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<span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">Dear Eelke Spaak:</span>
<div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">Thank you for the advise on memory efficiency coding. Although in my case I have tried single precision and it still doesn’t seem to change much. I was wondering if I could analyse different
channels one by one although I don’t think is possible for inverse solution. I am referring to <a href="http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory/" class="">http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory/</a>. </div>
<div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">My problem is only when computing ft_sourceanalysis only. I don’t know if trying another method rather than lcmv may be less computationally heavy. </div>
<div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);"><br class="">
</div>
<div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">Best, </div>
<div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">Andrade. </div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 23 Jun 2020, at 12:00, <a href="mailto:fieldtrip-request@science.ru.nl" class="">
fieldtrip-request@science.ru.nl</a> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Send fieldtrip mailing list submissions to<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a><br class="">
<br class="">
To subscribe or unsubscribe via the World Wide Web, visit<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
or, via email, send a message with subject or body 'help' to<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>fieldtrip-request@science.ru.nl<br class="">
<br class="">
You can reach the person managing the list at<br class="">
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When replying, please edit your Subject line so it is more specific<br class="">
than "Re: Contents of fieldtrip digest..."<br class="">
<br class="">
<br class="">
Today's Topics:<br class="">
<br class="">
1. Re: Running out of memory (RAM) (Eelke Spaak)<br class="">
2. Connectivity Dimensions (Michael Glassen - Biomedical Engineer)<br class="">
3. Re: Connectivity Dimensions (Schoffelen, J.M. (Jan Mathijs))<br class="">
4. Re: Errors with downsampling and artifact rejection (Gaëlle Leys)<br class="">
5. Re: Errors with downsampling and artifact rejection<br class="">
(Stephen Whitmarsh)<br class="">
6. Re: fieldtrip Digest, Vol 115, Issue 23 (Andrade Rey René)<br class="">
7. Re: Errors with downsampling and artifact rejection<br class="">
(Schoffelen, J.M. (Jan Mathijs))<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Mon, 22 Jun 2020 15:27:19 +0200<br class="">
From: Eelke Spaak <e.spaak@donders.ru.nl><br class="">
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br class="">
Subject: Re: [FieldTrip] Running out of memory (RAM)<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><CABPNLUqmPjmyXR4gbRG3y-MLf97-SPGnRA+zp=SA4TBkCOugzw@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Andrade,<br class="">
<br class="">
You could have a look here for some tips on memory efficiency:<br class="">
http://www.fieldtriptoolbox.org/tutorial/memory/ Probably most relevant to<br class="">
you: change the data precision to single, rather than double (saves ~50%).<br class="">
<br class="">
Best,<br class="">
Eelke<br class="">
<br class="">
On Sun, 21 Jun 2020 at 22:34, Andrade Rey René <rene.andrade@edu.uah.es><br class="">
wrote:<br class="">
<br class="">
<blockquote type="cite" class="">Dear experts:<br class="">
I am running this code<br class="">
<br class="">
cfg = [];cfg.headmodel = headmodel;cfg.sourcemodel = leadfield;cfg.method = 'lcmv';cfg.lcmv.projectmom = 'yes'; % project dipole time series in direction of maximal power (see below)cfg.lcmv.kurtosis = 'yes'; % compute kurtosis at each locationsource = ft_sourceanalysis(cfg,
cov_matrix);<br class="">
<br class="">
<br class="">
Of http://www.fieldtriptoolbox.org/tutorial/epilepsy/. And I think I run<br class="">
out of memory because with “top” I can see the computer stops responding<br class="">
when near 85% of RAM memory(16GB).<br class="">
<br class="">
I cannot report any error because the only problem seems to be that either<br class="">
wrong code or wrong data or I don’t know.<br class="">
<br class="">
Best,<br class="">
Andrade.<br class="">
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
<br class="">
</blockquote>
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<br class="">
Message: 2<br class="">
Date: Mon, 22 Jun 2020 13:47:14 +0000<br class="">
From: "Michael Glassen - Biomedical Engineer"<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><MGlassen@kesslerfoundation.org><br class="">
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br class="">
Subject: [FieldTrip] Connectivity Dimensions<br class="">
Message-ID: <aae7aaea206143f3a87df61e1478a883@kesslerfoundation.org><br class="">
Content-Type: text/plain; charset="iso-8859-1"<br class="">
<br class="">
Hi all,<br class="">
<br class="">
<br class="">
I was looking to make some plots of directional connectivity data obtained from ft_connectivityanalysis, and I just wanted to double check the dimensions of pdcspctrm and dtfspctrm.<br class="">
<br class="">
<br class="">
The dimord is 'chan_chan_freq_time', but there isn't any indication of which chan dimension is the from direction and which is the to direction. I tried piecing it together by using ft_connectivityplot and comparing these to my own plots, and I'm pretty sure
that the dimensions are 'fromchan_tochan_freq_time' but I wanted to get confirmation before I moved forward.<br class="">
<br class="">
<br class="">
Best,<br class="">
<br class="">
Michael Glassen<br class="">
<br class="">
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<br class="">
Message: 3<br class="">
Date: Mon, 22 Jun 2020 13:52:32 +0000<br class="">
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen@donders.ru.nl><br class="">
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br class="">
Subject: Re: [FieldTrip] Connectivity Dimensions<br class="">
Message-ID: <B6521FD0-2B75-4E0B-AF0C-68CDF3CB411B@donders.ru.nl><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Michael,<br class="">
<br class="">
Consider it confirmed!<br class="">
<br class="">
Best wishes,<br class="">
JM<br class="">
<br class="">
<br class="">
On 22 Jun 2020, at 15:47, Michael Glassen - Biomedical Engineer <MGlassen@kesslerfoundation.org<mailto:MGlassen@kesslerfoundation.org>> wrote:<br class="">
<br class="">
Hi all,<br class="">
<br class="">
I was looking to make some plots of directional connectivity data obtained from ft_connectivityanalysis, and I just wanted to double check the dimensions of pdcspctrm and dtfspctrm.<br class="">
<br class="">
The dimord is 'chan_chan_freq_time', but there isn't any indication of which chan dimension is the from direction and which is the to direction. I tried piecing it together by using ft_connectivityplot and comparing these to my own plots, and I'm pretty sure
that the dimensions are 'fromchan_tochan_freq_time' but I wanted to get confirmation before I moved forward.<br class="">
<br class="">
Best,<br class="">
Michael Glassen<br class="">
<br class="">
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
<br class="">
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<br class="">
Message: 4<br class="">
Date: Mon, 22 Jun 2020 14:47:00 +0000<br class="">
From: Gaëlle Leys <gaelle.leys@kuleuven.be><br class="">
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br class="">
Subject: Re: [FieldTrip] Errors with downsampling and artifact<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>rejection<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><a967d7106acf41d182449785c9466db7@ICTS-S-EXMBX17.luna.kuleuven.be><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Stephen, <br class="">
<br class="">
I have included the data structures and cfg's involved in the functions.<br class="">
<br class="">
1)<span class="Apple-tab-span" style="white-space:pre"> </span>A. data structure for resampling data (raw data after reading it in):<br class="">
data_eeg = <br class="">
struct with fields:<br class="">
hdr: [1×1 struct]<br class="">
label: {129×1 cell}<br class="">
time: {[1×245726 double]}<br class="">
trial: {[129×245726 double]}<br class="">
fsample: 1000<br class="">
sampleinfo: [1 245726]<br class="">
elec: [1×1 struct]<br class="">
cfg: [1×1 struct]<br class="">
<br class="">
1)<span class="Apple-tab-span" style="white-space:pre"> </span>B. cfg for resampling data (I’m using all the default options for resampling):<br class="">
