005C2D@donders.ru.nl> References: <4E3F9B02-6C6D-4EA0-BADF-85A33B005C2D@donders.ru.nl> Message-ID: Dear Robert Thank you for your fast answer I'll check it. Best Regards Omis On Mon, Jul 9, 2012 at 12:10 PM, Robert Oostenveld < r.oostenveld at donders.ru.nl> wrote: > Dear Omid > > The option cfg.montage in ft_preprocessing allows you to convert your data > between a monopolar to a bipolar montage. See the help of ft_preprocessing > and the help of ft_apply_montage (which is the lower-level function that > does the actual work). > > best regards, > Robert > > > On 9 Jul 2012, at 7:06, omid abbasi wrote: > > > Dear Member lists > > > > I have .txt file of monopolar montage of EEG (EEG1020, 19 channel). How > can i have bipolar montage of it? What's the relationship between bipolar > montage and monopolar montage? > > > > Best Regards > > Omid > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 9 11:48:18 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 09 Jul 2012 11:48:18 +0200 Subject: [FieldTrip] band pass and segmentation In-Reply-To: <1341330157.2152.YahooMailNeo@web28705.mail.ir2.yahoo.com> References: <1341330157.2152.YahooMailNeo@web28705.mail.ir2.yahoo.com> Message-ID: <4FFAA8E2.70100@donders.ru.nl> Hi Ivano, I don't understand your request exactly, could you attach an example figure and explain your issue by using that? Then I (or someone else) might be able to help you out. Best, Jörn On 7/3/2012 5:42 PM, Ivano Triggiani wrote: > Hi all, > > I tried to use a simple cfg.bpfilter (0.1 - 40) for an EEG that I > divide into 2 secs époques and giving a look it seems that at the > board of every window the signal is reduced (just like following a > parabolic trend). Is this a problem of the brutal segmentation > (respect to a good windowing) or there's something else? > > Ivano > > > > _______________________________________________ > 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 Mon Jul 9 12:17:33 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 09 Jul 2012 12:17:33 +0200 Subject: [FieldTrip] Fwd: Re: band pass and segmentation In-Reply-To: <1341828068.24326.YahooMailNeo@web28706.mail.ir2.yahoo.com> References: <1341828068.24326.YahooMailNeo@web28706.mail.ir2.yahoo.com> Message-ID: <4FFAAFBD.4080107@donders.ru.nl> Dear Ivano, I am forwarding your message and my reply to the discussion list again, so that others might benefit or add information. What you see looks to me pretty much like a filter artifact, which is common to occur at the edges of your signal. In order to reduce these, you can think of changing the order of your filter or, more ideal in my opinion, use filterpadding. You can either let FieldTrip do that by specifying cfg.padding or by defining your trials in a wider range (e.g. add 1s pre and post time of interest) and then only plot the time of interest, with the knowledge that the 1s padding before and after is corrupted by filter artifacts. Best, Jörn -------- Original Message -------- Subject: Re: [FieldTrip] band pass and segmentation Date: Mon, 9 Jul 2012 11:01:08 +0100 (BST) From: Ivano Triggiani Reply-To: Ivano Triggiani To: "Jörn M. Horschig" Hi Jorn, in attach an example. you can see in the third slide on the right the channel that "goes down". Thanks, Ivano ------------------------------------------------------------------------ "No man can wear one face to himself and another to the multitude, without finally getting bewildered as to which one is true." Nathaniel Hawthorne ------------------------------------------------------------------------ *Da:* ""Jörn M. Horschig"" *A:* Ivano Triggiani ; FieldTrip discussion list *Inviato:* Lunedì 9 Luglio 2012 11:48 *Oggetto:* Re: [FieldTrip] band pass and segmentation Hi Ivano, I don't understand your request exactly, could you attach an example figure and explain your issue by using that? Then I (or someone else) might be able to help you out. Best, Jörn On 7/3/2012 5:42 PM, Ivano Triggiani wrote: > Hi all, > > I tried to use a simple cfg.bpfilter (0.1 - 40) for an EEG that I > divide into 2 secs époques and giving a look it seems that at the > board of every window the signal is reduced (just like following a > parabolic trend). Is this a problem of the brutal segmentation > (respect to a good windowing) or there's something else? > > Ivano > > > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: Fieldtrip_EEG.ppt Type: application/vnd.ms-powerpoint Size: 169984 bytes Desc: not available URL: From vitoria.piai at gmail.com Mon Jul 9 15:18:47 2012 From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=) Date: Mon, 09 Jul 2012 15:18:47 +0200 Subject: [FieldTrip] plot functions and illustrator: set(gcf, 'interpreter', 'zbuffer') Message-ID: <4FFADA37.5070004@gmail.com> Hi, On the FT page, Roemer said that using set(gcf,'interpreter','zbuffer') may resolve problems when exporting from matlab as .eps and opening in Illustrator. That works fine for sensor-level data, for example TFRs with ft_singleplotTFR. But it doesn't work when, for example, using ft_sourceplot (I've akes around and I don't seem to be the only one having this problem). But ok, so far so good, I can get around it. But now I have an analysis I ran with LCMV for which I wanted to plot the results. Interestingly, if I use ft_singleplotTFR in this case, I cannot fix the bug with set(gcf,'interpreter','zbuffer'). It seems to behave like when using ft_sourceplot, instead of behaving as ft_singleplot when plotting sensor-level data. Has anyone dealt with this bug before? I mean, not being able to fix it with set(gcf,'interpreter','zbuffer')? Thanx a lot, Vitoria -- ** Please consider the environment - do you really need to print? ** From kmanning at robarts.ca Mon Jul 9 15:19:16 2012 From: kmanning at robarts.ca (Kathryn Manning) Date: Mon, 9 Jul 2012 09:19:16 -0400 Subject: [FieldTrip] Connectivity analysis In-Reply-To: References: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> Message-ID: <9EC69CEB-0315-4823-B241-71ED4649B9D5@robarts.ca> Thanks for your help! Best wishes, Kathryn On 2012-07-07, at 2:01 PM, jan-mathijs schoffelen wrote: Hi Kathryn, I believe that ft_connectivityanalysis is capable of dealing with frequency domain data that contain a time dimension. I assume here that you would like to compute coherence, rather than correlation. Last time I checked, ft_connectivityanalysis could not compute an ordinary correlation coefficient. Best wishes, Jan-Mathijs On Jul 6, 2012, at 6:59 PM, Kathryn Manning wrote: Dear FieldTrip list members, I am comparing the connectivity patterns in the brain measured using fMRI and electrophysiological recordings. I am trying to correlate the LFP signals as a function of time, using a sliding window analysis. I'm able to generate plots using ft_connectivityplot but this is as a function of frequency. From what I can tell the 'mtmconvol' method generates data with a time aspect in it's dimord, but are there any functions available in fieldtrip in order to calculate the correlation as a function of time? Any help would be greatly appreciated, thank you so much. Kathryn _______________________________________________ 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 stephen.whitmarsh at gmail.com Mon Jul 9 15:45:03 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Mon, 9 Jul 2012 15:45:03 +0200 Subject: [FieldTrip] plot functions and illustrator: set(gcf, 'interpreter', 'zbuffer') In-Reply-To: <4FFADA37.5070004@gmail.com> References: <4FFADA37.5070004@gmail.com> Message-ID: Hi Vitoria, Not really answering your questions, but from my experience I wouldn't export vector graphics of source data - just too many vectors. Instead why not export to high resolution (e.g. '-r600') png instead? I know my computer can certainly deal with those with less memory problems, I don't need to do anything vector-like on those images that I can't do on a bitmap. Cheers! Stephen p.s. same goes for fine-grained TFR's On 9 July 2012 15:18, Vitória Magalhães Piai wrote: > Hi, > > On the FT page, Roemer said that using set(gcf,'interpreter','**zbuffer') > may resolve problems when exporting from matlab as .eps and opening in > Illustrator. > > That works fine for sensor-level data, for example TFRs with > ft_singleplotTFR. But it doesn't work when, for example, using > ft_sourceplot (I've akes around and I don't seem to be the only one having > this problem). But ok, so far so good, I can get around it. > > But now I have an analysis I ran with LCMV for which I wanted to plot the > results. Interestingly, if I use ft_singleplotTFR in this case, I cannot > fix the bug with set(gcf,'interpreter','**zbuffer'). It seems to behave > like when using ft_sourceplot, instead of behaving as ft_singleplot when > plotting sensor-level data. > > Has anyone dealt with this bug before? I mean, not being able to fix it > with set(gcf,'interpreter','**zbuffer')? > > Thanx a lot, Vitoria > > > -- > ** Please consider the environment - do you really need to print? ** > > ______________________________**_________________ > 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 styll at med.ovgu.de Mon Jul 9 15:51:41 2012 From: styll at med.ovgu.de (styll at med.ovgu.de) Date: Mon, 9 Jul 2012 15:51:41 +0200 Subject: [FieldTrip] Problems with ft_app​ endata - merging dat​ asets​ Message-ID: <2854bfbc1930cfbba485e0aeb7488e16.squirrel@neuro2.med.uni-magdeburg.de> Hello, I probably have a problem with the use of ft_appendata. I want to merge 4 MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, etc.) of the same subject after I defined my trials of interest and preprocessed the 4 datasets individually. If I use ft_databrowser for a look into every single dataset, all trials (10 in each run/dataset) seems to be OK with the correct sequence: defined prestim time range, trigger and poststim time range. If I check the merged dataset I can go through all of the 40 trials, but there is no sequence like: prestim time range, trigger and poststim-time. Here is my pipeline for the first steps: %%%% run1 cfg.dataset=' \train01_64\run1\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run1'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_1 = ft_preprocessing(cfg) %%%% run2 cfg.dataset=' \train01_64\run2\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run2'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_2 = ft_preprocessing(cfg) the same for run3 and run4 %%%% merging the data cfg=[]; merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, prepro_run_4) Do I miss something or is there in error in my pipeline or in my strategy Best regards Sascha From styll at med.ovgu.de Mon Jul 9 15:56:52 2012 From: styll at med.ovgu.de (styll at med.ovgu.de) Date: Mon, 9 Jul 2012 15:56:52 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> Message-ID: <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> Hello, I probably have a problem with the use of ft_appendata. I want to merge 4 MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, etc.) of the same subject after I defined my trials of interest and preprocessed the 4 datasets individually. If I use ft_databrowser for a look into every single dataset, all trials (10 in each run/dataset) seems to be OK with the correct sequence: defined prestim time range, trigger and poststim time range. If I check the merged dataset I can go through all of the 40 trials, but there is no sequence like: prestim time range, trigger and poststim-time. Here is my pipeline for the first steps: %%%% run1 cfg.dataset=' \train01_64\run1\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run1'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_1 = ft_preprocessing(cfg) %%%% run2 cfg.dataset=' \train01_64\run2\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run2'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_2 = ft_preprocessing(cfg) the same for run3 and run4 %%%% merging the data cfg=[]; merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, prepro_run_4) Do I miss something or is there in error in my pipeline or in my strategy Best regards Sascha From dporada at uos.de Mon Jul 9 18:29:37 2012 From: dporada at uos.de (Porada Danja) Date: Mon, 9 Jul 2012 18:29:37 +0200 Subject: [FieldTrip] explained variance by ICA components Message-ID: <113D5DB2-88D7-4632-9F41-3DA2F409CF4B@uos.de> Hi, I computed an ICA on my MEG data. When I plot the components with the databrowser they are sorted according to variance in the data they accounted for. Or am I wrong? Where are those values saved? I want to know for each component how much variance it explains. Best, Danja From marco.rotonda at gmail.com Mon Jul 9 20:15:34 2012 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Mon, 9 Jul 2012 20:15:34 +0200 Subject: [FieldTrip] LARS and LASSO for connectivity Message-ID: Dear FieldTrip experts, I wasn't so happy to choose some ROIs with a priori knowledge in a GC analysis. So I searched a bit and I've found this wonderful solution which take care of all the voxels: http://www.ncbi.nlm.nih.gov/pubmed/21439388 Full-brain auto-regressive modeling (FARM) using fMRI Since there is already ft_mvaranalysis and ft_connectivityanalysis do you think that is possible to integrate the FARM approach into those functions? Regards, Marco From marco.rotonda at gmail.com Mon Jul 9 21:25:34 2012 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Mon, 9 Jul 2012 21:25:34 +0200 Subject: [FieldTrip] LARS and LASSO for connectivity Message-ID: Dear FieldTrip experts, I wasn't so happy to choose only some ROIs in a GC analysis. So I searched a bit and I've found this wonderful solution which take care of all the voxels: http://www.ncbi.nlm.nih.gov/pubmed/21439388 Full-brain auto-regressive modeling (FARM) using fMRI Since there are already ft_mvaranalysis and ft_connectivityanalysis, do you think that is possible to integrate the FARM approach into those functions? Regards, Marco From ith at deakin.edu.au Tue Jul 10 05:42:55 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Tue, 10 Jul 2012 03:42:55 +0000 Subject: [FieldTrip] plotting dipoles on an anatomical mri In-Reply-To: References: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> Message-ID: <5A1787011651BC42A4D41856DBC2E0603E047A96@mbox-f-3.du.deakin.edu.au> Dear Robert, Thank you very much for the very quick reply and the explaining. I am a bit struggling in the exact usage of ft_slice_plot function. I was trying to dig up on an example usage but was unable to find any. What does exactly in the use ft_plot_slice(dat, ...) , dat argument stands for? Can you please explain me on how to plot a 2D slice using the function? Thank you very much again. Regards Imali From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Robert Oostenveld Sent: Monday, 9 July 2012 6:02 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] plotting dipoles on an anatomical mri Dear Imali The ft_sourceplot function was not designed to plot 3D data in combination with dipoles. If you use method=ortho, you can get the 3 intersections in the 3D volume at the location of the dipole. For the best control over the details of the plot, which you need for your specific application of combining dipoles and volumetric data, I suggest that you look at the ft_plot_slice function. If you do three ft_plot_slice calls for the three orientations (x,y,z) at the location of the dipole and combine that with ft_plot_dipole, you will probably visualize the 3D relation between the two types of data the clearest. Note that ft_plot_slice plots any slice in 3D, so you should use the 3D rotate option of the MATLAB figure. best regards, Robert On 9 Jul 2012, at 9:26, IMALI THANUJA HETTIARACHCHI wrote: Dear fieldTrip users, I am doing a dipole fit with the ft_dipolefitting function and I can plot and visualize the results with ft_plot_dipole, further I also want to compare the results with a beamformer results so, I tried plotting the ft_dipolefitting results with ft_sourceplot. I cannot yet very well understand how ft_sourceplot works, I understand that the dipole should be assigned with some value but cannot figure out how to do this. Can someone please give me some help in doing this? Following is the code I am using, where should I modify? cfg = []; cfg.location = dip_fitted.dip.pos; cfg.method='ortho'; ft_sourceplot(cfg,mri) where mri is the standard_mri.mat . I work in the MNI coordinates and my locations are in mm's. Thank you very much in advance. Kind regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr _______________________________________________ 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 biomag.network.practical at gmail.com Tue Jul 10 09:21:37 2012 From: biomag.network.practical at gmail.com (Biomag Networks Satellite 25 Aug 2012) Date: Tue, 10 Jul 2012 09:21:37 +0200 Subject: [FieldTrip] Biomag Satellite Announcement: Open for Registration In-Reply-To: References: Message-ID: Dear Biomag community, A final reminder that you can still sign up for this Biomag Satellite Workshop on Practical Considerations for Network Analysis, until the end of this week (July 13 final deadline)! Please see link and details below. Best regards, Ole Jensen, Sarang Dalal, and Johanna Zumer On Mon, Apr 2, 2012 at 4:44 PM, Biomag Networks Satellite 25 Aug 2012 < biomag.network.practical at gmail.com> wrote: > 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 ith at deakin.edu.au Tue Jul 10 10:05:51 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Tue, 10 Jul 2012 08:05:51 +0000 Subject: [FieldTrip] Beamformer results for simulated data Message-ID: <5A1787011651BC42A4D41856DBC2E0603E047B22@mbox-f-3.du.deakin.edu.au> Dear fieldTrip Users, I am trying to run a dipole fit with the nonlinear grid search and a beamformer scan on a simulated data set, to compare the results. My simulated dipole is at the MNI coordinates [32.8 -85.8 28]. It is shown in red in DIP_1.jpg. The ft_dipolefitting results for the simulated dipole is in green in DIP_1.jpg. When I do the lcmv beamformer scan on the same simulated data and plot them I get results as in POW_1.jpg for avg.pow parameter and NAI_1.jpg for avg.nai parameter. Following is the code I use for the above purpose; cfg = []; cfg.vol = curry_vol; cfg.elec = sens; cfg.grid=template_grid; cfg.method = 'lcmv'; cfg.lambda='5%'; cfg.projectnoise='yes'; source = ft_sourceanalysis(cfg, timelock); load standard_mri.mat mri = ft_volumereslice([], mri); %% Figure POW_1.jpg % Aligning the measure of power increase with the structural MRI of subject cfg=[]; cfg.downsample=2; cfg.parameter='avg.pow'; source_int=ft_sourceinterpolate(cfg,source,mri); % Plot the interpolated data cfg=[]; cfg.method='slice'; cfg.funparameter='avg.pow'; figure,ft_sourceplot(cfg,source_int) %% Figure NAI_1.jpg % compute the neural activity index, i.e. projected power divided by % projected noise sourceNAI=source; sourceNAI.avg.nai=source.avg.pow./source.avg.noise; %neural activity index calculation cfg=[]; cfg.downsample=2; cfg.parameter='avg.nai'; sourceNAI_int=ft_sourceinterpolate(cfg,sourceNAI,mri); cfg = []; cfg.method = 'slice'; cfg.funparameter = 'avg.nai'; cfg.maskparameter=cfg.funparameter; figure ,ft_sourceplot(cfg, sourceNAI_int); Can you please direct me to what I am doing wrong or missing in my code to get sensible beamformer scan results. When I read the source_int.avg.pow and sourceNAI_int.avg.nai most of the values are NaN's. Many amny thanks in advance. Regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr [Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 29155 bytes Desc: image001.jpg URL: From jm.horschig at donders.ru.nl Tue Jul 10 12:20:35 2012 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 10 Jul 2012 12:20:35 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> Message-ID: <4FFC01F3.8010103@donders.ru.nl> Dear Sascha, What you do is perfectly fine, but what you want is not possible in FieldTrip (yet?). FieldTrip is designed such that triggers (and all other events) are stored with respect to sample number from the beginning of the recording, i.e. datafile on disk. However, when you merge datasets, FieldTrip cannot infer to what dataset a specific sample number belongs - in your case it could be coming from 4 different datasets - and thus dismisses this information completely. So, what you would need to as a workaround is to save the events with respect to your trials of interest (and dataset), and after merging, create a fake sampleinfo and event structure. Then, you would need to create events with samples respective to the fake sampleinfo. This is a somewhat tedious work, and only a hack to get what you want, but it's the only way so far :) But be aware that this work might result in a lot of nasty errors if you are not careful enough. If you do not know what I mean, feel free to send me a mail and I can try my best to explain what I mean with a short example script. Best, Jörn On 7/9/2012 3:56 PM, styll at med.ovgu.de wrote: > Hello, > > I probably have a problem with the use of ft_appendata. I want to merge 4 > MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, > etc.) of the same subject after I defined my trials of interest and > preprocessed the 4 datasets individually. If I use ft_databrowser for a > look into every single dataset, all trials (10 in each run/dataset) seems > to be OK with the correct sequence: defined prestim time range, trigger > and poststim time range. If I check the merged dataset I can go through > all of the 40 trials, but there is no sequence like: prestim time range, > trigger and poststim-time. Here is my pipeline for the first steps: > > %%%% run1 > cfg.dataset='…\train01_64\run1\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run1'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_1 = ft_preprocessing(cfg) > > %%%% run2 > cfg.dataset='…\train01_64\run2\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run2'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_2 = ft_preprocessing(cfg) > > the same for run3 and run4 > > %%%% merging the data > > cfg=[]; > merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, > prepro_run_4) > > Do I miss something or is there in error in my pipeline or in my strategy… > > Best regards > > Sascha > > > _______________________________________________ > 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 jm.horschig at donders.ru.nl Tue Jul 10 12:49:48 2012 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 10 Jul 2012 12:49:48 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> Message-ID: <4FFC08CC.2050302@donders.ru.nl> Hi Sascha, I just got reminded (thx Yuka-san) that you could use a ctf command to combine CTF datasets (of course, only if you got data from a CTF system): newCombinedDs [options] This program takes two or more datasets that have exactly the same collection parameters and combines them to make one dataset. Best, Jörn On 7/9/2012 3:56 PM, styll at med.ovgu.de wrote: > Hello, > > I probably have a problem with the use of ft_appendata. I want to merge 4 > MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, > etc.) of the same subject after I defined my trials of interest and > preprocessed the 4 datasets individually. If I use ft_databrowser for a > look into every single dataset, all trials (10 in each run/dataset) seems > to be OK with the correct sequence: defined prestim time range, trigger > and poststim time range. If I check the merged dataset I can go through > all of the 40 trials, but there is no sequence like: prestim time range, > trigger and poststim-time. Here is my pipeline for the first steps: > > %%%% run1 > cfg.dataset='…\train01_64\run1\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run1'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_1 = ft_preprocessing(cfg) > > %%%% run2 > cfg.dataset='…\train01_64\run2\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run2'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_2 = ft_preprocessing(cfg) > > the same for run3 and run4 > > %%%% merging the data > > cfg=[]; > merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, > prepro_run_4) > > Do I miss something or is there in error in my pipeline or in my strategy… > > Best regards > > Sascha > > > _______________________________________________ > 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 elilife at gmail.com Tue Jul 10 16:57:25 2012 From: elilife at gmail.com (Eliana Garcia) Date: Tue, 10 Jul 2012 16:57:25 +0200 Subject: [FieldTrip] problems with speed of processing Message-ID: Hello Dear Fieldtrip Community, I am having now problems with processing my data. I am analyzing a quite big data set with 400 trials that are composed by 10 sec (re-sampled at 150Hz). I am doing first a demean, then planar gradient transformation, time-frequency analysis using multitapers and then combine the planar gradient again. For the first subject always runs normally, but for the second one matlab gets really slow. I am taking care in deleting the variables that I create with big amount of data after I don't need them any more, so I am using just one big file that is being safe at the end (average time-frequency across trials) for each of the subjects. Every time matlab starts to analyze a new subject I am using clear all (with exceptions like directory and name of subject) but stills with every new subject it gets slower and slower. Do you have any advises to make the analysis faster? Sometimes is too slow and the computer normally crashes after 3 subjects. Thank you very much for the attention. Best, -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Tue Jul 10 18:01:30 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Tue, 10 Jul 2012 18:01:30 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: Dear Eliana, You could try creating a function that does all this preprocessing and then writes the output to file. If you then call this function in a (subject) loop you are sure that Matlab will free up the memory it used for that function. Perhaps it helps, Stephen On 10 July 2012 16:57, Eliana Garcia wrote: > Hello Dear Fieldtrip Community, > > I am having now problems with processing my data. I am analyzing a quite > big data set with 400 trials that are composed by 10 sec (re-sampled at > 150Hz). I am doing first a demean, then planar gradient transformation, > time-frequency analysis using multitapers and then combine the planar > gradient again. For the first subject always runs normally, but for the > second one matlab gets really slow. I am taking care in deleting the > variables that I create with big amount of data after I don't need them any > more, so I am using just one big file that is being safe at the end > (average time-frequency across trials) for each of the subjects. Every time > matlab starts to analyze a new subject I am using clear all (with > exceptions like directory and name of subject) but stills with every new > subject it gets slower and slower. > > Do you have any advises to make the analysis faster? Sometimes is too slow > and the computer normally crashes after 3 subjects. > > Thank you very much for the attention. > > Best, > > -- > Eliana García Cossio > Applied Neurotechnology Lab. > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > _______________________________________________ > 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 elilife at gmail.com Tue Jul 10 18:40:23 2012 From: elilife at gmail.com (Eliana Garcia) Date: Tue, 10 Jul 2012 18:40:23 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: Dear Stephen, Thanks for the suggestion. I have already one function that is doing all the preprocessing and saving as well. But this seams not to solve the issue. Thanks, Eliana On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh < stephen.whitmarsh at gmail.com> wrote: > Dear Eliana, > > You could try creating a function that does all this preprocessing and > then writes the output to file. > If you then call this function in a (subject) loop you are sure that > Matlab will free up the memory it used for that function. > > Perhaps it helps, > > Stephen > > On 10 July 2012 16:57, Eliana Garcia wrote: > >> Hello Dear Fieldtrip Community, >> >> I am having now problems with processing my data. I am analyzing a quite >> big data set with 400 trials that are composed by 10 sec (re-sampled at >> 150Hz). I am doing first a demean, then planar gradient transformation, >> time-frequency analysis using multitapers and then combine the planar >> gradient again. For the first subject always runs normally, but for the >> second one matlab gets really slow. I am taking care in deleting the >> variables that I create with big amount of data after I don't need them any >> more, so I am using just one big file that is being safe at the end >> (average time-frequency across trials) for each of the subjects. Every time >> matlab starts to analyze a new subject I am using clear all (with >> exceptions like directory and name of subject) but stills with every new >> subject it gets slower and slower. >> >> Do you have any advises to make the analysis faster? Sometimes is too >> slow and the computer normally crashes after 3 subjects. >> >> Thank you very much for the attention. >> >> Best, >> >> -- >> Eliana García Cossio >> Applied Neurotechnology Lab. >> Graduate School of Neural and Behavioural Science - Max Planck Research >> School >> Institute of Medical Psychology and Behavioural Neurobiology >> Universität Tübingen >> (+0049) 01 577-8587604 >> Otfried-Müller-Str. 47, 72076 >> Tübingen- Germany >> >> >> _______________________________________________ >> 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 > -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdeiss at ucsd.edu Tue Jul 10 20:49:49 2012 From: sdeiss at ucsd.edu (Steve Deiss) Date: Tue, 10 Jul 2012 11:49:49 -0700 Subject: [FieldTrip] read_biosig_header.m Message-ID: <4FFC794D.40508@ucsd.edu> The fieldtrip version we have calls function 'read_biosig_header' which calls 'sopen' with the following sequence. biosig = sopen(filename,'r'); For some reason it loses the digital triggers on channel 1 in our data after issuing the following warning: "Reading data file header... WARNING SOPEN(EDF): Physical Max/Min values of EDF data are not necessarily defining the dynamic range. Hence, OVERFLOWDETECTION might not work correctly. See also EEG2HIST and read http://dx.doi.org/10.1016/S1388-2457(99)00172-8 (A. Schlgl et al. Quality Control ... Clin. Neurophysiol. 1999, Dec; 110(12): 2165 - 2170). A copy is available here, too: http://www.dpmi.tugraz.at/schloegl/publications/neurophys1999_2165.pdf " If we let EEGLAB read the data, its function 'pop_biosig' calls 'sopen' with biosig = sopen(filename,'r',0,'OVERFLOWDETECTION:OFF'); The data read in here includes the triggers so that we can go on to epoch and process the data. We are not yet ready to upgrade to the very latest fieldtrip. So I would like to know if there is an easy way to determine if the latest version of fieldtrip changed anything in the way sopen is called from read_biosig_header? If it matches what EEGLAB does here, we can match that as a temporary fix. I'll try to download and unpack it to see, but if this is a known problem, fixed or not, I'd appreciate any tips. Thanks Steve From rn77 at sussex.ac.uk Wed Jul 11 05:25:36 2012 From: rn77 at sussex.ac.uk (Roshan Nair) Date: Wed, 11 Jul 2012 04:25:36 +0100 Subject: [FieldTrip] Importing '.mat' data in to fieldtrip Message-ID: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> Hi, I have MEG/EEG data in '.mat' format(Biomag 2012 data analysis dataset). The data is already epoched. It was straightforward to convert it in to the required fieldtrip structure - {label, fsample, trial, time} and run ft_databrowser on it. No problems so far. However, I feel I might be going wrong with the following:- 1. The trials include data for STI(stimulus) channels(I believe its an Elekta Neuromag Vectorview 306 system)? Is there a 'fieldtrip' way to represent this. Is this what 'data.trialinfo' is for? If so, how should I populate the trialinfo field. 2. The dataset comes with a file called 'design' with one entry(an integer) per trial. This is the category of the stimulus(living/non-living)presented to the subject for each trial. This is the output my classifier will be trained on. I'm assuming fieldtrip has some standard way of including this. I noticed, the multivariate analysis mentions a parameter called 'design'. Sorry, if thats confusing, but, I'm new to fieldtrip and MEG data. Thanks! Roshan From styll at med.ovgu.de Wed Jul 11 09:42:25 2012 From: styll at med.ovgu.de (styll at med.ovgu.de) Date: Wed, 11 Jul 2012 09:42:25 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <4FFC01F3.8010103@donders.ru.nl> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> <4FFC01F3.8010103@donders.ru.nl> Message-ID: <7436cf587bad96dc9ce7f72f058391fc.squirrel@neuro2.med.uni-magdeburg.de> Hi Jörn, thank you for useful information. I will try to set up the workaround that you mentioned in your mail. In the case of problems I contact you by mail :0) Best regards Sascha > Dear Sascha, > > What you do is perfectly fine, but what you want is not possible in > FieldTrip (yet?). FieldTrip is designed such that triggers (and all > other events) are stored with respect to sample number from the > beginning of the recording, i.e. datafile on disk. However, when you > merge datasets, FieldTrip cannot infer to what dataset a specific sample > number belongs - in your case it could be coming from 4 different > datasets - and thus dismisses this information completely. > > So, what you would need to as a workaround is to save the events with > respect to your trials of interest (and dataset), and after merging, > create a fake sampleinfo and event structure. Then, you would need to > create events with samples respective to the fake sampleinfo. This is a > somewhat tedious work, and only a hack to get what you want, but it's > the only way so far :) But be aware that this work might result in a lot > of nasty errors if you are not careful enough. > > If you do not know what I mean, feel free to send me a mail and I can > try my best to explain what I mean with a short example script. > > Best, > Jörn > > On 7/9/2012 3:56 PM, styll at med.ovgu.de wrote: >> Hello, >> >> I probably have a problem with the use of ft_appendata. I want to merge >> 4 >> MEG datasets (i.e. 4 runs, all the same number of channels, sampling >> rate, >> etc.) of the same subject after I defined my trials of interest and >> preprocessed the 4 datasets individually. If I use ft_databrowser for a >> look into every single dataset, all trials (10 in each run/dataset) >> seems >> to be OK with the correct sequence: defined prestim time range, trigger >> and poststim time range. If I check the merged dataset I can go through >> all of the 40 trials, but there is no sequence like: prestim time range, >> trigger and poststim-time. Here is my pipeline for the first steps: >> >> %%%% run1 >> cfg.dataset=' \train01_64\run1\c,rfDC'; >> cfg.trialdef.prestim=1; %%% in sec >> cfg.trialdef.poststim=5; %%% in sec >> cfg.trialfun = 'traildef_train01_all_pics_run1'; >> data_run1 = ft_definetrial(cfg) >> >> cfg.channel = {'MEG'}; >> cfg.dftfilter='yes'; >> prepro_run_1 = ft_preprocessing(cfg) >> >> %%%% run2 >> cfg.dataset=' \train01_64\run2\c,rfDC'; >> cfg.trialdef.prestim=1; %%% in sec >> cfg.trialdef.poststim=5; %%% in sec >> cfg.trialfun = 'traildef_train01_all_pics_run2'; >> data_run1 = ft_definetrial(cfg) >> >> cfg.channel = {'MEG'}; >> cfg.dftfilter='yes'; >> prepro_run_2 = ft_preprocessing(cfg) >> >> the same for run3 and run4 >> >> %%%% merging the data >> >> cfg=[]; >> merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, >> prepro_run_3, >> prepro_run_4) >> >> Do I miss something or is there in error in my pipeline or in my >> strategy >> >> Best regards >> >> Sascha >> >> >> _______________________________________________ >> 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 Wed Jul 11 10:20:58 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 11 Jul 2012 10:20:58 +0200 Subject: [FieldTrip] read_biosig_header.m In-Reply-To: <4FFC794D.40508@ucsd.edu> References: <4FFC794D.40508@ucsd.edu> Message-ID: <4FFD376A.8050206@donders.ru.nl> Dear Steve, Although I cannot help you directly and do not know about the specific error you got, you can find all code changes on http://code.google.com/p/fieldtrip/ For the biosig file you are referring to, please look here: http://code.google.com/p/fieldtrip/source/diff?path=/trunk/fileio/private/read_biosig_header.m&format=side&r=5429 (but as you can see, nothing changed there) Hope someone else can help out (Robert is on vacation right now, so maybe someone else can help) Best, Jörn On 7/10/2012 8:49 PM, Steve Deiss wrote: > The fieldtrip version we have calls function 'read_biosig_header' > which calls 'sopen' with the following sequence. > biosig = sopen(filename,'r'); > For some reason it loses the digital triggers on channel 1 in our data > after issuing the following warning: > > "Reading data file header... > WARNING SOPEN(EDF): Physical Max/Min values of EDF data are not > necessarily defining the dynamic range. > Hence, OVERFLOWDETECTION might not work correctly. See also > EEG2HIST and read > http://dx.doi.org/10.1016/S1388-2457(99)00172-8 (A. Schlgl et al. > Quality Control ... Clin. Neurophysiol. 1999, Dec; 110(12): 2165 - 2170). > A copy is available here, too: > http://www.dpmi.tugraz.at/schloegl/publications/neurophys1999_2165.pdf " > > If we let EEGLAB read the data, its function 'pop_biosig' calls > 'sopen' with > biosig = sopen(filename,'r',0,'OVERFLOWDETECTION:OFF'); > The data read in here includes the triggers so that we can go on to > epoch and process the data. > > We are not yet ready to upgrade to the very latest fieldtrip. So I > would like to know if there is an easy way to > determine if the latest version of fieldtrip changed anything in the > way sopen is called from read_biosig_header? > If it matches what EEGLAB does here, we can match that as a temporary > fix. > > I'll try to download and unpack it to see, but if this is a known > problem, fixed or not, I'd appreciate any tips. > > Thanks > Steve > _______________________________________________ > 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 jm.horschig at donders.ru.nl Wed Jul 11 10:30:58 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 11 Jul 2012 10:30:58 +0200 Subject: [FieldTrip] Importing '.mat' data in to fieldtrip In-Reply-To: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> References: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> Message-ID: <4FFD39C2.8030205@donders.ru.nl> Dear Roshan, 0) Welcome to FieldTrip ;) 1) FieldTrip usuaully reads in the stimulus channel and refers to the triggers as events. See also here: http://fieldtrip.fcdonders.nl/faq/what_is_the_relation_between_events_such_as_triggers_and_trials trialinfo can be used for that when you have segmented trials. Actually, there is no obligation how trialinfo should look like, you can put whatever information in that you want. I got stimulus trigger, stimulus offset sample, response sample, response trigger and some additional flags in there, so everything that facilitates in sorting trials according to some criteria. To find out what data you have, you can try to use ft_senstype 2) you might want to look at the Donders Machine Learning Toolbox, which is under external/dmlt. For the design, I assume it's an ordinary design matrix, so maybe you want to read the walkthrough and these tutorials: http://fieldtrip.fcdonders.nl/walkthrough?s[]=design#statistics http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock?s[]=design http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq?s[]=design Good luck with the data and have fun with FieldTrip. Best, Jörn On 7/11/2012 5:25 AM, Roshan Nair wrote: > Hi, > > I have MEG/EEG data in '.mat' format(Biomag 2012 data analysis dataset). > The data is already epoched. It was straightforward to convert it in to the > required fieldtrip structure - {label, fsample, trial, time} and run > ft_databrowser on it. No problems so far. > > However, I feel I might be going wrong with the following:- > 1. The trials include data for STI(stimulus) channels(I believe its an > Elekta Neuromag Vectorview 306 system)? Is there a 'fieldtrip' way to > represent this. Is this what 'data.trialinfo' is for? If so, how should I > populate the trialinfo field. > 2. The dataset comes with a file called 'design' with one entry(an > integer) per trial. This is the category of the > stimulus(living/non-living)presented to the subject for each trial. This is > the output my classifier will be trained on. I'm assuming fieldtrip has > some standard way of including this. I noticed, the multivariate analysis > mentions a parameter called 'design'. > > Sorry, if thats confusing, but, I'm new to fieldtrip and MEG data. > > Thanks! > > Roshan > _______________________________________________ > 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 Michael.Stephan at esi-frankfurt.de Wed Jul 11 11:40:17 2012 From: Michael.Stephan at esi-frankfurt.de (Michael Stephan) Date: Wed, 11 Jul 2012 11:40:17 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: <4FFD4A01.6090807@esi-frankfurt.de> Dear Eliana, if your data sets vary in size you should sort them according to size and then process them starting with the largest data set. -- Michael Stephan Ernst Strüngmann Institute for Neuroscience in Cooperation with Max Planck Society Deutschordenstraße 46 D-60528 Frankfurt am Main eMail: Michael.Stephan at esi-frankfurt.de > Hello Dear Fieldtrip Community, > > I am having now problems with processing my data. I am analyzing a quite > big data set with 400 trials that are composed by 10 sec (re-sampled at > 150Hz). I am doing first a demean, then planar gradient transformation, > time-frequency analysis using multitapers and then combine the planar > gradient again. For the first subject always runs normally, but for the > second one matlab gets really slow. I am taking care in deleting the > variables that I create with big amount of data after I don't need them > any more, so I am using just one big file that is being safe at the end > (average time-frequency across trials) for each of the subjects. Every > time matlab starts to analyze a new subject I am using clear all (with > exceptions like directory and name of subject) but stills with every new > subject it gets slower and slower. > > Do you have any advises to make the analysis faster? Sometimes is too > slow and the computer normally crashes after 3 subjects. > > Thank you very much for the attention. > > Best, > > -- > Eliana García Cossio > Applied Neurotechnology Lab. > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From irina.simanova at mpi.nl Wed Jul 11 17:20:41 2012 From: irina.simanova at mpi.nl (Irina Simanova) Date: Wed, 11 Jul 2012 17:20:41 +0200 Subject: [FieldTrip] freqstatistics ivar and uvar In-Reply-To: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> References: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> Message-ID: <30D34709-7D37-4A58-9072-CBF708A78052@mpi.nl> Dear all, I have a very basic question on freqstatistics. I want to compare the TFR's in 3 experimental conditions over 12 subjects. I run the freqstatistics with cfg.method = 'depsamplesF'. cfg.uvar = 1 cfg.ivar = 2 cfg.design = [1:12 1:12 1:12; ones(1,12) 2*ones(1,12) 3*ones(1,12)] I am confused with the the following lines that FT prints out: repeated measurement in variable 1 over 12 levels number of repeated measurements in each level is 3 3 3 3 3 3 3 3 3 3 3 3 I assume it is correct, since it's exactly the same output as I get with the tutorial within-subjects statistics example. But why is not it the other way around? There are 3 levels of the independent variable, and the number of samples in each level is 12? Thank you! Best, Irina Here is the code: cfg = []; cfg.latency = [0 1.5]; cfg.channel = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesF'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.tail = 1; cfg.clustertail = 1; cfg.alpha = 0.05; cfg.numrandomization = 100; cfg.neighbours = neighbours; cfg.parameter = 'powspctrm'; cfg.design = design; cfg.uvar = 1; cfg.ivar = 2; [stat] = ft_freqstatistics(cfg, TFRgrand_1, TFRgrand_2, TFRgrand_3); computing statistic over the frequency range [3.962 39.937] computing statistic over the time range [0.000 1.500] selection powspctrm along dimension 2 selection powspctrm along dimension 3 selection powspctrm along dimension 4 using "ft_statistics_montecarlo" for the statistical testing using "statfun_depsamplesF" for the single-sample statistics constructing randomized design total number of measurements = 36 total number of variables = 2 number of independent variables = 1 number of unit variables = 1 number of within-cell variables = 0 number of control variables = 0 using a permutation resampling approach repeated measurement in variable 1 over 12 levels number of repeated measurements in each level is 3 3 3 3 3 3 3 3 3 3 3 3 computing a parametric threshold for clustering computing statistic From Bill.Budd at newcastle.edu.au Thu Jul 12 01:33:38 2012 From: Bill.Budd at newcastle.edu.au (Bill Budd) Date: Thu, 12 Jul 2012 09:33:38 +1000 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Hi Eliana I see something similar when using SPM8 to process data. I’ve heard that this might be because SPM8 uses fieldtrip functions to import my continuous EEG files (Biosemi/bdf) and these functions may not release memory in matlab after closing. When looping my preprocessing functions over multiple subjects I have the exactly same problem in SPM that you see in fieldtrip. This may not be causing your problem (or mine) but wondered if the processing your refer to also involves importing raw MEG data? The PCs I’m using have plenty of RAM/disk space (Win7/matlab 2011b). Be great to find a solution to this as it slows done processing multi subject data significantly! Cheers -Bill From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eliana Garcia Sent: Wednesday, 11 July 2012 2:40 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] problems with speed of processing Dear Stephen, Thanks for the suggestion. I have already one function that is doing all the preprocessing and saving as well. But this seams not to solve the issue. Thanks, Eliana On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh wrote: Dear Eliana, You could try creating a function that does all this preprocessing and then writes the output to file. If you then call this function in a (subject) loop you are sure that Matlab will free up the memory it used for that function. Perhaps it helps, Stephen On 10 July 2012 16:57, Eliana Garcia wrote: Hello Dear Fieldtrip Community, I am having now problems with processing my data. I am analyzing a quite big data set with 400 trials that are composed by 10 sec (re-sampled at 150Hz). I am doing first a demean, then planar gradient transformation, time-frequency analysis using multitapers and then combine the planar gradient again. For the first subject always runs normally, but for the second one matlab gets really slow. I am taking care in deleting the variables that I create with big amount of data after I don't need them any more, so I am using just one big file that is being safe at the end (average time-frequency across trials) for each of the subjects. Every time matlab starts to analyze a new subject I am using clear all (with exceptions like directory and name of subject) but stills with every new subject it gets slower and slower. Do you have any advises to make the analysis faster? Sometimes is too slow and the computer normally crashes after 3 subjects. Thank you very much for the attention. Best, -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany _______________________________________________ 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 -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Jul 12 08:17:48 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 12 Jul 2012 08:17:48 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> References: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Message-ID: Hi, Please, note that "clear all" clears variables, but does not free up memory, especially for files read from disk. You can check the memory usage with the command "top" in Linux command line. You'll see that nothing changes even if you use "clear all". I agree with Stephen that you need to write smaller functions for each subjects. Something like: for i = 1:numel(subj) do_analysis(subj) end Where "do_analysis.m" is a function you wrote to do all the analysis. In this way, Matlab takes care of memory management by itself (it frees the memory once the function has been executed). A more elaborate solution is to use the "qsub" functions included in fieldtrip. Try this: addpath /path/to/fieldtrip/qsub fname = 'do_analysis'; subj = {1, 2, 3, 4, 5}; qsubcellfun(fname, x1, 'memreq', 1024^3, 'timreq', 60*60, 'backend', 'local'); This will start a new Matlab session (and use a new Matlab license) and it will close it when the function has been executed. There should be no memory leaks at all. See "help qsubcellfun" for more info. Remember to use 'backend' 'local' unless you have access to Oracle Grid Engine or Torque. Hope this helps. 