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!
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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
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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
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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
>
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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
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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
>
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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
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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
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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
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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
>
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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
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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
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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
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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/
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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
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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
>
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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
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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
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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/
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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
>
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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
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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]
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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
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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
>
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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
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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
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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
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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
>
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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
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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
>
>
>
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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]
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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
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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
>
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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
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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. Ive 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 Im 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
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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.
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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
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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,
Im 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
--------------------------------------------------
--------------------------------------------------
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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
>
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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? **
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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
>
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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
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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
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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
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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
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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
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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"