<br class="">
Cfg=[];<br class="">
[data_eeg] = ft_resampledata(cfg, data_eeg); % defaults are all OK<br class="">
<br class="">
2)<span class="Apple-tab-span" style="white-space:pre"> </span>A. data structure for artifact rejection (my data already epoched):<br class="">
data_eeg = <br class="">
struct with fields:<br class="">
hdr: [1×1 struct]<br class="">
label: {129×1 cell}<br class="">
time: {1×108 cell}<br class="">
trial: {1×108 cell}<br class="">
fsample: 1000<br class="">
sampleinfo: [108×2 double]<br class="">
elec: [1×1 struct]<br class="">
cfg: [1×1 struct]<br class="">
<br class="">
<br class="">
2)<span class="Apple-tab-span" style="white-space:pre"> </span>B. cfg for artifact rejection (taken from the automatic artifact rejection example):<br class="">
% jump<br class="">
cfg = [];<br class="">
cfg.trl = trl;<br class="">
cfg.datafile = '100_1_20200305.mff';<br class="">
cfg.headerfile = '100_1_20200305.mff';<br class="">
cfg.continuous = 'yes';<br class="">
<br class="">
% channel selection, cutoff and padding<br class="">
cfg.artfctdef.zvalue.channel = 'EEG';<br class="">
cfg.artfctdef.zvalue.cutoff = 20;<br class="">
cfg.artfctdef.zvalue.trlpadding = 0;<br class="">
cfg.artfctdef.zvalue.artpadding = 0;<br class="">
cfg.artfctdef.zvalue.fltpadding = 0;<br class="">
<br class="">
% algorithmic parameters<br class="">
cfg.artfctdef.zvalue.cumulative = 'yes';<br class="">
cfg.artfctdef.zvalue.medianfilter = 'yes';<br class="">
cfg.artfctdef.zvalue.medianfiltord = 9;<br class="">
cfg.artfctdef.zvalue.absdiff = 'yes';<br class="">
<br class="">
% make the process interactive<br class="">
cfg.artfctdef.zvalue.interactive = 'yes';<br class="">
<br class="">
[cfg, artifact_jump] = ft_artifact_zvalue(cfg); %plot error and error using zeros<br class="">
%[cfg, artifact_jump] = ft_artifact_zvalue(cfg, data_eeg); %no plot error, but each trial has the same graph, also error using zeros<br class="">
<br class="">
<br class="">
Kind regards, <br class="">
Gaëlle Leys<br class="">
<br class="">
<br class="">
<br class="">
-----Original Message-----<br class="">
From: fieldtrip <fieldtrip-bounces@science.ru.nl> On Behalf Of fieldtrip-request@science.ru.nl<br class="">
Sent: zaterdag 20 juni 2020 12:00<br class="">
To: fieldtrip@science.ru.nl<br class="">
Subject: fieldtrip Digest, Vol 115, Issue 22<br class="">
<br class="">
Send fieldtrip mailing list submissions to<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>fieldtrip@science.ru.nl<br class="">
<br class="">
To subscribe or unsubscribe via the World Wide Web, visit<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
or, via email, send a message with subject or body 'help' to<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>fieldtrip-request@science.ru.nl<br class="">
<br class="">
You can reach the person managing the list at<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>fieldtrip-owner@science.ru.nl<br class="">
<br class="">
When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..."<br class="">
<br class="">
<br class="">
Today's Topics:<br class="">
<br class="">
1. Errors with downsampling and artifact rejection (Gaëlle Leys)<br class="">
2. Re: Errors with downsampling and artifact rejection<br class="">
(Stephen Whitmarsh)<br class="">
3. MNI coordinates for the EEG easycap-M1 layout<br class="">
(SILVA PEREIRA, SILVANA)<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Fri, 19 Jun 2020 12:48:26 +0000<br class="">
From: Gaëlle Leys <gaelle.leys@kuleuven.be><br class="">
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br class="">
Subject: [FieldTrip] Errors with downsampling and artifact rejection<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><ccb89b4d31af42d3b4cd22485438f4ef@ICTS-S-EXMBX17.luna.kuleuven.be><br class="">
Content-Type: text/plain; charset="iso-8859-1"<br class="">
<br class="">
Dear Fieldtrip community,<br class="">
<br class="">
I have recently started with Fieldtrip for my EEG data processing and I am encountering some problems which I can't seem to resolve.<br class="">
I'm working with mff files from an EGI EEG system. I have no problem reading in and preprocessing the data. However, when trying to downsample and setup the automatic artifact removal, I'm getting some errors.<br class="">
<br class="">
<br class="">
1) When trying to downsample with the default options, these are the errors that I get:<br class="">
Error using resample>getSamples (line 357) The number of elements of Tx must match the number of rows of X when X is a matrix<br class="">
<br class="">
Error in resample>nonUniformResample (line 123) [x, tx] = getSamples(varargin{1:2});<br class="">
<br class="">
Error in resample (line 116)<br class="">
[varargout{1:max(1,nargout)}] = nonUniformResample(method,varargin{:});<br class="">
<br class="">
Error in ft_resampledata (line 228)<br class="">
newdat = transpose(resample(transpose(olddat),fsres,fsorig));<br class="">
<br class="">
I have tried downsampling before filtering, after filtering, on continuous data, or already segmented data. None of these things seem to resolve the error.<br class="">
<br class="">
<br class="">
2) When trying to set up the automatic artifact removal process and choosing yes for the interactive plot, I get a plotting error:<br class="">
<br class="">
Error using plot<br class="">
<br class="">
Vectors must be the same length.<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue>redraw_cb (line 973)<br class="">
<br class="">
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'b', 'displayname', 'data');<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue (line 512)<br class="">
<br class="">
redraw_cb(h);<br class="">
<br class="">
I've noticed that the xval and yval are different numbers, which of course doesn't allow plotting. It seems like the xval changes according to the epoch length, however the yval remains the same and equals the amount of samples in my continuous data.<br class="">
<br class="">
<br class="">
3) When choosing no for the interactive plot, I also get an error:<br class="">
Error using zeros<br class="">
Size inputs must be integers.<br class="">
<br class="">
Error in ft_artifact_zvalue (line 568)<br class="">
dum = zeros(1,max(opt.trl(:,2)));<br class="">
<br class="">
I've been looking into the functions and where it goes wrong, but I can't seem to pinpoint what exactly is causing these issues. Anyone here that can help or provide me some tips?<br class="">
<br class="">
Thanks in advance!<br class="">
<br class="">
Kind regards,<br class="">
<br class="">
Gaëlle Leys<br class="">
<br class="">
Research Associate<br class="">
Brain & Cognition<br class="">
Tiensestraat 102 box 3714<br class="">
3000 Leuven<br class="">
Room PSI 02.33<br class="">
tel. +32 16 37 61 98<br class="">
<br class="">
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<br class="">
Message: 2<br class="">
Date: Fri, 19 Jun 2020 15:08:21 +0200<br class="">
From: Stephen Whitmarsh <stephen.whitmarsh@gmail.com><br class="">
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br class="">
Subject: Re: [FieldTrip] Errors with downsampling and artifact<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>rejection<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><CAFrxm=w44QZ0C7xB4cpsqdy0D0ou5UcpHNM-q3bjyaqwwJxRwg@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Gaëlle,<br class="">
<br class="">
To understand the problem it would be helpful to have 1) description of the data structures going in ft_resampledata (just type in command line and copy-paste the output) and the artefact detection function you are using, and 2) the configuration (cfg) you
are using for those functions.<br class="">
<br class="">
Cheers,<br class="">
Stephen<br class="">
<br class="">
<br class="">
Op vr 19 jun. 2020 om 14:56 schreef Gaëlle Leys <gaelle.leys@kuleuven.be>:<br class="">
<br class="">
<blockquote type="cite" class="">Dear Fieldtrip community,<br class="">
<br class="">
<br class="">
<br class="">
I have recently started with Fieldtrip for my EEG data processing and <br class="">
I am encountering some problems which I can’t seem to resolve.<br class="">
<br class="">
I’m working with mff files from an EGI EEG system. I have no problem <br class="">
reading in and preprocessing the data. However, when trying to <br class="">
downsample and setup the automatic artifact removal, I’m getting some errors.<br class="">
<br class="">
<br class="">
<br class="">
1) When trying to downsample with the default options, these are the<br class="">