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, Jul 12, 2012 at 1:33 AM, Bill Budd wrote: > Hi Eliana > > > > I see something similar when using SPM8 to process data. I’ve heard that > this might be because SPM8 uses fieldtrip functions to import my continuous > EEG files (Biosemi/bdf) and these functions may not release memory in matlab > after closing. When looping my preprocessing functions over multiple > subjects I have the exactly same problem in SPM that you see in fieldtrip. > This may not be causing your problem (or mine) but wondered if the > processing your refer to also involves importing raw MEG data? > > > > The PCs I’m using have plenty of RAM/disk space (Win7/matlab 2011b). > > > > Be great to find a solution to this as it slows done processing multi > subject data significantly! > > > > Cheers > > > > -Bill > > > > > > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eliana Garcia > Sent: Wednesday, 11 July 2012 2:40 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] problems with speed of processing > > > > Dear Stephen, > > > > Thanks for the suggestion. I have already one function that is doing all the > preprocessing and saving as well. But this seams not to solve the issue. > > > > Thanks, > > Eliana > > > > On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh > wrote: > > Dear Eliana, > > > > You could try creating a function that does all this preprocessing and then > writes the output to file. > > If you then call this function in a (subject) loop you are sure that Matlab > will free up the memory it used for that function. > > > > Perhaps it helps, > > > > Stephen > > > > On 10 July 2012 16:57, Eliana Garcia wrote: > > Hello Dear Fieldtrip Community, > > > > I am having now problems with processing my data. I am analyzing a quite big > data set with 400 trials that are composed by 10 sec (re-sampled at 150Hz). > I am doing first a demean, then planar gradient transformation, > time-frequency analysis using multitapers and then combine the planar > gradient again. For the first subject always runs normally, but for the > second one matlab gets really slow. I am taking care in deleting the > variables that I create with big amount of data after I don't need them any > more, so I am using just one big file that is being safe at the end (average > time-frequency across trials) for each of the subjects. Every time matlab > starts to analyze a new subject I am using clear all (with exceptions like > directory and name of subject) but stills with every new subject it gets > slower and slower. > > > > Do you have any advises to make the analysis faster? Sometimes is too slow > and the computer normally crashes after 3 subjects. > > > > Thank you very much for the attention. > > > > Best, > > > > -- > > Eliana García Cossio > Applied Neurotechnology Lab. > > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > > > > _______________________________________________ > 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 > > > > > > -- > > Eliana García Cossio > Applied Neurotechnology Lab. > > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From d.oudebos at gmail.com Thu Jul 12 11:15:07 2012 From: d.oudebos at gmail.com (Danny Plass-Oude Bos) Date: Thu, 12 Jul 2012 11:15:07 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? Message-ID: Hi Fieldtrippers, I am using the stand-alone fieldtripbuffer emotiv2ft, in combination with python for signal analysis. As far as I understand, you can only use one Emotiv EPOC with this implementation. I'd like to use multiple epocs at the some time, and preferably on the same computer. Does anybody know if this is possible somehow with emotiv2ft? Or does anybody has other experience / ideas on this problem? Kind regards, Danny. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elilife at gmail.com Thu Jul 12 12:00:02 2012 From: elilife at gmail.com (Eliana Garcia) Date: Thu, 12 Jul 2012 12:00:02 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Message-ID: Thank you all for this interesting advices. I am not using Fieldtrip in this case to read the raw data (for this I am using a function from BCI2000), just for signal processing. The qsubcellfun function is new for me. I will implement it, this will solve the problem of memory as Giovanni mentioned. Thanks again, Eliana On Thu, Jul 12, 2012 at 8:17 AM, Gio Piantoni wrote: > Hi, > > Please, note that "clear all" clears variables, but does not free up > memory, especially for files read from disk. You can check the memory > usage with the command "top" in Linux command line. You'll see that > nothing changes even if you use "clear all". > I agree with Stephen that you need to write smaller functions for each > subjects. Something like: > > for i = 1:numel(subj) > do_analysis(subj) > end > Where "do_analysis.m" is a function you wrote to do all the analysis. > In this way, Matlab takes care of memory management by itself (it > frees the memory once the function has been executed). > > A more elaborate solution is to use the "qsub" functions included in > fieldtrip. Try this: > addpath /path/to/fieldtrip/qsub > fname = 'do_analysis'; > subj = {1, 2, 3, 4, 5}; > qsubcellfun(fname, x1, 'memreq', 1024^3, 'timreq', 60*60, 'backend', > 'local'); > > This will start a new Matlab session (and use a new Matlab license) > and it will close it when the function has been executed. There should > be no memory leaks at all. See "help qsubcellfun" for more info. > Remember to use 'backend' 'local' unless you have access to Oracle > Grid Engine or Torque. > > Hope this helps. > 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, Jul 12, 2012 at 1:33 AM, Bill Budd > wrote: > > Hi Eliana > > > > > > > > I see something similar when using SPM8 to process data. I’ve heard that > > this might be because SPM8 uses fieldtrip functions to import my > continuous > > EEG files (Biosemi/bdf) and these functions may not release memory in > matlab > > after closing. When looping my preprocessing functions over multiple > > subjects I have the exactly same problem in SPM that you see in > fieldtrip. > > This may not be causing your problem (or mine) but wondered if the > > processing your refer to also involves importing raw MEG data? > > > > > > > > The PCs I’m using have plenty of RAM/disk space (Win7/matlab 2011b). > > > > > > > > Be great to find a solution to this as it slows done processing multi > > subject data significantly! > > > > > > > > Cheers > > > > > > > > -Bill > > > > > > > > > > > > From: fieldtrip-bounces at science.ru.nl > > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eliana Garcia > > Sent: Wednesday, 11 July 2012 2:40 AM > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] problems with speed of processing > > > > > > > > Dear Stephen, > > > > > > > > Thanks for the suggestion. I have already one function that is doing all > the > > preprocessing and saving as well. But this seams not to solve the issue. > > > > > > > > Thanks, > > > > Eliana > > > > > > > > On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh > > wrote: > > > > Dear Eliana, > > > > > > > > You could try creating a function that does all this preprocessing and > then > > writes the output to file. > > > > If you then call this function in a (subject) loop you are sure that > Matlab > > will free up the memory it used for that function. > > > > > > > > Perhaps it helps, > > > > > > > > Stephen > > > > > > > > On 10 July 2012 16:57, Eliana Garcia wrote: > > > > Hello Dear Fieldtrip Community, > > > > > > > > I am having now problems with processing my data. I am analyzing a quite > big > > data set with 400 trials that are composed by 10 sec (re-sampled at > 150Hz). > > I am doing first a demean, then planar gradient transformation, > > time-frequency analysis using multitapers and then combine the planar > > gradient again. For the first subject always runs normally, but for the > > second one matlab gets really slow. I am taking care in deleting the > > variables that I create with big amount of data after I don't need them > any > > more, so I am using just one big file that is being safe at the end > (average > > time-frequency across trials) for each of the subjects. Every time matlab > > starts to analyze a new subject I am using clear all (with exceptions > like > > directory and name of subject) but stills with every new subject it gets > > slower and slower. > > > > > > > > Do you have any advises to make the analysis faster? Sometimes is too > slow > > and the computer normally crashes after 3 subjects. > > > > > > > > Thank you very much for the attention. > > > > > > > > Best, > > > > > > > > -- > > > > Eliana García Cossio > > Applied Neurotechnology Lab. > > > > Graduate School of Neural and Behavioural Science - Max Planck Research > > School > > Institute of Medical Psychology and Behavioural Neurobiology > > Universität Tübingen > > > > (+0049) 01 577-8587604 > > Otfried-Müller-Str. 47, 72076 > > Tübingen- Germany > > > > > > > > > > > > _______________________________________________ > > 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 > > > > > > > > > > > > -- > > > > Eliana García Cossio > > Applied Neurotechnology Lab. > > > > Graduate School of Neural and Behavioural Science - Max Planck Research > > School > > Institute of Medical Psychology and Behavioural Neurobiology > > Universität Tübingen > > > > (+0049) 01 577-8587604 > > Otfried-Müller-Str. 47, 72076 > > Tübingen- Germany > > > > > > > > > > _______________________________________________ > > 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 > -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabian.tomaschek at uni-tuebingen.de Thu Jul 12 15:25:11 2012 From: fabian.tomaschek at uni-tuebingen.de (=?iso-8859-1?Q?Fabian_Tomaschek_-_Universit=E4t_T=FCbingen?=) Date: Thu, 12 Jul 2012 15:25:11 +0200 Subject: [FieldTrip] Problems with "ft_megplanar" and fourier spectra. In-Reply-To: References: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Message-ID: <001501cd6031$c3f352e0$4bd9f8a0$@tomaschek@uni-tuebingen.de> Hi All, I’m currently performing a timefrequency analyis and its statistics as described on "http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis?s[]=wavelet&s[ ]=analysis" and "http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq". I got to the point where I should do "ft_megplanar" with my data. However, an error saying "'freq data should contain Fourier spectra'" occurs. Looking into the function, I saw that it requires a field called "fourierspctrm". However, I do not know where to get that field. Nor does "http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq" say anything about fourier spectra. Do you know any help? Thanks a lot. Fabian Es grüßt aus Tübingen Fabian Tomaschek -------------------------------------------------- -------------------------------------------------- Mobil: 0178 6312772 Institute: 07071 29-87529 Dept of Neurology University of Tuebingen Hoppe-Seyler-Str. 3 D-72076 Tuebingen -------------------------------------------------- -------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdeiss at ucsd.edu Thu Jul 12 19:01:14 2012 From: sdeiss at ucsd.edu (Steve Deiss) Date: Thu, 12 Jul 2012 10:01:14 -0700 Subject: [FieldTrip] read_biosig_header.m In-Reply-To: <4FFD376A.8050206@donders.ru.nl> References: <4FFC794D.40508@ucsd.edu> <4FFD376A.8050206@donders.ru.nl> Message-ID: <4FFF02DA.1090802@ucsd.edu> Thanks for this note. Changing the call in read_biosig_header and read_biosig_data does make the problem go away, ie., the digital trigger channel is not zeroed. I do not know what other side effects there could be. So I am a little wary. Steve On 07/11/12 01:20, "Jörn M. Horschig" wrote: > Dear Steve, > > Although I cannot help you directly and do not know about the specific > error you got, you can find all code changes on > http://code.google.com/p/fieldtrip/ > > For the biosig file you are referring to, please look here: > http://code.google.com/p/fieldtrip/source/diff?path=/trunk/fileio/private/read_biosig_header.m&format=side&r=5429 > > (but as you can see, nothing changed there) > > Hope someone else can help out (Robert is on vacation right now, so > maybe someone else can help) > > Best, > Jörn > > On 7/10/2012 8:49 PM, Steve Deiss wrote: >> The fieldtrip version we have calls function 'read_biosig_header' >> which calls 'sopen' with the following sequence. >> biosig = sopen(filename,'r'); >> For some reason it loses the digital triggers on channel 1 in our >> data after issuing the following warning: >> >> "Reading data file header... >> WARNING SOPEN(EDF): Physical Max/Min values of EDF data are not >> necessarily defining the dynamic range. >> Hence, OVERFLOWDETECTION might not work correctly. See also >> EEG2HIST and read >> http://dx.doi.org/10.1016/S1388-2457(99)00172-8 (A. Schlgl et al. >> Quality Control ... Clin. Neurophysiol. 1999, Dec; 110(12): 2165 - >> 2170). >> A copy is available here, too: >> http://www.dpmi.tugraz.at/schloegl/publications/neurophys1999_2165.pdf " >> >> If we let EEGLAB read the data, its function 'pop_biosig' calls >> 'sopen' with >> biosig = sopen(filename,'r',0,'OVERFLOWDETECTION:OFF'); >> The data read in here includes the triggers so that we can go on to >> epoch and process the data. >> >> We are not yet ready to upgrade to the very latest fieldtrip. So I >> would like to know if there is an easy way to >> determine if the latest version of fieldtrip changed anything in the >> way sopen is called from read_biosig_header? >> If it matches what EEGLAB does here, we can match that as a temporary >> fix. >> >> I'll try to download and unpack it to see, but if this is a known >> problem, fixed or not, I'd appreciate any tips. >> >> Thanks >> Steve >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Steve Deiss, M.Sc. MMIL Lab (Dale and Halgren), UCSD, La Jolla, CA, USA Neuroimaging Research Associate 858-246-1194 From b.reuderink at donders.ru.nl Fri Jul 13 07:48:52 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 13 Jul 2012 07:48:52 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? In-Reply-To: References: Message-ID: Hi Danny, How do you want to use multiple Emotivs? Do you want to stream them to one buffer in a synchronized manner, do you want your application to access two buffers, one for each Emotiv? The latter is more feasible I think, and could be implemented using two computers. I think one of the main issues would be connecting a FieldTrip buffer to a specific Emotiv headset if multiple receiver dongles are present on one computer. Best, Boris On Thu, Jul 12, 2012 at 11:15 AM, Danny Plass-Oude Bos wrote: > Hi Fieldtrippers, > > I am using the stand-alone fieldtripbuffer emotiv2ft, in combination with > python for signal analysis. > As far as I understand, you can only use one Emotiv EPOC with this > implementation. I'd like to use multiple epocs at the some time, and > preferably on the same computer. > Does anybody know if this is possible somehow with emotiv2ft? Or does > anybody has other experience / ideas on this problem? > > Kind regards, > > Danny. > > _______________________________________________ > 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 d.oudebos at gmail.com Fri Jul 13 09:39:58 2012 From: d.oudebos at gmail.com (Danny Plass-Oude Bos) Date: Fri, 13 Jul 2012 09:39:58 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? In-Reply-To: References: Message-ID: Hi Boris :) For me it doesn't matter if it is one buffer or multiple, as long as I can get the data, and know from which head set it is -- I'm not sure if the current buffer supports that kind of thing? The reason why I'd prefer not to have one computer for each head set, is because I'd like to use 8 head sets... Emotiv's own software can deal with multiple head sets. You can start up multiple control panels, and select which device it should listen to. So far, I have not been able to discover how to do a similar thing from the Emotiv SDK, however -- I guess that is also what you people would need to know to get the buffer working for multiple sets? Best, Danny. 2012/7/13 Boris Reuderink > Hi Danny, > > How do you want to use multiple Emotivs? Do you want to stream them to > one buffer in a synchronized manner, do you want your application to > access two buffers, one for each Emotiv? The latter is more feasible I > think, and could be implemented using two computers. > > I think one of the main issues would be connecting a FieldTrip buffer > to a specific Emotiv headset if multiple receiver dongles are present > on one computer. > > Best, > > Boris > > On Thu, Jul 12, 2012 at 11:15 AM, Danny Plass-Oude Bos > wrote: > > Hi Fieldtrippers, > > > > I am using the stand-alone fieldtripbuffer emotiv2ft, in combination with > > python for signal analysis. > > As far as I understand, you can only use one Emotiv EPOC with this > > implementation. I'd like to use multiple epocs at the some time, and > > preferably on the same computer. > > Does anybody know if this is possible somehow with emotiv2ft? Or does > > anybody has other experience / ideas on this problem? > > > > Kind regards, > > > > Danny. > > > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Fri Jul 13 12:20:38 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 13 Jul 2012 12:20:38 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? In-Reply-To: References: Message-ID: Whoa, 8 :). Okay. I was thinking of starting an emotiv2ft per headset somehow, but with 8 headsets that gets tedious and error-prone. Let's discuss a more principled solution in person. On Fri, Jul 13, 2012 at 9:39 AM, Danny Plass-Oude Bos wrote: > Hi Boris :) > > For me it doesn't matter if it is one buffer or multiple, as long as I can > get the data, and know from which head set it is -- I'm not sure if the > current buffer supports that kind of thing? > The reason why I'd prefer not to have one computer for each head set, is > because I'd like to use 8 head sets... > > Emotiv's own software can deal with multiple head sets. You can start up > multiple control panels, and select which device it should listen to. > So far, I have not been able to discover how to do a similar thing from the > Emotiv SDK, however -- I guess that is also what you people would need to > know to get the buffer working for multiple sets? > > Best, > > Danny. > > > > 2012/7/13 Boris Reuderink >> >> Hi Danny, >> >> How do you want to use multiple Emotivs? Do you want to stream them to >> one buffer in a synchronized manner, do you want your application to >> access two buffers, one for each Emotiv? The latter is more feasible I >> think, and could be implemented using two computers. >> >> I think one of the main issues would be connecting a FieldTrip buffer >> to a specific Emotiv headset if multiple receiver dongles are present >> on one computer. >> >> Best, >> >> Boris >> >> On Thu, Jul 12, 2012 at 11:15 AM, Danny Plass-Oude Bos >> wrote: >> > Hi Fieldtrippers, >> > >> > I am using the stand-alone fieldtripbuffer emotiv2ft, in combination >> > with >> > python for signal analysis. >> > As far as I understand, you can only use one Emotiv EPOC with this >> > implementation. I'd like to use multiple epocs at the some time, and >> > preferably on the same computer. >> > Does anybody know if this is possible somehow with emotiv2ft? Or does >> > anybody has other experience / ideas on this problem? >> > >> > Kind regards, >> > >> > Danny. >> > >> > _______________________________________________ >> > 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 > > > > _______________________________________________ > 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 vitoria.piai at gmail.com Fri Jul 13 15:07:10 2012 From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=) Date: Fri, 13 Jul 2012 15:07:10 +0200 Subject: [FieldTrip] timelockgrandaverage on planar gradients Message-ID: <50001D7E.9010609@gmail.com> Dear all, Until some weeks ago, I used to proceed with the following steps to compute ERFs: % For each subject dat = ft_preprocessing(cfgp, input); dat = ft_timelockanalysis(cfgtl, dat); cfg.method = 'template'; cfg.neighbours = ft_prepare_neighbours(cfg, dat); cfg.planarmethod = 'sincos'; cond = ft_megplanar(cfg, dat) cplanar{suj} = ft_combineplanar([], cond); ga = ft_timelockgrandaverage([], cplanar{:}); I excluded some channels for some subjects. I re-ran this script and now I'm left only with the channels that are common to all subjects. (I'm using the DCCN internal fieldtrip version). But I'm pretty sure it used to work until some time ago such that in the GA, I had all the planar gradients still. I understand where it comes from, coz I get the warning that gradiometer info is being discarded coz it cannot be averaged. I've found a previous post that came close (but still not there yet): http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003471.html But I'm not being able to understand the explanation in the tutorial about how to proceed: "Before calculating the grand average the data of each subject can be realigned to standard sensor positions with *ft_megrealign *", but then it's unclear to me what cfg.template should be when using ft_megrealign. So I tried (suggested by JM from another previous post) /"Alternatively, you could construct a gradiometer structure which //contains a meaningful average of the coil positions and orientations." / I made a grad in which grad.chanpos was an average of my participants [302x3]. I tried cfg.template = grad; cfg.template = grad.chanpos; cfg.template = grad.chanori; but I'm probably doing something wrong coz it didn't work still. In all three cases, the error is in ft_megrealign at 174 "cell contents reference from a non-cell array object". So I guess my questions are: - what should the template be? What am I doing wrong? - do I need to make a grad structure myself with all the averages or will the template do, once I get it right? Thanx loads, Vitória -- ** Please consider the environment - do you really need to print? ** -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Mon Jul 16 12:20:57 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Mon, 16 Jul 2012 12:20:57 +0200 Subject: [FieldTrip] Improvements in FieldTrip's real-time processing Message-ID: Dear FieldTrippers, I would like to bring to you attention that we have reorganzed and improved FieldTrip's programs for acquisition and real-time signal processing. The most important change for users is the new directory structure. For each platform, we now have a directory containing all the executables for that platform*: - realtime/bin/win32 for Windows, - realtime/bin/glnxa64 for Linux (64 bit), - realtime/bin/maci64 for OS-X (64 bit). To get started with real-time processing, you can take a look at the examples (http://fieldtrip.fcdonders.nl/development/realtime#example_scripts) and the background information (http://fieldtrip.fcdonders.nl/development/realtime) on the FieldTrip wiki. Besides restructuring the file layout, we have fixed a number of bugs, most notable being: - bug #1525 duplicated samples with low-latency settings [1], - bug #933 freezing buffer server due to deadlock in threading [2], - bug #1246 incorrect reading of configuration scripts [3], - bug #1020 memory problem in event handling [4]. We strongly recommend to download a fresh release of FieldTrip (http://fieldtrip.fcdonders.nl/download), and use the files from this new version. Best regards, Boris Reuderink [1] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1525 [2] http://bugzilla.fcdonders.nl/show_bug.cgi?id=933 [3] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1246 [4] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1020 * Please note that for now, the neuromag files are still in realtime/src/acquisition/neuromag/bin . -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From profabdo at gmail.com Mon Jul 16 13:33:20 2012 From: profabdo at gmail.com (Prof. Abdalla Mohamed) Date: Mon, 16 Jul 2012 13:33:20 +0200 Subject: [FieldTrip] Improvements in FieldTrip's real-time processing In-Reply-To: References: Message-ID: Dear Sir, I am not able to download fresh release FieldTrip and I got error of invalid e-mail address. Please may help me. Thanking you,we remain. Prof. Abdalla Mohamed, Systems & Biomedical Engineering Dept., Cairo University, Egypt. On Mon, Jul 16, 2012 at 12:20 PM, Boris Reuderink wrote: > Dear FieldTrippers, > > I would like to bring to you attention that we have reorganzed and > improved FieldTrip's programs for acquisition and real-time signal > processing. > > The most important change for users is the new directory structure. > For each platform, we now have a directory containing all the > executables for that platform*: > - realtime/bin/win32 for Windows, > - realtime/bin/glnxa64 for Linux (64 bit), > - realtime/bin/maci64 for OS-X (64 bit). > > To get started with real-time processing, you can take a look at the > examples ( > http://fieldtrip.fcdonders.nl/development/realtime#example_scripts) > and the background information > (http://fieldtrip.fcdonders.nl/development/realtime) on the FieldTrip > wiki. > > Besides restructuring the file layout, we have fixed a number of bugs, > most notable being: > - bug #1525 duplicated samples with low-latency settings [1], > - bug #933 freezing buffer server due to deadlock in threading [2], > - bug #1246 incorrect reading of configuration scripts [3], > - bug #1020 memory problem in event handling [4]. > > We strongly recommend to download a fresh release of FieldTrip > (http://fieldtrip.fcdonders.nl/download), and use the files from this > new version. > > Best regards, > > Boris Reuderink > > [1] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1525 > [2] http://bugzilla.fcdonders.nl/show_bug.cgi?id=933 > [3] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1246 > [4] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1020 > > > * Please note that for now, the neuromag files are still in > realtime/src/acquisition/neuromag/bin . > > -- > twitter.com/#!/breuderink | > github.com/breuderink | borisreuderink.nl > _______________________________________________ > 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 b.reuderink at donders.ru.nl Mon Jul 16 15:01:15 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Mon, 16 Jul 2012 15:01:15 +0200 Subject: [FieldTrip] Improvements in FieldTrip's real-time processing In-Reply-To: References: Message-ID: Dear Prof. Abdalla Mohamed, I just tried to download FieldTrip, and supplied a fake email address from http://10minutemail.com/ (as suggested on http://fieldtrip.fcdonders.nl/download.php), and I can download FieldTrip just fine. Perhaps you could try with a fake email adress as well? Best regards, Boris Reuderink On Mon, Jul 16, 2012 at 1:33 PM, Prof. Abdalla Mohamed wrote: > Dear Sir, > I am not able to download fresh release FieldTrip and I got error of invalid > e-mail address. > Please may help me. > Thanking you,we remain. > Prof. Abdalla Mohamed, > Systems & Biomedical Engineering Dept., > Cairo University, Egypt. > > On Mon, Jul 16, 2012 at 12:20 PM, Boris Reuderink > wrote: >> >> Dear FieldTrippers, >> >> I would like to bring to you attention that we have reorganzed and >> improved FieldTrip's programs for acquisition and real-time signal >> processing. >> >> The most important change for users is the new directory structure. >> For each platform, we now have a directory containing all the >> executables for that platform*: >> - realtime/bin/win32 for Windows, >> - realtime/bin/glnxa64 for Linux (64 bit), >> - realtime/bin/maci64 for OS-X (64 bit). >> >> To get started with real-time processing, you can take a look at the >> examples >> (http://fieldtrip.fcdonders.nl/development/realtime#example_scripts) >> and the background information >> (http://fieldtrip.fcdonders.nl/development/realtime) on the FieldTrip >> wiki. >> >> Besides restructuring the file layout, we have fixed a number of bugs, >> most notable being: >> - bug #1525 duplicated samples with low-latency settings [1], >> - bug #933 freezing buffer server due to deadlock in threading [2], >> - bug #1246 incorrect reading of configuration scripts [3], >> - bug #1020 memory problem in event handling [4]. >> >> We strongly recommend to download a fresh release of FieldTrip >> (http://fieldtrip.fcdonders.nl/download), and use the files from this >> new version. >> >> Best regards, >> >> Boris Reuderink >> >> [1] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1525 >> [2] http://bugzilla.fcdonders.nl/show_bug.cgi?id=933 >> [3] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1246 >> [4] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1020 >> >> >> * Please note that for now, the neuromag files are still in >> realtime/src/acquisition/neuromag/bin . >> >> -- >> twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl >> >> _______________________________________________ >> 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 -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From m.vandenieuwenhuijzen at fcdonders.ru.nl Mon Jul 16 19:03:57 2012 From: m.vandenieuwenhuijzen at fcdonders.ru.nl (Marieke van de Nieuwenhuijzen) Date: Mon, 16 Jul 2012 19:03:57 +0200 (CEST) Subject: [FieldTrip] graphical problem with ft_sourceplot In-Reply-To: <668686231.1061677.1342456205553.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <805894218.1061785.1342458237893.JavaMail.root@draco.zimbra.ru.nl> Dear all, I am trying to use ft_sourceplot to plot modelvalues ranging from negative to positive. The blobs of interest are the ones close to both the positive and negative extremes, so I want to mask the values surrounding zero. However, I can't seem to mask these values properly. The code I'm using is: cfg = []; cfg.method = 'slice'; cfg.funparameter = 'model'; cfg.maskparameter = cfg.funparameter cfg.colorlim = 'maxabs'; cfg.opacitymap = 'vdown' cfg.opacitylim = 'maxabs'; figure; ft_sourceplot(cfg,sourceInterpolated); Although this code masks the values around zero, it only plots the underlying MRI scan partially. It looks like only those voxels of the MRI scan that contain gridpoints which are located inside the brain according to grid_singleshell.inside are plotted in the underlying MRI. In fact, this is exactly how I would expect the functional overlay to behave (which it does), but not the underlying MRI scan. If I set cfg.opavitymap to 'rampup' I don't get this graphical glitch, i.e. the anatomical MRI scan is plotted completely. However, as this doesn't mask the zero values, using this setting is not an option for me. I am aware of the artefacts that can occur when using opacity. However, setting the renderer to zbuffer doesn't solve the problem at all. In fact, if I do this the anatomical scan isn't plotted at all, and the zero values are not masked. If I specify cfg.method as 'ortho' instead of 'slice', the resulting plot looks good (the complete anatomical MRI is plotted and the values around zero are masked), apart from some green line pieces surrounding the brain. Setting the renderer to zbuffer here does seem to get rid of those lines, but ignores the masking of the values around zero. Does any of you perhaps know how to get rid of the glitch (if it is indeed a glitch) when using the aforementioned code? Best, Marieke From hgould at memphis.edu Tue Jul 17 14:36:26 2012 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 17 Jul 2012 12:36:26 +0000 Subject: [FieldTrip] mexw files Message-ID: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com> I have just found fieldtrip and have started to work on the tutorial. I am trying to read the data for subject 1 in the tutorial and recieve the following error: cfg1 = ft_definetrial(cfg1); Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20120715\private\warning_once at 75 In ft_defaults at 91 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > In ft_defaults at 99 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > In ft_defaults at 99 In ft_definetrial at 111 ??? Invalid MEX-file 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); I have checked and the .mexw32 file is there What am I doing wrong? Herb Gould -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Tue Jul 17 15:04:26 2012 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Tue, 17 Jul 2012 15:04:26 +0200 (CEST) Subject: [FieldTrip] mexw files In-Reply-To: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com> Message-ID: <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> Hi Herbert, It seems you have multiple versions of SPM on your path, which may confuse FieldTrip. Could you try inserting the commands below in the matlab command window, before inserting the tutorial code? Best regards, Arjen restoredefaultpath addpath C:\FieldTrip\fieldtrip-20120715 ft_defaults ----- Oorspronkelijk bericht ----- > Van: "Herbert J Gould (hgould)" > Aan: fieldtrip at science.ru.nl > Verzonden: Dinsdag 17 juli 2012 14:36:26 > Onderwerp: [FieldTrip] mexw files > I have just found fieldtrip and have started to work on the tutorial. > I am trying to read the data for subject 1 in the tutorial and recieve > the following error: >   > cfg1         = ft_definetrial(cfg1); > Warning: multiple versions of SPM on your path will confuse FieldTrip > > In fieldtrip-20120715\private\warning_once at 75 >   In ft_defaults at 91 >   In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > > In ft_defaults at 99 >   In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > > In ft_defaults at 99 >   In ft_definetrial at 111 > ??? Invalid MEX-file > 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified > procedure could not be found. > . > Error in ==> ft_checkconfig at 71 > renamed         = ft_getopt(varargin, 'renamed'); > Error in ==> ft_definetrial at 116 > cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); >   > I have checked and the .mexw32 file is there What am I doing wrong? >   > Herb Gould > _______________________________________________ > 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 hgould at memphis.edu Tue Jul 17 15:22:47 2012 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 17 Jul 2012 13:22:47 +0000 Subject: [FieldTrip] mexw files In-Reply-To: <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> References: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com>, <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com> Dear Arjen, Thank you that took care of the SPM issue but it still leaves the .mexw32 issue. However it now is looking for the file in a different location >> restoredefaultpath >> addpath c:\FieldTrip\fieldtrip-20120715 >> ft_defaults ??? Invalid MEX-file 'c:\FieldTrip\fieldtrip-20120715\utilities\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); Error in ==> tutorial1 at 8 cfg1 = ft_definetrial(cfg1); >> Herb Gould ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, July 17, 2012 8:04 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] mexw files Hi Herbert, It seems you have multiple versions of SPM on your path, which may confuse FieldTrip. Could you try inserting the commands below in the matlab command window, before inserting the tutorial code? Best regards, Arjen restoredefaultpath addpath C:\FieldTrip\fieldtrip-20120715 ft_defaults ________________________________ Van: "Herbert J Gould (hgould)" Aan: fieldtrip at science.ru.nl Verzonden: Dinsdag 17 juli 2012 14:36:26 Onderwerp: [FieldTrip] mexw files I have just found fieldtrip and have started to work on the tutorial. I am trying to read the data for subject 1 in the tutorial and recieve the following error: cfg1 = ft_definetrial(cfg1); Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20120715\private\warning_once at 75 In ft_defaults at 91 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > In ft_defaults at 99 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > In ft_defaults at 99 In ft_definetrial at 111 ??? Invalid MEX-file 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); I have checked and the .mexw32 file is there What am I doing wrong? Herb Gould _______________________________________________ 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 jm.horschig at donders.ru.nl Tue Jul 17 15:47:43 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 17 Jul 2012 15:47:43 +0200 Subject: [FieldTrip] mexw files In-Reply-To: <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com> References: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com>, <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com> Message-ID: <50056CFF.7080103@donders.ru.nl> Dear Herb, it seems like the mex-file you are using is corrupt. Either it is from a corrupt download (in which case you'd need to download fieldtrip once more) or there is, or there is some other incompatibility between your windows/matlab combination that we have not encountered. Could you try downloading FieldTrip again and see whether the error persists? If it does persist, you could go to the src/ directory and type 'mex ft_getopt.c' to re-mex the file (in Matlab). Then copy the mexw32 file from that folder to utilities/. This is not an optimal solution, because you will probably encounter similar issues with other mexw32 files. If that works for you, it would be nice if you sent me (or someone else from the dev team) the file so that we can check whether the file is indeed different. Either way, please let us know whether (and if so how) you can resolve the problem. Best, Jörn On 7/17/2012 3:22 PM, Herbert J Gould (hgould) wrote: > > Dear Arjen, > > Thank you that took care of the SPM issue but it still leaves the > .mexw32 issue. However it now is looking for the file in a different > location > > >> restoredefaultpath > >> addpath c:\FieldTrip\fieldtrip-20120715 > >> ft_defaults > ??? Invalid MEX-file > 'c:\FieldTrip\fieldtrip-20120715\utilities\ft_getopt.mexw32': The > specified procedure could not be found. > > . > > Error in ==> ft_checkconfig at 71 > renamed = ft_getopt(varargin, 'renamed'); > > Error in ==> ft_definetrial at 116 > cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); > > Error in ==> tutorial1 at 8 > cfg1 = ft_definetrial(cfg1); > > >> > > Herb Gould > ------------------------------------------------------------------------ > *From:* fieldtrip-bounces at science.ru.nl > [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. > [a.stolk at fcdonders.ru.nl] > *Sent:* Tuesday, July 17, 2012 8:04 AM > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] mexw files > > Hi Herbert, > > It seems you have multiple versions of SPM on your path, which may > confuse FieldTrip. Could you try inserting the commands below in the > matlab command window, before inserting the tutorial code? > > Best regards, > > Arjen > > restoredefaultpath > > addpath C:\FieldTrip\fieldtrip-20120715 > > ft_defaults > > ------------------------------------------------------------------------ > > *Van: *"Herbert J Gould (hgould)" > *Aan: *fieldtrip at science.ru.nl > *Verzonden: *Dinsdag 17 juli 2012 14:36:26 > *Onderwerp: *[FieldTrip] mexw files > > I have just found fieldtrip and have started to work on the > tutorial. I am trying to read the data for subject 1 in the > tutorial and recieve the following error: > > cfg1 = ft_definetrial(cfg1); > Warning: multiple versions of SPM on your path will confuse FieldTrip > > In fieldtrip-20120715\private\warning_once at 75 > In ft_defaults at 91 > In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > > In ft_defaults at 99 > In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > > In ft_defaults at 99 > In ft_definetrial at 111 > ??? Invalid MEX-file > 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The > specified procedure could not be found. > > . > > Error in ==> ft_checkconfig at 71 > renamed = ft_getopt(varargin, 'renamed'); > > Error in ==> ft_definetrial at 116 > cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); > > I have checked and the .mexw32 file is there What am I doing wrong? > > Herb Gould > > > _______________________________________________ > 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 sguillor at ucla.edu Tue Jul 17 20:18:24 2012 From: sguillor at ucla.edu (S Guillory) Date: Tue, 17 Jul 2012 14:18:24 -0400 Subject: [FieldTrip] errors with ft_definetrial Message-ID: Hello, I'm trying to timelock to a specific event in an epoch and I'm having some difficulty setting it up in matlab. When not specifying an event, i.e. using '?', it identifies two types of events 'trial' and 'trigger' as well as the values. The problem I'm having is that there are two different triggers per trial and I am interested in only one of them, however when I specify cfg.trialdef.eventtype = 'trigger' and the cfg.trialdef.eventvalue = 'triggername', I get an error that no trials were defined. Is there a way to isolate the specific trigger without having to code a trial function. Thank you in advance for your time. -Sylvia -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Tue Jul 17 21:39:06 2012 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Tue, 17 Jul 2012 21:39:06 +0200 (CEST) Subject: [FieldTrip] errors with ft_definetrial In-Reply-To: Message-ID: <1895003729.997389.1342553946159.JavaMail.root@sculptor.zimbra.ru.nl> Hi Sylvia, What values exactly do you get for the 'trial' and 'trigger' event types? If, for instance, you have the values 1 and 2 (e.g. for conditions 1 and 2 respectively) for the 'trigger' event type, you can specifically read condition 1 by using: cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 1;  and more generally cfg.trialdef.prestim = 1; % one second before trigger with value 1 cfg.trialdef.poststim = 2; % two seconds after trigger with value 1 Hope this solves your problem? Arjen ----- Oorspronkelijk bericht ----- > Van: "S Guillory" > Aan: fieldtrip at donders.ru.nl > Verzonden: Dinsdag 17 juli 2012 20:18:24 > Onderwerp: [FieldTrip] errors with ft_definetrial > Hello, >  I'm trying to timelock to a specific event in an epoch and I'm > having some difficulty setting it up in matlab. When not specifying an > event, i.e. using '?', it identifies two types of events 'trial' > and 'trigger' as well as the values. The problem I'm having is that > there are two different triggers per trial and I am interested in only > one of them, however when I specify cfg.trialdef.eventtype = 'trigger' > and the cfg.trialdef.eventvalue = 'triggername', I get an error that > no trials were defined. Is there a way to isolate the specific > trigger without having to code a trial function. Thank you in advance > for your time. >  -Sylvia > _______________________________________________ > 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 hgould at memphis.edu Tue Jul 17 22:39:03 2012 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 17 Jul 2012 20:39:03 +0000 Subject: [FieldTrip] mexw files In-Reply-To: <50056CFF.7080103@donders.ru.nl> References: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com>, <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com>, <50056CFF.7080103@donders.ru.nl> Message-ID: <5306C43FAB1DB14992CDDF2D7EDB981B13A824BB@CH1PRD0410MB356.namprd04.prod.outlook.com> Dear Jorn, I downloaded the 20120716 version of Fieldtrip and the same problem occurred. Next I did the mex of ft_getopt.c and transfered it to Utilities. Still no joy as the same problem occured again. I am working on an older laptop running xp with an old 7.1 version of Matlab. I will be back in my lab next week where I can try it out on better equipment and newer software. Herb ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of "Jörn M. Horschig" [jm.horschig at donders.ru.nl] Sent: Tuesday, July 17, 2012 8:47 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] mexw files Dear Herb, it seems like the mex-file you are using is corrupt. Either it is from a corrupt download (in which case you'd need to download fieldtrip once more) or there is, or there is some other incompatibility between your windows/matlab combination that we have not encountered. Could you try downloading FieldTrip again and see whether the error persists? If it does persist, you could go to the src/ directory and type 'mex ft_getopt.c' to re-mex the file (in Matlab). Then copy the mexw32 file from that folder to utilities/. This is not an optimal solution, because you will probably encounter similar issues with other mexw32 files. If that works for you, it would be nice if you sent me (or someone else from the dev team) the file so that we can check whether the file is indeed different. Either way, please let us know whether (and if so how) you can resolve the problem. Best, Jörn On 7/17/2012 3:22 PM, Herbert J Gould (hgould) wrote: Dear Arjen, Thank you that took care of the SPM issue but it still leaves the .mexw32 issue. However it now is looking for the file in a different location >> restoredefaultpath >> addpath c:\FieldTrip\fieldtrip-20120715 >> ft_defaults ??? Invalid MEX-file 'c:\FieldTrip\fieldtrip-20120715\utilities\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); Error in ==> tutorial1 at 8 cfg1 = ft_definetrial(cfg1); >> Herb Gould ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, July 17, 2012 8:04 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] mexw files Hi Herbert, It seems you have multiple versions of SPM on your path, which may confuse FieldTrip. Could you try inserting the commands below in the matlab command window, before inserting the tutorial code? Best regards, Arjen restoredefaultpath addpath C:\FieldTrip\fieldtrip-20120715 ft_defaults ________________________________ Van: "Herbert J Gould (hgould)" Aan: fieldtrip at science.ru.nl Verzonden: Dinsdag 17 juli 2012 14:36:26 Onderwerp: [FieldTrip] mexw files I have just found fieldtrip and have started to work on the tutorial. I am trying to read the data for subject 1 in the tutorial and recieve the following error: cfg1 = ft_definetrial(cfg1); Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20120715\private\warning_once at 75 In ft_defaults at 91 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > In ft_defaults at 99 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > In ft_defaults at 99 In ft_definetrial at 111 ??? Invalid MEX-file 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); I have checked and the .mexw32 file is there What am I doing wrong? Herb Gould _______________________________________________ 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 ith at deakin.edu.au Thu Jul 19 06:44:38 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Thu, 19 Jul 2012 04:44:38 +0000 Subject: [FieldTrip] Question regarding ft_connectivitysimulation Message-ID: <5A1787011651BC42A4D41856DBC2E0603E048720@mbox-f-3.du.deakin.edu.au> Dear fieldTrippers, I am trying to generate some simulated signals from a known connectivity structure with ft_connectivitysimulation, and secondly to assign these signals to known dipole locations when using in ft_dipolesimulation. Is there any way I can assign a frequency to the signals in ft_connectivityanalysis, so that I can assign different known frequency signals for dipoles? Any help is really appreciated. Thank you very much. Kind regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr [Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 29155 bytes Desc: image001.jpg URL: From e.maris at psych.ru.nl Fri Jul 20 00:30:26 2012 From: e.maris at psych.ru.nl (Eric Maris) Date: Fri, 20 Jul 2012 00:30:26 +0200 (CEST) Subject: [FieldTrip] PhD position "Mechanisms of top-down control in the accumulation of sensory evidence" Message-ID: <02d301cd65fe$17ff7a90$47fe6fb0$@maris@psych.ru.nl> Dear Discussion List subscribers, I would to post an advertisement for a PhD position at the Donders Institute for Brain, Cognition and Behavior. Mechanisms of top-down control in the accumulation of sensory evidence Many studies have shown neurophysiological correlates of top-down factors in perception (e.g., attention and expectation) which are already active prior to the sampling of sensory evidence. One of the puzzling observations in this line of investigation is the rather weak relation between these anticipatory neurophysiological signals (typically, modulations of oscillatory activity) and perception (most importantly, accuracy). The overall objective of this project is to identify additional neurophysiological processes that explain behavioral accuracy and its modulation by attention. The main working hypothesis that guides us in this search is that one should not only investigate anticipatory neural activity but also the neural activity during the accumulation of sensory evidence. The objectives of this research project will be addressed in experiments in which extracranial neural signals are recorded using Magnetoencephalography (MEG). Within the Donders Institute (DI), you will belong to the research group Neurophysiology of Active Perception (PI Eric Maris). As this is a collaborative project within the DI, you will also be affiliated to the research groups Prediction & Attention (PI Floris de Lange) and Neuronal Oscillations (PI Ole Jensen). A successful candidate has a Master' s degree in a field at the interface of behavior and neurobiology (Cognitive Neuroscience, Neurobiology, Cognitive Science) and excellent analytic and quantitative skills. Programming skills (e.g., Matlab) are required, and it is an advantage if you have experience in running EEG or MEG experiments. Please include with your application: - a curriculum vitae, including academic qualifications, grades, a list of publications (if applicable), and the names and contact details of two referees; - a letter explaining your motivation, your interest in the project, and your competence in the research field;" Employment start date: 2012-10-15 Contract length: 4 years Contact Information: Dr. Eric Maris E-mail: e.maris at donders.ru.nl Website: http://www.nphyscog.