<div dir="ltr">Dear Nick and Jan-Mathijs, <div><br></div><div>thanks for your emails. Here is the part of the code that details the cfg inputs. I basically stuck to what was in the tutorial:</div><div><br></div><div><div>cfg = [];</div><div>cfg.channel = 'all';</div><div><br></div><div>% prepare neighbouring channels</div><div><br></div><div>cfg_neighb = [];</div><div>cfg_neighb.method = 'distance'; </div><div>cfg.channel = 'all';</div><div>cfg_neighb.feedback = 'yes';</div><div>cfg_neighb.layout = 'easycapM3.mat'; </div><div><br></div><div>neighbours = ft_prepare_neighbours(cfg_neighb, Correct{1});</div><div><br></div><div>% settings for statistics</div><div><br></div><div>cfg = [];</div><div>cfg.channel = {'EEG'};</div><div>cfg.latency = [0 1];</div><div><br></div><div>cfg.method = 'montecarlo';</div><div>cfg.statistic = 'depsamplesT';</div><div>cfg.correctm = 'cluster';</div><div>cfg.clusteralpha = 0.05;</div><div>cfg.clusterstatistic = 'maxsum';</div><div>cfg.minnbchan = 2;</div><div>cfg.neighbours = neighbours; </div><div>cfg.tail = 0;</div><div>cfg.clustertail = 0;</div><div>cfg.alpha = 0.5;</div><div>cfg.numrandomization = 500;</div><div><br></div><div>% prepare design</div><div>subj = 24;</div><div>design = zeros(2,2*subj);</div><div>for i = 1:subj</div><div> design(1,i) = i;</div><div>end</div><div>for i = 1:subj</div><div> design(1,subj+i) = i;</div><div>end</div><div>design(2,1:subj) = 1;</div><div>design(2,subj+1:2*subj) = 2;</div><div><br></div><div>cfg.design = design;</div><div>cfg.uvar = 1;</div><div>cfg.ivar = 2;</div></div><div><br></div><div>Best,</div><div>Anne</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Dec 11, 2015 at 12:00 PM, <span dir="ltr"><<a href="mailto:fieldtrip-request@science.ru.nl" target="_blank">fieldtrip-request@science.ru.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send fieldtrip mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Stats matrix incomplete - cluster-based permutation test<br>
(Anne Mickan)<br>
2. Re: Stats matrix incomplete - cluster-based permutation test<br>
(Nicholas A. Peatfield)<br>
3. Re: Stats matrix incomplete - cluster-based permutation test<br>
(Schoffelen, J.M. (Jan Mathijs))<br>
4. Re: filed trip (aishwarya selvaraj)<br>
5. Re: filed trip (Pelt, S. van (Stan))<br>
6. possible bug in tutorial code for creating sourcemodel (Juan)<br>
7. Re: possible bug in tutorial code for creating sourcemodel<br>
(Schoffelen, J.M. (Jan Mathijs))<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 10 Dec 2015 18:14:10 +0100<br>
From: Anne Mickan <<a href="mailto:amickan1990@gmail.com">amickan1990@gmail.com</a>><br>
To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
Subject: [FieldTrip] Stats matrix incomplete - cluster-based<br>
permutation test<br>
Message-ID:<br>
<<a href="mailto:CANX43OJN4h_1jEuDKMNwQC4sHeW%2BE2_StnS3WLkEbOkVpMerQA@mail.gmail.com">CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear all,<br>
<br>
I'm just starting to work on a cluster-based permutation test script based<br>
on the tutorial for within-subject designs on the fieldtrip website. I ran<br>
into an issue when computing the [stat] matrix. I used the code as it was<br>
on the website:<br>
<br>
[stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});<br>
<br>
with the Correct and Incorrect matrices looking as follows:<br>
<br>
Correct{1}<br>
<br>
avg: [34x600 double]<br>
time: [1x600 double]<br>
fsample: '500'<br>
label: {34x1 cell}<br>
dimord: 'chan_time'<br>
dof: [34x600 double]<br>
var: [34x600 double]<br>
<br>
The function runs without problems, i.e I don't get any error messages.<br>
However, the result seems incomplete.<br>
<br>
stat =<br>