errors that I get:<br class="">
<br class="">
Error using resample>getSamples (line 357)<br class="">
<br class="">
The number of elements of Tx must match the number of rows of X when X <br class="">
is a matrix<br class="">
<br class="">
<br class="">
<br class="">
Error in resample>nonUniformResample (line 123)<br class="">
<br class="">
[x, tx] = getSamples(varargin{1:2});<br class="">
<br class="">
<br class="">
<br class="">
Error in resample (line 116)<br class="">
<br class="">
[varargout{1:max(1,nargout)}] = <br class="">
nonUniformResample(method,varargin{:});<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_resampledata (line 228)<br class="">
<br class="">
newdat = transpose(resample(transpose(olddat),fsres,fsorig));<br class="">
<br class="">
<br class="">
<br class="">
I have tried downsampling before filtering, after <br class="">
filtering, on continuous data, or already segmented data. None of <br class="">
these things seem to resolve the error.<br class="">
<br class="">
<br class="">
<br class="">
2) When trying to set up the automatic artifact removal process and<br class="">
choosing yes for the interactive plot, I get a plotting error:<br class="">
<br class="">
Error using plot<br class="">
<br class="">
Vectors must be the same length.<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue>redraw_cb (line 973)<br class="">
<br class="">
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'b', <br class="">
'displayname', 'data');<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue (line 512)<br class="">
<br class="">
redraw_cb(h);<br class="">
<br class="">
<br class="">
<br class="">
I’ve noticed that the xval and yval are different numbers, <br class="">
which of course doesn’t allow plotting. It seems like the xval changes <br class="">
according to the epoch length, however the yval remains the same and <br class="">
equals the amount of samples in my continuous data.<br class="">
<br class="">
<br class="">
<br class="">
3) When choosing no for the interactive plot, I also get an error:<br class="">
<br class="">
Error using zeros<br class="">
<br class="">
Size inputs must be integers.<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue (line 568)<br class="">
<br class="">
dum = zeros(1,max(opt.trl(:,2)));<br class="">
<br class="">
<br class="">
<br class="">
I’ve been looking into the functions and where it goes wrong, but I <br class="">
can’t seem to pinpoint what exactly is causing these issues. Anyone <br class="">
here that can help or provide me some tips?<br class="">
<br class="">
<br class="">
<br class="">
Thanks in advance!<br class="">
<br class="">
<br class="">
<br class="">
Kind regards,<br class="">
<br class="">
<br class="">
<br class="">
Gaëlle Leys<br class="">
<br class="">
<br class="">
<br class="">
Research Associate<br class="">
Brain & Cognition<br class="">
Tiensestraat 102 box 3714<br class="">
3000 Leuven<br class="">
<br class="">
Room PSI 02.33<br class="">
tel. +32 16 37 61 98<br class="">
<br class="">
<br class="">
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
<br class="">
</blockquote>
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<br class="">
Message: 3<br class="">
Date: Fri, 19 Jun 2020 18:58:36 +0200<br class="">
From: "SILVA PEREIRA, SILVANA" <silvana.silva@upf.edu><br class="">
To: fieldtrip@science.ru.nl<br class="">
Subject: [FieldTrip] MNI coordinates for the EEG easycap-M1 layout<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><CA+_MWm1NufDWa-fjR71OzQ5ab88ioyUT8OJ-QFYX9ABr7gNQrA@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear community,<br class="">
<br class="">
I've been struggling to find the 3D positions (montages) for the<br class="">
Acticap-64ch-standard2 on the web, which is a modified version of the easycap-M1, but I have not succeeded. In the Fieldtrip page http://www.fieldtriptoolbox.org/template/electrode/ you have the following:<br class="">
<br class="">
You can find the template 3-D electrode sets included in FieldTrip here <https://github.com/fieldtrip/fieldtrip/tree/master/template/electrode>.<br class="">
<br class="">
But in that link you only find a txt file with theta-phi coordinates (easycap-M1.txt). Is there any place where I could find these positions in MNI space?<br class="">
<br class="">
Thank you and best regards,<br class="">
Silvana<br class="">
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_______________________________________________<br class="">
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<br class="">
<br class="">
------------------------------<br class="">
<br class="">
End of fieldtrip Digest, Vol 115, Issue 22<br class="">
******************************************<br class="">
<br class="">
<br class="">
<br class="">
------------------------------<br class="">
<br class="">
Message: 5<br class="">
Date: Mon, 22 Jun 2020 17:35:42 +0200<br class="">
From: Stephen Whitmarsh <stephen.whitmarsh@gmail.com><br class="">
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br class="">
Subject: Re: [FieldTrip] Errors with downsampling and artifact<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>rejection<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><CAFrxm=wFXM-y1XBHbrVCTPwgjD2OWSG0c3Wx+v=Roiy7dprdPA@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Gaëlle,<br class="">
<br class="">
You are using default settings for downsampling, which will then try to<br class="">
downsample to 256Hz. Your original samplerate is 1000Hz, so that isn't a<br class="">
neat integer division.<br class="">
I tried the following, and could reproduce your problem:<br class="">
<br class="">
Fs = 1000;<br class="">
data_eeg = [];<br class="">
data_eeg.label = {'a','b','c'};<br class="">
data_eeg.time{1} = 0:1/Fs:10;<br class="">
data_eeg.trial{1} = rand(length(data_eeg.label),length(data_eeg.time{1}));<br class="">
data_eeg.Fs = Fs;<br class="">
data_eeg.sampleinfo = [1, length(data_eeg.time{1})];<br class="">
<br class="">
% Doesn't work:<br class="">
cfg = [];<br class="">
[data_eeg] = ft_resampledata(cfg, data_eeg);<br class="">
<br class="">
% Does work:<br class="">
cfg = [];<br class="">
cfg.resamplefs = 250;<br class="">
[data_eeg] = ft_resampledata(cfg, data_eeg);<br class="">
<br class="">
So that deals with your first problem. Not sure why it has a problem with<br class="">
the downsampling to non-integer values, but it's good practice and much<br class="">
faster to stick to that anyway.<br class="">
<br class="">
Not sure what to do with the artefact detection though, or what you<br class="">
expect; it seems you are running it with some contradictory settings/ways<br class="">
perhaps:<br class="">
- use cfg.dataset if reading from disk directly OR give datastructure to<br class="">
function is you already have data in memory<br class="">
- use cfg.continuous when data is not segmented<br class="">
- the comment "jump" suggests you use settings for SQUID jumps, i.e.<br class="">
optimized for MEG, but that should not give an error :-)<br class="">
<br class="">
I suspect you probably want to run artefact detection on your<br class="">
segmented data, so remove those references to the data on disk (datafile,<br class="">
headerfile), and the trl from the cfg, and give your segmented data as an<br class="">
argument as you did here:<br class="">
%[cfg, artifact_jump] = ft_artifact_zvalue(cfg, data_eeg); %no plot error,<br class="">
but each trial has the same graph, also error using zeros<br class="">
<br class="">
Let us know how it goes,<br class="">
<br class="">
All the best,<br class="">
Stephen<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
Op ma 22 jun. 2020 om 17:02 schreef Gaëlle Leys <gaelle.leys@kuleuven.be>:<br class="">
<br class="">
<blockquote type="cite" class="">Dear Stephen,<br class="">
<br class="">
I have included the data structures and cfg's involved in the functions.<br class="">
<br class="">
1) A. data structure for resampling data (raw data after reading it<br class="">
in):<br class="">
data_eeg =<br class="">
struct with fields:<br class="">
hdr: [1×1 struct]<br class="">
label: {129×1 cell}<br class="">
time: {[1×245726 double]}<br class="">
trial: {[129×245726 double]}<br class="">
fsample: 1000<br class="">
sampleinfo: [1 245726]<br class="">
elec: [1×1 struct]<br class="">
cfg: [1×1 struct]<br class="">
<br class="">
1) B. cfg for resampling data (I’m using all the default options for<br class="">
resampling):<br class="">
<br class="">
Cfg=[];<br class="">
[data_eeg] = ft_resampledata(cfg, data_eeg); % defaults are all OK<br class="">
<br class="">