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From dporada at uos.de Fri Jul 20 07:48:31 2012 From: dporada at uos.de (Porada Danja) Date: Fri, 20 Jul 2012 07:48:31 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds Message-ID: <0D507729-5866-4635-845A-E5C45F210830@uos.de> Hi, I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). Here is the problem: For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? And I have another question: Do I have to calculate the planar gradient before computing the grand average? Best, Danja From jm.horschig at donders.ru.nl Fri Jul 20 11:59:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 20 Jul 2012 11:59:37 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds In-Reply-To: <0D507729-5866-4635-845A-E5C45F210830@uos.de> References: <0D507729-5866-4635-845A-E5C45F210830@uos.de> Message-ID: <50092C09.7080109@donders.ru.nl> Hi Danja, you can could either compute the average yourself: /data.avg = squeeze(nanmean(data.trial, 1)); data.dimord = 'chan_time';/ Note that the covariance might be invalid here, not sure what ft_regressconfound does here. or call /data = ft_checkdata(data, 'datatype', 'raw')/ which converts the timelocked data back to raw data format, and you can call /ft_timelockanalysis /again with /cfg.keeptrials = 'no'/ (the latter would be my favourite) Regarding the planar gradient, I'd say no. Keep in mind that the planar gradient computation results in all values > 0, thus e.g. noise might not cancel out as efficiently and a simple t-test against with the classical null hypothesis becomes invalid. I don't do ERP analysis though, so if someone can provide a good reason for doing the transformation nonetheless, I might be convinced otherwise ;) Best, Jörn On 7/20/2012 7:48 AM, Porada Danja wrote: > Hi, > > I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). > > Here is the problem: > For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? > > > And I have another question: Do I have to calculate the planar gradient before computing the grand average? > > > Best, > Danja > _______________________________________________ > 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 dporada at uos.de Fri Jul 20 12:28:01 2012 From: dporada at uos.de (Porada Danja) Date: Fri, 20 Jul 2012 12:28:01 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds In-Reply-To: <800_1342766933_q6K6mqFs001171_0D507729-5866-4635-845A-E5C45F210830@uos.de> References: <800_1342766933_q6K6mqFs001171_0D507729-5866-4635-845A-E5C45F210830@uos.de> Message-ID: I just found out that I only have to use the field avg as input for ft_grandaverage... But I'm still wondering whether it is necessary to calculate the planar gradient before computing the grand average. Best, Danja Am 20.07.2012 um 07:48 schrieb Porada Danja: > Hi, > > I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). > > Here is the problem: > For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? > > > And I have another question: Do I have to calculate the planar gradient before computing the grand average? > > > Best, > Danja > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From stephen.whitmarsh at gmail.com Fri Jul 20 13:13:47 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 20 Jul 2012 13:13:47 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds In-Reply-To: References: <800_1342766933_q6K6mqFs001171_0D507729-5866-4635-845A-E5C45F210830@uos.de> Message-ID: Dear Danja, As Jorn said calculating the planar on ERF data creates some additional 'issues', mainly because the signal, as well as the noise, will always be positive (because of the pythagoras' square operation), and the noise will therefore be additive - i.e. it won't 'average out'. However, with similar amount of trials and other such caretaking comparisons between conditions it is in principle possible. As I see it there are two main reasons for going to planar: 1) more interpretable locations (of maximum amplitude difference): It relieves one from the neccecity to visually process the dipole pattern (positive and negative poles) as showing two sides of a single dipole with the source probably in between. 2) since you lose the orientation of the dipole in the planar transformation - an ideal anterior-posterior will give the same pattern as a left-right dipole when the maximum slope between the two poles lie on the same location - this can help you to average over subjects that might have different orientations but are located above similar regions. In addition the dipole pattern is in effect spatially smoothed (depending on how many neighbours you use), which might help your average as well. Cheers, Stephen On 20 July 2012 12:28, Porada Danja wrote: > I just found out that I only have to use the field avg as input for ft_grandaverage... > > But I'm still wondering whether it is necessary to calculate the planar gradient before computing the grand average. > > Best, > Danja > > Am 20.07.2012 um 07:48 schrieb Porada Danja: > >> Hi, >> >> I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). >> >> Here is the problem: >> For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? >> >> >> And I have another question: Do I have to calculate the planar gradient before computing the grand average? >> >> >> Best, >> Danja >> _______________________________________________ >> 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 sanchomoro at gmail.com Fri Jul 20 17:21:22 2012 From: sanchomoro at gmail.com (Sancho Moro) Date: Fri, 20 Jul 2012 17:21:22 +0200 Subject: [FieldTrip] Post-doctoral position in Multisensory integration/EEG Message-ID: *Post-doctoral position in Multisensory integration/EEG* * * Applications are invited for a full-time post-doctoral research position in the MULTISENSORY RESEARCH GROUP , led by Salvador Soto-Faraco, at the Pompeu Fabra University (Barcelona). The position is covered by a European Research Council grant on Multisensory Integration and Attention. *The project* addresses the interplay between multisensory integration processes and attention mechanisms. This research spans several functions (speech, temporal and spatial processing, in vision, audition and touch, and body representation) and research approaches (psychophysics, neuroimaging, and brain stimulation with TMS). *We seek* a person with solid experience who leads a research line focused on brain oscillatory dynamics. Involvement in some organizational and management aspects is expected. The candidate must (1) *have solid demonstrable experience (i.e., publications) in the field of oscillatory analysis using EEG and/or MEG*, (2) strong background in cognitive neuroscience, neuroscience, and/or cognitive psychology, and (3) scientific motivation about multisensory integration, perception and attention. *We offer* onsite ERP/EEG, TMS, and psychophysical testing facilities, neuronavigation system, a wide range of visual auditory and somatosensory stimulation equipment, and the use of fMRI and MEG recording facilities externally. The position will be funded and renewable on yearly basis for up to three years. Starting date: Feb 2013 or before. Salary: up to 36,000Eur/Year *How to apply* Applications should include: - a C.V. including a list of publications - the names of two referees who would willing to write letters of recommendation - a short cover letter describing research interests Check out www.mrg.upf.edu for info on the group. For informal enquiries about the position and applications, please contact Salvador Soto-Faraco at applications.MRGLab at gmail.com. Applications will be accepted until the position is filled. Please, mention that you are applying to the POSTDOCTORAL position in the email subject -- Salvador Soto Faraco ICREA Research Professor Dept. de Tecnologies de la Informació i les Comunicacions Universitat Pompeu Fabra C. Tanger, 122-140, room 55.108 Postal address: Roc Boronat 138 08018 Barcelona Spain Phone: +34 93.542.25.34 <%2B34%2093.542.25.34> Fax: +34 93..542.25.17 E-Mail: salvador.soto at icrea.cat http://www.mrg.upf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From xbai3 at uthsc.edu Sat Jul 21 01:28:49 2012 From: xbai3 at uthsc.edu (Bai, XiaoXiao) Date: Fri, 20 Jul 2012 23:28:49 +0000 Subject: [FieldTrip] About co-register the individual sudbject MRI and sensor locations Message-ID: <5D2CC5653262C14188174E20065A4C4EC8D457@hscmbx6.uthsc.tennessee.edu> Dear Sir/Madam, I am a new fieldtrip user and want to apply the beamformer method in Fieldtrip for the MEG data from 4D/BTI system. Now I can get a individual subject MRI in analysis/spm format from CURRY software. This is my code for create volume head model for the beamformer, mri_nom = ft_read_mri(mrifile); cfg = []; [segmentedmri] = ft_volumesegment(cfg, mri_nom); cfg = []; cfg.method = 'singleshell'; vol = ft_prepare_headmodel(cfg, segmentedmri); The vol and sensor locations were displayed and attached with here. How can I co-register the vol with sensors based on headshpe file (hs_file) for computing lead field for next step? Thanks a lot. Best regards, Xiaoxiao [X] [X] [X] Division of Clinical Neurosciences, Department of Pediatrics University of Tennessee Health Science Center, College of Medicine & Neuroscience Institute, LeBonheur Children's Hospital 777 Washington Avenue, P335 Memphis, TN 38105, USA Phone: 901-287-4612 Fax: 901-287-5325 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sensor and volume.png Type: image/x-png Size: 21343 bytes Desc: sensor and volume.png URL: From victor.veliks at gmail.com Sun Jul 22 22:28:07 2012 From: victor.veliks at gmail.com (viktor veliks) Date: Sun, 22 Jul 2012 23:28:07 +0300 Subject: [FieldTrip] Post-doctoral position in Multisensory integration/EEG In-Reply-To: References: Message-ID: Dear Salvador Soto-Faraco I would like to apply for the job you have published in FieldTrip list - post-doctoral research position in the MULTISENSORY RESEARCH GROUP. In attachment You may see my motivation letter with my skills, CV and list with 2 references. Sincerely, Dr.biol. Viktors Veliks On Fri, Jul 20, 2012 at 6:21 PM, Sancho Moro wrote: > Post-doctoral position in Multisensory integration/EEG > > > > Applications are invited for a full-time post-doctoral research position in > the MULTISENSORY RESEARCH GROUP, led by Salvador Soto-Faraco, at the Pompeu > Fabra University (Barcelona). The position is covered by a European Research > Council grant on Multisensory Integration and Attention. > > > > The project addresses the interplay between multisensory integration > processes and attention mechanisms. This research spans several functions > (speech, temporal and spatial processing, in vision, audition and touch, and > body representation) and research approaches (psychophysics, neuroimaging, > and brain stimulation with TMS). > > > > We seek a person with solid experience who leads a research line focused on > brain oscillatory dynamics. Involvement in some organizational and > management aspects is expected. The candidate must (1) have solid > demonstrable experience (i.e., publications) in the field of oscillatory > analysis using EEG and/or MEG, (2) strong background in cognitive > neuroscience, neuroscience, and/or cognitive psychology, and (3) scientific > motivation about multisensory integration, perception and attention. > > > > We offer onsite ERP/EEG, TMS, and psychophysical testing facilities, > neuronavigation system, a wide range of visual auditory and somatosensory > stimulation equipment, and the use of fMRI and MEG recording facilities > externally. The position will be funded and renewable on yearly basis for > up to three years. > > > > Starting date: Feb 2013 or before. > > Salary: up to 36,000Eur/Year > > > > How to apply > > Applications should include: > > - a C.V. including a list of publications > > - the names of two referees who would willing to write letters of > recommendation > > - a short cover letter describing research interests > > Check out www.mrg.upf.edu for info on the group. For informal enquiries > about the position and applications, please contact Salvador Soto-Faraco at > applications.MRGLab at gmail.com. Applications will be accepted until the > position is filled. > > Please, mention that you are applying to the POSTDOCTORAL position in the > email subject > > > > > > -- > Salvador Soto Faraco > ICREA Research Professor > Dept. de Tecnologies de la Informació i les Comunicacions > Universitat Pompeu Fabra > C. Tanger, 122-140, room 55.108 > > Postal address: > Roc Boronat 138 > 08018 Barcelona > Spain > > > Phone: +34 93.542.25.34 > Fax: +34 93..542.25.17 > E-Mail: salvador.soto at icrea.cat > http://www.mrg.upf.edu > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From omidabbasi2000 at gmail.com Tue Jul 24 17:49:05 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Tue, 24 Jul 2012 20:19:05 +0430 Subject: [FieldTrip] help to apply field trip (topography plotting) In-Reply-To: References: Message-ID: Dear Steve I have a project in ERP analyzing. I provide a task for it. Any 2 sec, a square appear in the left side of screen or in the right side of screen. And subject have to look to other side of screen. I don't have any software to analyze it. I write some code for it but i think i haven't enough information about ERP analyzing. Some latency and amplitude like P300 and N100 is important for me. Do you have any information about ERP analyzing. I know i take your time with my basic question, but i think the only person that can help me is you. Thank you very much Best Regards On Sat, Jul 7, 2012 at 5:16 AM, Stephen Politzer-Ahles < politzerahless at gmail.com> wrote: > Hi Omid, > > Welcome to Fieldtrip. You can find a lot of information about how to use > Fieldtrip at http://fieldtrip.fcdonders.nl/walkthrough and > http://fieldtrip.fcdonders.nl/tutorial. In your case, you need to get > your data imported into Fieldtrip's format in MATLAB ( > http://fieldtrip.fcdonders.nl/tutorial/preprocessing), as well as your > channel layout (http://fieldtrip.fcdonders.nl/tutorial/layout) before > proceeding to plotting. > > Good luck, > Steve > > >> Message: 1 >> Date: Thu, 5 Jul 2012 16:36:23 +0430 >> From: omid abbasi >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] help to apply field trip (topography plotting) >> Message-ID: >> < >> CAPc_m1utoA_ZqC8_0q44hz5FX3yMfWP-gfke5Mes9_sEUOuyrA at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear Developer >> >> At first, I thank you for useful source code. >> >> This is Omid. I'm a student that work on biological signal processing. I >> want to use your source code for plotting data topography of brain. I >> downloaded your code from this link ( >> http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but >> i >> can't use it in my project, because i have 19 signals from 19 sites on the >> brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your >> code in my project with different channel and data? >> >> It would grateful for me if you could help me to apply your code in my >> project. >> >> Best Regards >> > > _______________________________________________ > 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 ajavitt at NKI.RFMH.ORG Thu Jul 19 17:05:37 2012 From: ajavitt at NKI.RFMH.ORG (Javitt, Aaron) Date: Thu, 19 Jul 2012 11:05:37 -0400 Subject: [FieldTrip] Automatic Artifact Rejection Message-ID: <2586A1048152BE4D861E64A98700AD420B374DBB@nki-mail.NKI.rfmh.org> I am attempting to use automatic artifact rejection based on uV threshold levels (ft_artifact_threshold). When I run ft_rejectartifact some of the datasets run just fine but on others, all the trials are rejected which then causes an error and the program crashes. Since I have a lot of files to analyze I didn't want to go through all of the files by hand, is there a way to know which datasets are going to have all of the trials rejected when ft_rejectartifact is called before I actually call it. -Aaron 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Wed Jul 25 23:43:59 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Wed, 25 Jul 2012 22:43:59 +0100 Subject: [FieldTrip] SPM M/EEG 2012 course lectures now available online In-Reply-To: References: Message-ID: Dear colleagues, Sorry for possible cross-posting. We are pleased to announce that video recordings and presentations from the May 2012 SPM for M/EEG Course at the Wellcome Trust Centre for Neuroimaging, are now freely available online at http://www.fil.ion.ucl.ac.uk/spm/course/video/#MEEG12 The new recordings complement the previously recorded set of lectures covering SPM for fMRI, PET and VBM. We hope that this resource will be useful for SPM M/EEG users as well as for the broader neuroimaging community. With best wishes, Vladimir Litvak Lecturer, Wellcome Trust Centre for Neuroimaging on behalf of SPM faculty From dargilboa at gmail.com Thu Jul 26 01:29:25 2012 From: dargilboa at gmail.com (Dar Gilboa) Date: Thu, 26 Jul 2012 02:29:25 +0300 Subject: [FieldTrip] Help with EEG ROI Timecourse Analysis Message-ID: Hello, I'm a new user of Fieldtrip, and I want to write a script that performs source reconstruction on an EEG data file (initially in TRC or EDF format) and extracts ROI timecourses based on the AAL parcellation (Tzourio-Mazoyer et al. 2002). I have matlab files with details of the parcellation, which assign an ROI number to each voxel in a matrix. I assume the parcellation can be inputted using ft_prepare_atlas. I was wondering if someone has done something similar to this so I don't have to start from scratch, or if anyone has some helpful advice. Thanks, Dar -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.weiss at klinikum.uni-tuebingen.de Thu Jul 26 06:41:10 2012 From: daniel.weiss at klinikum.uni-tuebingen.de (Klinik) Date: Thu, 26 Jul 2012 06:41:10 +0200 Subject: [FieldTrip] SPM M/EEG 2012 course lectures now available online In-Reply-To: References: Message-ID: ! Von meinem iPhone gesendet Am 25.07.2012 um 23:43 schrieb Vladimir Litvak : > Dear colleagues, > > Sorry for possible cross-posting. > > We are pleased to announce that video recordings and presentations > from the May 2012 SPM for M/EEG Course at the Wellcome Trust Centre > for Neuroimaging, are now freely available online at > > http://www.fil.ion.ucl.ac.uk/spm/course/video/#MEEG12 > > The new recordings complement the previously recorded set of lectures > covering SPM for fMRI, PET and VBM. We hope that this resource will be > useful for SPM M/EEG users as well as for the broader neuroimaging > community. > > With best wishes, > > Vladimir Litvak > Lecturer, Wellcome Trust Centre for Neuroimaging > on behalf of SPM faculty > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From marco.buiatti at gmail.com Thu Jul 26 12:36:39 2012 From: marco.buiatti at gmail.com (Marco Buiatti) Date: Thu, 26 Jul 2012 12:36:39 +0200 Subject: [FieldTrip] interactions between two factors In-Reply-To: References: Message-ID: Dear FieldTrippers, some time ago I have posted the message below concerning how to compute the statistical interaction between two factors in an EEG study with the FieldTrip cluster-based statistical analysis. Since I believe it is a problem of general interest, I was confident I would have received some replies, no matter how critics. But I had no reply and I am trying to guess why: - the problem is trivial, I should go back to my statistics books and solve it myself; - the problem is ill-posed, I should go back to my statistics books and reformulate it correctly; - the problem is tabou, no one dares commits to a solution because it could be a wrong one. - the problem is solved: I should read message number #. Thanks a lot for your feedback, Best, Marco On 25 May 2012 15:58, Marco Buiatti wrote: > Dear FieldTrippers, > > I am analysing an EEG study with 2x4 factors: one varies between 4 > parametrically varying levels (1 to 4), the second between two levels. > > I have three questions concerning the use of Fieldtrip cluster-based > non parametric statistical analysis in this case: > > 1) How to compute the interaction between the two factors. Let's start > from the simplest case of a 2x2 design, factors varying between values > A1 and A2 for the first factor, B1 and B2 for the second. Please tell > me if it is correct to compute the interaction by: > - computing the difference diffA=ERP(A1)-ERP(A2) separately in > condition B1 and B2, for every subject > - performing a within-subjects statistical analysis between diffA in > condition B1 and diffA in condition B2 (function > statfun_depsamplesT.m). > > 2) Now consider that factor A varies parametrically between values 1 > to 4. For the main effect of this factor, I have used the Fieldtrip > function statfun_depsamplesregrT.m and I'm satisfied with it. Is it > correct to compute the interaction by > - computing the regression > regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside > function statfun_depsamplesregrT.m) separately in condition B1 and B2, > for every subject > - performing a within-subjects statistical analysis between regrA in > condition B1 and regrA in condition B2 (function > statfun_depsamplesT.m)? > > 3) Since BEFORE looking at the data (this is to prevent Eric's > contestation...) I expect a dipolar topography for the regression > (data are in average reference), I would like to combine into a joint > cluster negative and positive clusters. I have tried by changing > statfun_depsamplesregrT.m by just taking the absolute value of the > regression, but I get weird results (a huge, non significant cluster). > Is it possible that since values are now all positive, I should use a > different statistical test at the single bin level? Any other > suggestions? > > Thanks in advance for your help, > > Marco > > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** -- Marco Buiatti, PhD CEA/DSV/I2BM / NeuroSpin INSERM U992 - Cognitive Neuroimaging Unit Bât 145 - Point Courrier 156 Gif sur Yvette F-91191 FRANCE Ph: +33(0)169.08.65.21 Fax: +33(0)169.08.79.73 E-mail: marco.buiatti at gmail.com http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti *********************************************** From lihqih at gmail.com Thu Jul 26 16:58:51 2012 From: lihqih at gmail.com (qi li) Date: Thu, 26 Jul 2012 10:58:51 -0400 Subject: [FieldTrip] lateral view plot Message-ID: Hi there, Can fieldtrip make the plot like brain lateral view or something like suma such that descriptive statistics can be mapped on? Thanks a lot! Qi From jm.horschig at donders.ru.nl Thu Jul 26 17:23:25 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 26 Jul 2012 17:23:25 +0200 Subject: [FieldTrip] lateral view plot In-Reply-To: References: Message-ID: <501160ED.4050307@donders.ru.nl> Hi Qi, you can see here what's possible: http://fieldtrip.fcdonders.nl/tutorial/plotting?s[]=source&s[]=plot#plotting_data_at_the_source_level or in the tutorial: http://fieldtrip.fcdonders.nl/tutorial/beamformer?#neural_activity_index http://fieldtrip.fcdonders.nl/tutorial/beamformer?#plotting_options see also ft_sourceplot: http://fieldtrip.fcdonders.nl/reference/ft_sourceplot You can use cfg.funparameter and cfg.maskparameter to specify what you want to plot. Have fun ;) Jörn On 7/26/2012 4:58 PM, qi li wrote: > Hi there, > > Can fieldtrip make the plot like brain lateral view or something like > suma such that descriptive statistics can be mapped on? Thanks a lot! > > Qi > _______________________________________________ > 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 arno at cerco.ups-tlse.fr Thu Jul 26 18:35:49 2012 From: arno at cerco.ups-tlse.fr (Arnaud Delorme) Date: Thu, 26 Jul 2012 09:35:49 -0700 Subject: [FieldTrip] interactions between two factors In-Reply-To: References: Message-ID: Dear Marco, I believe the first answer is the correct one. The problem is somewhat trivial but not implemented yet. The LIMO toolbox will let you perform 2-way statistics with cluster correction for multiple comparisons. Best, Arno On Jul 26, 2012, at 3:36 AM, Marco Buiatti wrote: > Dear FieldTrippers, > > some time ago I have posted the message below concerning how to > compute the statistical interaction between two factors in an EEG > study with the FieldTrip cluster-based statistical analysis. Since I > believe it is a problem of general interest, I was confident I would > have received some replies, no matter how critics. But I had no reply > and I am trying to guess why: > > - the problem is trivial, I should go back to my statistics books and > solve it myself; > - the problem is ill-posed, I should go back to my statistics books > and reformulate it correctly; > - the problem is tabou, no one dares commits to a solution because it > could be a wrong one. > - the problem is solved: I should read message number #. > > Thanks a lot for your feedback, > > Best, > > Marco > > On 25 May 2012 15:58, Marco Buiatti wrote: >> Dear FieldTrippers, >> >> I am analysing an EEG study with 2x4 factors: one varies between 4 >> parametrically varying levels (1 to 4), the second between two levels. >> >> I have three questions concerning the use of Fieldtrip cluster-based >> non parametric statistical analysis in this case: >> >> 1) How to compute the interaction between the two factors. Let's start >> from the simplest case of a 2x2 design, factors varying between values >> A1 and A2 for the first factor, B1 and B2 for the second. Please tell >> me if it is correct to compute the interaction by: >> - computing the difference diffA=ERP(A1)-ERP(A2) separately in >> condition B1 and B2, for every subject >> - performing a within-subjects statistical analysis between diffA in >> condition B1 and diffA in condition B2 (function >> statfun_depsamplesT.m). >> >> 2) Now consider that factor A varies parametrically between values 1 >> to 4. For the main effect of this factor, I have used the Fieldtrip >> function statfun_depsamplesregrT.m and I'm satisfied with it. Is it >> correct to compute the interaction by >> - computing the regression >> regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside >> function statfun_depsamplesregrT.m) separately in condition B1 and B2, >> for every subject >> - performing a within-subjects statistical analysis between regrA in >> condition B1 and regrA in condition B2 (function >> statfun_depsamplesT.m)? >> >> 3) Since BEFORE looking at the data (this is to prevent Eric's >> contestation...) I expect a dipolar topography for the regression >> (data are in average reference), I would like to combine into a joint >> cluster negative and positive clusters. I have tried by changing >> statfun_depsamplesregrT.m by just taking the absolute value of the >> regression, but I get weird results (a huge, non significant cluster). >> Is it possible that since values are now all positive, I should use a >> different statistical test at the single bin level? Any other >> suggestions? >> >> Thanks in advance for your help, >> >> Marco >> >> >> >> -- >> Marco Buiatti, PhD >> >> CEA/DSV/I2BM / NeuroSpin >> INSERM U992 - Cognitive Neuroimaging Unit >> Bât 145 - Point Courrier 156 >> Gif sur Yvette F-91191 FRANCE >> Ph: +33(0)169.08.65.21 >> Fax: +33(0)169.08.79.73 >> E-mail: marco.buiatti at gmail.com >> http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti >> >> *********************************************** > > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Arnaud Delorme, PhD Centre de Recherche Cerveau et Cognition - UMR 5549 Pavillon Baudot, Hopital Purpan, BP 25202 31052 Toulouse Cedex, France From arno at cerco.ups-tlse.fr Thu Jul 26 18:35:49 2012 From: arno at cerco.ups-tlse.fr (Arnaud Delorme) Date: Thu, 26 Jul 2012 09:35:49 -0700 Subject: [FieldTrip] interactions between two factors In-Reply-To: References: Message-ID: Dear Marco, I believe the first answer is the correct one. The problem is somewhat trivial but not implemented yet. The LIMO toolbox will let you perform 2-way statistics with cluster correction for multiple comparisons. Best, Arno On Jul 26, 2012, at 3:36 AM, Marco Buiatti wrote: > Dear FieldTrippers, > > some time ago I have posted the message below concerning how to > compute the statistical interaction between two factors in an EEG > study with the FieldTrip cluster-based statistical analysis. Since I > believe it is a problem of general interest, I was confident I would > have received some replies, no matter how critics. But I had no reply > and I am trying to guess why: > > - the problem is trivial, I should go back to my statistics books and > solve it myself; > - the problem is ill-posed, I should go back to my statistics books > and reformulate it correctly; > - the problem is tabou, no one dares commits to a solution because it > could be a wrong one. > - the problem is solved: I should read message number #. > > Thanks a lot for your feedback, > > Best, > > Marco > > On 25 May 2012 15:58, Marco Buiatti wrote: >> Dear FieldTrippers, >> >> I am analysing an EEG study with 2x4 factors: one varies between 4 >> parametrically varying levels (1 to 4), the second between two levels. >> >> I have three questions concerning the use of Fieldtrip cluster-based >> non parametric statistical analysis in this case: >> >> 1) How to compute the interaction between the two factors. Let's start >> from the simplest case of a 2x2 design, factors varying between values >> A1 and A2 for the first factor, B1 and B2 for the second. Please tell >> me if it is correct to compute the interaction by: >> - computing the difference diffA=ERP(A1)-ERP(A2) separately in >> condition B1 and B2, for every subject >> - performing a within-subjects statistical analysis between diffA in >> condition B1 and diffA in condition B2 (function >> statfun_depsamplesT.m). >> >> 2) Now consider that factor A varies parametrically between values 1 >> to 4. For the main effect of this factor, I have used the Fieldtrip >> function statfun_depsamplesregrT.m and I'm satisfied with it. Is it >> correct to compute the interaction by >> - computing the regression >> regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside >> function statfun_depsamplesregrT.m) separately in condition B1 and B2, >> for every subject >> - performing a within-subjects statistical analysis between regrA in >> condition B1 and regrA in condition B2 (function >> statfun_depsamplesT.m)? >> >> 3) Since BEFORE looking at the data (this is to prevent Eric's >> contestation...) I expect a dipolar topography for the regression >> (data are in average reference), I would like to combine into a joint >> cluster negative and positive clusters. I have tried by changing >> statfun_depsamplesregrT.m by just taking the absolute value of the >> regression, but I get weird results (a huge, non significant cluster). >> Is it possible that since values are now all positive, I should use a >> different statistical test at the single bin level? Any other >> suggestions? >> >> Thanks in advance for your help, >> >> Marco >> >> >> >> -- >> Marco Buiatti, PhD >> >> CEA/DSV/I2BM / NeuroSpin >> INSERM U992 - Cognitive Neuroimaging Unit >> Bât 145 - Point Courrier 156 >> Gif sur Yvette F-91191 FRANCE >> Ph: +33(0)169.08.65.21 >> Fax: +33(0)169.08.79.73 >> E-mail: marco.buiatti at gmail.com >> http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti >> >> *********************************************** > > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Arnaud Delorme, PhD Centre de Recherche Cerveau et Cognition - UMR 5549 Pavillon Baudot, Hopital Purpan, BP 25202 31052 Toulouse Cedex, France From politzerahless at gmail.com Fri Jul 27 16:25:07 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Fri, 27 Jul 2012 09:25:07 -0500 Subject: [FieldTrip] interactions between two factors Message-ID: Hello Marco, For how to test an interaction in a 2x2 design, see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-January/003447.html(and some additional information at http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003338.html, http://mailman.science.ru.nl/pipermail/fieldtrip/2011-September/004244.html, and Anderson & Braak 2003 in *Journal of Statistical Computation & Simulation*). I'm not sure about the other two issues you mentioned, though. Best, Steve Message: 1 > Date: Thu, 26 Jul 2012 12:36:39 +0200 > From: Marco Buiatti > To: fieldtrip at donders.ru.nl > Subject: Re: [FieldTrip] interactions between two factors > Message-ID: > < > CA+wnTO2TL7XtzsKX2QciqXZO9hVxGUZTPjXwoYtS54ztRc0KeQ at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear FieldTrippers, > > some time ago I have posted the message below concerning how to > compute the statistical interaction between two factors in an EEG > study with the FieldTrip cluster-based statistical analysis. Since I > believe it is a problem of general interest, I was confident I would > have received some replies, no matter how critics. But I had no reply > and I am trying to guess why: > > - the problem is trivial, I should go back to my statistics books and > solve it myself; > - the problem is ill-posed, I should go back to my statistics books > and reformulate it correctly; > - the problem is tabou, no one dares commits to a solution because it > could be a wrong one. > - the problem is solved: I should read message number #. > > Thanks a lot for your feedback, > > Best, > > Marco > > On 25 May 2012 15:58, Marco Buiatti wrote: > > Dear FieldTrippers, > > > > I am analysing an EEG study with 2x4 factors: one varies between 4 > > parametrically varying levels (1 to 4), the second between two levels. > > > > I have three questions concerning the use of Fieldtrip cluster-based > > non parametric statistical analysis in this case: > > > > 1) How to compute the interaction between the two factors. Let's start > > from the simplest case of a 2x2 design, factors varying between values > > A1 and A2 for the first factor, B1 and B2 for the second. Please tell > > me if it is correct to compute the interaction by: > > - computing the difference diffA=ERP(A1)-ERP(A2) separately in > > condition B1 and B2, for every subject > > - performing a within-subjects statistical analysis between diffA in > > condition B1 and diffA in condition B2 (function > > statfun_depsamplesT.m). > > > > 2) Now consider that factor A varies parametrically between values 1 > > to 4. For the main effect of this factor, I have used the Fieldtrip > > function statfun_depsamplesregrT.m and I'm satisfied with it. Is it > > correct to compute the interaction by > > - computing the regression > > regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside > > function statfun_depsamplesregrT.m) separately in condition B1 and B2, > > for every subject > > - performing a within-subjects statistical analysis between regrA in > > condition B1 and regrA in condition B2 (function > > statfun_depsamplesT.m)? > > > > 3) Since BEFORE looking at the data (this is to prevent Eric's > > contestation...) I expect a dipolar topography for the regression > > (data are in average reference), I would like to combine into a joint > > cluster negative and positive clusters. I have tried by changing > > statfun_depsamplesregrT.m by just taking the absolute value of the > > regression, but I get weird results (a huge, non significant cluster). > > Is it possible that since values are now all positive, I should use a > > different statistical test at the single bin level? Any other > > suggestions? > > > > Thanks in advance for your help, > > > > Marco > > > > > > > > -- > > Marco Buiatti, PhD > > > > CEA/DSV/I2BM / NeuroSpin > > INSERM U992 - Cognitive Neuroimaging Unit > > B?t 145 - Point Courrier 156 > > Gif sur Yvette F-91191 FRANCE > > Ph: +33(0)169.08.65.21 > > Fax: +33(0)169.08.79.73 > > E-mail: marco.buiatti at gmail.com > > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erdosttorun at gmail.com Sat Jul 28 22:47:21 2012 From: erdosttorun at gmail.com (erdost torun) Date: Sat, 28 Jul 2012 23:47:21 +0300 Subject: [FieldTrip] May I use fieldtrip on social science time series data? Message-ID: Hello everyone! I wonder whether I could use fieldtrip toolbox to do wavelet based causality analysis on Social science data, such as birth rates or malaria statistics. From the fieldtrip webpage, I understand that researches using fieldtrip mainly focus on MEG, EEG, and invasive electrophysiological data. Hence, I want to be sure that fieldtrip is suitable for other time series. Thank you in advance. All the best, Erdost From eelke.spaak at donders.ru.nl Mon Jul 30 13:21:46 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 30 Jul 2012 13:21:46 +0200 Subject: [FieldTrip] May I use fieldtrip on social science time series data? In-Reply-To: References: Message-ID: Hello Erdost, Indeed, FieldTrip is designed specifically for the analysis of electrophysiological neuroscientific data. However, I don't see a reason why you should not use it for analysing different time series as well, if you think this will be useful to you. Best, Eelke On 28 July 2012 22:47, erdost torun wrote: > Hello everyone! > > I wonder whether I could use fieldtrip toolbox to do wavelet based > causality analysis on Social science data, such as birth rates or > malaria statistics. From the fieldtrip webpage, I understand that > researches using fieldtrip mainly focus on MEG, EEG, and invasive > electrophysiological data. Hence, I want to be sure that fieldtrip is > suitable for other time series. Thank you in advance. > > All the best, > > Erdost > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Mon Jul 30 15:43:59 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 30 Jul 2012 15:43:59 +0200 Subject: [FieldTrip] May I use fieldtrip on social science time series data? In-Reply-To: References: Message-ID: <50168F9F.6060400@donders.ru.nl> Dear Erdost, I agree as well with Eelke. In particular, apart from some methods (e.g. source reconstruction), there is no explicit assumption made about the origin of the data. While the algorithms are per se suited for any type of data, the options might be specific for your data. So, e.g. be sure to not demean or detrend your data when preprocessing (check what the defaults are for each function!). If would be great to let us all know if you publish your results in a particular scientific journal. Best of luck&success, Jörn On 7/28/2012 10:47 PM, erdost torun wrote: > Hello everyone! > > I wonder whether I could use fieldtrip toolbox to do wavelet based > causality analysis on Social science data, such as birth rates or > malaria statistics. From the fieldtrip webpage, I understand that > researches using fieldtrip mainly focus on MEG, EEG, and invasive > electrophysiological data. Hence, I want to be sure that fieldtrip is > suitable for other time series. Thank you in advance. > > All the best, > > Erdost > _______________________________________________ > 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 polomacnenad at gmail.com Mon Jul 30 16:10:54 2012 From: polomacnenad at gmail.com (Nenad Polomac) Date: Mon, 30 Jul 2012 16:10:54 +0200 Subject: [FieldTrip] MEG-anatomical MRI image coregistration Message-ID: Hello, I am analyzing MEG CTF data. I want to do source localisation and I have two particular questions regarding the anatomical MRI images. 1. Is it allowed to use anatomical MRI images from a two different MRI devices in a one source localisation study? We already have routinely obtain anatomical images for some patients and those are obtained on the 1.5 Tesla MRI. And for other patients we will record anatomical MRI on 3 Tesla. So, what do you think can we use this data in the same source analysis study. 2. The anatomical MRI images from a few subject were not marked with the vitamin E during imaging for relevant skull points (nasion and ear canals). So, I think to mark them now in some imaging software. The MEG data were properly marked during acquisition for this skull points. What is your opinion about accuracy of software based marking. How big localisation error might be? Thank you in advance! Kind regards! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Mon Jul 30 16:48:33 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Mon, 30 Jul 2012 16:48:33 +0200 Subject: [FieldTrip] MEG-anatomical MRI image coregistration In-Reply-To: References: Message-ID: Dear Nenad, My 2 cents: 1) As long as you are convinced that both give appropriately accurate segmentations - something easily checked along the way by superimposing stripped brain,stull etc on the original scan - I don't see any reason against using them together in one study. Also, as you will probably not work on the high resolution of your T3 (i.e. 1mm isomorphic), but on downsampled grids for beamformer (i.e. 5 mm isomorphic), below the resolution of your 1.5T scans, differences in resolution should not confound your results on source level. Ofcourse in some specific cases in between- or within-group comparisons you could do a control analysis, e.g. using scan device as a covariate in your analysis, just to be sure, but I can think of only some very specific situations where that could be the case. 2) The localisation error would be related to how close you think you can co-register [sic]. I would consider that addive uncertainty above the localisation errors you'll unavoidably already have with your recording (movement) and source reconstruction (i.e. point-spread of the beamformer and such). I don't know what you mean exactly with 'software-based marking'. If you know where your MEG coils where in respect to anatomical landmarks, you can intelligently 'guess' where they are on the anatomical and just put them there by hand (nasion would be pretty close, ears probably put them e.g. 1.5 cm anterior to ear canals). The added uncertainty will be the degree of uncertainty you have being able to do that, right? If with 'software-based marking' you mean the use of a polemus device than that would probably be better. In any case, being conservative i would say the by-eye-method would increase your uncertainly by another cm or 2, instead of about a cm when appropriately using vitamin markers. I have no data to back that claim up though. Good luck! Stephen On 30 July 2012 16:10, Nenad Polomac wrote: > Hello, > > I am analyzing MEG CTF data. I want to do source localisation and I have two > particular questions regarding the anatomical MRI images. > > 1. Is it allowed to use anatomical MRI images from a two different MRI > devices in a one source localisation study? We already have routinely obtain > anatomical images for some patients and those are obtained on the 1.5 Tesla > MRI. And for other patients we will record anatomical MRI on 3 Tesla. So, > what do you think can we use this data in the same source analysis study. > > 2. The anatomical MRI images from a few subject were not marked with the > vitamin E during imaging for relevant skull points (nasion and ear canals). > So, I think to mark them now in some imaging software. The MEG data were > properly marked during acquisition for this skull points. > What is your opinion about accuracy of software based marking. How big > localisation error might be? > > Thank you in advance! > > Kind regards! > > Nenad > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From nenga at gmx.net Mon Jul 30 18:29:38 2012 From: nenga at gmx.net (Carina Oehrn) Date: Mon, 30 Jul 2012 18:29:38 +0200 Subject: [FieldTrip] granger causality Message-ID: <20120730162938.56630@gmx.net> Hi there, I have got an iEEG dataset and would like to look at the directionality of interactions between two channels in two different conditions using granger causality. Hopefully somebody here can help me :-) 1.) I know that I can calculate the appropriate model order and window length with the bsmart toolbox. But from the documentation I somehow do not get the format of data I should use for this calculation. When I enter the time-frequency data (which I want to use to estimate granger causality) (size: 2 x 2 x freq x time points), it doesn't work. Any advise? I have a sampling rate of 1000. What sort of time window and maximal model order would make sense do you think? 2)I would like to keep the time domain analyzing my data. What do you think would be an appropriate sliding time window using the 'ft_mvaranalysis' function? And what does it mean exactly? By choosing the model order, I am already determining the maximal time lag between the two functions. Are the values then estimated for the whole time window? 3)What do you think about statistics? Would it makes sense to use the non-parametric cluster approach to shuffle within patients and do a group analysis that way? Thank you so much in advance! Best, Carina As a summary,I am doing following steps with field trip: cfg = []; cfg.dftfilter ='yes' prep_cond1{subj} = ft_preprocessing(cfg, data); cfg = []; cfg.order = 5; cfg.toolbox = 'bsmart'; cfg.t_ftimwin = 0.05 cfg.toi = -1:0.001:3.5; mdata_cond1{subj}= ft_mvaranalysis(cfg, prep_cond1{subj}); cfg = []; cfg.method = 'mvar'; cfg.foi = 4:100; cond1_freq{subj}= ft_freqanalysis_mvar(cfg,mdata_cond1{subj}); cfg = []; cfg.method = 'granger'; cond1_granger{subj} = ft_connectivityanalysis(cfg, cond1_freq{subj}); From erdosttorun at gmail.com Tue Jul 31 13:33:58 2012 From: erdosttorun at gmail.com (erdost torun) Date: Tue, 31 Jul 2012 14:33:58 +0300 Subject: [FieldTrip] May I use fieldtrip on social science time series data? Message-ID: Dear Eelke and Jorne, Thank you both for your intesest. I plan to implement Wavelet-based Granger Causality on Social Science data through Fieldtrip toolbox. Hope I can make it correctly. If I publish any paper on it, I will share the results with you. Thank you so much All the best, Erdost Torun Dokuz Eylul University Dept of International Business and Trade From stephen.whitmarsh at gmail.com Tue Jul 31 17:35:52 2012 From: stephen.whitmarsh at gmail.com (stephen whitmarsh) Date: Tue, 31 Jul 2012 15:35:52 +0000 (UTC) Subject: [FieldTrip] Invitation to connect on LinkedIn Message-ID: <1955016892.13426275.1343748952505.JavaMail.app@ela4-app0131.prod> LinkedIn ------------ FieldTrip, I'd like to add you to my professional network on LinkedIn. - stephen stephen whitmarsh aio at Radboud Netherlands Confirm that you know stephen whitmarsh: https://www.linkedin.com/e/-kyqm8y-h5b5fjjo-12/isd/8060512829/VSO4ebwG/?hs=false&tok=1jOyZbi12DKRk1 -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/-kyqm8y-h5b5fjjo-12/o2zr3wMN-KUziWnbF0JpKw1y-MN7WW_ZDEc0/goo/fieldtrip%40science%2Eru%2Enl/20061/I2717672971_1/?hs=false&tok=3aVU5rC6CDKRk1 (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Tue Jul 31 22:45:16 2012 From: lihqih at gmail.com (qi li) Date: Tue, 31 Jul 2012 16:45:16 -0400 Subject: [FieldTrip] sourceplot Message-ID: Hi, I am having trouble to call the ft_sourceplot after ft_sourceanalysis. After sourceanalysis I have a source struct ans = time: [1x399 double] pos: [8196x3 double] inside: [1x8196 double] outside: [1x0 double] method: 'average' avg: [1x1 struct] cfg: [1x1 struct] unit: 'cm' Avg field has the following structure ans = mom: {1x8196 cell} pow: [8196x399 double] I want to plot the pow in the brian, so I use cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'avg.pow'; cfg.maskparameter = cfg.funparameter; cfg.funcolorlim = [0.0 1.2]; cfg.opacitylim = [0.0 1.2]; cfg.opacitymap = 'rampup'; figure ft_sourceplot(cfg, source); but the message says 'Error using ft_checkdata (line 307) This function requires volume data as input. Error in ft_volumedownsample (line 58) source = ft_checkdata(source, 'datatype', 'volume', 'feedback', 'no'); Error in ft_sourceplot (line 290) data = ft_volumedownsample(tmpcfg, data);' What does volume data point to? Thanks! From mahdi_meng at yahoo.com Sun Jul 1 18:23:06 2012 From: mahdi_meng at yahoo.com (m m) Date: Sun, 1 Jul 2012 09:23:06 -0700 (PDT) Subject: [FieldTrip] FW: Hi Friend! Message-ID: <1341159786.76669.androidMobile@web122403.mail.ne1.yahoo.com>

I guess your job search is going well. I just wanted to tell you to a new job opp in locality.