prob: [25x1 double]<br>
posclusters: []<br>
posclusterslabelmat: [25x1 double]<br>
posdistribution: [1x500 double]<br>
negclusters: [1x1 struct]<br>
negclusterslabelmat: [25x1 double]<br>
negdistribution: [1x500 double]<br>
cirange: [25x1 double]<br>
mask: [25x1 logical]<br>
stat: [25x1 double]<br>
ref: [25x1 double]<br>
dimord: 'chan_time'<br>
label: {25x1 cell}<br>
time: 0<br>
cfg: [1x1 struct]<br>
<br>
Specifically, I later run into trouble with the stat.posclusterslabelmat<br>
and stat.negclusterslabelmat matrices which should apparantly contain far<br>
more values something more like 25x500 instead of 25x1. When calling<br>
neg_int = all(neg(:, m(k):m(k+1)), 2)<br>
I get the "Index exceeds matrix dimensions" error message which I assume<br>
has to do with the fact that "neg" does not have the appropriate matrix<br>
dimensions<br>
(neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )<br>
<br>
Where is the error / where should I look for the error?<br>
<br>
Some further design details:<br>
Nsubj = 24<br>
2 conditions = Correct, Incorrect<br>
Within-subject design<br>
sampling rate = 500<br>
34 channels<br>
<br>
I hope I gave enough / the necessary information for someone to help me<br>
out.<br>
<br>
Thanks in advance!<br>
<br>
Best,<br>
Anne<br>
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<br>
Message: 2<br>
Date: Thu, 10 Dec 2015 11:13:10 -0800<br>
From: "Nicholas A. Peatfield" <<a href="mailto:nick.peatfield@gmail.com">nick.peatfield@gmail.com</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] Stats matrix incomplete - cluster-based<br>
permutation test<br>
Message-ID:<br>
<CADzq99=<a href="mailto:3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com">3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Anne,<br>
<br>
To get an answer/suggestion you should provide the part of your script<br>
detailing your cfg inputs.<br>
<br>
Cheers,<br>
<br>
Nick<br>
<br>
On 10 December 2015 at 09:14, Anne Mickan <<a href="mailto:amickan1990@gmail.com">amickan1990@gmail.com</a>> wrote:<br>
<br>
> Dear all,<br>
><br>
> I'm just starting to work on a cluster-based permutation test script based<br>
> on the tutorial for within-subject designs on the fieldtrip website. I ran<br>
> into an issue when computing the [stat] matrix. I used the code as it was<br>
> on the website:<br>
><br>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});<br>
><br>
> with the Correct and Incorrect matrices looking as follows:<br>
><br>
> Correct{1}<br>
><br>
> avg: [34x600 double]<br>
> time: [1x600 double]<br>
> fsample: '500'<br>
> label: {34x1 cell}<br>
> dimord: 'chan_time'<br>
> dof: [34x600 double]<br>
> var: [34x600 double]<br>
><br>
> The function runs without problems, i.e I don't get any error messages.<br>
> However, the result seems incomplete.<br>
><br>
> stat =<br>
> prob: [25x1 double]<br>
> posclusters: []<br>
> posclusterslabelmat: [25x1 double]<br>
> posdistribution: [1x500 double]<br>
> negclusters: [1x1 struct]<br>
> negclusterslabelmat: [25x1 double]<br>
> negdistribution: [1x500 double]<br>
> cirange: [25x1 double]<br>
> mask: [25x1 logical]<br>
> stat: [25x1 double]<br>
> ref: [25x1 double]<br>
> dimord: 'chan_time'<br>
> label: {25x1 cell}<br>
> time: 0<br>
> cfg: [1x1 struct]<br>
><br>
> Specifically, I later run into trouble with the stat.posclusterslabelmat<br>
> and stat.negclusterslabelmat matrices which should apparantly contain far<br>
> more values something more like 25x500 instead of 25x1. When calling<br>
> neg_int = all(neg(:, m(k):m(k+1)), 2)<br>
> I get the "Index exceeds matrix dimensions" error message which I assume<br>
> has to do with the fact that "neg" does not have the appropriate matrix<br>