2) A. data structure for artifact rejection (my data already epoched):<br class="">
data_eeg =<br class="">
struct with fields:<br class="">
hdr: [1×1 struct]<br class="">
label: {129×1 cell}<br class="">
time: {1×108 cell}<br class="">
trial: {1×108 cell}<br class="">
fsample: 1000<br class="">
sampleinfo: [108×2 double]<br class="">
elec: [1×1 struct]<br class="">
cfg: [1×1 struct]<br class="">
<br class="">
<br class="">
2) B. cfg for artifact rejection (taken from the automatic artifact<br class="">
rejection example):<br class="">
% jump<br class="">
cfg = [];<br class="">
cfg.trl = trl;<br class="">
cfg.datafile = '100_1_20200305.mff';<br class="">
cfg.headerfile = '100_1_20200305.mff';<br class="">
cfg.continuous = 'yes';<br class="">
<br class="">
% channel selection, cutoff and padding<br class="">
cfg.artfctdef.zvalue.channel = 'EEG';<br class="">
cfg.artfctdef.zvalue.cutoff = 20;<br class="">
cfg.artfctdef.zvalue.trlpadding = 0;<br class="">
cfg.artfctdef.zvalue.artpadding = 0;<br class="">
cfg.artfctdef.zvalue.fltpadding = 0;<br class="">
<br class="">
% algorithmic parameters<br class="">
cfg.artfctdef.zvalue.cumulative = 'yes';<br class="">
cfg.artfctdef.zvalue.medianfilter = 'yes';<br class="">
cfg.artfctdef.zvalue.medianfiltord = 9;<br class="">
cfg.artfctdef.zvalue.absdiff = 'yes';<br class="">
<br class="">
% make the process interactive<br class="">
cfg.artfctdef.zvalue.interactive = 'yes';<br class="">
<br class="">
[cfg, artifact_jump] = ft_artifact_zvalue(cfg); %plot error and error<br class="">
using zeros<br class="">
%[cfg, artifact_jump] = ft_artifact_zvalue(cfg, data_eeg); %no plot error,<br class="">
but each trial has the same graph, also error using zeros<br class="">
<br class="">
<br class="">
Kind regards,<br class="">
Gaëlle Leys<br class="">
<br class="">
<br class="">
<br class="">
-----Original Message-----<br class="">
From: fieldtrip <fieldtrip-bounces@science.ru.nl> On Behalf Of<br class="">
fieldtrip-request@science.ru.nl<br class="">
Sent: zaterdag 20 juni 2020 12:00<br class="">
To: fieldtrip@science.ru.nl<br class="">
Subject: fieldtrip Digest, Vol 115, Issue 22<br class="">
<br class="">
Send fieldtrip mailing list submissions to<br class="">
fieldtrip@science.ru.nl<br class="">
<br class="">
To subscribe or unsubscribe via the World Wide Web, visit<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
or, via email, send a message with subject or body 'help' to<br class="">
fieldtrip-request@science.ru.nl<br class="">
<br class="">
You can reach the person managing the list at<br class="">
fieldtrip-owner@science.ru.nl<br class="">
<br class="">
When replying, please edit your Subject line so it is more specific than<br class="">
"Re: Contents of fieldtrip digest..."<br class="">
<br class="">
<br class="">
Today's Topics:<br class="">
<br class="">
1. Errors with downsampling and artifact rejection (Gaëlle Leys)<br class="">
2. Re: Errors with downsampling and artifact rejection<br class="">
(Stephen Whitmarsh)<br class="">
3. MNI coordinates for the EEG easycap-M1 layout<br class="">
(SILVA PEREIRA, SILVANA)<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Fri, 19 Jun 2020 12:48:26 +0000<br class="">
From: Gaëlle Leys <gaelle.leys@kuleuven.be><br class="">
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br class="">
Subject: [FieldTrip] Errors with downsampling and artifact rejection<br class="">
Message-ID:<br class="">
<ccb89b4d31af42d3b4cd22485438f4ef@ICTS-S-EXMBX17.luna.kuleuven.be><br class="">
Content-Type: text/plain; charset="iso-8859-1"<br class="">
<br class="">
Dear Fieldtrip community,<br class="">
<br class="">
I have recently started with Fieldtrip for my EEG data processing and I am<br class="">
encountering some problems which I can't seem to resolve.<br class="">
I'm working with mff files from an EGI EEG system. I have no problem<br class="">
reading in and preprocessing the data. However, when trying to downsample<br class="">
and setup the automatic artifact removal, I'm getting some errors.<br class="">
<br class="">
<br class="">
1) When trying to downsample with the default options, these are the<br class="">
errors that I get:<br class="">
Error using resample>getSamples (line 357) The number of elements of Tx<br class="">
must match the number of rows of X when X is a matrix<br class="">
<br class="">
Error in resample>nonUniformResample (line 123) [x, tx] =<br class="">
getSamples(varargin{1:2});<br class="">
<br class="">
Error in resample (line 116)<br class="">
[varargout{1:max(1,nargout)}] = nonUniformResample(method,varargin{:});<br class="">
<br class="">
Error in ft_resampledata (line 228)<br class="">
newdat = transpose(resample(transpose(olddat),fsres,fsorig));<br class="">
<br class="">
I have tried downsampling before filtering, after<br class="">
filtering, on continuous data, or already segmented data. None of these<br class="">
things seem to resolve the error.<br class="">
<br class="">
<br class="">
2) When trying to set up the automatic artifact removal process and<br class="">
choosing yes for the interactive plot, I get a plotting error:<br class="">
<br class="">
Error using plot<br class="">
<br class="">
Vectors must be the same length.<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue>redraw_cb (line 973)<br class="">
<br class="">
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'b',<br class="">
'displayname', 'data');<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue (line 512)<br class="">
<br class="">
redraw_cb(h);<br class="">
<br class="">
I've noticed that the xval and yval are different numbers, which<br class="">
of course doesn't allow plotting. It seems like the xval changes according<br class="">
to the epoch length, however the yval remains the same and equals the<br class="">
amount of samples in my continuous data.<br class="">
<br class="">
<br class="">
3) When choosing no for the interactive plot, I also get an error:<br class="">
Error using zeros<br class="">
Size inputs must be integers.<br class="">
<br class="">
Error in ft_artifact_zvalue (line 568)<br class="">
dum = zeros(1,max(opt.trl(:,2)));<br class="">
<br class="">
I've been looking into the functions and where it goes wrong, but I can't<br class="">
seem to pinpoint what exactly is causing these issues. Anyone here that can<br class="">
help or provide me some tips?<br class="">
<br class="">
Thanks in advance!<br class="">
<br class="">
Kind regards,<br class="">
<br class="">
Gaëlle Leys<br class="">
<br class="">
Research Associate<br class="">
Brain & Cognition<br class="">
Tiensestraat 102 box 3714<br class="">
3000 Leuven<br class="">
Room PSI 02.33<br class="">
tel. +32 16 37 61 98<br class="">
<br class="">
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<blockquote type="cite" class=""><br class="">
</blockquote>
<br class="">
------------------------------<br class="">
<br class="">
Message: 2<br class="">
Date: Fri, 19 Jun 2020 15:08:21 +0200<br class="">
From: Stephen Whitmarsh <stephen.whitmarsh@gmail.com><br class="">
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br class="">
Subject: Re: [FieldTrip] Errors with downsampling and artifact<br class="">
rejection<br class="">
Message-ID:<br class="">
<CAFrxm=<br class="">
w44QZ0C7xB4cpsqdy0D0ou5UcpHNM-q3bjyaqwwJxRwg@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Gaëlle,<br class="">
<br class="">
To understand the problem it would be helpful to have 1) description of<br class="">
the data structures going in ft_resampledata (just type in command line and<br class="">
copy-paste the output) and the artefact detection function you are using,<br class="">
and 2) the configuration (cfg) you are using for those functions.<br class="">
<br class="">
Cheers,<br class="">
Stephen<br class="">
<br class="">
<br class="">
Op vr 19 jun. 2020 om 14:56 schreef Gaëlle Leys <gaelle.leys@kuleuven.be>:<br class="">
<br class="">
<blockquote type="cite" class="">Dear Fieldtrip community,<br class="">
<br class="">
<br class="">
<br class="">
I have recently started with Fieldtrip for my EEG data processing and<br class="">
I am encountering some problems which I can’t seem to resolve.<br class="">
<br class="">
I’m working with mff files from an EGI EEG system. I have no problem<br class="">
reading in and preprocessing the data. However, when trying to<br class="">
downsample and setup the automatic artifact removal, I’m getting some<br class="">
</blockquote>
errors.<br class="">
<blockquote type="cite" class=""><br class="">
<br class="">
<br class="">
1) When trying to downsample with the default options, these are the<br class="">