We have had several of our members take this opp and I have heard lots of perfect success stories.

The local paper has an article featuring one of our clients, Kelly Richards. It will also you all you all the important information you need to get started.
The link is http://specialoffers.com.br/angerabandoned/Daniel_Alien5/?a=198461&s=dprocessing and I think the story will be featured on the home-page until tomorrow.

TTYL!

-------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Sun Jul 1 22:15:56 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Sun, 01 Jul 2012 13:15:56 -0700 Subject: [FieldTrip] calculating correlation Message-ID: <4FF0AFFC.1040500@berkeley.edu> Hi FTers, I'd like to do two sorts of correlation calculations, and was wondering if there's any easy way to do this within FieldTrip. 1) I'd like to calculate the correlation between performance over trials and power within a specific frequency over trials. So I have the performance measure per trial, and my chan*freq measure after freqanalysis. So for each channel I have a series of power values (trials) and I have a series of performance measures (per trial), and now like to know (first within, and then over subjects) which channel's frequency power follows (correlates) with the performance. From the walkthrough I understand I can give in these performance measures through the design (cfg.design=[0.10.20.30.40.50.40.30.10.2];cfg.ivar=1;), but which method to use for ft_freqstatistics? I don't see statistics = 'correlation' or 'pearson' or 'spearman' in method = 'analytic. Also how to make the design to correlate over trials? 2) I'd like to calculate the correlation between the score on repeated questionnaire over participants with power within a frequency. So I have several power values per participant for each channel, and the repeated scores on the questionnaire for each participant. And now I'd like to calculate a value per channel reflecting the correlation over the repeats of the questionnaire and over participants. Any idea on FieldTrip settings? Both in general, is there a correlation statistics implemented, and more specifically for my question, how would I make the appropriate designs? Thanks so much! Ingrid -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 2 08:53:51 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 2 Jul 2012 08:53:51 +0200 Subject: [FieldTrip] calculating correlation In-Reply-To: <4FF0AFFC.1040500@berkeley.edu> References: <4FF0AFFC.1040500@berkeley.edu> Message-ID: <1AA66D8B-3685-4A8F-AED3-A1FF8C7A8D21@donders.ru.nl> Hi Ingrid, This calls for a statfun_corr or even a statfun_glm! It so happens that I have some of these sitting on my hard drive. As you know I am fond of beer, chocolate and co-authorships, so I am sure we can strike a deal. I have not yet had the opportunity to contribute these statfuns to FieldTrip, but now I sense a win-win-win situation: win 1 is for me (beer/chocolate/co-authorships/etc), win 2 is for you (you can compute your statistic of interest) and win 3 for the community (where you test the code, write documentation on the wiki etcetc). How does that sound for a plan? Cheers, JM On Jul 1, 2012, at 10:15 PM, Ingrid Nieuwenhuis wrote: > Hi FTers, > > I'd like to do two sorts of correlation calculations, and was wondering if there's any easy way to do this within FieldTrip. > > 1) I'd like to calculate the correlation between performance over trials and power within a specific frequency over trials. So I have the performance measure per trial, and my chan*freq measure after freqanalysis. So for each channel I have a series of power values (trials) and I have a series of performance measures (per trial), and now like to know (first within, and then over subjects) which channel's frequency power follows (correlates) with the performance. > > From the walkthrough I understand I can give in these performance measures through the design (cfg.design = [0.1 0.2 0.3 0.4 0.5 0.4 0.3 0.1 0.2]; cfg.ivar= 1;), but which method to use for ft_freqstatistics? I don't see statistics = 'correlation' or 'pearson' or 'spearman' in method = 'analytic. Also how to make the design to correlate over trials? > > 2) I'd like to calculate the correlation between the score on repeated questionnaire over participants with power within a frequency. So I have several power values per participant for each channel, and the repeated scores on the questionnaire for each participant. And now I'd like to calculate a value per channel reflecting the correlation over the repeats of the questionnaire and over participants. > > Any idea on FieldTrip settings? Both in general, is there a correlation statistics implemented, and more specifically for my question, how would I make the appropriate designs? > > Thanks so much! > Ingrid > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > _______________________________________________ > 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 johanna.zumer at donders.ru.nl Mon Jul 2 11:54:11 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Mon, 2 Jul 2012 11:54:11 +0200 Subject: [FieldTrip] Source localization using DICS for EEG data from combined MEG/EEG recordings In-Reply-To: References: Message-ID: Dear Marcel, I might have seen a similar error before when the number of channels in 'elec' do not match the number of channels in 'freq'. Could that be the cause? Also, does it matter that you are setting cfg.grad=elec, rather than cfg.elec=elec? To debug, it might be best to first call leadfield=ft_prepare_leadfield() to ensure that is computed correctly, and then set that output to cfg.grid.leadfield=leadfield, in your call to ft_sourceanalysis. cheers, Johanna 2012/6/26 Marcel Heers > Dear all, > > I am trying to perform source localization in the frequency domain > from EEG data using DICS. The data were recorded combined with MEG > (Neuromag data format). The volume conductor is a 3 shell realistic > head model created with bemcp. > When running DICS with the following settings > > cfg = []; > cfg.method = 'dics'; > cfg.grad = elec; > cfg.frequency = 14; > cfg.vol = vol_eeg; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = 5; > source = ft_sourceanalysis(cfg, freq); > > > I am am getting the following error message: > > ??? Error using ==> svd > Input to SVD must not contain NaN or Inf. > > Error in ==> beamformer_dics>pinv at 568 > [U,S,V] = svd(A,0); > > Error in ==> beamformer_dics at 314 > filt = pinv(lf' * invCf * lf) * lf' * invCf; % > Gross eqn. 3, use > PINV/SVD to cover rank deficient leadfield > > Error in ==> ft_sourceanalysis at 584 > dip(i) = beamformer_dics(grid, sens, vol, [], > squeeze(Cf(i,:,:)), optarg{:}); > > > and I am not sure what might be the cause. > > Maybe anyone can help me! Thank you in advance! > > Marcel > _______________________________________________ > 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 Don.Rojas at ucdenver.edu Mon Jul 2 14:34:31 2012 From: Don.Rojas at ucdenver.edu (Rojas, Don) Date: Mon, 2 Jul 2012 06:34:31 -0600 Subject: [FieldTrip] Source localization using DICS for EEG data from combined MEG/EEG recordings In-Reply-To: References: Message-ID: <9FCD53FD-5A0E-48F8-87B2-08717F732CC9@ucdenver.edu> Marcel, Also, you might check your volume conductor. I've seen a similar error when there were NaNs in the surface normals. Don Sent from my iPad On Jul 2, 2012, at 4:12 AM, "Johanna Zumer" > wrote: Dear Marcel, I might have seen a similar error before when the number of channels in 'elec' do not match the number of channels in 'freq'. Could that be the cause? Also, does it matter that you are setting cfg.grad=elec, rather than cfg.elec=elec? To debug, it might be best to first call leadfield=ft_prepare_leadfield() to ensure that is computed correctly, and then set that output to cfg.grid.leadfield=leadfield, in your call to ft_sourceanalysis. cheers, Johanna 2012/6/26 Marcel Heers > Dear all, I am trying to perform source localization in the frequency domain from EEG data using DICS. The data were recorded combined with MEG (Neuromag data format). The volume conductor is a 3 shell realistic head model created with bemcp. When running DICS with the following settings cfg = []; cfg.method = 'dics'; cfg.grad = elec; cfg.frequency = 14; cfg.vol = vol_eeg; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = 5; source = ft_sourceanalysis(cfg, freq); I am am getting the following error message: ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> beamformer_dics>pinv at 568 [U,S,V] = svd(A,0); Error in ==> beamformer_dics at 314 filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank deficient leadfield Error in ==> ft_sourceanalysis at 584 dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:}); and I am not sure what might be the cause. Maybe anyone can help me! Thank you in advance! Marcel _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornabel at googlemail.com Mon Jul 2 14:52:58 2012 From: cornabel at googlemail.com (Cornelius Abel) Date: Mon, 2 Jul 2012 14:52:58 +0200 Subject: [FieldTrip] reverse source interpolate? In-Reply-To: <36BAC777-CD99-4F3E-95D1-A133F5CC2372@donders.ru.nl> References: <4FEB2620.3050505@googlemail.com> <36BAC777-CD99-4F3E-95D1-A133F5CC2372@donders.ru.nl> Message-ID: Hi mailing list, I'm still struggling with the conversion of coordinates between source and interpolated source space. For example, if i have the position of a single grid point how do i get the corresponding voxel in the interpolated source structure. Or the other way around, how to get the grid point which corresponds to a voxel (e.g the max voxel) in the interpolated source structure. I think this should be a common problem when working with virtual electrodes, shouldn't it? To make things easier i put together a example with the data from the source tutorial where i tried to calculated the grid pos of the max voxel in the interpolated source. clear all; load sourcePost_nocon; % source structure from tutorial mri = ft_read_mri('Subject01.mri'); % mri of subject01 from tutorial sourceNAI = sourcePost_nocon; sourceNAI.avg.pow = sourcePost_nocon.avg.pow ./ sourcePost_nocon.avg.noise; sourceNAI=rmfield(sourceNAI,'freq'); % had to remove that to let cfg = []; cfg.downsample = 2; cfg.parameter = 'avg.pow'; sourceNAIInt = ft_sourceinterpolate(cfg, sourceNAI , mri); % Find position of max activity [dum, maxindx] = max(sourceNAIInt.avg.pow(:)); [xi, yi, zi] = ind2sub(sourceNAIInt.dim, maxindx); posInt=[xi, yi, zi]; % Plot interpolated source with position of max activity cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'avg.pow'; cfg.locationcoordinates = 'voxel'; cfg.location = posInt; % location of max activity is marked correctly. figure; ft_sourceplot(cfg,sourceNAIInt); % Transform coordinate back to uninterpolated source??? dpos = warp_apply(inv(mri.transform), posInt, 'homogeneous'); % Plot uninterpolated source with position aquired from interpolated source cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'avg.pow'; cfg.locationcoordinates = 'voxel'; cfg.location = dpos; % unfortunately this coordinate is obviously wrong!!! WHY? figure; ft_sourceplot(cfg,sourceNAI); Unfortunately the solution of Jan Mathijs did not work, nor did mine :( Any ideas??? Cornelius 2012/6/28 jan-mathijs schoffelen > Hi Cornelius, > > Probably you should use: cfg.locationcoordinates to be 'head'. > > Best, > > JM > > On Jun 28, 2012, at 11:19 AM, Cornelius Abel wrote: > > Hi jan mathijs, hello mailing list, > > thanks for your answer. I think i got your idea with finding the minimum > in this squared differences. This should the work with positions of any > scaling, right? > However it gives me strange results when trying to get voxel indices in > the "raw" source using voxel indices aquired from interpolated source. > But even using the ctf coordinates in mm doesn't work. > > Here is a short script showing what i did, i also attached the necessary > mat files. > > greetings, Cornelius > > > clear all; > load testdata.mat; > > % Interpolate source on anatomy > cfg = []; > cfg.parameter = 'avg.itc'; > cfg.interpmethod = 'linear'; > sourceInt = ft_sourceinterpolate(cfg, source,mri); > > % Find position of max voxel in interpolated source > [maxval, maxindx] = max(sourceInt.avg.itc(:)); > [x,y,z]=ind2sub(size(sourceInt.avg.itc),maxindx); > pos=[x y z]; > > % plot this position in interpolated source > figure; > cfg = []; > cfg.method = 'ortho'; > cfg.funparameter = 'avg.itc'; > cfg.locationcoordinates = 'voxel'; > cfg.location = pos; > ft_sourceplot(cfg, sourceInt); > > % Calculate respective position in 'raw' source struct > dpos = source.pos - repmat(pos, size(source.pos,1),1); > [m,ind] = min(sum(dpos.^2,2)); > spos=source.pos(ind,:); > > % Plot position in 'raw' source. > % This gives not the position of max activity!!! > figure; > cfg = []; > cfg.method = 'ortho'; > cfg.funparameter = 'avg.itc'; > cfg.locationcoordinates = 'voxel'; > cfg.location = spos; > ft_sourceplot(cfg, source); > > > > 2012/6/27 jan-mathijs schoffelen > >> Hi Cornelius, >> >> There is no need to 'uninterpolate' because the coordinates are already >> expressed in the correct coordinate system. What you probably want is to >> find the index to the voxel in the original source-structure closest to >> your 'hotspot' in the interpolated image. >> This can be achieved by something like this: >> >> write down the coordinates of your favourite position in the interpolated >> image (in world coordinates, here I assume that you are still in MEG >> coordinate system and have not normalized to MNI space), call this pos >> >> pos = pos./10 (from mm to cm) >> >> dpos = source.pos - repmat(pos, size(source.pos,1),1); >> [m,ind] = min(sum(dpos.^2,2)); >> >> source is the original source structure. >> ind is the index you are looking for. >> >> If you have interpolate to the MNI-template grid you need to replace the >> source.pos with the set of grid positions from your template grid (i.e. >> expressed in MNI coordinates). >> >> >> Cheers, >> >> JM >> >> >> On Jun 27, 2012, at 5:26 PM, cornelius abel wrote: >> >> Hello, >> >> does anybody know how to get the uninterpolated source position giving >> the coordinates aquired after interpolation with an anatomy. >> In principle i want to get an individual source time course at the >> position i picked from the interpolated grand average source plot. Therfore >> i need the corresponding filter and its position in the source structure. >> >> I tried to get the position by applying the inverse transformation matrix >> of the used anatomy like: >> pos_before_interpolation=warp_apply(inv(anatomy.transform), >> position_after_interpolation); >> >> but that did not give usefull results :( >> >> Any ideas how it could be done? >> >> Greetings, Cornelius >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 drivolta81 at gmail.com Mon Jul 2 17:04:08 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Mon, 2 Jul 2012 17:04:08 +0200 Subject: [FieldTrip] Job advertisement: Research associate at the University of Glasgow Message-ID: *Research Associate, Institute of Neuroscience and Psychology, University of Glasgow* The Institute of Neuroscience and Psychology, University of Glasgow, has a vacancy for a Research Associate post for 3 years. The position contributes to a project entitled “Neural synchrony in neuropsychiatry and brain development”. Specifically, the job requires the analysis of existing MEG-data sets, data-acquisition and implementation of novel analytic tools, contributing to the design and programming of MEG experiments. *Responsibilities:* 1. To analyse MEG-data using complex time-frequency and source-localization techniques. 2. To assist in the supervision of data-acquisition and analysis-protocols. 3. To establish links with the MEG-expertise in the Institute and with international groups working in the field. 4. To recruit experimental subjects and to run the agreed behavioural and MEG-experiments, dealing with all aspects of testing the participants and storing data. 5. To perform statistical analyses of the experiments and to produce experimental reports describing these results. 6. To establish an expert reputation and track record in field/discipline. 7. Write up papers and identify high impact national and international journals for publication. 8. To contribute to the identification of potential funding sources and to assist in the securing of funding from external bodies to support future research. 9. To contribute fully to the planning and supervision of undergraduate students and postgraduate (PhD) students through day to day mentoring and longer term in planning research objectives. *Requirements:* 1. Ph.D or equivalent. 2. Extensive and up-to-date practical and theoretical knowledge in MEG or EEG. 3. Excellent knowledge of experimental statistics. 4. Excellent knowledge of source-localization techniques. 5. Excellent knowledge of Matlab and experimental control software. * * * * *Salary Range*** £31,948 - £35,938** * * *More Information:* 1. The position is available now (July 2012) 2. To apply, visit the University of Glasgow staff jobs website: * http://www.gla.ac.uk/about/jobs/* . Search for position 002148 3. For further info please contact: Dr. Peter Uhlhaas, peter.uhlhaas at brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Mon Jul 2 18:20:13 2012 From: drivolta81 at gmail.com (Davide Rivolta) Date: Mon, 2 Jul 2012 18:20:13 +0200 Subject: [FieldTrip] Info about the power-line noise Message-ID: Dear fieldtrippers, I recently run into the attached figures (S01 files). It seems a failure of the power-line noise filter. I used the following settings quite succesfully for other subjects: cfg.dftfilter = 'yes'; cfg.padding = 10; An example of good figures are the "KAT" files. These data come from a visual task where people see moving concentrical gratings. Each trial has a different length that range between around 0.5 until 3 seconds. Would the bandstop filter be the only possible solution here? Thanks, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: S01_TFR1_high.png Type: image/png Size: 12615 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: S01_power_.png Type: image/png Size: 13211 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: KAT_TFR1_low.png Type: image/png Size: 11199 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: KAT_power_spectra1_high.png Type: image/png Size: 13236 bytes Desc: not available URL: From inieuwenhuis at berkeley.edu Mon Jul 2 18:38:37 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 02 Jul 2012 09:38:37 -0700 Subject: [FieldTrip] calculating correlation In-Reply-To: <1AA66D8B-3685-4A8F-AED3-A1FF8C7A8D21@donders.ru.nl> References: <4FF0AFFC.1040500@berkeley.edu> <1AA66D8B-3685-4A8F-AED3-A1FF8C7A8D21@donders.ru.nl> Message-ID: <4FF1CE8D.5020305@berkeley.edu> Hi JM! haha, sounds good, I'll contact you :) Cheers, Ingrid On 7/1/2012 11:53 PM, jan-mathijs schoffelen wrote: > Hi Ingrid, > > This calls for a statfun_corr or even a statfun_glm! It so happens > that I have some of these sitting on my hard drive. As you know I am > fond of beer, chocolate and co-authorships, so I am sure we can strike > a deal. I have not yet had the opportunity to contribute these > statfuns to FieldTrip, but now I sense a win-win-win situation: win 1 > is for me (beer/chocolate/co-authorships/etc), win 2 is for you (you > can compute your statistic of interest) and win 3 for the community > (where you test the code, write documentation on the wiki etcetc). How > does that sound for a plan? > > Cheers, > > JM > > On Jul 1, 2012, at 10:15 PM, Ingrid Nieuwenhuis wrote: > >> Hi FTers, >> >> I'd like to do two sorts of correlation calculations, and was >> wondering if there's any easy way to do this within FieldTrip. >> >> 1) I'd like to calculate the correlation between performance over >> trials and power within a specific frequency over trials. So I have >> the performance measure per trial, and my chan*freq measure after >> freqanalysis. So for each channel I have a series of power values >> (trials) and I have a series of performance measures (per trial), and >> now like to know (first within, and then over subjects) which >> channel's frequency power follows (correlates) with the performance. >> >> From the walkthrough >> I understand >> I can give in these performance measures through the design >> (cfg.design=[0.10.20.30.40.50.40.30.10.2];cfg.ivar=1;), but which >> method to use for ft_freqstatistics? I don't see statistics = >> 'correlation' or 'pearson' or 'spearman' in method = 'analytic. Also >> how to make the design to correlate over trials? >> >> 2) I'd like to calculate the correlation between the score on >> repeated questionnaire over participants with power within a >> frequency. So I have several power values per participant for each >> channel, and the repeated scores on the questionnaire for each >> participant. And now I'd like to calculate a value per channel >> reflecting the correlation over the repeats of the questionnaire and >> over participants. >> >> Any idea on FieldTrip settings? Both in general, is there a >> correlation statistics implemented, and more specifically for my >> question, how would I make the appropriate designs? >> >> Thanks so much! >> Ingrid >> -- >> Ingrid Nieuwenhuis PhD >> Postdoctoral Fellow >> Sleep and Neuroimaging Laboratory >> Department of Psychology >> University of California, Berkeley >> California 94720-1650 >> Tolman Hall, room 5305 >> _______________________________________________ >> 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 -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Mon Jul 2 19:39:16 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Mon, 2 Jul 2012 18:39:16 +0100 Subject: [FieldTrip] calculating correlation In-Reply-To: <4FF0AFFC.1040500@berkeley.edu> References: <4FF0AFFC.1040500@berkeley.edu> Message-ID: Hi Ingrid, You're trying to test two very different things. 1) power-behavior correlation over trials, and differences between subjects are just unexplained variance. 2) power-behavior correlation across subjects. For 2) problem, I don't have anything to add to what Jan-Mathijs said. Correlation/GLM is very easy outside Fieldtrip but I hope Jan-Mathijs will include the GLM functions, it sounds very cool. For your "repeated questionnaires", I'd use a summary score (difference score for example) and do a simple correlation. For 1) problem, you could do a 2-level analysis, like SPM does for fMRI data: 1- you do correlation at the single-subject level, 2- you do a t-test on the slope (or your GLM column of interest), to test if it's different from zero. I don't know of Fieldtrip tools for this but I don't like this approach too much, because you lose quite some power and you don't model the trial-level noise. I've had some success using linear mixed-effects models for these types of research questions. There is the package lme4 in R which is very powerful. The only pain is to export data from Matlab and read them in R. You can get t-values from the linear mixed-effects models for each electrode/time point/freq point (unless you average over some dimension). Then you can use the cluster-level correction as implemented in Fieldtrip by flipping the sign of the t-statistics. There is some learning to do to use linear mixed-effects models but there are very flexible. Let me know if you need help with that. You can bribe me with the same things Jan-Mathijs likes... Hope this helps, 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 Sun, Jul 1, 2012 at 9:15 PM, Ingrid Nieuwenhuis wrote: > Hi FTers, > > I'd like to do two sorts of correlation calculations, and was wondering if > there's any easy way to do this within FieldTrip. > > 1) I'd like to calculate the correlation between performance over trials and > power within a specific frequency over trials. So I have the performance > measure per trial, and my chan*freq measure after freqanalysis. So for each > channel I have a series of power values (trials) and I have a series of > performance measures (per trial), and now like to know (first within, and > then over subjects) which channel's frequency power follows (correlates) > with the performance. > > From the walkthrough I understand I can give in these performance measures > through the design (cfg.design = [0.1 0.2 0.3 0.4 0.5 0.4 0.3 0.1 0.2]; > cfg.ivar= 1;), but which method to use for ft_freqstatistics? I don't see > statistics = 'correlation' or 'pearson' or 'spearman' in method = 'analytic. > Also how to make the design to correlate over trials? > > 2) I'd like to calculate the correlation between the score on repeated > questionnaire over participants with power within a frequency. So I have > several power values per participant for each channel, and the repeated > scores on the questionnaire for each participant. And now I'd like to > calculate a value per channel reflecting the correlation over the repeats of > the questionnaire and over participants. > > Any idea on FieldTrip settings? Both in general, is there a correlation > statistics implemented, and more specifically for my question, how would I > make the appropriate designs? > > Thanks so much! > Ingrid > > -- > Ingrid Nieuwenhuis PhD > Postdoctoral Fellow > Sleep and Neuroimaging Laboratory > Department of Psychology > University of California, Berkeley > California 94720-1650 > Tolman Hall, room 5305 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From inieuwenhuis at berkeley.edu Mon Jul 2 19:58:04 2012 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 02 Jul 2012 10:58:04 -0700 Subject: [FieldTrip] calculating correlation In-Reply-To: References: <4FF0AFFC.1040500@berkeley.edu> Message-ID: <4FF1E12C.7010004@berkeley.edu> Hi Gio! Guys, where are the good old times of unconditional sharing between scientists for the greater good? ;) Must be the economy... Anyways, thanks! I'm just starting to learn R actually, I'll check out the lme4. Might be useful to include some FieldTrip to R functionality. I'll get in touch when I need help :) Cheers, Ingrid On 7/2/2012 10:39 AM, Gio Piantoni wrote: > Hi Ingrid, > > You're trying to test two very different things. > 1) power-behavior correlation over trials, and differences between > subjects are just unexplained variance. > 2) power-behavior correlation across subjects. > > For 2) problem, I don't have anything to add to what Jan-Mathijs said. > Correlation/GLM is very easy outside Fieldtrip but I hope Jan-Mathijs > will include the GLM functions, it sounds very cool. For your > "repeated questionnaires", I'd use a summary score (difference score > for example) and do a simple correlation. > > For 1) problem, you could do a 2-level analysis, like SPM does for > fMRI data: 1- you do correlation at the single-subject level, 2- you > do a t-test on the slope (or your GLM column of interest), to test if > it's different from zero. I don't know of Fieldtrip tools for this but > I don't like this approach too much, because you lose quite some power > and you don't model the trial-level noise. > I've had some success using linear mixed-effects models for these > types of research questions. There is the package lme4 in R which is > very powerful. The only pain is to export data from Matlab and read > them in R. You can get t-values from the linear mixed-effects models > for each electrode/time point/freq point (unless you average over some > dimension). Then you can use the cluster-level correction as > implemented in Fieldtrip by flipping the sign of the t-statistics. > There is some learning to do to use linear mixed-effects models but > there are very flexible. > Let me know if you need help with that. You can bribe me with the same > things Jan-Mathijs likes... > > Hope this helps, > > Gio > -- Ingrid Nieuwenhuis PhD Postdoctoral Fellow Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From johanna.zumer at donders.ru.nl Mon Jul 2 22:07:08 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Mon, 2 Jul 2012 22:07:08 +0200 Subject: [FieldTrip] Beamformer: different length of baseline and post baseline interval In-Reply-To: <1659120385.1619.1340961051346.JavaMail.root@zimbra> References: <1376177301.1612.1340961039830.JavaMail.root@zimbra> <1659120385.1619.1340961051346.JavaMail.root@zimbra> Message-ID: Dear Anna, Ideally for the common filter, you want the same amount of data T(s) per condition, where T = N x tw (and N is number of trials and tw is timewindow length). In your case, if the baselines for each conditions can be combined into one general baseline, and if you happen to have 100 trials per condition, then T_baseline = 3 x 100 x 0.5s = 150s. If you then use 1.5s length post-baseline, then T_each_condition = 100 x 1.5s = 150s, so you now have equal T for each condition for the common filter. However, in order to have an equal effect of tapers and edge-effects on the different conditions, you should use equal time window lengths in freqanalysis. Thus it would be better to split your post-baseline data into 3 segments of 500ms each before calling ft_freqanalysis, which again gives T = 100 x 0.5 x 3 = 150s. Cheers, Johanna 2012/6/29 Anna Wilsch > > Dear Fieldtrippers, > > I'm trying to beamform my MEG data by building a common filter including > three conditions and a baseline for each condition. The baseline intervals > have a duration of 500 ms. I was wondering if it is ok if the post-baseline > data are longer than that (1000 - 2000 ms). Does it have any negative > impact on the cross-spectral-density matrix and/or the common filter? Would > that still be a valid operation to do or is it necessary that baseline and > post baseline data have the same length? > Thank you for your comments. > > Cheers, > Anna > > > Anna Wilsch, Dipl.-Psych. > Auditory Cognition Research Group > Max Planck Institute for Human Cognitive and Brain Sciences > Stephanstr. 1a - Leipzig, Germany > (p) +49 (0)341 9940 2641 > (e) wilsch at cbs.mpg.de > > _______________________________________________ > 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 stan.vanpelt at fcdonders.ru.nl Tue Jul 3 09:17:47 2012 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Tue, 3 Jul 2012 09:17:47 +0200 (CEST) Subject: [FieldTrip] Info about the power-line noise In-Reply-To: Message-ID: <997455910.845940.1341299867043.JavaMail.root@sculptor.zimbra.ru.nl> Hi Davide, Nice data (aside from what is indeed probably line noise). I see four approaches you could take, but not sure if it helps. You could just be unlucky with a very fluctuating line noise in this recording (see http://fieldtrip.fcdonders.nl/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter). The options I see: - Check if there is actually a datapadding up to 10 s. With already preprocessed data (e.g., after 3rd order gradiometer correction), it is not directly possible to data pad for subsequent dft-filtering. It happened to me not so long ago, that's why I ask. I made a workaround by first creating trials of 10s length, then do the dft-filetering, and after that cut the actual trials out. - If not already done, apply 3rd-order gradiometer correction first (ft_denoise_synthetic, or in the CTF DataEditor) - Use a bandstop-filter instead of the dft - Source-project the data. With my data that usually also gets rid of most line noise (I use LCMV to reconstruct a virtual sensor time course) Hope that helps. Stan ----- Oorspronkelijk bericht ----- > Van: "Davide Rivolta" > Aan: "Email discussion list for the FieldTrip project" > > Verzonden: Maandag 2 juli 2012 18:20:13 > Onderwerp: [FieldTrip] Info about the power-line noise > Dear fieldtrippers, > I recently run into the attached figures (S01 files). It seems a > failure of the power-line noise filter. > I used the following settings quite succesfully for other subjects: > cfg.dftfilter = 'yes'; > cfg.padding = 10; > An example of good figures are the "KAT" files. > These data come from a visual task where people see moving > concentrical gratings. Each trial has a different length that range > between around 0.5 until 3 seconds. > Would the bandstop filter be the only possible solution here? > Thanks, > Davide > _______________________________________________ > 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 ivano_triggiani at yahoo.it Tue Jul 3 17:42:37 2012 From: ivano_triggiani at yahoo.it (Ivano Triggiani) Date: Tue, 3 Jul 2012 16:42:37 +0100 (BST) Subject: [FieldTrip] band pass and segmentation In-Reply-To: References: Message-ID: <1341330157.2152.YahooMailNeo@web28705.mail.ir2.yahoo.com> Hi all, I tried to use a simple cfg.bpfilter (0.1 - 40) for an EEG that I divide into 2 secs époques and giving a look it seems that at the board of every window the signal is reduced (just like following a parabolic trend). Is this a problem of the brutal segmentation (respect to a good windowing) or there's something else? Ivano -------------- next part -------------- An HTML attachment was scrubbed... URL: From andreas.wutz-1 at unitn.it Tue Jul 3 23:44:09 2012 From: andreas.wutz-1 at unitn.it (Wutz, Andreas) Date: Tue, 3 Jul 2012 23:44:09 +0200 Subject: [FieldTrip] Structure of 4D-Fourierspectrum with Multi-Taper Message-ID: Dear all, in requesting from a ft_freqanalysis with output ='fourier' and 2 multitapers, I figured out that in the 4D matrix in the field 'fourierspctrm' the first dimension refers to the number of tapers that are calculated (Number of trials -times- number of tapers). My question refers to the organization of this dimension. Are in the example with 2 tapers the two tapers from the same trial next to each other? Or do we have first, the outputs from the first taper for all the trials and then, all the trials for the 2nd taper? I would like to calculate the circular mean of the phase angles across trials and therefore would need to combine the outputs of the two tapers per trial. Is there already some fieldtrip function to do this? How should it be done? Thank you very much. Best Andreas Andreas Wutz PhD Student CIMeC - Center for Mind/Brain Sciences Università degli studi di Trento From jan.schoffelen at donders.ru.nl Wed Jul 4 09:19:30 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 4 Jul 2012 09:19:30 +0200 Subject: [FieldTrip] Structure of 4D-Fourierspectrum with Multi-Taper References: Message-ID: <6C2FF2A6-B080-424C-A01F-048215D181CD@donders.ru.nl> Hi Andreas, The tapers per trial are grouped together, i.e. it is according to the first scenario you sketch. Note that averaging fourier-coefficients across tapers is not correct, because each of the tapers induces a non-trivial phase shift. Phase differences however can be averaged across tapers, but for this you need a reference signal. Best, Jan-Mathijs On Jul 3, 2012, at 11:44 PM, Wutz, Andreas wrote: > Dear all, > > in requesting from a ft_freqanalysis with output ='fourier' and 2 multitapers, I figured out that in the 4D matrix in the field 'fourierspctrm' the first dimension refers to the number of tapers that are calculated (Number of trials -times- number of tapers). My question refers to the organization of this dimension. Are in the example with 2 tapers the two tapers from the same trial next to each other? Or do we have first, the outputs from the first taper for all the trials and then, all the trials for the 2nd taper? I would like to calculate the circular mean of the phase angles across trials and therefore would need to combine the outputs of the two tapers per trial. Is there already some fieldtrip function to do this? How should it be done? > > Thank you very much. > Best > Andreas > > Andreas Wutz > PhD Student > CIMeC - Center for Mind/Brain Sciences > Università degli studi di Trento > _______________________________________________ > 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 jm.horschig at donders.ru.nl Wed Jul 4 15:35:52 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 04 Jul 2012 15:35:52 +0200 Subject: [FieldTrip] Questions on High pass and Dft filtering In-Reply-To: References: Message-ID: <4FF446B8.8040600@donders.ru.nl> HI Philipp, > The issue with the continuous data is the following: I tried using > cfg = []; > cfg.channel = {'EEG'}; > cfg.datafile = dataset; > cfg.headerfile = dataset; > cfg.dataset = dataset; > > cfg.continuous = 'yes'; > > (cfg.padding = 10;) > cfg.dftfilter = 'yes'; > > filteredContinuousData = ft_preprocessing(cfg); > > but looking at averaged timelocked data for the subject, the data looks > identical to the result I get using no filter at all, i.e., contaminated by > strong line noise. Including padding makes no difference either, therefore > the brackets. I tested this with my own data as well with as synthetic signal. The line noise is reduced by a factor of ~8 (I looked at the Fourier spectrum of the filtered and the unfiltered signal).The problem you encounter is either caused by nonstationarity of the 50Hz component (i.e. a drift in power, see FAQ), or maybe your acquisition system is misspecifying the sampling frequency a bit - Robert says this might happen, see: http://bugzilla.fcdonders.nl/show_bug.cgi?id=1571 In any case, it might help for you if you specify cfg.dftfreq = [49.6:0.2:50.4 100 150] or similar (depends on your padding parameter). That might help to filter a bit 'better' (but maybe a bandstop filter works better here). Best, Jörn -- 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 frsantos at fpce.up.pt Wed Jul 4 18:35:36 2012 From: frsantos at fpce.up.pt (Fernando Ricardo Santos) Date: Wed, 4 Jul 2012 16:35:36 +0000 Subject: [FieldTrip] Introductory EEG/ERP Summer School in Porto, Portugal Message-ID: <2BAB036A9BAEA44984A131DFCE446108722337EB@SRVMBX02.fpceup.psi.up.pt> Dear FieldTrip users, The Laboratory of Neuropsychopsysiology (University of Porto, Portugal) is organizing "I CAN – 1st Cognitive and Affective Neurophysiology Summer School: Acquisition, processing and analysis of EEG signal" -- September 3-8, 2012. This summer school is focused on the application of Electroencephalography (EEG) and Event Related Potential (ERP) techniques to the study of cognitive and affective processes. The course will cover an introduction to the EEG and ERP techniques, acquisition of electrophysiological data of brain activity, signal processing, and statistical analysis of the data. All the modules will have a practical hands-on component and all lectures will be held in English. Scientific Coordination: -Professor João Marques-Teixeira Course tutors: -Fernando Ferreira-Santos -Pedro R. Almeida Venue and dates: Faculty of Psychology and Educational Sciences of the University of Porto (Portugal), from the 3rd to the 8th of September of 2012. For additional information on the Summer School please follow the link: http://www.fpce.up.pt/labpsi/summerschool/ Thank you and best wishes to all, -- Fernando Ferreira-Santos Laboratory of Neuropsychophysiology Faculty of Psychology and Education Sciences University of Porto Rua Dr. Manuel Pereira da Silva 4200-392 Porto (Portugal) Tel. +351 226079700 (ext. 301) Email: frsantos at fpce.up.pt http://www.fpce.up.pt/labpsi/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From omidabbasi2000 at gmail.com Thu Jul 5 14:06:23 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Thu, 5 Jul 2012 16:36:23 +0430 Subject: [FieldTrip] help to apply field trip (topography plotting) In-Reply-To: References: Message-ID: Dear Developer At first, I thank you for useful source code. This is Omid. I'm a student that work on biological signal processing. I want to use your source code for plotting data topography of brain. I downloaded your code from this link ( http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but i can't use it in my project, because i have 19 signals from 19 sites on the brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your code in my project with different channel and data? It would grateful for me if you could help me to apply your code in my project. Best Regards Omid -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ulrich.Pomper at charite.de Fri Jul 6 12:59:05 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Fri, 6 Jul 2012 12:59:05 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? Message-ID: Dear list members, I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. Any help with this issue is greatly aprreciated! Cheers, Ulrich From johanna.zumer at donders.ru.nl Fri Jul 6 14:36:04 2012 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Fri, 6 Jul 2012 14:36:04 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: Message-ID: Dear Ulrich, Only if the leadfields are the same, can you use the common filter. If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. Cheers, Johanna 2012/7/6 Pomper, Ulrich > Dear list members, > I want to compare source data between two different groups (patients and > controls). Each patient has an age and gender-matched control. > Is it correct to compute a common filter for each pair of subjects? The > TF-topographies do look different within each pair, so I would assume that > the sources are somewhat different. However, as I'm going to statistically > compare the two groups it would be nice to have common filters, as > otherwise any finding could be due to different filters as opposed to > different sources. > > Any help with this issue is greatly aprreciated! > Cheers, Ulrich > _______________________________________________ > 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 Ulrich.Pomper at charite.de Fri Jul 6 15:21:23 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Fri, 6 Jul 2012 15:21:23 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: , Message-ID: Dear Johanna, thanks for your quick reply! To clarify things: This is an EEG study, using a standard MNI-based headmodel for all subjects. I have a between subjects factor group (patients, controls) and a within subjects factor condition (A, B). Also, I can use a within subject contrast (active versus baseline) for the source analysis. Currently, I use one common filter for baseline and active data as well as both conditions for each subject. So I end up using one common filter per subject. My question I whether it would be more correct to additionally pool the data from matched subjects into one single filter. Thus resulting in one common filter per pair. Cheers, Ulrich ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer [johanna.zumer at donders.ru.nl] Sent: Friday, July 06, 2012 2:36 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Common beamforming filters for different groups? Dear Ulrich, Only if the leadfields are the same, can you use the common filter. If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. Cheers, Johanna 2012/7/6 Pomper, Ulrich > Dear list members, I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. Any help with this issue is greatly aprreciated! Cheers, Ulrich _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus From kmanning at robarts.ca Fri Jul 6 18:59:20 2012 From: kmanning at robarts.ca (Kathryn Manning) Date: Fri, 6 Jul 2012 12:59:20 -0400 Subject: [FieldTrip] Connectivity analysis Message-ID: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> Dear FieldTrip list members, I am comparing the connectivity patterns in the brain measured using fMRI and electrophysiological recordings. I am trying to correlate the LFP signals as a function of time, using a sliding window analysis. I'm able to generate plots using ft_connectivityplot but this is as a function of frequency. From what I can tell the 'mtmconvol' method generates data with a time aspect in it's dimord, but are there any functions available in fieldtrip in order to calculate the correlation as a function of time? Any help would be greatly appreciated, thank you so much. Kathryn From Don.Rojas at ucdenver.edu Fri Jul 6 19:02:41 2012 From: Don.Rojas at ucdenver.edu (Rojas, Don) Date: Fri, 6 Jul 2012 11:02:41 -0600 