errors that I get:<br class="">
<br class="">
Error using resample>getSamples (line 357)<br class="">
<br class="">
The number of elements of Tx must match the number of rows of X when X<br class="">
is a matrix<br class="">
<br class="">
<br class="">
<br class="">
Error in resample>nonUniformResample (line 123)<br class="">
<br class="">
[x, tx] = getSamples(varargin{1:2});<br class="">
<br class="">
<br class="">
<br class="">
Error in resample (line 116)<br class="">
<br class="">
[varargout{1:max(1,nargout)}] =<br class="">
nonUniformResample(method,varargin{:});<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_resampledata (line 228)<br class="">
<br class="">
newdat = transpose(resample(transpose(olddat),fsres,fsorig));<br class="">
<br class="">
<br class="">
<br class="">
I have tried downsampling before filtering, after<br class="">
filtering, on continuous data, or already segmented data. None of<br class="">
these things seem to resolve the error.<br class="">
<br class="">
<br class="">
<br class="">
2) When trying to set up the automatic artifact removal process and<br class="">
choosing yes for the interactive plot, I get a plotting error:<br class="">
<br class="">
Error using plot<br class="">
<br class="">
Vectors must be the same length.<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue>redraw_cb (line 973)<br class="">
<br class="">
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'b',<br class="">
'displayname', 'data');<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue (line 512)<br class="">
<br class="">
redraw_cb(h);<br class="">
<br class="">
<br class="">
<br class="">
I’ve noticed that the xval and yval are different numbers,<br class="">
which of course doesn’t allow plotting. It seems like the xval changes<br class="">
according to the epoch length, however the yval remains the same and<br class="">
equals the amount of samples in my continuous data.<br class="">
<br class="">
<br class="">
<br class="">
3) When choosing no for the interactive plot, I also get an error:<br class="">
<br class="">
Error using zeros<br class="">
<br class="">
Size inputs must be integers.<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue (line 568)<br class="">
<br class="">
dum = zeros(1,max(opt.trl(:,2)));<br class="">
<br class="">
<br class="">
<br class="">
I’ve been looking into the functions and where it goes wrong, but I<br class="">
can’t seem to pinpoint what exactly is causing these issues. Anyone<br class="">
here that can help or provide me some tips?<br class="">
<br class="">
<br class="">
<br class="">
Thanks in advance!<br class="">
<br class="">
<br class="">
<br class="">
Kind regards,<br class="">
<br class="">
<br class="">
<br class="">
Gaëlle Leys<br class="">
<br class="">
<br class="">
<br class="">
Research Associate<br class="">
Brain & Cognition<br class="">
Tiensestraat 102 box 3714<br class="">
3000 Leuven<br class="">
<br class="">
Room PSI 02.33<br class="">
tel. +32 16 37 61 98<br class="">
<br class="">
<br class="">
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
<br class="">
</blockquote>
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<blockquote type="cite" class=""><br class="">
</blockquote>
<br class="">
------------------------------<br class="">
<br class="">
Message: 3<br class="">
Date: Fri, 19 Jun 2020 18:58:36 +0200<br class="">
From: "SILVA PEREIRA, SILVANA" <silvana.silva@upf.edu><br class="">
To: fieldtrip@science.ru.nl<br class="">
Subject: [FieldTrip] MNI coordinates for the EEG easycap-M1 layout<br class="">
Message-ID:<br class="">
<<br class="">
CA+_MWm1NufDWa-fjR71OzQ5ab88ioyUT8OJ-QFYX9ABr7gNQrA@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear community,<br class="">
<br class="">
I've been struggling to find the 3D positions (montages) for the<br class="">
Acticap-64ch-standard2 on the web, which is a modified version of the<br class="">
easycap-M1, but I have not succeeded. In the Fieldtrip page<br class="">
http://www.fieldtriptoolbox.org/template/electrode/ you have the<br class="">
following:<br class="">
<br class="">
You can find the template 3-D electrode sets included in FieldTrip here <<br class="">
https://github.com/fieldtrip/fieldtrip/tree/master/template/electrode>.<br class="">
<br class="">
But in that link you only find a txt file with theta-phi coordinates<br class="">
(easycap-M1.txt). Is there any place where I could find these positions in<br class="">
MNI space?<br class="">
<br class="">
Thank you and best regards,<br class="">
Silvana<br class="">
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<blockquote type="cite" class=""><br class="">
</blockquote>
<br class="">
------------------------------<br class="">
<br class="">
Subject: Digest Footer<br class="">
<br class="">
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
<br class="">
<br class="">
------------------------------<br class="">
<br class="">
End of fieldtrip Digest, Vol 115, Issue 22<br class="">
******************************************<br class="">
<br class="">
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
<br class="">
</blockquote>
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<br class="">
------------------------------<br class="">
<br class="">
Message: 6<br class="">
Date: Mon, 22 Jun 2020 21:38:39 +0000<br class="">
From: Andrade Rey René <rene.andrade@edu.uah.es><br class="">
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br class="">
Subject: Re: [FieldTrip] fieldtrip Digest, Vol 115, Issue 23<br class="">
Message-ID: <0CED8809-357C-49C1-B255-9CCE26A7EC75@edu.uah.es><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Is it normal that 16GB of RAM aren't sufficient for a normal EEG? May be I am doing something wrong and that is the reason my RAM isn't enough.<br class="">
<br class="">
Sent from my iPhone<br class="">
<br class="">
<blockquote type="cite" class="">On 22 Jun 2020, at 12:16, "fieldtrip-request@science.ru.nl" <fieldtrip-request@science.ru.nl> wrote:<br class="">
<br class="">
Send fieldtrip mailing list submissions to<br class="">
fieldtrip@science.ru.nl<br class="">
<br class="">
To subscribe or unsubscribe via the World Wide Web, visit<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
or, via email, send a message with subject or body 'help' to<br class="">
fieldtrip-request@science.ru.nl<br class="">
<br class="">
You can reach the person managing the list at<br class="">
fieldtrip-owner@science.ru.nl<br class="">
<br class="">
When replying, please edit your Subject line so it is more specific<br class="">
than "Re: Contents of fieldtrip digest..."<br class="">
<br class="">
<br class="">
Today's Topics:<br class="">
<br class="">
1. Running out of memory (RAM) (Andrade Rey René)<br class="">
2. Re: Running out of memory (RAM) (Schoffelen, J.M. (Jan Mathijs))<br class="">
3. Re: DICS question (Schoffelen, J.M. (Jan Mathijs))<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Sun, 21 Jun 2020 20:34:49 +0000<br class="">
From: Andrade Rey René <rene.andrade@edu.uah.es><br class="">
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br class="">
Subject: [FieldTrip] Running out of memory (RAM)<br class="">
Message-ID: <C30BBEE6-8A40-4668-8F48-E8244C205963@edu.uah.es><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear experts:<br class="">
I am running this code<br class="">
<br class="">
<br class="">
cfg = [];<br class="">
cfg.headmodel = headmodel;<br class="">
cfg.sourcemodel = leadfield;<br class="">
cfg.method = 'lcmv';<br class="">
cfg.lcmv.projectmom = 'yes'; % project dipole time series in direction of maximal power (see below)<br class="">
cfg.lcmv.kurtosis = 'yes'; % compute kurtosis at each location<br class="">
source = ft_sourceanalysis(cfg, cov_matrix);<br class="">
<br class="">
Of http://www.fieldtriptoolbox.org/tutorial/epilepsy/. And I think I run out of memory because with “top” I can see the computer stops responding when near 85% of RAM memory(16GB).<br class="">
<br class="">
I cannot report any error because the only problem seems to be that either wrong code or wrong data or I don’t know.<br class="">
<br class="">
Best,<br class="">
Andrade.<br class="">
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<br class="">
Message: 2<br class="">
Date: Mon, 22 Jun 2020 06:51:30 +0000<br class="">
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen@donders.ru.nl><br class="">
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br class="">
Subject: Re: [FieldTrip] Running out of memory (RAM)<br class="">
Message-ID: <308CD012-C138-486C-9B4C-E7F7487D3426@donders.ru.nl><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Andrade,<br class="">
<br class="">
Without any more specific information, the only meaningful comment that can be given here, is ‘get yourself a more powerful computer’.<br class="">
<br class="">
Memory usage depends highly on the operating system (in particular: matlab on windows machines used to be much less memory friendly, but it’s been a while that I have been running real computations on a window machine so perhaps this has changed), the total
size of all variables that need to be kept in memory, etc.<br class="">
<br class="">
Best wishes,<br class="">
Jan-Mathijs<br class="">
<br class="">
<br class="">
<br class="">
On 21 Jun 2020, at 22:34, Andrade Rey René <rene.andrade@edu.uah.es<mailto:rene.andrade@edu.uah.es>> wrote:<br class="">
<br class="">
Dear experts:<br class="">
I am running this code<br class="">
<br class="">
<br class="">
cfg = [];<br class="">
cfg.headmodel = headmodel;<br class="">
cfg.sourcemodel = leadfield;<br class="">
cfg.method = 'lcmv';<br class="">
cfg.lcmv.projectmom = 'yes'; % project dipole time series in direction of maximal power (see below)<br class="">
cfg.lcmv.kurtosis = 'yes'; % compute kurtosis at each location<br class="">
source = ft_sourceanalysis(cfg, cov_matrix);<br class="">
<br class="">
Of http://www.fieldtriptoolbox.org/tutorial/epilepsy/. And I think I run out of memory because with “top” I can see the computer stops responding when near 85% of RAM memory(16GB).<br class="">
<br class="">
I cannot report any error because the only problem seems to be that either wrong code or wrong data or I don’t know.<br class="">
<br class="">
Best,<br class="">
Andrade.<br class="">
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
<br class="">
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<br class="">
Message: 3<br class="">
Date: Mon, 22 Jun 2020 07:52:03 +0000<br class="">
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen@donders.ru.nl><br class="">
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br class="">
Cc: Sanjeev Nara <s.nara@bcbl.eu>, "m.lizarazu@bcbl.eu"<br class="">
<m.lizarazu@bcbl.eu>, Nicola Molinaro <nicolaml@gmail.com>, Craig<br class="">
Richter <craiggrichter@gmail.com><br class="">
Subject: Re: [FieldTrip] DICS question<br class="">
Message-ID: <40F6A2CA-6DB9-453A-B33B-6E2413DA4EA8@donders.ru.nl><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Craig,<br class="">
<br class="">
Let me forward this e-mail to the discussion list, in order to widen the scope to all of Donostia and beyond.<br class="">
<br class="">
Indeed, the estimation of spectrally resolved GC requires a full bandwidth signal. I have not extensively played with the different options here, but the scenario that you describe, i.e. compute a DICS spatial filter on a narrow bandwidth-of-interest signal,
and subjecting the broadband sensor signals to this spatial filter, will, in my opinion, not be really optimal. The reason for this is that the beamformer then can only suppress interference from that particular bandwidth. Signal components that lie outside
this range might still leak into the estimated time courses, which may lead to distortion and invalid GC estimates.<br class="">
<br class="">
So, if you would be using an LCMV beamformer, I’d always recommend a broadband spatial filter, optionally on mildly highpass-filtered data. Then, the risk could be that the 1/f characteristic of the signals results in a covariance matrix whose signal components
are dominated by low-frequency stuff. One could then worry about suboptimal spatial filtering of the higher frequency components. This is probably true, and I have worried about this myself, but in my experience this is the least of the worries one should
have. (as a side note: I have played around with spectral whitening of the data prior to the beamforming. The reasoning behind this is that the individual variance components in the data are more evenly balanced across the frequency range, but the long story
short is that this does not seem to influence the final GC estimate).<br class="">
<br class="">
A larger worry would be the fact that source-estimated GC spectra very often have a canonical shape, unless you use extremely well-defined data such a visual attention experiment that induces strong gamma band oscillations. If you are into applying connectivity
analysis in a more ethereal context, such as a cognitive or language experiment, you will see that source-level GC spectra will be always dominated by the low-frequency components (i.e. most of the time you’ll find a large peak at low frequencies). This of
course can reflect genuine neuronal coupling, but my suspicion is that this is most of the time due to ‘weak signal asymmetries’, in other words due to asymmetries in SNR and location specific leakage of power. This can be further investigated using time-flipping
and an appropriate statistical evaluation. For inspiration, you can of course always consult my 2017 PNAS paper :).<br class="">
<br class="">
Another worry of course would be the fact that you’d be working with Elekta data :).<br class="">
<br class="">
Practically, what I typically do, is to compute the broadband spatial filter with LCMV, and apply these filters (as is, or dimensionality reduced after a parcellation step) to the sensor level cross-spectral density data (from DC to Nyquist). The spectral factorization
algorithm should be applied to the source-level data, which in my experience is most stable if you do this pairwise. I know that this is suboptimal in the context of an interpretation of direct versus indirect interactions, but I have always found this an
argument that is part of a non-discussion at this stage of the analysis. One should first trust the estimates overall, before a discussion about direct versus indirect coupling becomes relevant.<br class="">
<br class="">
Best wishes,<br class="">
JM<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
On 19 Jun 2020, at 18:06, Craig Richter <craiggrichter@gmail.com<mailto:craiggrichter@gmail.com>> wrote:<br class="">
<br class="">
Hey JM,<br class="">
<br class="">
How’s it going? Covid treating you ok? Been a bit crazy here, but normalcy is resuming.<br class="">
<br class="">
I have a question about DICS for you… :-/... Anyhow, so for coherence at a given frequency DICS is superior, since the spatial-filter is specific to that frequency, which is about the same as a building a noise-covariance matrix from a narrow-band filtered
signal? But to do source-level GC, we need the broadband time-series, so we’re forced to use the unfiltered data and LCMV. But… what if we know the frequency we want to analyse, so we build the spatial filter on this frequency, or narrow-band filtered data,
then compute virtual time series from the raw data, and compute GC. Then we simply look at our frequency of interest in the spectral results. Would this potentially generate a better GC estimate at the frequency of interest, or would it just mess everything
up?<br class="">
<br class="">
PS - I’ve cc’ed some other interested folks.<br class="">
<br class="">
Thanks!<br class="">
<br class="">
C.<br class="">
<br class="">
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_______________________________________________<br class="">
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End of fieldtrip Digest, Vol 115, Issue 23<br class="">
******************************************<br class="">
</blockquote>
<br class="">
<br class="">
<br class="">
------------------------------<br class="">
<br class="">
Message: 7<br class="">
Date: Tue, 23 Jun 2020 06:42:03 +0000<br class="">
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen@donders.ru.nl><br class="">
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br class="">
Subject: Re: [FieldTrip] Errors with downsampling and artifact<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>rejection<br class="">
Message-ID: <184602F0-A203-406F-B278-32CD899D4532@donders.ru.nl><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Hi Gaëlle,<br class="">
<br class="">
Adding to Stephen’s comment: reading through the code and comments (highly recommended to occasionally do this, then you get a feel what’s going on under the hood) I saw that there’s a discrepancy between the comments in the help section of ft_resampledata,
where it states that the default resamplefs=256, and the actually implemented default resamplefs, which is []. Apparently, MATLAB is lenient with respect to mathematical operations involving empty variables. Specifically, it doesn’t throw an error on lines