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: , Message-ID: Ulrich, It does not make sense to me to have a common filter per pair of subjects, only between conditions within a subject (which you say you are currently doing). Since, as Johanna suggested, you are using a standard brain and standard electrode locations, rather than individual ones, you can have a common leadfield matrix for all subjects. However, I don't think you can have a common beamformer filter, since that is computed for each subject based on the covariance or cross spectral density matrix, which would be unique to each subject. Therefore, the beamformer filter, which uses both the covariance and the leadfield, would be unique for each individual. You can save time simply by having a common leadfield matrix. Best, Don ----------------------- Don Rojas, Ph.D. Associate Professor of Psychiatry U. of Colorado Denver Anschutz Medical Campus Director, UCD Magnetoencephalography Lab 13001 E. 17th Pl F546 Aurora, CO 80045 303-724-4994 On Jul 6, 2012, at 7:21 AM, Pomper, Ulrich wrote: > Dear Johanna, > thanks for your quick reply! > > To clarify things: This is an EEG study, using a standard MNI-based headmodel for all subjects. > > I have a between subjects factor group (patients, controls) and a within subjects factor condition (A, B). Also, I can use a within subject contrast (active versus baseline) for the source analysis. > > Currently, I use one common filter for baseline and active data as well as both conditions for each subject. So I end up using one common filter per subject. > > My question I whether it would be more correct to additionally pool the data from matched subjects into one single filter. Thus resulting in one common filter per pair. > > > Cheers, Ulrich > > > > > > > > > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer [johanna.zumer at donders.ru.nl] > Sent: Friday, July 06, 2012 2:36 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Common beamforming filters for different groups? > > Dear Ulrich, > > Only if the leadfields are the same, can you use the common filter. > > If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. > > If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. > > Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? > > Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. > > Cheers, > Johanna > > > 2012/7/6 Pomper, Ulrich > > Dear list members, > I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. > Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. > > Any help with this issue is greatly aprreciated! > Cheers, Ulrich > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg > > Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From politzerahless at gmail.com Sat Jul 7 02:46:14 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Sat, 7 Jul 2012 08:46:14 +0800 Subject: [FieldTrip] help to apply field trip (topography plotting) Message-ID: Hi Omid, Welcome to Fieldtrip. You can find a lot of information about how to use Fieldtrip at http://fieldtrip.fcdonders.nl/walkthrough and http://fieldtrip.fcdonders.nl/tutorial. In your case, you need to get your data imported into Fieldtrip's format in MATLAB ( http://fieldtrip.fcdonders.nl/tutorial/preprocessing), as well as your channel layout (http://fieldtrip.fcdonders.nl/tutorial/layout) before proceeding to plotting. Good luck, Steve > Message: 1 > Date: Thu, 5 Jul 2012 16:36:23 +0430 > From: omid abbasi > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] help to apply field trip (topography plotting) > Message-ID: > < > CAPc_m1utoA_ZqC8_0q44hz5FX3yMfWP-gfke5Mes9_sEUOuyrA at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Developer > > At first, I thank you for useful source code. > > This is Omid. I'm a student that work on biological signal processing. I > want to use your source code for plotting data topography of brain. I > downloaded your code from this link ( > http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but i > can't use it in my project, because i have 19 signals from 19 sites on the > brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your > code in my project with different channel and data? > > It would grateful for me if you could help me to apply your code in my > project. > > Best Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From skelly2 at ccny.cuny.edu Sat Jul 7 07:00:40 2012 From: skelly2 at ccny.cuny.edu (skelly2 at ccny.cuny.edu) Date: Sat, 7 Jul 2012 01:00:40 -0400 (EDT) Subject: [FieldTrip] Postdoc position in systems neuroscience, City College of New York Message-ID: <201207070500.028516@pelican.admin.ccny.cuny.edu> Postdoctoral position in systems neuroscience, City College of New York A postdoctoral "Endeavor Scientist" position funded by the Child Mind Institute (CMI) is available starting this Fall in the lab of Simon Kelly at the City College of New York. The endeavor scientist will work on basic and clinical projects mainly using human electroencephalogram (EEG) recordings, under the joint supervision of Simon Kelly (http://bme.ccny.cuny.edu/people/faculty/skelly) of the Department of Biomedical Engineering, CCNY and Michael Milham (http://www.childmind.org/en/directory/clinicians/mmilham) of CMI. The position will involve analysis of data obtained from clinical and non-clinical populations at the Child Mind Institute and its collaborators, in addition to conducting basic studies of perception and cognition in the Kelly lab, particularly focusing on decision making and attention. A major goal will be to develop novel paradigms and data analysis approaches that allow neural signals to be linked with well-defined perceptual/cognitive computations, and to deploy these paradigms and approaches to studies at CMI. Clinical studies will be mainly in child and adolescent populations associated with clinically significant anxiety, attentional dysfunction, emotional dysregulation and learning impairments. Any innovative tools developed in the course of this position will be made publicly available. Applicants must have a Ph.D. in neuroscience or related field, including neural/biomedical engineering, applied mathematics and computer science. The candidate must have strong analytic/quantitative skills, be proficient in programming (especially Matlab), and have experience in psychophysics and EEG recording and analysis. Experience with fMRI is a strong plus, as some projects may involve a multimodal EEG/fMRI approach. The ideal candidate will be reliable, highly motivated, and will be equally productive when working independently or cooperatively. Applicants should send a curriculum vitae, contact information for three references, and a cover letter with a brief description of past research accomplishments as well as future research interests and career goals to Simon Kelly at skelly2 at ccny.cuny.edu. From jan.schoffelen at donders.ru.nl Sat Jul 7 20:01:23 2012 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Sat, 7 Jul 2012 20:01:23 +0200 Subject: [FieldTrip] Connectivity analysis In-Reply-To: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> References: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> Message-ID: Hi Kathryn, I believe that ft_connectivityanalysis is capable of dealing with frequency domain data that contain a time dimension. I assume here that you would like to compute coherence, rather than correlation. Last time I checked, ft_connectivityanalysis could not compute an ordinary correlation coefficient. Best wishes, Jan-Mathijs On Jul 6, 2012, at 6:59 PM, Kathryn Manning wrote: > Dear FieldTrip list members, > > I am comparing the connectivity patterns in the brain measured using fMRI and electrophysiological recordings. I am trying to correlate the LFP signals as a function of time, using a sliding window analysis. I'm able to generate plots using ft_connectivityplot but this is as a function of frequency. From what I can tell the 'mtmconvol' method generates data with a time aspect in it's dimord, but are there any functions available in fieldtrip in order to calculate the correlation as a function of time? > > Any help would be greatly appreciated, thank you so much. > > Kathryn > _______________________________________________ > 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 bertram0611 at pku.edu.cn Sun Jul 8 09:50:20 2012 From: bertram0611 at pku.edu.cn (=?utf-8?B?6JSh5p6X?=) Date: Sun, 8 Jul 2012 15:50:20 +0800 (CST) Subject: [FieldTrip] =?gbk?q?How_to_import_*=2Ecnt_datafile_from_NeuroScan?= =?gbk?q?=3F?= Message-ID: <283648358.226.1341733820039.JavaMail.root@bj-mail07.pku.edu.cn> Dear FieldTrip list members, I wanna analyse the *.cnt datafile from NeuroScan. But I don't know how to do that. Because there are not detailed scripts. In my exp, the trigger code is 14. I don't what is eventvalue that equals trigger code? My EEG was recorded from 62 Ag/AgCl electrodes mounted in an elastic cap (Quick-Cap, NeuroScan Inc.,Herndon, Virginia, USA). Recordings were referenced to the left mastoid, but rereferenced to linked mastoids offline. The horizontal and vertical electrooculogram was also monitored. Electrode impedances were kept below 5 kO. The EEG and electrooculogram were amplified with a band-pass from DC to 70Hz and the sample rate was 500 Hz.The epoch interval was 1200ms, ranging from 200ms before the onset of the critical word to 1000 ms after it.I used a 100-ms poststimulus baseline for the critical words. can you give an example that analysing *.cnt data. my script and problems as follows: cfg = [] cfg.datafile = 's01.cnt' cfg.headerfile = 's01.cnt' cfg.channel = 'all' cfg.eventvalue = '14' raw = ft_definetrial(cfg); Warning: no trialfun was specified, using trialfun_general > In ft_definetrial at 123 evaluating trialfunction 'trialfun_general' ??? Reference to non-existent field 'trialdef'. Error in ==> trialfun_general at 29 if isfield(cfg.trialdef, 'eventvalue') && isempty(cfg.trialdef.eventvalue ), cfg.trialdef = rmfield(cfg.trialdef, 'eventvalue' ); end Error in ==> ft_definetrial at 175 [trl, event] = feval(cfg.trialfun, cfg); best regards -- Lin Cai Department of Psychology, Peking University, Beijing 100871, P.R.China From politzerahless at gmail.com Sun Jul 8 12:32:02 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Sun, 8 Jul 2012 18:32:02 +0800 Subject: [FieldTrip] How to import *.cnt datafile from NeuroScan? Message-ID: Hello Lin, In your code you need to specify an event type. To find out what the event type is, you can run ft_definetrial() with cfg.trialdef.eventtype='?', and it will tell you what event types are present in the file (see my sample below): addpath 'C:\Program Files\MATLAB\R2010a\toolbox\fieldtrip-20120512'; cd 'C:\Users\SJPA\Documents\MATLAB'; cfg = []; cfg.dataset = 'myneuroscanfile.cnt'; cfg.trialdef.eventtype = '?' cfg = ft_definetrial(cfg); After that, you can use that event type, along with cfg.dataset and cfg.trialdef.eventvalue, to define trials and import the data; see my example below (this code will take a continuous file but it will epoch it while importing, so you will end up with epoched data; also note, as far as I know, you don't need to specify cfg.headerfile) addpath 'C:\Program Files\MATLAB\R2010a\toolbox\fieldtrip-20120512'; cd 'C:\Users\SJPA\Documents\MATLAB'; cfg = []; cfg.dataset = 'myneuroscanfile.cnt'; cfg.trialdef.eventtype = 'trial'; cfg.trialdef.eventvalue = [4 5 6 7]; cfg = ft_definetrial(cfg); cfg.channel = []; cfg.continuous = 'yes'; data = ft_preprocessing(cfg); I noticed your e-mail signature says you are at Peking University; I am actually also at the psychology department in PKU and will be here until July 17th, if you need assistance feel free to contact me! Best, Steve Politzer-Ahles > > Message: 2 > Date: Sun, 8 Jul 2012 15:50:20 +0800 (CST) > From: ?? > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] How to import *.cnt datafile from NeuroScan? > Message-ID: > <283648358.226.1341733820039.JavaMail.root at bj-mail07.pku.edu.cn> > Content-Type: text/plain; charset=utf-8 > > Dear FieldTrip list members, > > I wanna analyse the *.cnt datafile from NeuroScan. But I don't know how to > do that. Because there are not detailed scripts. In my exp, the trigger > code is 14. I don't what is eventvalue that equals trigger code? My EEG was > recorded from 62 Ag/AgCl electrodes mounted in an elastic cap (Quick-Cap, > NeuroScan Inc.,Herndon, Virginia, USA). Recordings were referenced to the > left mastoid, but rereferenced to linked mastoids offline. The horizontal > and vertical electrooculogram was also monitored. Electrode impedances were > kept below 5 kO. The EEG and electrooculogram were amplified with a > band-pass from DC to 70Hz and the sample rate was 500 Hz.The epoch interval > was 1200ms, ranging from 200ms before the onset of the critical word to > 1000 ms after it.I used a 100-ms poststimulus baseline for the critical > words. > can you give an example that analysing *.cnt data. > my script and problems as follows: > cfg = [] > cfg.datafile = 's01.cnt' > cfg.headerfile = 's01.cnt' > cfg.channel = 'all' > cfg.eventvalue = '14' > raw = ft_definetrial(cfg); > Warning: no trialfun was specified, using trialfun_general > > In ft_definetrial at 123 > evaluating trialfunction 'trialfun_general' > ??? Reference to non-existent field 'trialdef'. > > Error in ==> trialfun_general at 29 > if isfield(cfg.trialdef, 'eventvalue') && isempty(cfg.trialdef.eventvalue > ), > cfg.trialdef = rmfield(cfg.trialdef, 'eventvalue' ); end > > Error in ==> ft_definetrial at 175 > [trl, event] = feval(cfg.trialfun, cfg); > best regards > > -- > Lin Cai > Department of Psychology, Peking University, Beijing 100871, P.R.China > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 20, Issue 12 > ***************************************** > -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From omidabbasi2000 at gmail.com Sun Jul 8 13:28:31 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Sun, 8 Jul 2012 15:58:31 +0430 Subject: [FieldTrip] help to apply field trip (topography plotting) In-Reply-To: References: Message-ID: Dear Steve Thank you very much for your good guidance. I review these links and if i have any question i will ask you again. Best Regards Omid On Sat, Jul 7, 2012 at 5:16 AM, Stephen Politzer-Ahles < politzerahless at gmail.com> wrote: > Hi Omid, > > Welcome to Fieldtrip. You can find a lot of information about how to use > Fieldtrip at http://fieldtrip.fcdonders.nl/walkthrough and > http://fieldtrip.fcdonders.nl/tutorial. In your case, you need to get > your data imported into Fieldtrip's format in MATLAB ( > http://fieldtrip.fcdonders.nl/tutorial/preprocessing), as well as your > channel layout (http://fieldtrip.fcdonders.nl/tutorial/layout) before > proceeding to plotting. > > Good luck, > Steve > > >> Message: 1 >> Date: Thu, 5 Jul 2012 16:36:23 +0430 >> From: omid abbasi >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] help to apply field trip (topography plotting) >> Message-ID: >> < >> CAPc_m1utoA_ZqC8_0q44hz5FX3yMfWP-gfke5Mes9_sEUOuyrA at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear Developer >> >> At first, I thank you for useful source code. >> >> This is Omid. I'm a student that work on biological signal processing. I >> want to use your source code for plotting data topography of brain. I >> downloaded your code from this link ( >> http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but >> i >> can't use it in my project, because i have 19 signals from 19 sites on the >> brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your >> code in my project with different channel and data? >> >> It would grateful for me if you could help me to apply your code in my >> project. >> >> Best Regards >> > > _______________________________________________ > 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 omidabbasi2000 at gmail.com Mon Jul 9 07:06:35 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Mon, 9 Jul 2012 09:36:35 +0430 Subject: [FieldTrip] Bipolar montage Message-ID: Dear Member lists I have .txt file of monopolar montage of EEG (EEG1020, 19 channel). How can i have bipolar montage of it? What's the relationship between bipolar montage and monopolar montage? Best Regards Omid -------------- next part -------------- An HTML attachment was scrubbed... URL: From ith at deakin.edu.au Mon Jul 9 09:26:03 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Mon, 9 Jul 2012 07:26:03 +0000 Subject: [FieldTrip] plotting dipoles on an anatomical mri Message-ID: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> Dear fieldTrip users, I am doing a dipole fit with the ft_dipolefitting function and I can plot and visualize the results with ft_plot_dipole, further I also want to compare the results with a beamformer results so, I tried plotting the ft_dipolefitting results with ft_sourceplot. I cannot yet very well understand how ft_sourceplot works, I understand that the dipole should be assigned with some value but cannot figure out how to do this. Can someone please give me some help in doing this? Following is the code I am using, where should I modify? cfg = []; cfg.location = dip_fitted.dip.pos; cfg.method='ortho'; ft_sourceplot(cfg,mri) where mri is the standard_mri.mat . I work in the MNI coordinates and my locations are in mm's. Thank you very much in advance. Kind regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr [Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 29155 bytes Desc: image001.jpg URL: From r.oostenveld at donders.ru.nl Mon Jul 9 09:40:56 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 9 Jul 2012 09:40:56 +0200 Subject: [FieldTrip] Bipolar montage In-Reply-To: References: Message-ID: <4E3F9B02-6C6D-4EA0-BADF-85A33B005C2D@donders.ru.nl> Dear Omid The option cfg.montage in ft_preprocessing allows you to convert your data between a monopolar to a bipolar montage. See the help of ft_preprocessing and the help of ft_apply_montage (which is the lower-level function that does the actual work). best regards, Robert On 9 Jul 2012, at 7:06, omid abbasi wrote: > Dear Member lists > > I have .txt file of monopolar montage of EEG (EEG1020, 19 channel). How can i have bipolar montage of it? What's the relationship between bipolar montage and monopolar montage? > > Best Regards > Omid > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Ulrich.Pomper at charite.de Mon Jul 9 09:51:56 2012 From: Ulrich.Pomper at charite.de (Pomper, Ulrich) Date: Mon, 9 Jul 2012 09:51:56 +0200 Subject: [FieldTrip] Common beamforming filters for different groups? In-Reply-To: References: , , Message-ID: Thanks Don for you help! Best, Ulrich ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Rojas, Don [Don.Rojas at ucdenver.edu] Sent: Friday, July 06, 2012 7:02 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] Common beamforming filters for different groups? Ulrich, It does not make sense to me to have a common filter per pair of subjects, only between conditions within a subject (which you say you are currently doing). Since, as Johanna suggested, you are using a standard brain and standard electrode locations, rather than individual ones, you can have a common leadfield matrix for all subjects. However, I don't think you can have a common beamformer filter, since that is computed for each subject based on the covariance or cross spectral density matrix, which would be unique to each subject. Therefore, the beamformer filter, which uses both the covariance and the leadfield, would be unique for each individual. You can save time simply by having a common leadfield matrix. Best, Don ----------------------- Don Rojas, Ph.D. Associate Professor of Psychiatry U. of Colorado Denver Anschutz Medical Campus Director, UCD Magnetoencephalography Lab 13001 E. 17th Pl F546 Aurora, CO 80045 303-724-4994 On Jul 6, 2012, at 7:21 AM, Pomper, Ulrich wrote: > Dear Johanna, > thanks for your quick reply! > > To clarify things: This is an EEG study, using a standard MNI-based headmodel for all subjects. > > I have a between subjects factor group (patients, controls) and a within subjects factor condition (A, B). Also, I can use a within subject contrast (active versus baseline) for the source analysis. > > Currently, I use one common filter for baseline and active data as well as both conditions for each subject. So I end up using one common filter per subject. > > My question I whether it would be more correct to additionally pool the data from matched subjects into one single filter. Thus resulting in one common filter per pair. > > > Cheers, Ulrich > > > > > > > > > > ________________________________________ > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] On Behalf Of Johanna Zumer [johanna.zumer at donders.ru.nl] > Sent: Friday, July 06, 2012 2:36 PM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] Common beamforming filters for different groups? > > Dear Ulrich, > > Only if the leadfields are the same, can you use the common filter. > > If you have EEG data with standard electrode positions based on the cap layout (rather than measured electrode positions) and using the standard MNI MRI rather than subject specific MRI, then your leadfield will be the same for all subjects. Then for the covariance computation you might need to consider some normalization (z-transform) of the data (using some control window) so that differences in sensor values due to e.g. sensitivity of electrodes across subjects, won't bias the result. > > If you have MEG data, then the different head positions in the helmet will mean different lead fields. The only ways around that might be: if you do something similar to correcting for head movement within a single session (something like ft_headmovement but as far as I know is not implemented for this multi-subject /session case) or if you ensured similar head position between subject-pairs using ft_realtime_headlocalizer at the time of acquisition; and in combination with using the MNI MRI rather than individual subject MRI. > > Perhaps someone else on the list can comment as to which is better, if the common filter is a possibility? A common filter using sub-optimal reconstruction for each subject if based on non-subject-specific MRI etc, versus optimal reconstruction per subject but then issue of not a common filter? > > Another thing to do is to use the subject-specific inverse filter and do a contrast within that subject (active versus baseline) and take this contrast to the comparison at the paired-subjects group level. However, not all experiments have the possibility of within-subject active-versus-baseline. > > Cheers, > Johanna > > > 2012/7/6 Pomper, Ulrich > > Dear list members, > I want to compare source data between two different groups (patients and controls). Each patient has an age and gender-matched control. > Is it correct to compute a common filter for each pair of subjects? The TF-topographies do look different within each pair, so I would assume that the sources are somewhat different. However, as I'm going to statistically compare the two groups it would be nice to have common filters, as otherwise any finding could be due to different filters as opposed to different sources. > > Any help with this issue is greatly aprreciated! > Cheers, Ulrich > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg > > Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus > > _______________________________________________ > 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 -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus From r.oostenveld at donders.ru.nl Mon Jul 9 10:02:16 2012 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 9 Jul 2012 10:02:16 +0200 Subject: [FieldTrip] plotting dipoles on an anatomical mri In-Reply-To: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> References: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> Message-ID: Dear Imali The ft_sourceplot function was not designed to plot 3D data in combination with dipoles. If you use method=ortho, you can get the 3 intersections in the 3D volume at the location of the dipole. For the best control over the details of the plot, which you need for your specific application of combining dipoles and volumetric data, I suggest that you look at the ft_plot_slice function. If you do three ft_plot_slice calls for the three orientations (x,y,z) at the location of the dipole and combine that with ft_plot_dipole, you will probably visualize the 3D relation between the two types of data the clearest. Note that ft_plot_slice plots any slice in 3D, so you should use the 3D rotate option of the MATLAB figure. best regards, Robert On 9 Jul 2012, at 9:26, IMALI THANUJA HETTIARACHCHI wrote: > Dear fieldTrip users, > > I am doing a dipole fit with the ft_dipolefitting function and I can plot and visualize the results with ft_plot_dipole, further I also want to compare the results with a beamformer results so, I tried plotting the ft_dipolefitting results with ft_sourceplot. I cannot yet very well understand how ft_sourceplot works, I understand that the dipole should be assigned with some value but cannot figure out how to do this. > > Can someone please give me some help in doing this? Following is the code I am using, where should I modify? > > cfg = []; > cfg.location = dip_fitted.dip.pos; > cfg.method='ortho'; > ft_sourceplot(cfg,mri) > > where mri is the standard_mri.mat . I work in the MNI coordinates and my locations are in mm’s. > > > Thank you very much in advance. > > Kind regards > Imali > > Imali Thanuja Hettiarachchi > PhD Candidate > Centre for Intelligent Systems research > Deakin University, Geelong 3217, Australia. > Email: ith at deakin.edu.au > www.deakin.edu.au/cisr > > > > > > > _______________________________________________ > 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 omidabbasi2000 at gmail.com Mon Jul 9 10:35:45 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Mon, 9 Jul 2012 13:05:45 +0430 Subject: [FieldTrip] Bipolar montage In-Reply-To: <4E3F9B02-6C6D-4EA0-BADF-85A33B005C2D@donders.ru.nl> References: <4E3F9B02-6C6D-4EA0-BADF-85A33B005C2D@donders.ru.nl> Message-ID: Dear Robert Thank you for your fast answer I'll check it. Best Regards Omis On Mon, Jul 9, 2012 at 12:10 PM, Robert Oostenveld < r.oostenveld at donders.ru.nl> wrote: > Dear Omid > > The option cfg.montage in ft_preprocessing allows you to convert your data > between a monopolar to a bipolar montage. See the help of ft_preprocessing > and the help of ft_apply_montage (which is the lower-level function that > does the actual work). > > best regards, > Robert > > > On 9 Jul 2012, at 7:06, omid abbasi wrote: > > > Dear Member lists > > > > I have .txt file of monopolar montage of EEG (EEG1020, 19 channel). How > can i have bipolar montage of it? What's the relationship between bipolar > montage and monopolar montage? > > > > Best Regards > > Omid > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 9 11:48:18 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 09 Jul 2012 11:48:18 +0200 Subject: [FieldTrip] band pass and segmentation In-Reply-To: <1341330157.2152.YahooMailNeo@web28705.mail.ir2.yahoo.com> References: <1341330157.2152.YahooMailNeo@web28705.mail.ir2.yahoo.com> Message-ID: <4FFAA8E2.70100@donders.ru.nl> Hi Ivano, I don't understand your request exactly, could you attach an example figure and explain your issue by using that? Then I (or someone else) might be able to help you out. Best, Jörn On 7/3/2012 5:42 PM, Ivano Triggiani wrote: > Hi all, > > I tried to use a simple cfg.bpfilter (0.1 - 40) for an EEG that I > divide into 2 secs époques and giving a look it seems that at the > board of every window the signal is reduced (just like following a > parabolic trend). Is this a problem of the brutal segmentation > (respect to a good windowing) or there's something else? > > Ivano > > > > _______________________________________________ > 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 Mon Jul 9 12:17:33 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 09 Jul 2012 12:17:33 +0200 Subject: [FieldTrip] Fwd: Re: band pass and segmentation In-Reply-To: <1341828068.24326.YahooMailNeo@web28706.mail.ir2.yahoo.com> References: <1341828068.24326.YahooMailNeo@web28706.mail.ir2.yahoo.com> Message-ID: <4FFAAFBD.4080107@donders.ru.nl> Dear Ivano, I am forwarding your message and my reply to the discussion list again, so that others might benefit or add information. What you see looks to me pretty much like a filter artifact, which is common to occur at the edges of your signal. In order to reduce these, you can think of changing the order of your filter or, more ideal in my opinion, use filterpadding. You can either let FieldTrip do that by specifying cfg.padding or by defining your trials in a wider range (e.g. add 1s pre and post time of interest) and then only plot the time of interest, with the knowledge that the 1s padding before and after is corrupted by filter artifacts. Best, Jörn -------- Original Message -------- Subject: Re: [FieldTrip] band pass and segmentation Date: Mon, 9 Jul 2012 11:01:08 +0100 (BST) From: Ivano Triggiani Reply-To: Ivano Triggiani To: "Jörn M. Horschig" Hi Jorn, in attach an example. you can see in the third slide on the right the channel that "goes down". Thanks, Ivano ------------------------------------------------------------------------ "No man can wear one face to himself and another to the multitude, without finally getting bewildered as to which one is true." Nathaniel Hawthorne ------------------------------------------------------------------------ *Da:* ""Jörn M. Horschig"" *A:* Ivano Triggiani ; FieldTrip discussion list *Inviato:* Lunedì 9 Luglio 2012 11:48 *Oggetto:* Re: [FieldTrip] band pass and segmentation Hi Ivano, I don't understand your request exactly, could you attach an example figure and explain your issue by using that? Then I (or someone else) might be able to help you out. Best, Jörn On 7/3/2012 5:42 PM, Ivano Triggiani wrote: > Hi all, > > I tried to use a simple cfg.bpfilter (0.1 - 40) for an EEG that I > divide into 2 secs époques and giving a look it seems that at the > board of every window the signal is reduced (just like following a > parabolic trend). Is this a problem of the brutal segmentation > (respect to a good windowing) or there's something else? > > Ivano > > > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: Fieldtrip_EEG.ppt Type: application/vnd.ms-powerpoint Size: 169984 bytes Desc: not available URL: From vitoria.piai at gmail.com Mon Jul 9 15:18:47 2012 From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=) Date: Mon, 09 Jul 2012 15:18:47 +0200 Subject: [FieldTrip] plot functions and illustrator: set(gcf, 'interpreter', 'zbuffer') Message-ID: <4FFADA37.5070004@gmail.com> Hi, On the FT page, Roemer said that using set(gcf,'interpreter','zbuffer') may resolve problems when exporting from matlab as .eps and opening in Illustrator. That works fine for sensor-level data, for example TFRs with ft_singleplotTFR. But it doesn't work when, for example, using ft_sourceplot (I've akes around and I don't seem to be the only one having this problem). But ok, so far so good, I can get around it. But now I have an analysis I ran with LCMV for which I wanted to plot the results. Interestingly, if I use ft_singleplotTFR in this case, I cannot fix the bug with set(gcf,'interpreter','zbuffer'). It seems to behave like when using ft_sourceplot, instead of behaving as ft_singleplot when plotting sensor-level data. Has anyone dealt with this bug before? I mean, not being able to fix it with set(gcf,'interpreter','zbuffer')? Thanx a lot, Vitoria -- ** Please consider the environment - do you really need to print? ** From kmanning at robarts.ca Mon Jul 9 15:19:16 2012 From: kmanning at robarts.ca (Kathryn Manning) Date: Mon, 9 Jul 2012 09:19:16 -0400 Subject: [FieldTrip] Connectivity analysis In-Reply-To: References: <72B65507-202A-4E99-8800-D557E96D057B@robarts.ca> Message-ID: <9EC69CEB-0315-4823-B241-71ED4649B9D5@robarts.ca> Thanks for your help! Best wishes, Kathryn On 2012-07-07, at 2:01 PM, jan-mathijs schoffelen wrote: Hi Kathryn, I believe that ft_connectivityanalysis is capable of dealing with frequency domain data that contain a time dimension. I assume here that you would like to compute coherence, rather than correlation. Last time I checked, ft_connectivityanalysis could not compute an ordinary correlation coefficient. Best wishes, Jan-Mathijs On Jul 6, 2012, at 6:59 PM, Kathryn Manning wrote: Dear FieldTrip list members, I am comparing the connectivity patterns in the brain measured using fMRI and electrophysiological recordings. I am trying to correlate the LFP signals as a function of time, using a sliding window analysis. I'm able to generate plots using ft_connectivityplot but this is as a function of frequency. From what I can tell the 'mtmconvol' method generates data with a time aspect in it's dimord, but are there any functions available in fieldtrip in order to calculate the correlation as a function of time? Any help would be greatly appreciated, thank you so much. Kathryn _______________________________________________ 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 stephen.whitmarsh at gmail.com Mon Jul 9 15:45:03 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Mon, 9 Jul 2012 15:45:03 +0200 Subject: [FieldTrip] plot functions and illustrator: set(gcf, 'interpreter', 'zbuffer') In-Reply-To: <4FFADA37.5070004@gmail.com> References: <4FFADA37.5070004@gmail.com> Message-ID: Hi Vitoria, Not really answering your questions, but from my experience I wouldn't export vector graphics of source data - just too many vectors. Instead why not export to high resolution (e.g. '-r600') png instead? I know my computer can certainly deal with those with less memory problems, I don't need to do anything vector-like on those images that I can't do on a bitmap. Cheers! Stephen p.s. same goes for fine-grained TFR's On 9 July 2012 15:18, Vitória Magalhães Piai wrote: > Hi, > > On the FT page, Roemer said that using set(gcf,'interpreter','**zbuffer') > may resolve problems when exporting from matlab as .eps and opening in > Illustrator. > > That works fine for sensor-level data, for example TFRs with > ft_singleplotTFR. But it doesn't work when, for example, using > ft_sourceplot (I've akes around and I don't seem to be the only one having > this problem). But ok, so far so good, I can get around it. > > But now I have an analysis I ran with LCMV for which I wanted to plot the > results. Interestingly, if I use ft_singleplotTFR in this case, I cannot > fix the bug with set(gcf,'interpreter','**zbuffer'). It seems to behave > like when using ft_sourceplot, instead of behaving as ft_singleplot when > plotting sensor-level data. > > Has anyone dealt with this bug before? I mean, not being able to fix it > with set(gcf,'interpreter','**zbuffer')? > > Thanx a lot, Vitoria > > > -- > ** Please consider the environment - do you really need to print? ** > > ______________________________**_________________ > 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 styll at med.ovgu.de Mon Jul 9 15:51:41 2012 From: styll at med.ovgu.de (styll at med.ovgu.de) Date: Mon, 9 Jul 2012 15:51:41 +0200 Subject: [FieldTrip] Problems with ft_app​ endata - merging dat​ asets​ Message-ID: <2854bfbc1930cfbba485e0aeb7488e16.squirrel@neuro2.med.uni-magdeburg.de> Hello, I probably have a problem with the use of ft_appendata. I want to merge 4 MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, etc.) of the same subject after I defined my trials of interest and preprocessed the 4 datasets individually. If I use ft_databrowser for a look into every single dataset, all trials (10 in each run/dataset) seems to be OK with the correct sequence: defined prestim time range, trigger and poststim time range. If I check the merged dataset I can go through all of the 40 trials, but there is no sequence like: prestim time range, trigger and poststim-time. Here is my pipeline for the first steps: %%%% run1 cfg.dataset=' \train01_64\run1\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run1'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_1 = ft_preprocessing(cfg) %%%% run2 cfg.dataset=' \train01_64\run2\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run2'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_2 = ft_preprocessing(cfg) the same for run3 and run4 %%%% merging the data cfg=[]; merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, prepro_run_4) Do I miss something or is there in error in my pipeline or in my strategy Best regards Sascha From styll at med.ovgu.de Mon Jul 9 15:56:52 2012 From: styll at med.ovgu.de (styll at med.ovgu.de) Date: Mon, 9 Jul 2012 15:56:52 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> Message-ID: <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> Hello, I probably have a problem with the use of ft_appendata. I want to merge 4 MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, etc.) of the same subject after I defined my trials of interest and preprocessed the 4 datasets individually. If I use ft_databrowser for a look into every single dataset, all trials (10 in each run/dataset) seems to be OK with the correct sequence: defined prestim time range, trigger and poststim time range. If I check the merged dataset I can go through all of the 40 trials, but there is no sequence like: prestim time range, trigger and poststim-time. Here is my pipeline for the first steps: %%%% run1 cfg.dataset=' \train01_64\run1\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run1'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_1 = ft_preprocessing(cfg) %%%% run2 cfg.dataset=' \train01_64\run2\c,rfDC'; cfg.trialdef.prestim=1; %%% in sec cfg.trialdef.poststim=5; %%% in sec cfg.trialfun = 'traildef_train01_all_pics_run2'; data_run1 = ft_definetrial(cfg) cfg.channel = {'MEG'}; cfg.dftfilter='yes'; prepro_run_2 = ft_preprocessing(cfg) the same for run3 and run4 %%%% merging the data cfg=[]; merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, prepro_run_4) Do I miss something or is there in error in my pipeline or in my strategy Best regards Sascha From dporada at uos.de Mon Jul 9 18:29:37 2012 From: dporada at uos.de (Porada Danja) Date: Mon, 9 Jul 2012 18:29:37 +0200 Subject: [FieldTrip] explained variance by ICA components Message-ID: <113D5DB2-88D7-4632-9F41-3DA2F409CF4B@uos.de> Hi, I computed an ICA on my MEG data. When I plot the components with the databrowser they are sorted according to variance in the data they accounted for. Or am I wrong? Where are those values saved? I want to know for each component how much variance it explains. Best, Danja From marco.rotonda at gmail.com Mon Jul 9 20:15:34 2012 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Mon, 9 Jul 2012 20:15:34 +0200 Subject: [FieldTrip] LARS and LASSO for connectivity Message-ID: Dear FieldTrip experts, I wasn't so happy to choose some ROIs with a priori knowledge in a GC analysis. So I searched a bit and I've found this wonderful solution which take care of all the voxels: http://www.ncbi.nlm.nih.gov/pubmed/21439388 Full-brain auto-regressive modeling (FARM) using fMRI Since there is already ft_mvaranalysis and ft_connectivityanalysis do you think that is possible to integrate the FARM approach into those functions? Regards, Marco From marco.rotonda at gmail.com Mon Jul 9 21:25:34 2012 From: marco.rotonda at gmail.com (Marco Rotonda) Date: Mon, 9 Jul 2012 21:25:34 +0200 Subject: [FieldTrip] LARS and LASSO for connectivity Message-ID: Dear FieldTrip experts, I wasn't so happy to choose only some ROIs in a GC analysis. So I searched a bit and I've found this wonderful solution which take care of all the voxels: http://www.ncbi.nlm.nih.gov/pubmed/21439388 Full-brain auto-regressive modeling (FARM) using fMRI Since there are already ft_mvaranalysis and ft_connectivityanalysis, do you think that is possible to integrate the FARM approach into those functions? Regards, Marco From ith at deakin.edu.au Tue Jul 10 05:42:55 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Tue, 10 Jul 2012 03:42:55 +0000 Subject: [FieldTrip] plotting dipoles on an anatomical mri In-Reply-To: References: <5A1787011651BC42A4D41856DBC2E0603E047913@mbox-f-3.du.deakin.edu.au> Message-ID: <5A1787011651BC42A4D41856DBC2E0603E047A96@mbox-f-3.du.deakin.edu.au> Dear Robert, Thank you very much for the very quick reply and the explaining. I am a bit struggling in the exact usage of ft_slice_plot function. I was trying to dig up on an example usage but was unable to find any. What does exactly in the use ft_plot_slice(dat, ...) , dat argument stands for? Can you please explain me on how to plot a 2D slice using the function? Thank you very much again. Regards Imali From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Robert Oostenveld Sent: Monday, 9 July 2012 6:02 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] plotting dipoles on an anatomical mri Dear Imali The ft_sourceplot function was not designed to plot 3D data in combination with dipoles. If you use method=ortho, you can get the 3 intersections in the 3D volume at the location of the dipole. For the best control over the details of the plot, which you need for your specific application of combining dipoles and volumetric data, I suggest that you look at the ft_plot_slice function. If you do three ft_plot_slice calls for the three orientations (x,y,z) at the location of the dipole and combine that with ft_plot_dipole, you will probably visualize the 3D relation between the two types of data the clearest. Note that ft_plot_slice plots any slice in 3D, so you should use the 3D rotate option of the MATLAB figure. best regards, Robert On 9 Jul 2012, at 9:26, IMALI THANUJA HETTIARACHCHI wrote: Dear fieldTrip users, I am doing a dipole fit with the ft_dipolefitting function and I can plot and visualize the results with ft_plot_dipole, further I also want to compare the results with a beamformer results so, I tried plotting the ft_dipolefitting results with ft_sourceplot. I cannot yet very well understand how ft_sourceplot works, I understand that the dipole should be assigned with some value but cannot figure out how to do this. Can someone please give me some help in doing this? Following is the code I am using, where should I modify? cfg = []; cfg.location = dip_fitted.dip.pos; cfg.method='ortho'; ft_sourceplot(cfg,mri) where mri is the standard_mri.mat . I work in the MNI coordinates and my locations are in mm's. Thank you very much in advance. Kind regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr _______________________________________________ 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 biomag.network.practical at gmail.com Tue Jul 10 09:21:37 2012 From: biomag.network.practical at gmail.com (Biomag Networks Satellite 25 Aug 2012) Date: Tue, 10 Jul 2012 09:21:37 +0200 Subject: [FieldTrip] Biomag Satellite Announcement: Open for Registration In-Reply-To: References: Message-ID: Dear Biomag community, A final reminder that you can still sign up for this Biomag Satellite Workshop on Practical Considerations for Network Analysis, until the end of this week (July 13 final deadline)! Please see link and details below. Best regards, Ole Jensen, Sarang Dalal, and Johanna Zumer On Mon, Apr 2, 2012 at 4:44 PM, Biomag Networks Satellite 25 Aug 2012 < biomag.network.practical at gmail.com> wrote: > 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 ith at deakin.edu.au Tue Jul 10 10:05:51 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Tue, 10 Jul 2012 08:05:51 +0000 Subject: [FieldTrip] Beamformer results for simulated data Message-ID: <5A1787011651BC42A4D41856DBC2E0603E047B22@mbox-f-3.du.deakin.edu.au> Dear fieldTrip Users, I am trying to run a dipole fit with the nonlinear grid search and a beamformer scan on a simulated data set, to compare the results. My simulated dipole is at the MNI coordinates [32.8 -85.8 28]. It is shown in red in DIP_1.jpg. The ft_dipolefitting results for the simulated dipole is in green in DIP_1.jpg. When I do the lcmv beamformer scan on the same simulated data and plot them I get results as in POW_1.jpg for avg.pow parameter and NAI_1.jpg for avg.nai parameter. Following is the code I use for the above purpose; cfg = []; cfg.vol = curry_vol; cfg.elec = sens; cfg.grid=template_grid; cfg.method = 'lcmv'; cfg.lambda='5%'; cfg.projectnoise='yes'; source = ft_sourceanalysis(cfg, timelock); load standard_mri.mat mri = ft_volumereslice([], mri); %% Figure POW_1.jpg % Aligning the measure of power increase with the structural MRI of subject cfg=[]; cfg.downsample=2; cfg.parameter='avg.pow'; source_int=ft_sourceinterpolate(cfg,source,mri); % Plot the interpolated data cfg=[]; cfg.method='slice'; cfg.funparameter='avg.pow'; figure,ft_sourceplot(cfg,source_int) %% Figure NAI_1.jpg % compute the neural activity index, i.e. projected power divided by % projected noise sourceNAI=source; sourceNAI.avg.nai=source.avg.pow./source.avg.noise; %neural activity index calculation cfg=[]; cfg.downsample=2; cfg.parameter='avg.nai'; sourceNAI_int=ft_sourceinterpolate(cfg,sourceNAI,mri); cfg = []; cfg.method = 'slice'; cfg.funparameter = 'avg.nai'; cfg.maskparameter=cfg.funparameter; figure ,ft_sourceplot(cfg, sourceNAI_int); Can you please direct me to what I am doing wrong or missing in my code to get sensible beamformer scan results. When I read the source_int.avg.pow and sourceNAI_int.avg.nai most of the values are NaN's. Many amny thanks in advance. Regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr [Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 29155 bytes Desc: image001.jpg URL: From jm.horschig at donders.ru.nl Tue Jul 10 12:20:35 2012 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 10 Jul 2012 12:20:35 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> Message-ID: <4FFC01F3.8010103@donders.ru.nl> Dear Sascha, What you do is perfectly fine, but what you want is not possible in FieldTrip (yet?). FieldTrip is designed such that triggers (and all other events) are stored with respect to sample number from the beginning of the recording, i.e. datafile on disk. However, when you merge datasets, FieldTrip cannot infer to what dataset a specific sample number belongs - in your case it could be coming from 4 different datasets - and thus dismisses this information completely. So, what you would need to as a workaround is to save the events with respect to your trials of interest (and dataset), and after merging, create a fake sampleinfo and event structure. Then, you would need to create events with samples respective to the fake sampleinfo. This is a somewhat tedious work, and only a hack to get what you want, but it's the only way so far :) But be aware that this work might result in a lot of nasty errors if you are not careful enough. If you do not know what I mean, feel free to send me a mail and I can try my best to explain what I mean with a short example script. Best, Jörn On 7/9/2012 3:56 PM, styll at med.ovgu.de wrote: > Hello, > > I probably have a problem with the use of ft_appendata. I want to merge 4 > MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, > etc.) of the same subject after I defined my trials of interest and > preprocessed the 4 datasets individually. If I use ft_databrowser for a > look into every single dataset, all trials (10 in each run/dataset) seems > to be OK with the correct sequence: defined prestim time range, trigger > and poststim time range. If I check the merged dataset I can go through > all of the 40 trials, but there is no sequence like: prestim time range, > trigger and poststim-time. Here is my pipeline for the first steps: > > %%%% run1 > cfg.dataset='…\train01_64\run1\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run1'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_1 = ft_preprocessing(cfg) > > %%%% run2 > cfg.dataset='…\train01_64\run2\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run2'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_2 = ft_preprocessing(cfg) > > the same for run3 and run4 > > %%%% merging the data > > cfg=[]; > merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, > prepro_run_4) > > Do I miss something or is there in error in my pipeline or in my strategy… > > Best regards > > Sascha > > > _______________________________________________ > 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 jm.horschig at donders.ru.nl Tue Jul 10 12:49:48 2012 From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 10 Jul 2012 12:49:48 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> Message-ID: <4FFC08CC.2050302@donders.ru.nl> Hi Sascha, I just got reminded (thx Yuka-san) that you could use a ctf command to combine CTF datasets (of course, only if you got data from a CTF system): newCombinedDs [options] This program takes two or more datasets that have exactly the same collection parameters and combines them to make one dataset. Best, Jörn On 7/9/2012 3:56 PM, styll at med.ovgu.de wrote: > Hello, > > I probably have a problem with the use of ft_appendata. I want to merge 4 > MEG datasets (i.e. 4 runs, all the same number of channels, sampling rate, > etc.) of the same subject after I defined my trials of interest and > preprocessed the 4 datasets individually. If I use ft_databrowser for a > look into every single dataset, all trials (10 in each run/dataset) seems > to be OK with the correct sequence: defined prestim time range, trigger > and poststim time range. If I check the merged dataset I can go through > all of the 40 trials, but there is no sequence like: prestim time range, > trigger and poststim-time. Here is my pipeline for the first steps: > > %%%% run1 > cfg.dataset='…\train01_64\run1\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run1'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_1 = ft_preprocessing(cfg) > > %%%% run2 > cfg.dataset='…\train01_64\run2\c,rfDC'; > cfg.trialdef.prestim=1; %%% in sec > cfg.trialdef.poststim=5; %%% in sec > cfg.trialfun = 'traildef_train01_all_pics_run2'; > data_run1 = ft_definetrial(cfg) > > cfg.channel = {'MEG'}; > cfg.dftfilter='yes'; > prepro_run_2 = ft_preprocessing(cfg) > > the same for run3 and run4 > > %%%% merging the data > > cfg=[]; > merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, prepro_run_3, > prepro_run_4) > > Do I miss something or is there in error in my pipeline or in my strategy… > > Best regards > > Sascha > > > _______________________________________________ > 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 elilife at gmail.com Tue Jul 10 16:57:25 2012 From: elilife at gmail.com (Eliana Garcia) Date: Tue, 10 Jul 2012 16:57:25 +0200 Subject: [FieldTrip] problems with speed of processing Message-ID: Hello Dear Fieldtrip Community, I am having now problems with processing my data. I am analyzing a quite big data set with 400 trials that are composed by 10 sec (re-sampled at 150Hz). I am doing first a demean, then planar gradient transformation, time-frequency analysis using multitapers and then combine the planar gradient again. For the first subject always runs normally, but for the second one matlab gets really slow. I am taking care in deleting the variables that I create with big amount of data after I don't need them any more, so I am using just one big file that is being safe at the end (average time-frequency across trials) for each of the subjects. Every time matlab starts to analyze a new subject I am using clear all (with exceptions like directory and name of subject) but stills with every new subject it gets slower and slower. Do you have any advises to make the analysis faster? Sometimes is too slow and the computer normally crashes after 3 subjects. Thank you very much for the attention. Best, -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Tue Jul 10 18:01:30 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Tue, 10 Jul 2012 18:01:30 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: Dear Eliana, You could try creating a function that does all this preprocessing and then writes the output to file. If you then call this function in a (subject) loop you are sure that Matlab will free up the memory it used for that function. Perhaps it helps, Stephen On 10 July 2012 16:57, Eliana Garcia wrote: > Hello Dear Fieldtrip Community, > > I am having now problems with processing my data. I am analyzing a quite > big data set with 400 trials that are composed by 10 sec (re-sampled at > 150Hz). I am doing first a demean, then planar gradient transformation, > time-frequency analysis using multitapers and then combine the planar > gradient again. For the first subject always runs normally, but for the > second one matlab gets really slow. I am taking care in deleting the > variables that I create with big amount of data after I don't need them any > more, so I am using just one big file that is being safe at the end > (average time-frequency across trials) for each of the subjects. Every time > matlab starts to analyze a new subject I am using clear all (with > exceptions like directory and name of subject) but stills with every new > subject it gets slower and slower. > > Do you have any advises to make the analysis faster? Sometimes is too slow > and the computer normally crashes after 3 subjects. > > Thank you very much for the attention. > > Best, > > -- > Eliana García Cossio > Applied Neurotechnology Lab. > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > _______________________________________________ > 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 elilife at gmail.com Tue Jul 10 18:40:23 2012 From: elilife at gmail.com (Eliana Garcia) Date: Tue, 10 Jul 2012 18:40:23 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: Dear Stephen, Thanks for the suggestion. I have already one function that is doing all the preprocessing and saving as well. But this seams not to solve the issue. Thanks, Eliana On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh < stephen.whitmarsh at gmail.com> wrote: > Dear Eliana, > > You could try creating a function that does all this preprocessing and > then writes the output to file. > If you then call this function in a (subject) loop you are sure that > Matlab will free up the memory it used for that function. > > Perhaps it helps, > > Stephen > > On 10 July 2012 16:57, Eliana Garcia wrote: > >> Hello Dear Fieldtrip Community, >> >> I am having now problems with processing my data. I am analyzing a quite >> big data set with 400 trials that are composed by 10 sec (re-sampled at >> 150Hz). I am doing first a demean, then planar gradient transformation, >> time-frequency analysis using multitapers and then combine the planar >> gradient again. For the first subject always runs normally, but for the >> second one matlab gets really slow. I am taking care in deleting the >> variables that I create with big amount of data after I don't need them any >> more, so I am using just one big file that is being safe at the end >> (average time-frequency across trials) for each of the subjects. Every time >> matlab starts to analyze a new subject I am using clear all (with >> exceptions like directory and name of subject) but stills with every new >> subject it gets slower and slower. >> >> Do you have any advises to make the analysis faster? Sometimes is too >> slow and the computer normally crashes after 3 subjects. >> >> Thank you very much for the attention. >> >> Best, >> >> -- >> Eliana García Cossio >> Applied Neurotechnology Lab. >> Graduate School of Neural and Behavioural Science - Max Planck Research >> School >> Institute of Medical Psychology and Behavioural Neurobiology >> Universität Tübingen >> (+0049) 01 577-8587604 >> Otfried-Müller-Str. 47, 72076 >> Tübingen- Germany >> >> >> _______________________________________________ >> 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 > -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdeiss at ucsd.edu Tue Jul 10 20:49:49 2012 From: sdeiss at ucsd.edu (Steve Deiss) Date: Tue, 10 Jul 2012 11:49:49 -0700 Subject: [FieldTrip] read_biosig_header.m Message-ID: <4FFC794D.40508@ucsd.edu> The fieldtrip version we have calls function 'read_biosig_header' which calls 'sopen' with the following sequence. biosig = sopen(filename,'r'); For some reason it loses the digital triggers on channel 1 in our data after issuing the following warning: "Reading data file header... WARNING SOPEN(EDF): Physical Max/Min values of EDF data are not necessarily defining the dynamic range. Hence, OVERFLOWDETECTION might not work correctly. See also EEG2HIST and read http://dx.doi.org/10.1016/S1388-2457(99)00172-8 (A. Schlgl et al. Quality Control ... Clin. Neurophysiol. 1999, Dec; 110(12): 2165 - 2170). A copy is available here, too: http://www.dpmi.tugraz.at/schloegl/publications/neurophys1999_2165.pdf " If we let EEGLAB read the data, its function 'pop_biosig' calls 'sopen' with biosig = sopen(filename,'r',0,'OVERFLOWDETECTION:OFF'); The data read in here includes the triggers so that we can go on to epoch and process the data. We are not yet ready to upgrade to the very latest fieldtrip. So I would like to know if there is an easy way to determine if the latest version of fieldtrip changed anything in the way sopen is called from read_biosig_header? If it matches what EEGLAB does here, we can match that as a temporary fix. I'll try to download and unpack it to see, but if this is a known problem, fixed or not, I'd appreciate any tips. Thanks Steve From rn77 at sussex.ac.uk Wed Jul 11 05:25:36 2012 From: rn77 at sussex.ac.uk (Roshan Nair) Date: Wed, 11 Jul 2012 04:25:36 +0100 Subject: [FieldTrip] Importing '.mat' data in to fieldtrip Message-ID: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> Hi, I have MEG/EEG data in '.mat' format(Biomag 2012 data analysis dataset). The data is already epoched. It was straightforward to convert it in to the required fieldtrip structure - {label, fsample, trial, time} and run ft_databrowser on it. No problems so far. However, I feel I might be going wrong with the following:- 1. The trials include data for STI(stimulus) channels(I believe its an Elekta Neuromag Vectorview 306 system)? Is there a 'fieldtrip' way to represent this. Is this what 'data.trialinfo' is for? If so, how should I populate the trialinfo field. 2. The dataset comes with a file called 'design' with one entry(an integer) per trial. This is the category of the stimulus(living/non-living)presented to the subject for each trial. This is the output my classifier will be trained on. I'm assuming fieldtrip has some standard way of including this. I noticed, the multivariate analysis mentions a parameter called 'design'. Sorry, if thats confusing, but, I'm new to fieldtrip and MEG data. Thanks! Roshan From styll at med.ovgu.de Wed Jul 11 09:42:25 2012 From: styll at med.ovgu.de (styll at med.ovgu.de) Date: Wed, 11 Jul 2012 09:42:25 +0200 Subject: [FieldTrip] Problems with ft_appendata - merging datasets In-Reply-To: <4FFC01F3.8010103@donders.ru.nl> References: <9912259e997f1001f2109e1765557d95.squirrel@neuro2.med.uni-magdeburg.de> <8a0448ff088edf208ec38b8e5920cbeb.squirrel@neuro2.med.uni-magdeburg.de> <4FFC01F3.8010103@donders.ru.nl> Message-ID: <7436cf587bad96dc9ce7f72f058391fc.squirrel@neuro2.med.uni-magdeburg.de> Hi Jörn, thank you for useful information. I will try to set up the workaround that you mentioned in your mail. In the case of problems I contact you by mail :0) Best regards Sascha > Dear Sascha, > > What you do is perfectly fine, but what you want is not possible in > FieldTrip (yet?). FieldTrip is designed such that triggers (and all > other events) are stored with respect to sample number from the > beginning of the recording, i.e. datafile on disk. However, when you > merge datasets, FieldTrip cannot infer to what dataset a specific sample > number belongs - in your case it could be coming from 4 different > datasets - and thus dismisses this information completely. > > So, what you would need to as a workaround is to save the events with > respect to your trials of interest (and dataset), and after merging, > create a fake sampleinfo and event structure. Then, you would need to > create events with samples respective to the fake sampleinfo. This is a > somewhat tedious work, and only a hack to get what you want, but it's > the only way so far :) But be aware that this work might result in a lot > of nasty errors if you are not careful enough. > > If you do not know what I mean, feel free to send me a mail and I can > try my best to explain what I mean with a short example script. > > Best, > Jörn > > On 7/9/2012 3:56 PM, styll at med.ovgu.de wrote: >> Hello, >> >> I probably have a problem with the use of ft_appendata. I want to merge >> 4 >> MEG datasets (i.e. 4 runs, all the same number of channels, sampling >> rate, >> etc.) of the same subject after I defined my trials of interest and >> preprocessed the 4 datasets individually. If I use ft_databrowser for a >> look into every single dataset, all trials (10 in each run/dataset) >> seems >> to be OK with the correct sequence: defined prestim time range, trigger >> and poststim time range. If I check the merged dataset I can go through >> all of the 40 trials, but there is no sequence like: prestim time range, >> trigger and poststim-time. Here is my pipeline for the first steps: >> >> %%%% run1 >> cfg.dataset=' \train01_64\run1\c,rfDC'; >> cfg.trialdef.prestim=1; %%% in sec >> cfg.trialdef.poststim=5; %%% in sec >> cfg.trialfun = 'traildef_train01_all_pics_run1'; >> data_run1 = ft_definetrial(cfg) >> >> cfg.channel = {'MEG'}; >> cfg.dftfilter='yes'; >> prepro_run_1 = ft_preprocessing(cfg) >> >> %%%% run2 >> cfg.dataset=' \train01_64\run2\c,rfDC'; >> cfg.trialdef.prestim=1; %%% in sec >> cfg.trialdef.poststim=5; %%% in sec >> cfg.trialfun = 'traildef_train01_all_pics_run2'; >> data_run1 = ft_definetrial(cfg) >> >> cfg.channel = {'MEG'}; >> cfg.dftfilter='yes'; >> prepro_run_2 = ft_preprocessing(cfg) >> >> the same for run3 and run4 >> >> %%%% merging the data >> >> cfg=[]; >> merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2, >> prepro_run_3, >> prepro_run_4) >> >> Do I miss something or is there in error in my pipeline or in my >> strategy >> >> Best regards >> >> Sascha >> >> >> _______________________________________________ >> 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 Wed Jul 11 10:20:58 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 11 Jul 2012 10:20:58 +0200 Subject: [FieldTrip] read_biosig_header.m In-Reply-To: <4FFC794D.40508@ucsd.edu> References: <4FFC794D.40508@ucsd.edu> Message-ID: <4FFD376A.8050206@donders.ru.nl> Dear Steve, Although I cannot help you directly and do not know about the specific error you got, you can find all code changes on http://code.google.com/p/fieldtrip/ For the biosig file you are referring to, please look here: http://code.google.com/p/fieldtrip/source/diff?path=/trunk/fileio/private/read_biosig_header.m&format=side&r=5429 (but as you can see, nothing changed there) Hope someone else can help out (Robert is on vacation right now, so maybe someone else can help) Best, Jörn On 7/10/2012 8:49 PM, Steve Deiss wrote: > The fieldtrip version we have calls function 'read_biosig_header' > which calls 'sopen' with the following sequence. > biosig = sopen(filename,'r'); > For some reason it loses the digital triggers on channel 1 in our data > after issuing the following warning: > > "Reading data file header... > WARNING SOPEN(EDF): Physical Max/Min values of EDF data are not > necessarily defining the dynamic range. > Hence, OVERFLOWDETECTION might not work correctly. See also > EEG2HIST and read > http://dx.doi.org/10.1016/S1388-2457(99)00172-8 (A. Schlgl et al. > Quality Control ... Clin. Neurophysiol. 1999, Dec; 110(12): 2165 - 2170). > A copy is available here, too: > http://www.dpmi.tugraz.at/schloegl/publications/neurophys1999_2165.pdf " > > If we let EEGLAB read the data, its function 'pop_biosig' calls > 'sopen' with > biosig = sopen(filename,'r',0,'OVERFLOWDETECTION:OFF'); > The data read in here includes the triggers so that we can go on to > epoch and process the data. > > We are not yet ready to upgrade to the very latest fieldtrip. So I > would like to know if there is an easy way to > determine if the latest version of fieldtrip changed anything in the > way sopen is called from read_biosig_header? > If it matches what EEGLAB does here, we can match that as a temporary > fix. > > I'll try to download and unpack it to see, but if this is a known > problem, fixed or not, I'd appreciate any tips. > > Thanks > Steve > _______________________________________________ > 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 jm.horschig at donders.ru.nl Wed Jul 11 10:30:58 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 11 Jul 2012 10:30:58 +0200 Subject: [FieldTrip] Importing '.mat' data in to fieldtrip In-Reply-To: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> References: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> Message-ID: <4FFD39C2.8030205@donders.ru.nl> Dear Roshan, 0) Welcome to FieldTrip ;) 1) FieldTrip usuaully reads in the stimulus channel and refers to the triggers as events. See also here: http://fieldtrip.fcdonders.nl/faq/what_is_the_relation_between_events_such_as_triggers_and_trials trialinfo can be used for that when you have segmented trials. Actually, there is no obligation how trialinfo should look like, you can put whatever information in that you want. I got stimulus trigger, stimulus offset sample, response sample, response trigger and some additional flags in there, so everything that facilitates in sorting trials according to some criteria. To find out what data you have, you can try to use ft_senstype 2) you might want to look at the Donders Machine Learning Toolbox, which is under external/dmlt. For the design, I assume it's an ordinary design matrix, so maybe you want to read the walkthrough and these tutorials: http://fieldtrip.fcdonders.nl/walkthrough?s[]=design#statistics http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock?s[]=design http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq?s[]=design Good luck with the data and have fun with FieldTrip. Best, Jörn On 7/11/2012 5:25 AM, Roshan Nair wrote: > Hi, > > I have MEG/EEG data in '.mat' format(Biomag 2012 data analysis dataset). > The data is already epoched. It was straightforward to convert it in to the > required fieldtrip structure - {label, fsample, trial, time} and run > ft_databrowser on it. No problems so far. > > However, I feel I might be going wrong with the following:- > 1. The trials include data for STI(stimulus) channels(I believe its an > Elekta Neuromag Vectorview 306 system)? Is there a 'fieldtrip' way to > represent this. Is this what 'data.trialinfo' is for? If so, how should I > populate the trialinfo field. > 2. The dataset comes with a file called 'design' with one entry(an > integer) per trial. This is the category of the > stimulus(living/non-living)presented to the subject for each trial. This is > the output my classifier will be trained on. I'm assuming fieldtrip has > some standard way of including this. I noticed, the multivariate analysis > mentions a parameter called 'design'. > > Sorry, if thats confusing, but, I'm new to fieldtrip and MEG data. > > Thanks! > > Roshan > _______________________________________________ > 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 Michael.Stephan at esi-frankfurt.de Wed Jul 11 11:40:17 2012 From: Michael.Stephan at esi-frankfurt.de (Michael Stephan) Date: Wed, 11 Jul 2012 11:40:17 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: <4FFD4A01.6090807@esi-frankfurt.de> Dear Eliana, if your data sets vary in size you should sort them according to size and then process them starting with the largest data set. -- Michael Stephan Ernst Strüngmann Institute for Neuroscience in Cooperation with Max Planck Society Deutschordenstraße 46 D-60528 Frankfurt am Main eMail: Michael.Stephan at esi-frankfurt.de > Hello Dear Fieldtrip Community, > > I am having now problems with processing my data. I am analyzing a quite > big data set with 400 trials that are composed by 10 sec (re-sampled at > 150Hz). I am doing first a demean, then planar gradient transformation, > time-frequency analysis using multitapers and then combine the planar > gradient again. For the first subject always runs normally, but for the > second one matlab gets really slow. I am taking care in deleting the > variables that I create with big amount of data after I don't need them > any more, so I am using just one big file that is being safe at the end > (average time-frequency across trials) for each of the subjects. Every > time matlab starts to analyze a new subject I am using clear all (with > exceptions like directory and name of subject) but stills with every new > subject it gets slower and slower. > > Do you have any advises to make the analysis faster? Sometimes is too > slow and the computer normally crashes after 3 subjects. > > Thank you very much for the attention. > > Best, > > -- > Eliana García Cossio > Applied Neurotechnology Lab. > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From irina.simanova at mpi.nl Wed Jul 11 17:20:41 2012 From: irina.simanova at mpi.nl (Irina Simanova) Date: Wed, 11 Jul 2012 17:20:41 +0200 Subject: [FieldTrip] freqstatistics ivar and uvar In-Reply-To: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> References: <84379fb72d9686dc72126f3a729882ff@sussex.ac.uk> Message-ID: <30D34709-7D37-4A58-9072-CBF708A78052@mpi.nl> Dear all, I have a very basic question on freqstatistics. I want to compare the TFR's in 3 experimental conditions over 12 subjects. I run the freqstatistics with cfg.method = 'depsamplesF'. cfg.uvar = 1 cfg.ivar = 2 cfg.design = [1:12 1:12 1:12; ones(1,12) 2*ones(1,12) 3*ones(1,12)] I am confused with the the following lines that FT prints out: repeated measurement in variable 1 over 12 levels number of repeated measurements in each level is 3 3 3 3 3 3 3 3 3 3 3 3 I assume it is correct, since it's exactly the same output as I get with the tutorial within-subjects statistics example. But why is not it the other way around? There are 3 levels of the independent variable, and the number of samples in each level is 12? Thank you! Best, Irina Here is the code: cfg = []; cfg.latency = [0 1.5]; cfg.channel = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesF'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.tail = 1; cfg.clustertail = 1; cfg.alpha = 0.05; cfg.numrandomization = 100; cfg.neighbours = neighbours; cfg.parameter = 'powspctrm'; cfg.design = design; cfg.uvar = 1; cfg.ivar = 2; [stat] = ft_freqstatistics(cfg, TFRgrand_1, TFRgrand_2, TFRgrand_3); computing statistic over the frequency range [3.962 39.937] computing statistic over the time range [0.000 1.500] selection powspctrm along dimension 2 selection powspctrm along dimension 3 selection powspctrm along dimension 4 using "ft_statistics_montecarlo" for the statistical testing using "statfun_depsamplesF" for the single-sample statistics constructing randomized design total number of measurements = 36 total number of variables = 2 number of independent variables = 1 number of unit variables = 1 number of within-cell variables = 0 number of control variables = 0 using a permutation resampling approach repeated measurement in variable 1 over 12 levels number of repeated measurements in each level is 3 3 3 3 3 3 3 3 3 3 3 3 computing a parametric threshold for clustering computing statistic From Bill.Budd at newcastle.edu.au Thu Jul 12 01:33:38 2012 From: Bill.Budd at newcastle.edu.au (Bill Budd) Date: Thu, 12 Jul 2012 09:33:38 +1000 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: Message-ID: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Hi Eliana I see something similar when using SPM8 to process data. I’ve heard that this might be because SPM8 uses fieldtrip functions to import my continuous EEG files (Biosemi/bdf) and these functions may not release memory in matlab after closing. When looping my preprocessing functions over multiple subjects I have the exactly same problem in SPM that you see in fieldtrip. This may not be causing your problem (or mine) but wondered if the processing your refer to also involves importing raw MEG data? The PCs I’m using have plenty of RAM/disk space (Win7/matlab 2011b). Be great to find a solution to this as it slows done processing multi subject data significantly! Cheers -Bill From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eliana Garcia Sent: Wednesday, 11 July 2012 2:40 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] problems with speed of processing Dear Stephen, Thanks for the suggestion. I have already one function that is doing all the preprocessing and saving as well. But this seams not to solve the issue. Thanks, Eliana On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh wrote: Dear Eliana, You could try creating a function that does all this preprocessing and then writes the output to file. If you then call this function in a (subject) loop you are sure that Matlab will free up the memory it used for that function. Perhaps it helps, Stephen On 10 July 2012 16:57, Eliana Garcia wrote: Hello Dear Fieldtrip Community, I am having now problems with processing my data. I am analyzing a quite big data set with 400 trials that are composed by 10 sec (re-sampled at 150Hz). I am doing first a demean, then planar gradient transformation, time-frequency analysis using multitapers and then combine the planar gradient again. For the first subject always runs normally, but for the second one matlab gets really slow. I am taking care in deleting the variables that I create with big amount of data after I don't need them any more, so I am using just one big file that is being safe at the end (average time-frequency across trials) for each of the subjects. Every time matlab starts to analyze a new subject I am using clear all (with exceptions like directory and name of subject) but stills with every new subject it gets slower and slower. Do you have any advises to make the analysis faster? Sometimes is too slow and the computer normally crashes after 3 subjects. Thank you very much for the attention. Best, -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany _______________________________________________ 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 -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Jul 12 08:17:48 2012 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Thu, 12 Jul 2012 08:17:48 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> References: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Message-ID: Hi, Please, note that "clear all" clears variables, but does not free up memory, especially for files read from disk. You can check the memory usage with the command "top" in Linux command line. You'll see that nothing changes even if you use "clear all". I agree with Stephen that you need to write smaller functions for each subjects. Something like: for i = 1:numel(subj) do_analysis(subj) end Where "do_analysis.m" is a function you wrote to do all the analysis. In this way, Matlab takes care of memory management by itself (it frees the memory once the function has been executed). A more elaborate solution is to use the "qsub" functions included in fieldtrip. Try this: addpath /path/to/fieldtrip/qsub fname = 'do_analysis'; subj = {1, 2, 3, 4, 5}; qsubcellfun(fname, x1, 'memreq', 1024^3, 'timreq', 60*60, 'backend', 'local'); This will start a new Matlab session (and use a new Matlab license) and it will close it when the function has been executed. There should be no memory leaks at all. See "help qsubcellfun" for more info. Remember to use 'backend' 'local' unless you have access to Oracle Grid Engine or Torque. Hope this helps. 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, Jul 12, 2012 at 1:33 AM, Bill Budd wrote: > Hi Eliana > > > > I see something similar when using SPM8 to process data. I’ve heard that > this might be because SPM8 uses fieldtrip functions to import my continuous > EEG files (Biosemi/bdf) and these functions may not release memory in matlab > after closing. When looping my preprocessing functions over multiple > subjects I have the exactly same problem in SPM that you see in fieldtrip. > This may not be causing your problem (or mine) but wondered if the > processing your refer to also involves importing raw MEG data? > > > > The PCs I’m using have plenty of RAM/disk space (Win7/matlab 2011b). > > > > Be great to find a solution to this as it slows done processing multi > subject data significantly! > > > > Cheers > > > > -Bill > > > > > > From: fieldtrip-bounces at science.ru.nl > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eliana Garcia > Sent: Wednesday, 11 July 2012 2:40 AM > To: FieldTrip discussion list > Subject: Re: [FieldTrip] problems with speed of processing > > > > Dear Stephen, > > > > Thanks for the suggestion. I have already one function that is doing all the > preprocessing and saving as well. But this seams not to solve the issue. > > > > Thanks, > > Eliana > > > > On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh > wrote: > > Dear Eliana, > > > > You could try creating a function that does all this preprocessing and then > writes the output to file. > > If you then call this function in a (subject) loop you are sure that Matlab > will free up the memory it used for that function. > > > > Perhaps it helps, > > > > Stephen > > > > On 10 July 2012 16:57, Eliana Garcia wrote: > > Hello Dear Fieldtrip Community, > > > > I am having now problems with processing my data. I am analyzing a quite big > data set with 400 trials that are composed by 10 sec (re-sampled at 150Hz). > I am doing first a demean, then planar gradient transformation, > time-frequency analysis using multitapers and then combine the planar > gradient again. For the first subject always runs normally, but for the > second one matlab gets really slow. I am taking care in deleting the > variables that I create with big amount of data after I don't need them any > more, so I am using just one big file that is being safe at the end (average > time-frequency across trials) for each of the subjects. Every time matlab > starts to analyze a new subject I am using clear all (with exceptions like > directory and name of subject) but stills with every new subject it gets > slower and slower. > > > > Do you have any advises to make the analysis faster? Sometimes is too slow > and the computer normally crashes after 3 subjects. > > > > Thank you very much for the attention. > > > > Best, > > > > -- > > Eliana García Cossio > Applied Neurotechnology Lab. > > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > > > > _______________________________________________ > 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 > > > > > > -- > > Eliana García Cossio > Applied Neurotechnology Lab. > > Graduate School of Neural and Behavioural Science - Max Planck Research > School > Institute of Medical Psychology and Behavioural Neurobiology > Universität Tübingen > > (+0049) 01 577-8587604 > Otfried-Müller-Str. 47, 72076 > Tübingen- Germany > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From d.oudebos at gmail.com Thu Jul 12 11:15:07 2012 From: d.oudebos at gmail.com (Danny Plass-Oude Bos) Date: Thu, 12 Jul 2012 11:15:07 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? Message-ID: Hi Fieldtrippers, I am using the stand-alone fieldtripbuffer emotiv2ft, in combination with python for signal analysis. As far as I understand, you can only use one Emotiv EPOC with this implementation. I'd like to use multiple epocs at the some time, and preferably on the same computer. Does anybody know if this is possible somehow with emotiv2ft? Or does anybody has other experience / ideas on this problem? Kind regards, Danny. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elilife at gmail.com Thu Jul 12 12:00:02 2012 From: elilife at gmail.com (Eliana Garcia) Date: Thu, 12 Jul 2012 12:00:02 +0200 Subject: [FieldTrip] problems with speed of processing In-Reply-To: References: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Message-ID: Thank you all for this interesting advices. I am not using Fieldtrip in this case to read the raw data (for this I am using a function from BCI2000), just for signal processing. The qsubcellfun function is new for me. I will implement it, this will solve the problem of memory as Giovanni mentioned. Thanks again, Eliana On Thu, Jul 12, 2012 at 8:17 AM, Gio Piantoni wrote: > Hi, > > Please, note that "clear all" clears variables, but does not free up > memory, especially for files read from disk. You can check the memory > usage with the command "top" in Linux command line. You'll see that > nothing changes even if you use "clear all". > I agree with Stephen that you need to write smaller functions for each > subjects. Something like: > > for i = 1:numel(subj) > do_analysis(subj) > end > Where "do_analysis.m" is a function you wrote to do all the analysis. > In this way, Matlab takes care of memory management by itself (it > frees the memory once the function has been executed). > > A more elaborate solution is to use the "qsub" functions included in > fieldtrip. Try this: > addpath /path/to/fieldtrip/qsub > fname = 'do_analysis'; > subj = {1, 2, 3, 4, 5}; > qsubcellfun(fname, x1, 'memreq', 1024^3, 'timreq', 60*60, 'backend', > 'local'); > > This will start a new Matlab session (and use a new Matlab license) > and it will close it when the function has been executed. There should > be no memory leaks at all. See "help qsubcellfun" for more info. > Remember to use 'backend' 'local' unless you have access to Oracle > Grid Engine or Torque. > > Hope this helps. > 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, Jul 12, 2012 at 1:33 AM, Bill Budd > wrote: > > Hi Eliana > > > > > > > > I see something similar when using SPM8 to process data. I’ve heard that > > this might be because SPM8 uses fieldtrip functions to import my > continuous > > EEG files (Biosemi/bdf) and these functions may not release memory in > matlab > > after closing. When looping my preprocessing functions over multiple > > subjects I have the exactly same problem in SPM that you see in > fieldtrip. > > This may not be causing your problem (or mine) but wondered if the > > processing your refer to also involves importing raw MEG data? > > > > > > > > The PCs I’m using have plenty of RAM/disk space (Win7/matlab 2011b). > > > > > > > > Be great to find a solution to this as it slows done processing multi > > subject data significantly! > > > > > > > > Cheers > > > > > > > > -Bill > > > > > > > > > > > > From: fieldtrip-bounces at science.ru.nl > > [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eliana Garcia > > Sent: Wednesday, 11 July 2012 2:40 AM > > To: FieldTrip discussion list > > Subject: Re: [FieldTrip] problems with speed of processing > > > > > > > > Dear Stephen, > > > > > > > > Thanks for the suggestion. I have already one function that is doing all > the > > preprocessing and saving as well. But this seams not to solve the issue. > > > > > > > > Thanks, > > > > Eliana > > > > > > > > On Tue, Jul 10, 2012 at 6:01 PM, Stephen Whitmarsh > > wrote: > > > > Dear Eliana, > > > > > > > > You could try creating a function that does all this preprocessing and > then > > writes the output to file. > > > > If you then call this function in a (subject) loop you are sure that > Matlab > > will free up the memory it used for that function. > > > > > > > > Perhaps it helps, > > > > > > > > Stephen > > > > > > > > On 10 July 2012 16:57, Eliana Garcia wrote: > > > > Hello Dear Fieldtrip Community, > > > > > > > > I am having now problems with processing my data. I am analyzing a quite > big > > data set with 400 trials that are composed by 10 sec (re-sampled at > 150Hz). > > I am doing first a demean, then planar gradient transformation, > > time-frequency analysis using multitapers and then combine the planar > > gradient again. For the first subject always runs normally, but for the > > second one matlab gets really slow. I am taking care in deleting the > > variables that I create with big amount of data after I don't need them > any > > more, so I am using just one big file that is being safe at the end > (average > > time-frequency across trials) for each of the subjects. Every time matlab > > starts to analyze a new subject I am using clear all (with exceptions > like > > directory and name of subject) but stills with every new subject it gets > > slower and slower. > > > > > > > > Do you have any advises to make the analysis faster? Sometimes is too > slow > > and the computer normally crashes after 3 subjects. > > > > > > > > Thank you very much for the attention. > > > > > > > > Best, > > > > > > > > -- > > > > Eliana García Cossio > > Applied Neurotechnology Lab. > > > > Graduate School of Neural and Behavioural Science - Max Planck Research > > School > > Institute of Medical Psychology and Behavioural Neurobiology > > Universität Tübingen > > > > (+0049) 01 577-8587604 > > Otfried-Müller-Str. 47, 72076 > > Tübingen- Germany > > > > > > > > > > > > _______________________________________________ > > 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 > > > > > > > > > > > > -- > > > > Eliana García Cossio > > Applied Neurotechnology Lab. > > > > Graduate School of Neural and Behavioural Science - Max Planck Research > > School > > Institute of Medical Psychology and Behavioural Neurobiology > > Universität Tübingen > > > > (+0049) 01 577-8587604 > > Otfried-Müller-Str. 47, 72076 > > Tübingen- Germany > > > > > > > > > > _______________________________________________ > > 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 > -- Eliana García Cossio Applied Neurotechnology Lab. Graduate School of Neural and Behavioural Science - Max Planck Research School Institute of Medical Psychology and Behavioural Neurobiology Universität Tübingen (+0049) 01 577-8587604 Otfried-Müller-Str. 47, 72076 Tübingen- Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabian.tomaschek at uni-tuebingen.de Thu Jul 12 15:25:11 2012 From: fabian.tomaschek at uni-tuebingen.de (=?iso-8859-1?Q?Fabian_Tomaschek_-_Universit=E4t_T=FCbingen?