160/161 in ft_resampledata, where an empty variable is multiplied and divided by a scalar. Long story short, the silently accepted empty variable is the acual cause of the reported problem in ft_resampledata.<br class="">
<br class="">
I look forward to a PR that fixes this. I suggest making the documentation consistent, i.e. stating that cfg.resamplefs is an argument that needs to be defined, and explicitly check this in the code, i.e. throw an error if it isn’t defined. This is typically
done with a call to ft_checkconfig using the key-value pair ‘required’, and ‘resamplefs’ (in this case).<br class="">
<br class="">
Thanks for your contribution,<br class="">
<br class="">
Jan-Mathijs<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
On 22 Jun 2020, at 17:35, Stephen Whitmarsh <stephen.whitmarsh@gmail.com<mailto:stephen.whitmarsh@gmail.com>> wrote:<br class="">
<br class="">
Dear Gaëlle,<br class="">
<br class="">
You are using default settings for downsampling, which will then try to downsample to 256Hz. Your original samplerate is 1000Hz, so that isn't a neat integer division.<br class="">
I tried the following, and could reproduce your problem:<br class="">
<br class="">
Fs = 1000;<br class="">
data_eeg = [];<br class="">
data_eeg.label = {'a','b','c'};<br class="">
data_eeg.time{1} = 0:1/Fs:10;<br class="">
data_eeg.trial{1} = rand(length(data_eeg.label),length(data_eeg.time{1}));<br class="">
data_eeg.Fs = Fs;<br class="">
data_eeg.sampleinfo = [1, length(data_eeg.time{1})];<br class="">
<br class="">
% Doesn't work:<br class="">
cfg = [];<br class="">
[data_eeg] = ft_resampledata(cfg, data_eeg);<br class="">
<br class="">
% Does work:<br class="">
cfg = [];<br class="">
cfg.resamplefs = 250;<br class="">
[data_eeg] = ft_resampledata(cfg, data_eeg);<br class="">
<br class="">
So that deals with your first problem. Not sure why it has a problem with the downsampling to non-integer values, but it's good practice and much faster to stick to that anyway.<br class="">
<br class="">
Not sure what to do with the artefact detection though, or what you expect; it seems you are running it with some contradictory settings/ways perhaps:<br class="">
- use cfg.dataset if reading from disk directly OR give datastructure to function is you already have data in memory<br class="">
- use cfg.continuous when data is not segmented<br class="">
- the comment "jump" suggests you use settings for SQUID jumps, i.e. optimized for MEG, but that should not give an error :-)<br class="">
<br class="">
I suspect you probably want to run artefact detection on your segmented data, so remove those references to the data on disk (datafile, headerfile), and the trl from the cfg, and give your segmented data as an argument as you did here:<br class="">
%[cfg, artifact_jump] = ft_artifact_zvalue(cfg, data_eeg); %no plot error, but each trial has the same graph, also error using zeros<br class="">
<br class="">
Let us know how it goes,<br class="">
<br class="">
All the best,<br class="">
Stephen<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
Op ma 22 jun. 2020 om 17:02 schreef Gaëlle Leys <gaelle.leys@kuleuven.be<mailto:gaelle.leys@kuleuven.be>>:<br class="">
Dear Stephen,<br class="">
<br class="">
I have included the data structures and cfg's involved in the functions.<br class="">
<br class="">
1) A. data structure for resampling data (raw data after reading it in):<br class="">
data_eeg =<br class="">
struct with fields:<br class="">
hdr: [1×1 struct]<br class="">
label: {129×1 cell}<br class="">
time: {[1×245726 double]}<br class="">
trial: {[129×245726 double]}<br class="">
fsample: 1000<br class="">
sampleinfo: [1 245726]<br class="">
elec: [1×1 struct]<br class="">
cfg: [1×1 struct]<br class="">
<br class="">
1) B. cfg for resampling data (I’m using all the default options for resampling):<br class="">
<br class="">
Cfg=[];<br class="">
[data_eeg] = ft_resampledata(cfg, data_eeg); % defaults are all OK<br class="">
<br class="">
2) A. data structure for artifact rejection (my data already epoched):<br class="">
data_eeg =<br class="">
struct with fields:<br class="">
hdr: [1×1 struct]<br class="">
label: {129×1 cell}<br class="">
time: {1×108 cell}<br class="">
trial: {1×108 cell}<br class="">
fsample: 1000<br class="">
sampleinfo: [108×2 double]<br class="">
elec: [1×1 struct]<br class="">
cfg: [1×1 struct]<br class="">
<br class="">
<br class="">
2) B. cfg for artifact rejection (taken from the automatic artifact rejection example):<br class="">
% jump<br class="">
cfg = [];<br class="">
cfg.trl = trl;<br class="">
cfg.datafile = '100_1_20200305.mff';<br class="">
cfg.headerfile = '100_1_20200305.mff';<br class="">
cfg.continuous = 'yes';<br class="">
<br class="">
% channel selection, cutoff and padding<br class="">
cfg.artfctdef.zvalue.channel = 'EEG';<br class="">
cfg.artfctdef.zvalue.cutoff = 20;<br class="">
cfg.artfctdef.zvalue.trlpadding = 0;<br class="">
cfg.artfctdef.zvalue.artpadding = 0;<br class="">
cfg.artfctdef.zvalue.fltpadding = 0;<br class="">
<br class="">
% algorithmic parameters<br class="">
cfg.artfctdef.zvalue.cumulative = 'yes';<br class="">
cfg.artfctdef.zvalue.medianfilter = 'yes';<br class="">
cfg.artfctdef.zvalue.medianfiltord = 9;<br class="">
cfg.artfctdef.zvalue.absdiff = 'yes';<br class="">
<br class="">
% make the process interactive<br class="">
cfg.artfctdef.zvalue.interactive = 'yes';<br class="">
<br class="">
[cfg, artifact_jump] = ft_artifact_zvalue(cfg); %plot error and error using zeros<br class="">
%[cfg, artifact_jump] = ft_artifact_zvalue(cfg, data_eeg); %no plot error, but each trial has the same graph, also error using zeros<br class="">
<br class="">
<br class="">
Kind regards,<br class="">
Gaëlle Leys<br class="">
<br class="">
<br class="">
<br class="">
-----Original Message-----<br class="">
From: fieldtrip <fieldtrip-bounces@science.ru.nl<mailto:fieldtrip-bounces@science.ru.nl>> On Behalf Of fieldtrip-request@science.ru.nl<mailto:fieldtrip-request@science.ru.nl><br class="">
Sent: zaterdag 20 juni 2020 12:00<br class="">
To: fieldtrip@science.ru.nl<mailto:fieldtrip@science.ru.nl><br class="">
Subject: fieldtrip Digest, Vol 115, Issue 22<br class="">
<br class="">
Send fieldtrip mailing list submissions to<br class="">
fieldtrip@science.ru.nl<mailto:fieldtrip@science.ru.nl><br class="">
<br class="">
To subscribe or unsubscribe via the World Wide Web, visit<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
or, via email, send a message with subject or body 'help' to<br class="">
fieldtrip-request@science.ru.nl<mailto:fieldtrip-request@science.ru.nl><br class="">
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You can reach the person managing the list at<br class="">
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<br class="">
When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..."<br class="">
<br class="">
<br class="">
Today's Topics:<br class="">
<br class="">
1. Errors with downsampling and artifact rejection (Gaëlle Leys)<br class="">
2. Re: Errors with downsampling and artifact rejection<br class="">
(Stephen Whitmarsh)<br class="">
3. MNI coordinates for the EEG easycap-M1 layout<br class="">
(SILVA PEREIRA, SILVANA)<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Fri, 19 Jun 2020 12:48:26 +0000<br class="">
From: Gaëlle Leys <gaelle.leys@kuleuven.be<mailto:gaelle.leys@kuleuven.be>><br class="">
To: "fieldtrip@science.ru.nl<mailto:fieldtrip@science.ru.nl>" <fieldtrip@science.ru.nl<mailto:fieldtrip@science.ru.nl>><br class="">
Subject: [FieldTrip] Errors with downsampling and artifact rejection<br class="">
Message-ID:<br class="">
<ccb89b4d31af42d3b4cd22485438f4ef@ICTS-S-EXMBX17.luna.kuleuven.be<mailto:ccb89b4d31af42d3b4cd22485438f4ef@ICTS-S-EXMBX17.luna.kuleuven.be>><br class="">
Content-Type: text/plain; charset="iso-8859-1"<br class="">
<br class="">
Dear Fieldtrip community,<br class="">
<br class="">
I have recently started with Fieldtrip for my EEG data processing and I am encountering some problems which I can't seem to resolve.<br class="">
I'm working with mff files from an EGI EEG system. I have no problem reading in and preprocessing the data. However, when trying to downsample and setup the automatic artifact removal, I'm getting some errors.<br class="">
<br class="">
<br class="">
1) When trying to downsample with the default options, these are the errors that I get:<br class="">
Error using resample>getSamples (line 357) The number of elements of Tx must match the number of rows of X when X is a matrix<br class="">
<br class="">
Error in resample>nonUniformResample (line 123) [x, tx] = getSamples(varargin{1:2});<br class="">
<br class="">
Error in resample (line 116)<br class="">
[varargout{1:max(1,nargout)}] = nonUniformResample(method,varargin{:});<br class="">
<br class="">
Error in ft_resampledata (line 228)<br class="">
newdat = transpose(resample(transpose(olddat),fsres,fsorig));<br class="">
<br class="">
I have tried downsampling before filtering, after filtering, on continuous data, or already segmented data. None of these things seem to resolve the error.<br class="">
<br class="">
<br class="">
2) When trying to set up the automatic artifact removal process and choosing yes for the interactive plot, I get a plotting error:<br class="">
<br class="">
Error using plot<br class="">
<br class="">
Vectors must be the same length.<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue>redraw_cb (line 973)<br class="">
<br class="">
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'b', 'displayname', 'data');<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue (line 512)<br class="">
<br class="">
redraw_cb(h);<br class="">
<br class="">
I've noticed that the xval and yval are different numbers, which of course doesn't allow plotting. It seems like the xval changes according to the epoch length, however the yval remains the same and equals the amount of samples in my continuous data.<br class="">
<br class="">
<br class="">
3) When choosing no for the interactive plot, I also get an error:<br class="">
Error using zeros<br class="">
Size inputs must be integers.<br class="">
<br class="">
Error in ft_artifact_zvalue (line 568)<br class="">
dum = zeros(1,max(opt.trl(:,2)));<br class="">
<br class="">
I've been looking into the functions and where it goes wrong, but I can't seem to pinpoint what exactly is causing these issues. Anyone here that can help or provide me some tips?<br class="">
<br class="">
Thanks in advance!<br class="">
<br class="">
Kind regards,<br class="">
<br class="">
Gaëlle Leys<br class="">
<br class="">
Research Associate<br class="">
Brain & Cognition<br class="">
Tiensestraat 102 box 3714<br class="">
3000 Leuven<br class="">
Room PSI 02.33<br class="">
tel. +32 16 37 61 98<br class="">
<br class="">
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<br class="">
Message: 2<br class="">
Date: Fri, 19 Jun 2020 15:08:21 +0200<br class="">
From: Stephen Whitmarsh <stephen.whitmarsh@gmail.com<mailto:stephen.whitmarsh@gmail.com>><br class="">
To: FieldTrip discussion list <fieldtrip@science.ru.nl<mailto:fieldtrip@science.ru.nl>><br class="">
Subject: Re: [FieldTrip] Errors with downsampling and artifact<br class="">
rejection<br class="">
Message-ID:<br class="">
<CAFrxm=w44QZ0C7xB4cpsqdy0D0ou5UcpHNM-q3bjyaqwwJxRwg@mail.gmail.com<mailto:w44QZ0C7xB4cpsqdy0D0ou5UcpHNM-q3bjyaqwwJxRwg@mail.gmail.com>><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Gaëlle,<br class="">
<br class="">
To understand the problem it would be helpful to have 1) description of the data structures going in ft_resampledata (just type in command line and copy-paste the output) and the artefact detection function you are using, and 2) the configuration (cfg) you
are using for those functions.<br class="">
<br class="">
Cheers,<br class="">
Stephen<br class="">
<br class="">
<br class="">
Op vr 19 jun. 2020 om 14:56 schreef Gaëlle Leys <gaelle.leys@kuleuven.be<mailto:gaelle.leys@kuleuven.be>>:<br class="">
<br class="">
<blockquote type="cite" class="">Dear Fieldtrip community,<br class="">
<br class="">
<br class="">
<br class="">
I have recently started with Fieldtrip for my EEG data processing and<br class="">
I am encountering some problems which I can’t seem to resolve.<br class="">
<br class="">
I’m working with mff files from an EGI EEG system. I have no problem<br class="">
reading in and preprocessing the data. However, when trying to<br class="">
downsample and setup the automatic artifact removal, I’m getting some errors.<br class="">
<br class="">
<br class="">
<br class="">
1) When trying to downsample with the default options, these are the<br class="">
errors that I get:<br class="">
<br class="">
Error using resample>getSamples (line 357)<br class="">
<br class="">
The number of elements of Tx must match the number of rows of X when X<br class="">
is a matrix<br class="">
<br class="">
<br class="">
<br class="">
Error in resample>nonUniformResample (line 123)<br class="">
<br class="">
[x, tx] = getSamples(varargin{1:2});<br class="">
<br class="">
<br class="">
<br class="">
Error in resample (line 116)<br class="">
<br class="">
[varargout{1:max(1,nargout)}] =<br class="">
nonUniformResample(method,varargin{:});<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_resampledata (line 228)<br class="">
<br class="">
newdat = transpose(resample(transpose(olddat),fsres,fsorig));<br class="">
<br class="">
<br class="">
<br class="">
I have tried downsampling before filtering, after<br class="">
filtering, on continuous data, or already segmented data. None of<br class="">
these things seem to resolve the error.<br class="">
<br class="">
<br class="">
<br class="">
2) When trying to set up the automatic artifact removal process and<br class="">
choosing yes for the interactive plot, I get a plotting error:<br class="">
<br class="">
Error using plot<br class="">
<br class="">
Vectors must be the same length.<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue>redraw_cb (line 973)<br class="">
<br class="">
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'b',<br class="">
'displayname', 'data');<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue (line 512)<br class="">
<br class="">
redraw_cb(h);<br class="">
<br class="">
<br class="">
<br class="">
I’ve noticed that the xval and yval are different numbers,<br class="">
which of course doesn’t allow plotting. It seems like the xval changes<br class="">
according to the epoch length, however the yval remains the same and<br class="">
equals the amount of samples in my continuous data.<br class="">
<br class="">
<br class="">
<br class="">
3) When choosing no for the interactive plot, I also get an error:<br class="">
<br class="">
Error using zeros<br class="">
<br class="">
Size inputs must be integers.<br class="">
<br class="">
<br class="">
<br class="">
Error in ft_artifact_zvalue (line 568)<br class="">
<br class="">
dum = zeros(1,max(opt.trl(:,2)));<br class="">
<br class="">
<br class="">
<br class="">
I’ve been looking into the functions and where it goes wrong, but I<br class="">
can’t seem to pinpoint what exactly is causing these issues. Anyone<br class="">
here that can help or provide me some tips?<br class="">
<br class="">
<br class="">
<br class="">
Thanks in advance!<br class="">
<br class="">
<br class="">
<br class="">
Kind regards,<br class="">
<br class="">
<br class="">
<br class="">
Gaëlle Leys<br class="">
<br class="">
<br class="">
<br class="">
Research Associate<br class="">
Brain & Cognition<br class="">
Tiensestraat 102 box 3714<br class="">
3000 Leuven<br class="">
<br class="">
Room PSI 02.33<br class="">
tel. +32 16 37 61 98<br class="">
<br class="">
<br class="">
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
<br class="">
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Message: 3<br class="">
Date: Fri, 19 Jun 2020 18:58:36 +0200<br class="">
From: "SILVA PEREIRA, SILVANA" <silvana.silva@upf.edu<mailto:silvana.silva@upf.edu>><br class="">
To: fieldtrip@science.ru.nl<mailto:fieldtrip@science.ru.nl><br class="">
Subject: [FieldTrip] MNI coordinates for the EEG easycap-M1 layout<br class="">
Message-ID:<br class="">
<CA+_MWm1NufDWa-fjR71OzQ5ab88ioyUT8OJ-QFYX9ABr7gNQrA@mail.gmail.com<mailto:CA%2B_MWm1NufDWa-fjR71OzQ5ab88ioyUT8OJ-QFYX9ABr7gNQrA@mail.gmail.com>><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear community,<br class="">
<br class="">
I've been struggling to find the 3D positions (montages) for the<br class="">
Acticap-64ch-standard2 on the web, which is a modified version of the easycap-M1, but I have not succeeded. In the Fieldtrip page http://www.fieldtriptoolbox.org/template/electrode/ you have the following:<br class="">
<br class="">
You can find the template 3-D electrode sets included in FieldTrip here <https://github.com/fieldtrip/fieldtrip/tree/master/template/electrode>.<br class="">
<br class="">
But in that link you only find a txt file with theta-phi coordinates (easycap-M1.txt). Is there any place where I could find these positions in MNI space?<br class="">
<br class="">
Thank you and best regards,<br class="">
Silvana<br class="">
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