=) Date: Thu, 12 Jul 2012 15:25:11 +0200 Subject: [FieldTrip] Problems with "ft_megplanar" and fourier spectra. In-Reply-To: References: <03e101cd5fbd$98fd57d0$caf80770$@newcastle.edu.au> Message-ID: <001501cd6031$c3f352e0$4bd9f8a0$@tomaschek@uni-tuebingen.de> Hi All, I’m currently performing a timefrequency analyis and its statistics as described on "http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis?s[]=wavelet&s[ ]=analysis" and "http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq". I got to the point where I should do "ft_megplanar" with my data. However, an error saying "'freq data should contain Fourier spectra'" occurs. Looking into the function, I saw that it requires a field called "fourierspctrm". However, I do not know where to get that field. Nor does "http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq" say anything about fourier spectra. Do you know any help? Thanks a lot. Fabian Es grüßt aus Tübingen Fabian Tomaschek -------------------------------------------------- -------------------------------------------------- Mobil: 0178 6312772 Institute: 07071 29-87529 Dept of Neurology University of Tuebingen Hoppe-Seyler-Str. 3 D-72076 Tuebingen -------------------------------------------------- -------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdeiss at ucsd.edu Thu Jul 12 19:01:14 2012 From: sdeiss at ucsd.edu (Steve Deiss) Date: Thu, 12 Jul 2012 10:01:14 -0700 Subject: [FieldTrip] read_biosig_header.m In-Reply-To: <4FFD376A.8050206@donders.ru.nl> References: <4FFC794D.40508@ucsd.edu> <4FFD376A.8050206@donders.ru.nl> Message-ID: <4FFF02DA.1090802@ucsd.edu> Thanks for this note. Changing the call in read_biosig_header and read_biosig_data does make the problem go away, ie., the digital trigger channel is not zeroed. I do not know what other side effects there could be. So I am a little wary. Steve On 07/11/12 01:20, "Jörn M. Horschig" wrote: > Dear Steve, > > Although I cannot help you directly and do not know about the specific > error you got, you can find all code changes on > http://code.google.com/p/fieldtrip/ > > For the biosig file you are referring to, please look here: > http://code.google.com/p/fieldtrip/source/diff?path=/trunk/fileio/private/read_biosig_header.m&format=side&r=5429 > > (but as you can see, nothing changed there) > > Hope someone else can help out (Robert is on vacation right now, so > maybe someone else can help) > > Best, > Jörn > > On 7/10/2012 8:49 PM, Steve Deiss wrote: >> The fieldtrip version we have calls function 'read_biosig_header' >> which calls 'sopen' with the following sequence. >> biosig = sopen(filename,'r'); >> For some reason it loses the digital triggers on channel 1 in our >> data after issuing the following warning: >> >> "Reading data file header... >> WARNING SOPEN(EDF): Physical Max/Min values of EDF data are not >> necessarily defining the dynamic range. >> Hence, OVERFLOWDETECTION might not work correctly. See also >> EEG2HIST and read >> http://dx.doi.org/10.1016/S1388-2457(99)00172-8 (A. Schlgl et al. >> Quality Control ... Clin. Neurophysiol. 1999, Dec; 110(12): 2165 - >> 2170). >> A copy is available here, too: >> http://www.dpmi.tugraz.at/schloegl/publications/neurophys1999_2165.pdf " >> >> If we let EEGLAB read the data, its function 'pop_biosig' calls >> 'sopen' with >> biosig = sopen(filename,'r',0,'OVERFLOWDETECTION:OFF'); >> The data read in here includes the triggers so that we can go on to >> epoch and process the data. >> >> We are not yet ready to upgrade to the very latest fieldtrip. So I >> would like to know if there is an easy way to >> determine if the latest version of fieldtrip changed anything in the >> way sopen is called from read_biosig_header? >> If it matches what EEGLAB does here, we can match that as a temporary >> fix. >> >> I'll try to download and unpack it to see, but if this is a known >> problem, fixed or not, I'd appreciate any tips. >> >> Thanks >> Steve >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Steve Deiss, M.Sc. MMIL Lab (Dale and Halgren), UCSD, La Jolla, CA, USA Neuroimaging Research Associate 858-246-1194 From b.reuderink at donders.ru.nl Fri Jul 13 07:48:52 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 13 Jul 2012 07:48:52 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? In-Reply-To: References: Message-ID: Hi Danny, How do you want to use multiple Emotivs? Do you want to stream them to one buffer in a synchronized manner, do you want your application to access two buffers, one for each Emotiv? The latter is more feasible I think, and could be implemented using two computers. I think one of the main issues would be connecting a FieldTrip buffer to a specific Emotiv headset if multiple receiver dongles are present on one computer. Best, Boris On Thu, Jul 12, 2012 at 11:15 AM, Danny Plass-Oude Bos wrote: > Hi Fieldtrippers, > > I am using the stand-alone fieldtripbuffer emotiv2ft, in combination with > python for signal analysis. > As far as I understand, you can only use one Emotiv EPOC with this > implementation. I'd like to use multiple epocs at the some time, and > preferably on the same computer. > Does anybody know if this is possible somehow with emotiv2ft? Or does > anybody has other experience / ideas on this problem? > > Kind regards, > > Danny. > > _______________________________________________ > 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 d.oudebos at gmail.com Fri Jul 13 09:39:58 2012 From: d.oudebos at gmail.com (Danny Plass-Oude Bos) Date: Fri, 13 Jul 2012 09:39:58 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? In-Reply-To: References: Message-ID: Hi Boris :) For me it doesn't matter if it is one buffer or multiple, as long as I can get the data, and know from which head set it is -- I'm not sure if the current buffer supports that kind of thing? The reason why I'd prefer not to have one computer for each head set, is because I'd like to use 8 head sets... Emotiv's own software can deal with multiple head sets. You can start up multiple control panels, and select which device it should listen to. So far, I have not been able to discover how to do a similar thing from the Emotiv SDK, however -- I guess that is also what you people would need to know to get the buffer working for multiple sets? Best, Danny. 2012/7/13 Boris Reuderink > Hi Danny, > > How do you want to use multiple Emotivs? Do you want to stream them to > one buffer in a synchronized manner, do you want your application to > access two buffers, one for each Emotiv? The latter is more feasible I > think, and could be implemented using two computers. > > I think one of the main issues would be connecting a FieldTrip buffer > to a specific Emotiv headset if multiple receiver dongles are present > on one computer. > > Best, > > Boris > > On Thu, Jul 12, 2012 at 11:15 AM, Danny Plass-Oude Bos > wrote: > > Hi Fieldtrippers, > > > > I am using the stand-alone fieldtripbuffer emotiv2ft, in combination with > > python for signal analysis. > > As far as I understand, you can only use one Emotiv EPOC with this > > implementation. I'd like to use multiple epocs at the some time, and > > preferably on the same computer. > > Does anybody know if this is possible somehow with emotiv2ft? Or does > > anybody has other experience / ideas on this problem? > > > > Kind regards, > > > > Danny. > > > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Fri Jul 13 12:20:38 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Fri, 13 Jul 2012 12:20:38 +0200 Subject: [FieldTrip] multiple emotivs on one pc with the fieldtripbuffer ? In-Reply-To: References: Message-ID: Whoa, 8 :). Okay. I was thinking of starting an emotiv2ft per headset somehow, but with 8 headsets that gets tedious and error-prone. Let's discuss a more principled solution in person. On Fri, Jul 13, 2012 at 9:39 AM, Danny Plass-Oude Bos wrote: > Hi Boris :) > > For me it doesn't matter if it is one buffer or multiple, as long as I can > get the data, and know from which head set it is -- I'm not sure if the > current buffer supports that kind of thing? > The reason why I'd prefer not to have one computer for each head set, is > because I'd like to use 8 head sets... > > Emotiv's own software can deal with multiple head sets. You can start up > multiple control panels, and select which device it should listen to. > So far, I have not been able to discover how to do a similar thing from the > Emotiv SDK, however -- I guess that is also what you people would need to > know to get the buffer working for multiple sets? > > Best, > > Danny. > > > > 2012/7/13 Boris Reuderink >> >> Hi Danny, >> >> How do you want to use multiple Emotivs? Do you want to stream them to >> one buffer in a synchronized manner, do you want your application to >> access two buffers, one for each Emotiv? The latter is more feasible I >> think, and could be implemented using two computers. >> >> I think one of the main issues would be connecting a FieldTrip buffer >> to a specific Emotiv headset if multiple receiver dongles are present >> on one computer. >> >> Best, >> >> Boris >> >> On Thu, Jul 12, 2012 at 11:15 AM, Danny Plass-Oude Bos >> wrote: >> > Hi Fieldtrippers, >> > >> > I am using the stand-alone fieldtripbuffer emotiv2ft, in combination >> > with >> > python for signal analysis. >> > As far as I understand, you can only use one Emotiv EPOC with this >> > implementation. I'd like to use multiple epocs at the some time, and >> > preferably on the same computer. >> > Does anybody know if this is possible somehow with emotiv2ft? Or does >> > anybody has other experience / ideas on this problem? >> > >> > Kind regards, >> > >> > Danny. >> > >> > _______________________________________________ >> > 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 > > > > _______________________________________________ > 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 vitoria.piai at gmail.com Fri Jul 13 15:07:10 2012 From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=) Date: Fri, 13 Jul 2012 15:07:10 +0200 Subject: [FieldTrip] timelockgrandaverage on planar gradients Message-ID: <50001D7E.9010609@gmail.com> Dear all, Until some weeks ago, I used to proceed with the following steps to compute ERFs: % For each subject dat = ft_preprocessing(cfgp, input); dat = ft_timelockanalysis(cfgtl, dat); cfg.method = 'template'; cfg.neighbours = ft_prepare_neighbours(cfg, dat); cfg.planarmethod = 'sincos'; cond = ft_megplanar(cfg, dat) cplanar{suj} = ft_combineplanar([], cond); ga = ft_timelockgrandaverage([], cplanar{:}); I excluded some channels for some subjects. I re-ran this script and now I'm left only with the channels that are common to all subjects. (I'm using the DCCN internal fieldtrip version). But I'm pretty sure it used to work until some time ago such that in the GA, I had all the planar gradients still. I understand where it comes from, coz I get the warning that gradiometer info is being discarded coz it cannot be averaged. I've found a previous post that came close (but still not there yet): http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003471.html But I'm not being able to understand the explanation in the tutorial about how to proceed: "Before calculating the grand average the data of each subject can be realigned to standard sensor positions with *ft_megrealign *", but then it's unclear to me what cfg.template should be when using ft_megrealign. So I tried (suggested by JM from another previous post) /"Alternatively, you could construct a gradiometer structure which //contains a meaningful average of the coil positions and orientations." / I made a grad in which grad.chanpos was an average of my participants [302x3]. I tried cfg.template = grad; cfg.template = grad.chanpos; cfg.template = grad.chanori; but I'm probably doing something wrong coz it didn't work still. In all three cases, the error is in ft_megrealign at 174 "cell contents reference from a non-cell array object". So I guess my questions are: - what should the template be? What am I doing wrong? - do I need to make a grad structure myself with all the averages or will the template do, once I get it right? Thanx loads, Vitória -- ** Please consider the environment - do you really need to print? ** -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.reuderink at donders.ru.nl Mon Jul 16 12:20:57 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Mon, 16 Jul 2012 12:20:57 +0200 Subject: [FieldTrip] Improvements in FieldTrip's real-time processing Message-ID: Dear FieldTrippers, I would like to bring to you attention that we have reorganzed and improved FieldTrip's programs for acquisition and real-time signal processing. The most important change for users is the new directory structure. For each platform, we now have a directory containing all the executables for that platform*: - realtime/bin/win32 for Windows, - realtime/bin/glnxa64 for Linux (64 bit), - realtime/bin/maci64 for OS-X (64 bit). To get started with real-time processing, you can take a look at the examples (http://fieldtrip.fcdonders.nl/development/realtime#example_scripts) and the background information (http://fieldtrip.fcdonders.nl/development/realtime) on the FieldTrip wiki. Besides restructuring the file layout, we have fixed a number of bugs, most notable being: - bug #1525 duplicated samples with low-latency settings [1], - bug #933 freezing buffer server due to deadlock in threading [2], - bug #1246 incorrect reading of configuration scripts [3], - bug #1020 memory problem in event handling [4]. We strongly recommend to download a fresh release of FieldTrip (http://fieldtrip.fcdonders.nl/download), and use the files from this new version. Best regards, Boris Reuderink [1] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1525 [2] http://bugzilla.fcdonders.nl/show_bug.cgi?id=933 [3] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1246 [4] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1020 * Please note that for now, the neuromag files are still in realtime/src/acquisition/neuromag/bin . -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From profabdo at gmail.com Mon Jul 16 13:33:20 2012 From: profabdo at gmail.com (Prof. Abdalla Mohamed) Date: Mon, 16 Jul 2012 13:33:20 +0200 Subject: [FieldTrip] Improvements in FieldTrip's real-time processing In-Reply-To: References: Message-ID: Dear Sir, I am not able to download fresh release FieldTrip and I got error of invalid e-mail address. Please may help me. Thanking you,we remain. Prof. Abdalla Mohamed, Systems & Biomedical Engineering Dept., Cairo University, Egypt. On Mon, Jul 16, 2012 at 12:20 PM, Boris Reuderink wrote: > Dear FieldTrippers, > > I would like to bring to you attention that we have reorganzed and > improved FieldTrip's programs for acquisition and real-time signal > processing. > > The most important change for users is the new directory structure. > For each platform, we now have a directory containing all the > executables for that platform*: > - realtime/bin/win32 for Windows, > - realtime/bin/glnxa64 for Linux (64 bit), > - realtime/bin/maci64 for OS-X (64 bit). > > To get started with real-time processing, you can take a look at the > examples ( > http://fieldtrip.fcdonders.nl/development/realtime#example_scripts) > and the background information > (http://fieldtrip.fcdonders.nl/development/realtime) on the FieldTrip > wiki. > > Besides restructuring the file layout, we have fixed a number of bugs, > most notable being: > - bug #1525 duplicated samples with low-latency settings [1], > - bug #933 freezing buffer server due to deadlock in threading [2], > - bug #1246 incorrect reading of configuration scripts [3], > - bug #1020 memory problem in event handling [4]. > > We strongly recommend to download a fresh release of FieldTrip > (http://fieldtrip.fcdonders.nl/download), and use the files from this > new version. > > Best regards, > > Boris Reuderink > > [1] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1525 > [2] http://bugzilla.fcdonders.nl/show_bug.cgi?id=933 > [3] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1246 > [4] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1020 > > > * Please note that for now, the neuromag files are still in > realtime/src/acquisition/neuromag/bin . > > -- > twitter.com/#!/breuderink | > github.com/breuderink | borisreuderink.nl > _______________________________________________ > 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 b.reuderink at donders.ru.nl Mon Jul 16 15:01:15 2012 From: b.reuderink at donders.ru.nl (Boris Reuderink) Date: Mon, 16 Jul 2012 15:01:15 +0200 Subject: [FieldTrip] Improvements in FieldTrip's real-time processing In-Reply-To: References: Message-ID: Dear Prof. Abdalla Mohamed, I just tried to download FieldTrip, and supplied a fake email address from http://10minutemail.com/ (as suggested on http://fieldtrip.fcdonders.nl/download.php), and I can download FieldTrip just fine. Perhaps you could try with a fake email adress as well? Best regards, Boris Reuderink On Mon, Jul 16, 2012 at 1:33 PM, Prof. Abdalla Mohamed wrote: > Dear Sir, > I am not able to download fresh release FieldTrip and I got error of invalid > e-mail address. > Please may help me. > Thanking you,we remain. > Prof. Abdalla Mohamed, > Systems & Biomedical Engineering Dept., > Cairo University, Egypt. > > On Mon, Jul 16, 2012 at 12:20 PM, Boris Reuderink > wrote: >> >> Dear FieldTrippers, >> >> I would like to bring to you attention that we have reorganzed and >> improved FieldTrip's programs for acquisition and real-time signal >> processing. >> >> The most important change for users is the new directory structure. >> For each platform, we now have a directory containing all the >> executables for that platform*: >> - realtime/bin/win32 for Windows, >> - realtime/bin/glnxa64 for Linux (64 bit), >> - realtime/bin/maci64 for OS-X (64 bit). >> >> To get started with real-time processing, you can take a look at the >> examples >> (http://fieldtrip.fcdonders.nl/development/realtime#example_scripts) >> and the background information >> (http://fieldtrip.fcdonders.nl/development/realtime) on the FieldTrip >> wiki. >> >> Besides restructuring the file layout, we have fixed a number of bugs, >> most notable being: >> - bug #1525 duplicated samples with low-latency settings [1], >> - bug #933 freezing buffer server due to deadlock in threading [2], >> - bug #1246 incorrect reading of configuration scripts [3], >> - bug #1020 memory problem in event handling [4]. >> >> We strongly recommend to download a fresh release of FieldTrip >> (http://fieldtrip.fcdonders.nl/download), and use the files from this >> new version. >> >> Best regards, >> >> Boris Reuderink >> >> [1] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1525 >> [2] http://bugzilla.fcdonders.nl/show_bug.cgi?id=933 >> [3] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1246 >> [4] http://bugzilla.fcdonders.nl/show_bug.cgi?id=1020 >> >> >> * Please note that for now, the neuromag files are still in >> realtime/src/acquisition/neuromag/bin . >> >> -- >> twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl >> >> _______________________________________________ >> 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 -- twitter.com/#!/breuderink | github.com/breuderink | borisreuderink.nl From m.vandenieuwenhuijzen at fcdonders.ru.nl Mon Jul 16 19:03:57 2012 From: m.vandenieuwenhuijzen at fcdonders.ru.nl (Marieke van de Nieuwenhuijzen) Date: Mon, 16 Jul 2012 19:03:57 +0200 (CEST) Subject: [FieldTrip] graphical problem with ft_sourceplot In-Reply-To: <668686231.1061677.1342456205553.JavaMail.root@draco.zimbra.ru.nl> Message-ID: <805894218.1061785.1342458237893.JavaMail.root@draco.zimbra.ru.nl> Dear all, I am trying to use ft_sourceplot to plot modelvalues ranging from negative to positive. The blobs of interest are the ones close to both the positive and negative extremes, so I want to mask the values surrounding zero. However, I can't seem to mask these values properly. The code I'm using is: cfg = []; cfg.method = 'slice'; cfg.funparameter = 'model'; cfg.maskparameter = cfg.funparameter cfg.colorlim = 'maxabs'; cfg.opacitymap = 'vdown' cfg.opacitylim = 'maxabs'; figure; ft_sourceplot(cfg,sourceInterpolated); Although this code masks the values around zero, it only plots the underlying MRI scan partially. It looks like only those voxels of the MRI scan that contain gridpoints which are located inside the brain according to grid_singleshell.inside are plotted in the underlying MRI. In fact, this is exactly how I would expect the functional overlay to behave (which it does), but not the underlying MRI scan. If I set cfg.opavitymap to 'rampup' I don't get this graphical glitch, i.e. the anatomical MRI scan is plotted completely. However, as this doesn't mask the zero values, using this setting is not an option for me. I am aware of the artefacts that can occur when using opacity. However, setting the renderer to zbuffer doesn't solve the problem at all. In fact, if I do this the anatomical scan isn't plotted at all, and the zero values are not masked. If I specify cfg.method as 'ortho' instead of 'slice', the resulting plot looks good (the complete anatomical MRI is plotted and the values around zero are masked), apart from some green line pieces surrounding the brain. Setting the renderer to zbuffer here does seem to get rid of those lines, but ignores the masking of the values around zero. Does any of you perhaps know how to get rid of the glitch (if it is indeed a glitch) when using the aforementioned code? Best, Marieke From hgould at memphis.edu Tue Jul 17 14:36:26 2012 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 17 Jul 2012 12:36:26 +0000 Subject: [FieldTrip] mexw files Message-ID: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com> I have just found fieldtrip and have started to work on the tutorial. I am trying to read the data for subject 1 in the tutorial and recieve the following error: cfg1 = ft_definetrial(cfg1); Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20120715\private\warning_once at 75 In ft_defaults at 91 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > In ft_defaults at 99 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > In ft_defaults at 99 In ft_definetrial at 111 ??? Invalid MEX-file 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); I have checked and the .mexw32 file is there What am I doing wrong? Herb Gould -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Tue Jul 17 15:04:26 2012 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Tue, 17 Jul 2012 15:04:26 +0200 (CEST) Subject: [FieldTrip] mexw files In-Reply-To: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com> Message-ID: <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> Hi Herbert, It seems you have multiple versions of SPM on your path, which may confuse FieldTrip. Could you try inserting the commands below in the matlab command window, before inserting the tutorial code? Best regards, Arjen restoredefaultpath addpath C:\FieldTrip\fieldtrip-20120715 ft_defaults ----- Oorspronkelijk bericht ----- > Van: "Herbert J Gould (hgould)" > Aan: fieldtrip at science.ru.nl > Verzonden: Dinsdag 17 juli 2012 14:36:26 > Onderwerp: [FieldTrip] mexw files > I have just found fieldtrip and have started to work on the tutorial. > I am trying to read the data for subject 1 in the tutorial and recieve > the following error: >   > cfg1         = ft_definetrial(cfg1); > Warning: multiple versions of SPM on your path will confuse FieldTrip > > In fieldtrip-20120715\private\warning_once at 75 >   In ft_defaults at 91 >   In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > > In ft_defaults at 99 >   In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > > In ft_defaults at 99 >   In ft_definetrial at 111 > ??? Invalid MEX-file > 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified > procedure could not be found. > . > Error in ==> ft_checkconfig at 71 > renamed         = ft_getopt(varargin, 'renamed'); > Error in ==> ft_definetrial at 116 > cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); >   > I have checked and the .mexw32 file is there What am I doing wrong? >   > Herb Gould > _______________________________________________ > 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 hgould at memphis.edu Tue Jul 17 15:22:47 2012 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 17 Jul 2012 13:22:47 +0000 Subject: [FieldTrip] mexw files In-Reply-To: <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> References: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com>, <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com> Dear Arjen, Thank you that took care of the SPM issue but it still leaves the .mexw32 issue. However it now is looking for the file in a different location >> restoredefaultpath >> addpath c:\FieldTrip\fieldtrip-20120715 >> ft_defaults ??? Invalid MEX-file 'c:\FieldTrip\fieldtrip-20120715\utilities\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); Error in ==> tutorial1 at 8 cfg1 = ft_definetrial(cfg1); >> Herb Gould ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, July 17, 2012 8:04 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] mexw files Hi Herbert, It seems you have multiple versions of SPM on your path, which may confuse FieldTrip. Could you try inserting the commands below in the matlab command window, before inserting the tutorial code? Best regards, Arjen restoredefaultpath addpath C:\FieldTrip\fieldtrip-20120715 ft_defaults ________________________________ Van: "Herbert J Gould (hgould)" Aan: fieldtrip at science.ru.nl Verzonden: Dinsdag 17 juli 2012 14:36:26 Onderwerp: [FieldTrip] mexw files I have just found fieldtrip and have started to work on the tutorial. I am trying to read the data for subject 1 in the tutorial and recieve the following error: cfg1 = ft_definetrial(cfg1); Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20120715\private\warning_once at 75 In ft_defaults at 91 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > In ft_defaults at 99 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > In ft_defaults at 99 In ft_definetrial at 111 ??? Invalid MEX-file 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); I have checked and the .mexw32 file is there What am I doing wrong? Herb Gould _______________________________________________ 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 jm.horschig at donders.ru.nl Tue Jul 17 15:47:43 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 17 Jul 2012 15:47:43 +0200 Subject: [FieldTrip] mexw files In-Reply-To: <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com> References: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com>, <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com> Message-ID: <50056CFF.7080103@donders.ru.nl> Dear Herb, it seems like the mex-file you are using is corrupt. Either it is from a corrupt download (in which case you'd need to download fieldtrip once more) or there is, or there is some other incompatibility between your windows/matlab combination that we have not encountered. Could you try downloading FieldTrip again and see whether the error persists? If it does persist, you could go to the src/ directory and type 'mex ft_getopt.c' to re-mex the file (in Matlab). Then copy the mexw32 file from that folder to utilities/. This is not an optimal solution, because you will probably encounter similar issues with other mexw32 files. If that works for you, it would be nice if you sent me (or someone else from the dev team) the file so that we can check whether the file is indeed different. Either way, please let us know whether (and if so how) you can resolve the problem. Best, Jörn On 7/17/2012 3:22 PM, Herbert J Gould (hgould) wrote: > > Dear Arjen, > > Thank you that took care of the SPM issue but it still leaves the > .mexw32 issue. However it now is looking for the file in a different > location > > >> restoredefaultpath > >> addpath c:\FieldTrip\fieldtrip-20120715 > >> ft_defaults > ??? Invalid MEX-file > 'c:\FieldTrip\fieldtrip-20120715\utilities\ft_getopt.mexw32': The > specified procedure could not be found. > > . > > Error in ==> ft_checkconfig at 71 > renamed = ft_getopt(varargin, 'renamed'); > > Error in ==> ft_definetrial at 116 > cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); > > Error in ==> tutorial1 at 8 > cfg1 = ft_definetrial(cfg1); > > >> > > Herb Gould > ------------------------------------------------------------------------ > *From:* fieldtrip-bounces at science.ru.nl > [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. > [a.stolk at fcdonders.ru.nl] > *Sent:* Tuesday, July 17, 2012 8:04 AM > *To:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] mexw files > > Hi Herbert, > > It seems you have multiple versions of SPM on your path, which may > confuse FieldTrip. Could you try inserting the commands below in the > matlab command window, before inserting the tutorial code? > > Best regards, > > Arjen > > restoredefaultpath > > addpath C:\FieldTrip\fieldtrip-20120715 > > ft_defaults > > ------------------------------------------------------------------------ > > *Van: *"Herbert J Gould (hgould)" > *Aan: *fieldtrip at science.ru.nl > *Verzonden: *Dinsdag 17 juli 2012 14:36:26 > *Onderwerp: *[FieldTrip] mexw files > > I have just found fieldtrip and have started to work on the > tutorial. I am trying to read the data for subject 1 in the > tutorial and recieve the following error: > > cfg1 = ft_definetrial(cfg1); > Warning: multiple versions of SPM on your path will confuse FieldTrip > > In fieldtrip-20120715\private\warning_once at 75 > In ft_defaults at 91 > In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > > In ft_defaults at 99 > In ft_definetrial at 111 > Warning: one version of SPM is found here: > C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > > In ft_defaults at 99 > In ft_definetrial at 111 > ??? Invalid MEX-file > 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The > specified procedure could not be found. > > . > > Error in ==> ft_checkconfig at 71 > renamed = ft_getopt(varargin, 'renamed'); > > Error in ==> ft_definetrial at 116 > cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); > > I have checked and the .mexw32 file is there What am I doing wrong? > > Herb Gould > > > _______________________________________________ > 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 sguillor at ucla.edu Tue Jul 17 20:18:24 2012 From: sguillor at ucla.edu (S Guillory) Date: Tue, 17 Jul 2012 14:18:24 -0400 Subject: [FieldTrip] errors with ft_definetrial Message-ID: Hello, I'm trying to timelock to a specific event in an epoch and I'm having some difficulty setting it up in matlab. When not specifying an event, i.e. using '?', it identifies two types of events 'trial' and 'trigger' as well as the values. The problem I'm having is that there are two different triggers per trial and I am interested in only one of them, however when I specify cfg.trialdef.eventtype = 'trigger' and the cfg.trialdef.eventvalue = 'triggername', I get an error that no trials were defined. Is there a way to isolate the specific trigger without having to code a trial function. Thank you in advance for your time. -Sylvia -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Tue Jul 17 21:39:06 2012 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Tue, 17 Jul 2012 21:39:06 +0200 (CEST) Subject: [FieldTrip] errors with ft_definetrial In-Reply-To: Message-ID: <1895003729.997389.1342553946159.JavaMail.root@sculptor.zimbra.ru.nl> Hi Sylvia, What values exactly do you get for the 'trial' and 'trigger' event types? If, for instance, you have the values 1 and 2 (e.g. for conditions 1 and 2 respectively) for the 'trigger' event type, you can specifically read condition 1 by using: cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 1;  and more generally cfg.trialdef.prestim = 1; % one second before trigger with value 1 cfg.trialdef.poststim = 2; % two seconds after trigger with value 1 Hope this solves your problem? Arjen ----- Oorspronkelijk bericht ----- > Van: "S Guillory" > Aan: fieldtrip at donders.ru.nl > Verzonden: Dinsdag 17 juli 2012 20:18:24 > Onderwerp: [FieldTrip] errors with ft_definetrial > Hello, >  I'm trying to timelock to a specific event in an epoch and I'm > having some difficulty setting it up in matlab. When not specifying an > event, i.e. using '?', it identifies two types of events 'trial' > and 'trigger' as well as the values. The problem I'm having is that > there are two different triggers per trial and I am interested in only > one of them, however when I specify cfg.trialdef.eventtype = 'trigger' > and the cfg.trialdef.eventvalue = 'triggername', I get an error that > no trials were defined. Is there a way to isolate the specific > trigger without having to code a trial function. Thank you in advance > for your time. >  -Sylvia > _______________________________________________ > 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 hgould at memphis.edu Tue Jul 17 22:39:03 2012 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 17 Jul 2012 20:39:03 +0000 Subject: [FieldTrip] mexw files In-Reply-To: <50056CFF.7080103@donders.ru.nl> References: <5306C43FAB1DB14992CDDF2D7EDB981B13A8219E@CH1PRD0410MB356.namprd04.prod.outlook.com>, <1319598403.993208.1342530266821.JavaMail.root@sculptor.zimbra.ru.nl> <5306C43FAB1DB14992CDDF2D7EDB981B13A821D2@CH1PRD0410MB356.namprd04.prod.outlook.com>, <50056CFF.7080103@donders.ru.nl> Message-ID: <5306C43FAB1DB14992CDDF2D7EDB981B13A824BB@CH1PRD0410MB356.namprd04.prod.outlook.com> Dear Jorn, I downloaded the 20120716 version of Fieldtrip and the same problem occurred. Next I did the mex of ft_getopt.c and transfered it to Utilities. Still no joy as the same problem occured again. I am working on an older laptop running xp with an old 7.1 version of Matlab. I will be back in my lab next week where I can try it out on better equipment and newer software. Herb ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of "Jörn M. Horschig" [jm.horschig at donders.ru.nl] Sent: Tuesday, July 17, 2012 8:47 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] mexw files Dear Herb, it seems like the mex-file you are using is corrupt. Either it is from a corrupt download (in which case you'd need to download fieldtrip once more) or there is, or there is some other incompatibility between your windows/matlab combination that we have not encountered. Could you try downloading FieldTrip again and see whether the error persists? If it does persist, you could go to the src/ directory and type 'mex ft_getopt.c' to re-mex the file (in Matlab). Then copy the mexw32 file from that folder to utilities/. This is not an optimal solution, because you will probably encounter similar issues with other mexw32 files. If that works for you, it would be nice if you sent me (or someone else from the dev team) the file so that we can check whether the file is indeed different. Either way, please let us know whether (and if so how) you can resolve the problem. Best, Jörn On 7/17/2012 3:22 PM, Herbert J Gould (hgould) wrote: Dear Arjen, Thank you that took care of the SPM issue but it still leaves the .mexw32 issue. However it now is looking for the file in a different location >> restoredefaultpath >> addpath c:\FieldTrip\fieldtrip-20120715 >> ft_defaults ??? Invalid MEX-file 'c:\FieldTrip\fieldtrip-20120715\utilities\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); Error in ==> tutorial1 at 8 cfg1 = ft_definetrial(cfg1); >> Herb Gould ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stolk, A. [a.stolk at fcdonders.ru.nl] Sent: Tuesday, July 17, 2012 8:04 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] mexw files Hi Herbert, It seems you have multiple versions of SPM on your path, which may confuse FieldTrip. Could you try inserting the commands below in the matlab command window, before inserting the tutorial code? Best regards, Arjen restoredefaultpath addpath C:\FieldTrip\fieldtrip-20120715 ft_defaults ________________________________ Van: "Herbert J Gould (hgould)" Aan: fieldtrip at science.ru.nl Verzonden: Dinsdag 17 juli 2012 14:36:26 Onderwerp: [FieldTrip] mexw files I have just found fieldtrip and have started to work on the tutorial. I am trying to read the data for subject 1 in the tutorial and recieve the following error: cfg1 = ft_definetrial(cfg1); Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20120715\private\warning_once at 75 In ft_defaults at 91 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm2\spm.m > In ft_defaults at 99 In ft_definetrial at 111 Warning: one version of SPM is found here: C:\FieldTrip\fieldtrip-20120715\external\spm8\spm.m > In ft_defaults at 99 In ft_definetrial at 111 ??? Invalid MEX-file 'C:\FieldTrip\fieldtrip-20120715\src\ft_getopt.mexw32': The specified procedure could not be found. . Error in ==> ft_checkconfig at 71 renamed = ft_getopt(varargin, 'renamed'); Error in ==> ft_definetrial at 116 cfg = ft_checkconfig(cfg, 'dataset2files', {'yes'}); I have checked and the .mexw32 file is there What am I doing wrong? Herb Gould _______________________________________________ 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 ith at deakin.edu.au Thu Jul 19 06:44:38 2012 From: ith at deakin.edu.au (IMALI THANUJA HETTIARACHCHI) Date: Thu, 19 Jul 2012 04:44:38 +0000 Subject: [FieldTrip] Question regarding ft_connectivitysimulation Message-ID: <5A1787011651BC42A4D41856DBC2E0603E048720@mbox-f-3.du.deakin.edu.au> Dear fieldTrippers, I am trying to generate some simulated signals from a known connectivity structure with ft_connectivitysimulation, and secondly to assign these signals to known dipole locations when using in ft_dipolesimulation. Is there any way I can assign a frequency to the signals in ft_connectivityanalysis, so that I can assign different known frequency signals for dipoles? Any help is really appreciated. Thank you very much. Kind regards Imali Imali Thanuja Hettiarachchi PhD Candidate Centre for Intelligent Systems research Deakin University, Geelong 3217, Australia. Email: ith at deakin.edu.au www.deakin.edu.au/cisr [Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 29155 bytes Desc: image001.jpg URL: From e.maris at psych.ru.nl Fri Jul 20 00:30:26 2012 From: e.maris at psych.ru.nl (Eric Maris) Date: Fri, 20 Jul 2012 00:30:26 +0200 (CEST) Subject: [FieldTrip] PhD position "Mechanisms of top-down control in the accumulation of sensory evidence" Message-ID: <02d301cd65fe$17ff7a90$47fe6fb0$@maris@psych.ru.nl> Dear Discussion List subscribers, I would to post an advertisement for a PhD position at the Donders Institute for Brain, Cognition and Behavior. Mechanisms of top-down control in the accumulation of sensory evidence Many studies have shown neurophysiological correlates of top-down factors in perception (e.g., attention and expectation) which are already active prior to the sampling of sensory evidence. One of the puzzling observations in this line of investigation is the rather weak relation between these anticipatory neurophysiological signals (typically, modulations of oscillatory activity) and perception (most importantly, accuracy). The overall objective of this project is to identify additional neurophysiological processes that explain behavioral accuracy and its modulation by attention. The main working hypothesis that guides us in this search is that one should not only investigate anticipatory neural activity but also the neural activity during the accumulation of sensory evidence. The objectives of this research project will be addressed in experiments in which extracranial neural signals are recorded using Magnetoencephalography (MEG). Within the Donders Institute (DI), you will belong to the research group Neurophysiology of Active Perception (PI Eric Maris). As this is a collaborative project within the DI, you will also be affiliated to the research groups Prediction & Attention (PI Floris de Lange) and Neuronal Oscillations (PI Ole Jensen). A successful candidate has a Master' s degree in a field at the interface of behavior and neurobiology (Cognitive Neuroscience, Neurobiology, Cognitive Science) and excellent analytic and quantitative skills. Programming skills (e.g., Matlab) are required, and it is an advantage if you have experience in running EEG or MEG experiments. Please include with your application: - a curriculum vitae, including academic qualifications, grades, a list of publications (if applicable), and the names and contact details of two referees; - a letter explaining your motivation, your interest in the project, and your competence in the research field;" Employment start date: 2012-10-15 Contract length: 4 years Contact Information: Dr. Eric Maris E-mail: e.maris at donders.ru.nl Website: http://www.nphyscog.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From dporada at uos.de Fri Jul 20 07:48:31 2012 From: dporada at uos.de (Porada Danja) Date: Fri, 20 Jul 2012 07:48:31 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds Message-ID: <0D507729-5866-4635-845A-E5C45F210830@uos.de> Hi, I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). Here is the problem: For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? And I have another question: Do I have to calculate the planar gradient before computing the grand average? Best, Danja From jm.horschig at donders.ru.nl Fri Jul 20 11:59:37 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 20 Jul 2012 11:59:37 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds In-Reply-To: <0D507729-5866-4635-845A-E5C45F210830@uos.de> References: <0D507729-5866-4635-845A-E5C45F210830@uos.de> Message-ID: <50092C09.7080109@donders.ru.nl> Hi Danja, you can could either compute the average yourself: /data.avg = squeeze(nanmean(data.trial, 1)); data.dimord = 'chan_time';/ Note that the covariance might be invalid here, not sure what ft_regressconfound does here. or call /data = ft_checkdata(data, 'datatype', 'raw')/ which converts the timelocked data back to raw data format, and you can call /ft_timelockanalysis /again with /cfg.keeptrials = 'no'/ (the latter would be my favourite) Regarding the planar gradient, I'd say no. Keep in mind that the planar gradient computation results in all values > 0, thus e.g. noise might not cancel out as efficiently and a simple t-test against with the classical null hypothesis becomes invalid. I don't do ERP analysis though, so if someone can provide a good reason for doing the transformation nonetheless, I might be convinced otherwise ;) Best, Jörn On 7/20/2012 7:48 AM, Porada Danja wrote: > Hi, > > I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). > > Here is the problem: > For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? > > > And I have another question: Do I have to calculate the planar gradient before computing the grand average? > > > Best, > Danja > _______________________________________________ > 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 dporada at uos.de Fri Jul 20 12:28:01 2012 From: dporada at uos.de (Porada Danja) Date: Fri, 20 Jul 2012 12:28:01 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds In-Reply-To: <800_1342766933_q6K6mqFs001171_0D507729-5866-4635-845A-E5C45F210830@uos.de> References: <800_1342766933_q6K6mqFs001171_0D507729-5866-4635-845A-E5C45F210830@uos.de> Message-ID: I just found out that I only have to use the field avg as input for ft_grandaverage... But I'm still wondering whether it is necessary to calculate the planar gradient before computing the grand average. Best, Danja Am 20.07.2012 um 07:48 schrieb Porada Danja: > Hi, > > I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). > > Here is the problem: > For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? > > > And I have another question: Do I have to calculate the planar gradient before computing the grand average? > > > Best, > Danja > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From stephen.whitmarsh at gmail.com Fri Jul 20 13:13:47 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 20 Jul 2012 13:13:47 +0200 Subject: [FieldTrip] Grandaverage after regressing out headposition confounds In-Reply-To: References: <800_1342766933_q6K6mqFs001171_0D507729-5866-4635-845A-E5C45F210830@uos.de> Message-ID: Dear Danja, As Jorn said calculating the planar on ERF data creates some additional 'issues', mainly because the signal, as well as the noise, will always be positive (because of the pythagoras' square operation), and the noise will therefore be additive - i.e. it won't 'average out'. However, with similar amount of trials and other such caretaking comparisons between conditions it is in principle possible. As I see it there are two main reasons for going to planar: 1) more interpretable locations (of maximum amplitude difference): It relieves one from the neccecity to visually process the dipole pattern (positive and negative poles) as showing two sides of a single dipole with the source probably in between. 2) since you lose the orientation of the dipole in the planar transformation - an ideal anterior-posterior will give the same pattern as a left-right dipole when the maximum slope between the two poles lie on the same location - this can help you to average over subjects that might have different orientations but are located above similar regions. In addition the dipole pattern is in effect spatially smoothed (depending on how many neighbours you use), which might help your average as well. Cheers, Stephen On 20 July 2012 12:28, Porada Danja wrote: > I just found out that I only have to use the field avg as input for ft_grandaverage... > > But I'm still wondering whether it is necessary to calculate the planar gradient before computing the grand average. > > Best, > Danja > > Am 20.07.2012 um 07:48 schrieb Porada Danja: > >> Hi, >> >> I would like to compute a grand average of the individual ERFs after I already used ft_regressconfounds (in order to deal with changes in head position during the experiment). >> >> Here is the problem: >> For regressing out head position confounds I have to keep the individual trials during the timelockanalysis. But for computing the grand average afterwards I need averages and not individual trials. Which is the best way to obtain the average? >> >> >> And I have another question: Do I have to calculate the planar gradient before computing the grand average? >> >> >> Best, >> Danja >> _______________________________________________ >> 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 sanchomoro at gmail.com Fri Jul 20 17:21:22 2012 From: sanchomoro at gmail.com (Sancho Moro) Date: Fri, 20 Jul 2012 17:21:22 +0200 Subject: [FieldTrip] Post-doctoral position in Multisensory integration/EEG Message-ID: *Post-doctoral position in Multisensory integration/EEG* * * Applications are invited for a full-time post-doctoral research position in the MULTISENSORY RESEARCH GROUP , led by Salvador Soto-Faraco, at the Pompeu Fabra University (Barcelona). The position is covered by a European Research Council grant on Multisensory Integration and Attention. *The project* addresses the interplay between multisensory integration processes and attention mechanisms. This research spans several functions (speech, temporal and spatial processing, in vision, audition and touch, and body representation) and research approaches (psychophysics, neuroimaging, and brain stimulation with TMS). *We seek* a person with solid experience who leads a research line focused on brain oscillatory dynamics. Involvement in some organizational and management aspects is expected. The candidate must (1) *have solid demonstrable experience (i.e., publications) in the field of oscillatory analysis using EEG and/or MEG*, (2) strong background in cognitive neuroscience, neuroscience, and/or cognitive psychology, and (3) scientific motivation about multisensory integration, perception and attention. *We offer* onsite ERP/EEG, TMS, and psychophysical testing facilities, neuronavigation system, a wide range of visual auditory and somatosensory stimulation equipment, and the use of fMRI and MEG recording facilities externally. The position will be funded and renewable on yearly basis for up to three years. Starting date: Feb 2013 or before. Salary: up to 36,000Eur/Year *How to apply* Applications should include: - a C.V. including a list of publications - the names of two referees who would willing to write letters of recommendation - a short cover letter describing research interests Check out www.mrg.upf.edu for info on the group. For informal enquiries about the position and applications, please contact Salvador Soto-Faraco at applications.MRGLab at gmail.com. Applications will be accepted until the position is filled. Please, mention that you are applying to the POSTDOCTORAL position in the email subject -- Salvador Soto Faraco ICREA Research Professor Dept. de Tecnologies de la Informació i les Comunicacions Universitat Pompeu Fabra C. Tanger, 122-140, room 55.108 Postal address: Roc Boronat 138 08018 Barcelona Spain Phone: +34 93.542.25.34 <%2B34%2093.542.25.34> Fax: +34 93..542.25.17 E-Mail: salvador.soto at icrea.cat http://www.mrg.upf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From xbai3 at uthsc.edu Sat Jul 21 01:28:49 2012 From: xbai3 at uthsc.edu (Bai, XiaoXiao) Date: Fri, 20 Jul 2012 23:28:49 +0000 Subject: [FieldTrip] About co-register the individual sudbject MRI and sensor locations Message-ID: <5D2CC5653262C14188174E20065A4C4EC8D457@hscmbx6.uthsc.tennessee.edu> Dear Sir/Madam, I am a new fieldtrip user and want to apply the beamformer method in Fieldtrip for the MEG data from 4D/BTI system. Now I can get a individual subject MRI in analysis/spm format from CURRY software. This is my code for create volume head model for the beamformer, mri_nom = ft_read_mri(mrifile); cfg = []; [segmentedmri] = ft_volumesegment(cfg, mri_nom); cfg = []; cfg.method = 'singleshell'; vol = ft_prepare_headmodel(cfg, segmentedmri); The vol and sensor locations were displayed and attached with here. How can I co-register the vol with sensors based on headshpe file (hs_file) for computing lead field for next step? Thanks a lot. Best regards, Xiaoxiao [X] [X] [X] Division of Clinical Neurosciences, Department of Pediatrics University of Tennessee Health Science Center, College of Medicine & Neuroscience Institute, LeBonheur Children's Hospital 777 Washington Avenue, P335 Memphis, TN 38105, USA Phone: 901-287-4612 Fax: 901-287-5325 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sensor and volume.png Type: image/x-png Size: 21343 bytes Desc: sensor and volume.png URL: From victor.veliks at gmail.com Sun Jul 22 22:28:07 2012 From: victor.veliks at gmail.com (viktor veliks) Date: Sun, 22 Jul 2012 23:28:07 +0300 Subject: [FieldTrip] Post-doctoral position in Multisensory integration/EEG In-Reply-To: References: Message-ID: Dear Salvador Soto-Faraco I would like to apply for the job you have published in FieldTrip list - post-doctoral research position in the MULTISENSORY RESEARCH GROUP. In attachment You may see my motivation letter with my skills, CV and list with 2 references. Sincerely, Dr.biol. Viktors Veliks On Fri, Jul 20, 2012 at 6:21 PM, Sancho Moro wrote: > Post-doctoral position in Multisensory integration/EEG > > > > Applications are invited for a full-time post-doctoral research position in > the MULTISENSORY RESEARCH GROUP, led by Salvador Soto-Faraco, at the Pompeu > Fabra University (Barcelona). The position is covered by a European Research > Council grant on Multisensory Integration and Attention. > > > > The project addresses the interplay between multisensory integration > processes and attention mechanisms. This research spans several functions > (speech, temporal and spatial processing, in vision, audition and touch, and > body representation) and research approaches (psychophysics, neuroimaging, > and brain stimulation with TMS). > > > > We seek a person with solid experience who leads a research line focused on > brain oscillatory dynamics. Involvement in some organizational and > management aspects is expected. The candidate must (1) have solid > demonstrable experience (i.e., publications) in the field of oscillatory > analysis using EEG and/or MEG, (2) strong background in cognitive > neuroscience, neuroscience, and/or cognitive psychology, and (3) scientific > motivation about multisensory integration, perception and attention. > > > > We offer onsite ERP/EEG, TMS, and psychophysical testing facilities, > neuronavigation system, a wide range of visual auditory and somatosensory > stimulation equipment, and the use of fMRI and MEG recording facilities > externally. The position will be funded and renewable on yearly basis for > up to three years. > > > > Starting date: Feb 2013 or before. > > Salary: up to 36,000Eur/Year > > > > How to apply > > Applications should include: > > - a C.V. including a list of publications > > - the names of two referees who would willing to write letters of > recommendation > > - a short cover letter describing research interests > > Check out www.mrg.upf.edu for info on the group. For informal enquiries > about the position and applications, please contact Salvador Soto-Faraco at > applications.MRGLab at gmail.com. Applications will be accepted until the > position is filled. > > Please, mention that you are applying to the POSTDOCTORAL position in the > email subject > > > > > > -- > Salvador Soto Faraco > ICREA Research Professor > Dept. de Tecnologies de la Informació i les Comunicacions > Universitat Pompeu Fabra > C. Tanger, 122-140, room 55.108 > > Postal address: > Roc Boronat 138 > 08018 Barcelona > Spain > > > Phone: +34 93.542.25.34 > Fax: +34 93..542.25.17 > E-Mail: salvador.soto at icrea.cat > http://www.mrg.upf.edu > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From omidabbasi2000 at gmail.com Tue Jul 24 17:49:05 2012 From: omidabbasi2000 at gmail.com (omid abbasi) Date: Tue, 24 Jul 2012 20:19:05 +0430 Subject: [FieldTrip] help to apply field trip (topography plotting) In-Reply-To: References: Message-ID: Dear Steve I have a project in ERP analyzing. I provide a task for it. Any 2 sec, a square appear in the left side of screen or in the right side of screen. And subject have to look to other side of screen. I don't have any software to analyze it. I write some code for it but i think i haven't enough information about ERP analyzing. Some latency and amplitude like P300 and N100 is important for me. Do you have any information about ERP analyzing. I know i take your time with my basic question, but i think the only person that can help me is you. Thank you very much Best Regards On Sat, Jul 7, 2012 at 5:16 AM, Stephen Politzer-Ahles < politzerahless at gmail.com> wrote: > Hi Omid, > > Welcome to Fieldtrip. You can find a lot of information about how to use > Fieldtrip at http://fieldtrip.fcdonders.nl/walkthrough and > http://fieldtrip.fcdonders.nl/tutorial. In your case, you need to get > your data imported into Fieldtrip's format in MATLAB ( > http://fieldtrip.fcdonders.nl/tutorial/preprocessing), as well as your > channel layout (http://fieldtrip.fcdonders.nl/tutorial/layout) before > proceeding to plotting. > > Good luck, > Steve > > >> Message: 1 >> Date: Thu, 5 Jul 2012 16:36:23 +0430 >> From: omid abbasi >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] help to apply field trip (topography plotting) >> Message-ID: >> < >> CAPc_m1utoA_ZqC8_0q44hz5FX3yMfWP-gfke5Mes9_sEUOuyrA at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear Developer >> >> At first, I thank you for useful source code. >> >> This is Omid. I'm a student that work on biological signal processing. I >> want to use your source code for plotting data topography of brain. I >> downloaded your code from this link ( >> http://fieldtrip.fcdonders.nl/tutorial/plotting) and read it's help. but >> i >> can't use it in my project, because i have 19 signals from 19 sites on the >> brain(EEG1020) but your example (GA_FC) has 152 sites. How i can use your >> code in my project with different channel and data? >> >> It would grateful for me if you could help me to apply your code in my >> project. >> >> Best Regards >> > > _______________________________________________ > 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 ajavitt at NKI.RFMH.ORG Thu Jul 19 17:05:37 2012 From: ajavitt at NKI.RFMH.ORG (Javitt, Aaron) Date: Thu, 19 Jul 2012 11:05:37 -0400 Subject: [FieldTrip] Automatic Artifact Rejection Message-ID: <2586A1048152BE4D861E64A98700AD420B374DBB@nki-mail.NKI.rfmh.org> I am attempting to use automatic artifact rejection based on uV threshold levels (ft_artifact_threshold). When I run ft_rejectartifact some of the datasets run just fine but on others, all the trials are rejected which then causes an error and the program crashes. Since I have a lot of files to analyze I didn't want to go through all of the files by hand, is there a way to know which datasets are going to have all of the trials rejected when ft_rejectartifact is called before I actually call it. -Aaron 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Wed Jul 25 23:43:59 2012 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Wed, 25 Jul 2012 22:43:59 +0100 Subject: [FieldTrip] SPM M/EEG 2012 course lectures now available online In-Reply-To: References: Message-ID: Dear colleagues, Sorry for possible cross-posting. We are pleased to announce that video recordings and presentations from the May 2012 SPM for M/EEG Course at the Wellcome Trust Centre for Neuroimaging, are now freely available online at http://www.fil.ion.ucl.ac.uk/spm/course/video/#MEEG12 The new recordings complement the previously recorded set of lectures covering SPM for fMRI, PET and VBM. We hope that this resource will be useful for SPM M/EEG users as well as for the broader neuroimaging community. With best wishes, Vladimir Litvak Lecturer, Wellcome Trust Centre for Neuroimaging on behalf of SPM faculty From dargilboa at gmail.com Thu Jul 26 01:29:25 2012 From: dargilboa at gmail.com (Dar Gilboa) Date: Thu, 26 Jul 2012 02:29:25 +0300 Subject: [FieldTrip] Help with EEG ROI Timecourse Analysis Message-ID: Hello, I'm a new user of Fieldtrip, and I want to write a script that performs source reconstruction on an EEG data file (initially in TRC or EDF format) and extracts ROI timecourses based on the AAL parcellation (Tzourio-Mazoyer et al. 2002). I have matlab files with details of the parcellation, which assign an ROI number to each voxel in a matrix. I assume the parcellation can be inputted using ft_prepare_atlas. I was wondering if someone has done something similar to this so I don't have to start from scratch, or if anyone has some helpful advice. Thanks, Dar -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.weiss at klinikum.uni-tuebingen.de Thu Jul 26 06:41:10 2012 From: daniel.weiss at klinikum.uni-tuebingen.de (Klinik) Date: Thu, 26 Jul 2012 06:41:10 +0200 Subject: [FieldTrip] SPM M/EEG 2012 course lectures now available online In-Reply-To: References: Message-ID: ! Von meinem iPhone gesendet Am 25.07.2012 um 23:43 schrieb Vladimir Litvak : > Dear colleagues, > > Sorry for possible cross-posting. > > We are pleased to announce that video recordings and presentations > from the May 2012 SPM for M/EEG Course at the Wellcome Trust Centre > for Neuroimaging, are now freely available online at > > http://www.fil.ion.ucl.ac.uk/spm/course/video/#MEEG12 > > The new recordings complement the previously recorded set of lectures > covering SPM for fMRI, PET and VBM. We hope that this resource will be > useful for SPM M/EEG users as well as for the broader neuroimaging > community. > > With best wishes, > > Vladimir Litvak > Lecturer, Wellcome Trust Centre for Neuroimaging > on behalf of SPM faculty > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From marco.buiatti at gmail.com Thu Jul 26 12:36:39 2012 From: marco.buiatti at gmail.com (Marco Buiatti) Date: Thu, 26 Jul 2012 12:36:39 +0200 Subject: [FieldTrip] interactions between two factors In-Reply-To: References: Message-ID: Dear FieldTrippers, some time ago I have posted the message below concerning how to compute the statistical interaction between two factors in an EEG study with the FieldTrip cluster-based statistical analysis. Since I believe it is a problem of general interest, I was confident I would have received some replies, no matter how critics. But I had no reply and I am trying to guess why: - the problem is trivial, I should go back to my statistics books and solve it myself; - the problem is ill-posed, I should go back to my statistics books and reformulate it correctly; - the problem is tabou, no one dares commits to a solution because it could be a wrong one. - the problem is solved: I should read message number #. Thanks a lot for your feedback, Best, Marco On 25 May 2012 15:58, Marco Buiatti wrote: > Dear FieldTrippers, > > I am analysing an EEG study with 2x4 factors: one varies between 4 > parametrically varying levels (1 to 4), the second between two levels. > > I have three questions concerning the use of Fieldtrip cluster-based > non parametric statistical analysis in this case: > > 1) How to compute the interaction between the two factors. Let's start > from the simplest case of a 2x2 design, factors varying between values > A1 and A2 for the first factor, B1 and B2 for the second. Please tell > me if it is correct to compute the interaction by: > - computing the difference diffA=ERP(A1)-ERP(A2) separately in > condition B1 and B2, for every subject > - performing a within-subjects statistical analysis between diffA in > condition B1 and diffA in condition B2 (function > statfun_depsamplesT.m). > > 2) Now consider that factor A varies parametrically between values 1 > to 4. For the main effect of this factor, I have used the Fieldtrip > function statfun_depsamplesregrT.m and I'm satisfied with it. Is it > correct to compute the interaction by > - computing the regression > regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside > function statfun_depsamplesregrT.m) separately in condition B1 and B2, > for every subject > - performing a within-subjects statistical analysis between regrA in > condition B1 and regrA in condition B2 (function > statfun_depsamplesT.m)? > > 3) Since BEFORE looking at the data (this is to prevent Eric's > contestation...) I expect a dipolar topography for the regression > (data are in average reference), I would like to combine into a joint > cluster negative and positive clusters. I have tried by changing > statfun_depsamplesregrT.m by just taking the absolute value of the > regression, but I get weird results (a huge, non significant cluster). > Is it possible that since values are now all positive, I should use a > different statistical test at the single bin level? Any other > suggestions? > > Thanks in advance for your help, > > Marco > > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** -- Marco Buiatti, PhD CEA/DSV/I2BM / NeuroSpin INSERM U992 - Cognitive Neuroimaging Unit Bât 145 - Point Courrier 156 Gif sur Yvette F-91191 FRANCE Ph: +33(0)169.08.65.21 Fax: +33(0)169.08.79.73 E-mail: marco.buiatti at gmail.com http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti *********************************************** From lihqih at gmail.com Thu Jul 26 16:58:51 2012 From: lihqih at gmail.com (qi li) Date: Thu, 26 Jul 2012 10:58:51 -0400 Subject: [FieldTrip] lateral view plot Message-ID: Hi there, Can fieldtrip make the plot like brain lateral view or something like suma such that descriptive statistics can be mapped on? Thanks a lot! Qi From jm.horschig at donders.ru.nl Thu Jul 26 17:23:25 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 26 Jul 2012 17:23:25 +0200 Subject: [FieldTrip] lateral view plot In-Reply-To: References: Message-ID: <501160ED.4050307@donders.ru.nl> Hi Qi, you can see here what's possible: http://fieldtrip.fcdonders.nl/tutorial/plotting?s[]=source&s[]=plot#plotting_data_at_the_source_level or in the tutorial: http://fieldtrip.fcdonders.nl/tutorial/beamformer?#neural_activity_index http://fieldtrip.fcdonders.nl/tutorial/beamformer?#plotting_options see also ft_sourceplot: http://fieldtrip.fcdonders.nl/reference/ft_sourceplot You can use cfg.funparameter and cfg.maskparameter to specify what you want to plot. Have fun ;) Jörn On 7/26/2012 4:58 PM, qi li wrote: > Hi there, > > Can fieldtrip make the plot like brain lateral view or something like > suma such that descriptive statistics can be mapped on? Thanks a lot! > > Qi > _______________________________________________ > 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 arno at cerco.ups-tlse.fr Thu Jul 26 18:35:49 2012 From: arno at cerco.ups-tlse.fr (Arnaud Delorme) Date: Thu, 26 Jul 2012 09:35:49 -0700 Subject: [FieldTrip] interactions between two factors In-Reply-To: References: Message-ID: Dear Marco, I believe the first answer is the correct one. The problem is somewhat trivial but not implemented yet. The LIMO toolbox will let you perform 2-way statistics with cluster correction for multiple comparisons. Best, Arno On Jul 26, 2012, at 3:36 AM, Marco Buiatti wrote: > Dear FieldTrippers, > > some time ago I have posted the message below concerning how to > compute the statistical interaction between two factors in an EEG > study with the FieldTrip cluster-based statistical analysis. Since I > believe it is a problem of general interest, I was confident I would > have received some replies, no matter how critics. But I had no reply > and I am trying to guess why: > > - the problem is trivial, I should go back to my statistics books and > solve it myself; > - the problem is ill-posed, I should go back to my statistics books > and reformulate it correctly; > - the problem is tabou, no one dares commits to a solution because it > could be a wrong one. > - the problem is solved: I should read message number #. > > Thanks a lot for your feedback, > > Best, > > Marco > > On 25 May 2012 15:58, Marco Buiatti wrote: >> Dear FieldTrippers, >> >> I am analysing an EEG study with 2x4 factors: one varies between 4 >> parametrically varying levels (1 to 4), the second between two levels. >> >> I have three questions concerning the use of Fieldtrip cluster-based >> non parametric statistical analysis in this case: >> >> 1) How to compute the interaction between the two factors. Let's start >> from the simplest case of a 2x2 design, factors varying between values >> A1 and A2 for the first factor, B1 and B2 for the second. Please tell >> me if it is correct to compute the interaction by: >> - computing the difference diffA=ERP(A1)-ERP(A2) separately in >> condition B1 and B2, for every subject >> - performing a within-subjects statistical analysis between diffA in >> condition B1 and diffA in condition B2 (function >> statfun_depsamplesT.m). >> >> 2) Now consider that factor A varies parametrically between values 1 >> to 4. For the main effect of this factor, I have used the Fieldtrip >> function statfun_depsamplesregrT.m and I'm satisfied with it. Is it >> correct to compute the interaction by >> - computing the regression >> regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside >> function statfun_depsamplesregrT.m) separately in condition B1 and B2, >> for every subject >> - performing a within-subjects statistical analysis between regrA in >> condition B1 and regrA in condition B2 (function >> statfun_depsamplesT.m)? >> >> 3) Since BEFORE looking at the data (this is to prevent Eric's >> contestation...) I expect a dipolar topography for the regression >> (data are in average reference), I would like to combine into a joint >> cluster negative and positive clusters. I have tried by changing >> statfun_depsamplesregrT.m by just taking the absolute value of the >> regression, but I get weird results (a huge, non significant cluster). >> Is it possible that since values are now all positive, I should use a >> different statistical test at the single bin level? Any other >> suggestions? >> >> Thanks in advance for your help, >> >> Marco >> >> >> >> -- >> Marco Buiatti, PhD >> >> CEA/DSV/I2BM / NeuroSpin >> INSERM U992 - Cognitive Neuroimaging Unit >> Bât 145 - Point Courrier 156 >> Gif sur Yvette F-91191 FRANCE >> Ph: +33(0)169.08.65.21 >> Fax: +33(0)169.08.79.73 >> E-mail: marco.buiatti at gmail.com >> http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti >> >> *********************************************** > > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Arnaud Delorme, PhD Centre de Recherche Cerveau et Cognition - UMR 5549 Pavillon Baudot, Hopital Purpan, BP 25202 31052 Toulouse Cedex, France From arno at cerco.ups-tlse.fr Thu Jul 26 18:35:49 2012 From: arno at cerco.ups-tlse.fr (Arnaud Delorme) Date: Thu, 26 Jul 2012 09:35:49 -0700 Subject: [FieldTrip] interactions between two factors In-Reply-To: References: Message-ID: Dear Marco, I believe the first answer is the correct one. The problem is somewhat trivial but not implemented yet. The LIMO toolbox will let you perform 2-way statistics with cluster correction for multiple comparisons. Best, Arno On Jul 26, 2012, at 3:36 AM, Marco Buiatti wrote: > Dear FieldTrippers, > > some time ago I have posted the message below concerning how to > compute the statistical interaction between two factors in an EEG > study with the FieldTrip cluster-based statistical analysis. Since I > believe it is a problem of general interest, I was confident I would > have received some replies, no matter how critics. But I had no reply > and I am trying to guess why: > > - the problem is trivial, I should go back to my statistics books and > solve it myself; > - the problem is ill-posed, I should go back to my statistics books > and reformulate it correctly; > - the problem is tabou, no one dares commits to a solution because it > could be a wrong one. > - the problem is solved: I should read message number #. > > Thanks a lot for your feedback, > > Best, > > Marco > > On 25 May 2012 15:58, Marco Buiatti wrote: >> Dear FieldTrippers, >> >> I am analysing an EEG study with 2x4 factors: one varies between 4 >> parametrically varying levels (1 to 4), the second between two levels. >> >> I have three questions concerning the use of Fieldtrip cluster-based >> non parametric statistical analysis in this case: >> >> 1) How to compute the interaction between the two factors. Let's start >> from the simplest case of a 2x2 design, factors varying between values >> A1 and A2 for the first factor, B1 and B2 for the second. Please tell >> me if it is correct to compute the interaction by: >> - computing the difference diffA=ERP(A1)-ERP(A2) separately in >> condition B1 and B2, for every subject >> - performing a within-subjects statistical analysis between diffA in >> condition B1 and diffA in condition B2 (function >> statfun_depsamplesT.m). >> >> 2) Now consider that factor A varies parametrically between values 1 >> to 4. For the main effect of this factor, I have used the Fieldtrip >> function statfun_depsamplesregrT.m and I'm satisfied with it. Is it >> correct to compute the interaction by >> - computing the regression >> regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside >> function statfun_depsamplesregrT.m) separately in condition B1 and B2, >> for every subject >> - performing a within-subjects statistical analysis between regrA in >> condition B1 and regrA in condition B2 (function >> statfun_depsamplesT.m)? >> >> 3) Since BEFORE looking at the data (this is to prevent Eric's >> contestation...) I expect a dipolar topography for the regression >> (data are in average reference), I would like to combine into a joint >> cluster negative and positive clusters. I have tried by changing >> statfun_depsamplesregrT.m by just taking the absolute value of the >> regression, but I get weird results (a huge, non significant cluster). >> Is it possible that since values are now all positive, I should use a >> different statistical test at the single bin level? Any other >> suggestions? >> >> Thanks in advance for your help, >> >> Marco >> >> >> >> -- >> Marco Buiatti, PhD >> >> CEA/DSV/I2BM / NeuroSpin >> INSERM U992 - Cognitive Neuroimaging Unit >> Bât 145 - Point Courrier 156 >> Gif sur Yvette F-91191 FRANCE >> Ph: +33(0)169.08.65.21 >> Fax: +33(0)169.08.79.73 >> E-mail: marco.buiatti at gmail.com >> http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti >> >> *********************************************** > > > > -- > Marco Buiatti, PhD > > CEA/DSV/I2BM / NeuroSpin > INSERM U992 - Cognitive Neuroimaging Unit > Bât 145 - Point Courrier 156 > Gif sur Yvette F-91191 FRANCE > Ph: +33(0)169.08.65.21 > Fax: +33(0)169.08.79.73 > E-mail: marco.buiatti at gmail.com > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > *********************************************** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Arnaud Delorme, PhD Centre de Recherche Cerveau et Cognition - UMR 5549 Pavillon Baudot, Hopital Purpan, BP 25202 31052 Toulouse Cedex, France From politzerahless at gmail.com Fri Jul 27 16:25:07 2012 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Fri, 27 Jul 2012 09:25:07 -0500 Subject: [FieldTrip] interactions between two factors Message-ID: Hello Marco, For how to test an interaction in a 2x2 design, see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-January/003447.html(and some additional information at http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003338.html, http://mailman.science.ru.nl/pipermail/fieldtrip/2011-September/004244.html, and Anderson & Braak 2003 in *Journal of Statistical Computation & Simulation*). I'm not sure about the other two issues you mentioned, though. Best, Steve Message: 1 > Date: Thu, 26 Jul 2012 12:36:39 +0200 > From: Marco Buiatti > To: fieldtrip at donders.ru.nl > Subject: Re: [FieldTrip] interactions between two factors > Message-ID: > < > CA+wnTO2TL7XtzsKX2QciqXZO9hVxGUZTPjXwoYtS54ztRc0KeQ at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear FieldTrippers, > > some time ago I have posted the message below concerning how to > compute the statistical interaction between two factors in an EEG > study with the FieldTrip cluster-based statistical analysis. Since I > believe it is a problem of general interest, I was confident I would > have received some replies, no matter how critics. But I had no reply > and I am trying to guess why: > > - the problem is trivial, I should go back to my statistics books and > solve it myself; > - the problem is ill-posed, I should go back to my statistics books > and reformulate it correctly; > - the problem is tabou, no one dares commits to a solution because it > could be a wrong one. > - the problem is solved: I should read message number #. > > Thanks a lot for your feedback, > > Best, > > Marco > > On 25 May 2012 15:58, Marco Buiatti wrote: > > Dear FieldTrippers, > > > > I am analysing an EEG study with 2x4 factors: one varies between 4 > > parametrically varying levels (1 to 4), the second between two levels. > > > > I have three questions concerning the use of Fieldtrip cluster-based > > non parametric statistical analysis in this case: > > > > 1) How to compute the interaction between the two factors. Let's start > > from the simplest case of a 2x2 design, factors varying between values > > A1 and A2 for the first factor, B1 and B2 for the second. Please tell > > me if it is correct to compute the interaction by: > > - computing the difference diffA=ERP(A1)-ERP(A2) separately in > > condition B1 and B2, for every subject > > - performing a within-subjects statistical analysis between diffA in > > condition B1 and diffA in condition B2 (function > > statfun_depsamplesT.m). > > > > 2) Now consider that factor A varies parametrically between values 1 > > to 4. For the main effect of this factor, I have used the Fieldtrip > > function statfun_depsamplesregrT.m and I'm satisfied with it. Is it > > correct to compute the interaction by > > - computing the regression > > regrA=regression(ERP(A1),ERP(A2),ERP(A3),ERP(A4)) (computed as inside > > function statfun_depsamplesregrT.m) separately in condition B1 and B2, > > for every subject > > - performing a within-subjects statistical analysis between regrA in > > condition B1 and regrA in condition B2 (function > > statfun_depsamplesT.m)? > > > > 3) Since BEFORE looking at the data (this is to prevent Eric's > > contestation...) I expect a dipolar topography for the regression > > (data are in average reference), I would like to combine into a joint > > cluster negative and positive clusters. I have tried by changing > > statfun_depsamplesregrT.m by just taking the absolute value of the > > regression, but I get weird results (a huge, non significant cluster). > > Is it possible that since values are now all positive, I should use a > > different statistical test at the single bin level? Any other > > suggestions? > > > > Thanks in advance for your help, > > > > Marco > > > > > > > > -- > > Marco Buiatti, PhD > > > > CEA/DSV/I2BM / NeuroSpin > > INSERM U992 - Cognitive Neuroimaging Unit > > B?t 145 - Point Courrier 156 > > Gif sur Yvette F-91191 FRANCE > > Ph: +33(0)169.08.65.21 > > Fax: +33(0)169.08.79.73 > > E-mail: marco.buiatti at gmail.com > > http://www.unicog.org/pm/pmwiki.php/Main/MarcoBuiatti > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erdosttorun at gmail.com Sat Jul 28 22:47:21 2012 From: erdosttorun at gmail.com (erdost torun) Date: Sat, 28 Jul 2012 23:47:21 +0300 Subject: [FieldTrip] May I use fieldtrip on social science time series data? Message-ID: Hello everyone! I wonder whether I could use fieldtrip toolbox to do wavelet based causality analysis on Social science data, such as birth rates or malaria statistics. From the fieldtrip webpage, I understand that researches using fieldtrip mainly focus on MEG, EEG, and invasive electrophysiological data. Hence, I want to be sure that fieldtrip is suitable for other time series. Thank you in advance. All the best, Erdost From eelke.spaak at donders.ru.nl Mon Jul 30 13:21:46 2012 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 30 Jul 2012 13:21:46 +0200 Subject: [FieldTrip] May I use fieldtrip on social science time series data? In-Reply-To: References: Message-ID: Hello Erdost, Indeed, FieldTrip is designed specifically for the analysis of electrophysiological neuroscientific data. However, I don't see a reason why you should not use it for analysing different time series as well, if you think this will be useful to you. Best, Eelke On 28 July 2012 22:47, erdost torun wrote: > Hello everyone! > > I wonder whether I could use fieldtrip toolbox to do wavelet based > causality analysis on Social science data, such as birth rates or > malaria statistics. From the fieldtrip webpage, I understand that > researches using fieldtrip mainly focus on MEG, EEG, and invasive > electrophysiological data. Hence, I want to be sure that fieldtrip is > suitable for other time series. Thank you in advance. > > All the best, > > Erdost > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jm.horschig at donders.ru.nl Mon Jul 30 15:43:59 2012 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 30 Jul 2012 15:43:59 +0200 Subject: [FieldTrip] May I use fieldtrip on social science time series data? In-Reply-To: References: Message-ID: <50168F9F.6060400@donders.ru.nl> Dear Erdost, I agree as well with Eelke. In particular, apart from some methods (e.g. source reconstruction), there is no explicit assumption made about the origin of the data. While the algorithms are per se suited for any type of data, the options might be specific for your data. So, e.g. be sure to not demean or detrend your data when preprocessing (check what the defaults are for each function!). If would be great to let us all know if you publish your results in a particular scientific journal. Best of luck&success, Jörn On 7/28/2012 10:47 PM, erdost torun wrote: > Hello everyone! > > I wonder whether I could use fieldtrip toolbox to do wavelet based > causality analysis on Social science data, such as birth rates or > malaria statistics. From the fieldtrip webpage, I understand that > researches using fieldtrip mainly focus on MEG, EEG, and invasive > electrophysiological data. Hence, I want to be sure that fieldtrip is > suitable for other time series. Thank you in advance. > > All the best, > > Erdost > _______________________________________________ > 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 polomacnenad at gmail.com Mon Jul 30 16:10:54 2012 From: polomacnenad at gmail.com (Nenad Polomac) Date: Mon, 30 Jul 2012 16:10:54 +0200 Subject: [FieldTrip] MEG-anatomical MRI image coregistration Message-ID: Hello, I am analyzing MEG CTF data. I want to do source localisation and I have two particular questions regarding the anatomical MRI images. 1. Is it allowed to use anatomical MRI images from a two different MRI devices in a one source localisation study? We already have routinely obtain anatomical images for some patients and those are obtained on the 1.5 Tesla MRI. And for other patients we will record anatomical MRI on 3 Tesla. So, what do you think can we use this data in the same source analysis study. 2. The anatomical MRI images from a few subject were not marked with the vitamin E during imaging for relevant skull points (nasion and ear canals). So, I think to mark them now in some imaging software. The MEG data were properly marked during acquisition for this skull points. What is your opinion about accuracy of software based marking. How big localisation error might be? Thank you in advance! Kind regards! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Mon Jul 30 16:48:33 2012 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Mon, 30 Jul 2012 16:48:33 +0200 Subject: [FieldTrip] MEG-anatomical MRI image coregistration In-Reply-To: References: Message-ID: Dear Nenad, My 2 cents: 1) As long as you are convinced that both give appropriately accurate segmentations - something easily checked along the way by superimposing stripped brain,stull etc on the original scan - I don't see any reason against using them together in one study. Also, as you will probably not work on the high resolution of your T3 (i.e. 1mm isomorphic), but on downsampled grids for beamformer (i.e. 5 mm isomorphic), below the resolution of your 1.5T scans, differences in resolution should not confound your results on source level. Ofcourse in some specific cases in between- or within-group comparisons you could do a control analysis, e.g. using scan device as a covariate in your analysis, just to be sure, but I can think of only some very specific situations where that could be the case. 2) The localisation error would be related to how close you think you can co-register [sic]. I would consider that addive uncertainty above the localisation errors you'll unavoidably already have with your recording (movement) and source reconstruction (i.e. point-spread of the beamformer and such). I don't know what you mean exactly with 'software-based marking'. If you know where your MEG coils where in respect to anatomical landmarks, you can intelligently 'guess' where they are on the anatomical and just put them there by hand (nasion would be pretty close, ears probably put them e.g. 1.5 cm anterior to ear canals). The added uncertainty will be the degree of uncertainty you have being able to do that, right? If with 'software-based marking' you mean the use of a polemus device than that would probably be better. In any case, being conservative i would say the by-eye-method would increase your uncertainly by another cm or 2, instead of about a cm when appropriately using vitamin markers. I have no data to back that claim up though. Good luck! Stephen On 30 July 2012 16:10, Nenad Polomac wrote: > Hello, > > I am analyzing MEG CTF data. I want to do source localisation and I have two > particular questions regarding the anatomical MRI images. > > 1. Is it allowed to use anatomical MRI images from a two different MRI > devices in a one source localisation study? We already have routinely obtain > anatomical images for some patients and those are obtained on the 1.5 Tesla > MRI. And for other patients we will record anatomical MRI on 3 Tesla. So, > what do you think can we use this data in the same source analysis study. > > 2. The anatomical MRI images from a few subject were not marked with the > vitamin E during imaging for relevant skull points (nasion and ear canals). > So, I think to mark them now in some imaging software. The MEG data were > properly marked during acquisition for this skull points. > What is your opinion about accuracy of software based marking. How big > localisation error might be? > > Thank you in advance! > > Kind regards! > > Nenad > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From nenga at gmx.net Mon Jul 30 18:29:38 2012 From: nenga at gmx.net (Carina Oehrn) Date: Mon, 30 Jul 2012 18:29:38 +0200 Subject: [FieldTrip] granger causality Message-ID: <20120730162938.56630@gmx.net> Hi there, I have got an iEEG dataset and would like to look at the directionality of interactions between two channels in two different conditions using granger causality. Hopefully somebody here can help me :-) 1.) I know that I can calculate the appropriate model order and window length with the bsmart toolbox. But from the documentation I somehow do not get the format of data I should use for this calculation. When I enter the time-frequency data (which I want to use to estimate granger causality) (size: 2 x 2 x freq x time points), it doesn't work. Any advise? I have a sampling rate of 1000. What sort of time window and maximal model order would make sense do you think? 2)I would like to keep the time domain analyzing my data. What do you think would be an appropriate sliding time window using the 'ft_mvaranalysis' function? And what does it mean exactly? By choosing the model order, I am already determining the maximal time lag between the two functions. Are the values then estimated for the whole time window? 3)What do you think about statistics? Would it makes sense to use the non-parametric cluster approach to shuffle within patients and do a group analysis that way? Thank you so much in advance! Best, Carina As a summary,I am doing following steps with field trip: cfg = []; cfg.dftfilter ='yes' prep_cond1{subj} = ft_preprocessing(cfg, data); cfg = []; cfg.order = 5; cfg.toolbox = 'bsmart'; cfg.t_ftimwin = 0.05 cfg.toi = -1:0.001:3.5; mdata_cond1{subj}= ft_mvaranalysis(cfg, prep_cond1{subj}); cfg = []; cfg.method = 'mvar'; cfg.foi = 4:100; cond1_freq{subj}= ft_freqanalysis_mvar(cfg,mdata_cond1{subj}); cfg = []; cfg.method = 'granger'; cond1_granger{subj} = ft_connectivityanalysis(cfg, cond1_freq{subj}); From erdosttorun at gmail.com Tue Jul 31 13:33:58 2012 From: erdosttorun at gmail.com (erdost torun) Date: Tue, 31 Jul 2012 14:33:58 +0300 Subject: [FieldTrip] May I use fieldtrip on social science time series data? Message-ID: Dear Eelke and Jorne, Thank you both for your intesest. I plan to implement Wavelet-based Granger Causality on Social Science data through Fieldtrip toolbox. Hope I can make it correctly. If I publish any paper on it, I will share the results with you. Thank you so much All the best, Erdost Torun Dokuz Eylul University Dept of International Business and Trade From stephen.whitmarsh at gmail.com Tue Jul 31 17:35:52 2012 From: stephen.whitmarsh at gmail.com (stephen whitmarsh) Date: Tue, 31 Jul 2012 15:35:52 +0000 (UTC) Subject: [FieldTrip] Invitation to connect on LinkedIn Message-ID: <1955016892.13426275.1343748952505.JavaMail.app@ela4-app0131.prod> LinkedIn ------------ FieldTrip, I'd like to add you to my professional network on LinkedIn. - stephen stephen whitmarsh aio at Radboud Netherlands Confirm that you know stephen whitmarsh: https://www.linkedin.com/e/-kyqm8y-h5b5fjjo-12/isd/8060512829/VSO4ebwG/?hs=false&tok=1jOyZbi12DKRk1 -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/-kyqm8y-h5b5fjjo-12/o2zr3wMN-KUziWnbF0JpKw1y-MN7WW_ZDEc0/goo/fieldtrip%40science%2Eru%2Enl/20061/I2717672971_1/?hs=false&tok=3aVU5rC6CDKRk1 (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lihqih at gmail.com Tue Jul 31 22:45:16 2012 From: lihqih at gmail.com (qi li) Date: Tue, 31 Jul 2012 16:45:16 -0400 Subject: [FieldTrip] sourceplot Message-ID: Hi, I am having trouble to call the ft_sourceplot after ft_sourceanalysis. After sourceanalysis I have a source struct ans = time: [1x399 double] pos: [8196x3 double] inside: [1x8196 double] outside: [1x0 double] method: 'average' avg: [1x1 struct] cfg: [1x1 struct] unit: 'cm' Avg field has the following structure ans = mom: {1x8196 cell} pow: [8196x399 double] I want to plot the pow in the brian, so I use cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'avg.pow'; cfg.maskparameter = cfg.funparameter; cfg.funcolorlim = [0.0 1.2]; cfg.opacitylim = [0.0 1.2]; cfg.opacitymap = 'rampup'; figure ft_sourceplot(cfg, source); but the message says 'Error using ft_checkdata (line 307) This function requires volume data as input. Error in ft_volumedownsample (line 58) source = ft_checkdata(source, 'datatype', 'volume', 'feedback', 'no'); Error in ft_sourceplot (line 290) data = ft_volumedownsample(tmpcfg, data);' What does volume data point to? Thanks!