> dimensions<br>
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )<br>
><br>
> Where is the error / where should I look for the error?<br>
><br>
> Some further design details:<br>
> Nsubj = 24<br>
> 2 conditions = Correct, Incorrect<br>
> Within-subject design<br>
> sampling rate = 500<br>
> 34 channels<br>
><br>
> I hope I gave enough / the necessary information for someone to help me<br>
> out.<br>
><br>
> Thanks in advance!<br>
><br>
> Best,<br>
> Anne<br>
><br>
><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
><br>
<br>
<br>
<br>
--<br>
Nicholas Peatfield, PhD<br>
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<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 10 Dec 2015 19:36:45 +0000<br>
From: "Schoffelen, J.M. (Jan Mathijs)" <<a href="mailto:jan.schoffelen@donders.ru.nl">jan.schoffelen@donders.ru.nl</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] Stats matrix incomplete - cluster-based<br>
permutation test<br>
Message-ID: <<a href="mailto:7CAF2781-D756-4C0B-9B56-F05642437AF9@fcdonders.ru.nl">7CAF2781-D756-4C0B-9B56-F05642437AF9@fcdonders.ru.nl</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Hi Anne,<br>
<br>
I agree with Nick, some more information would be helpful. At this stage my wild guess (assuming that you did not constrain your ?search space?, using cfg.channel and cfg.latency before calling ft_timelockstatistics) would be that there?s a major discrepancy in the descriptive dimensions of your data (i.e. the ?labels? and the time points) across the input arguments. FieldTrip does an explicit check on the labels and time points, it only proceeds to do calculations on the channels and time points that are present in each and every input argument. With respect to time points: this could even mean that numerical inaccuracies are the showstopper here. These inaccuracies could be easily introduced when e.g. downsampling.<br>
<br>
Best,<br>
Jan-Mathijs<br>
<br>
<br>
On Dec 10, 2015, at 8:13 PM, Nicholas A. Peatfield <<a href="mailto:nick.peatfield@gmail.com">nick.peatfield@gmail.com</a><mailto:<a href="mailto:nick.peatfield@gmail.com">nick.peatfield@gmail.com</a>>> wrote:<br>
<br>
Hi Anne,<br>
<br>
To get an answer/suggestion you should provide the part of your script detailing your cfg inputs.<br>
<br>
Cheers,<br>
<br>
Nick<br>
<br>
On 10 December 2015 at 09:14, Anne Mickan <<a href="mailto:amickan1990@gmail.com">amickan1990@gmail.com</a><mailto:<a href="mailto:amickan1990@gmail.com">amickan1990@gmail.com</a>>> wrote:<br>
Dear all,<br>
<br>
I'm just starting to work on a cluster-based permutation test script based on the tutorial for within-subject designs on the fieldtrip website. I ran into an issue when computing the [stat] matrix. I used the code as it was on the website:<br>
<br>
[stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});<br>
<br>
with the Correct and Incorrect matrices looking as follows:<br>
<br>
Correct{1}<br>
<br>
avg: [34x600 double]<br>
time: [1x600 double]<br>
fsample: '500'<br>
label: {34x1 cell}<br>
dimord: 'chan_time'<br>
dof: [34x600 double]<br>
var: [34x600 double]<br>
<br>
The function runs without problems, i.e I don't get any error messages. However, the result seems incomplete.<br>
<br>
stat =<br>
prob: [25x1 double]<br>
posclusters: []<br>
posclusterslabelmat: [25x1 double]<br>
posdistribution: [1x500 double]<br>
negclusters: [1x1 struct]<br>
negclusterslabelmat: [25x1 double]<br>
negdistribution: [1x500 double]<br>
cirange: [25x1 double]<br>
mask: [25x1 logical]<br>
stat: [25x1 double]<br>
ref: [25x1 double]<br>
dimord: 'chan_time'<br>
label: {25x1 cell}<br>
time: 0<br>
cfg: [1x1 struct]<br>
<br>
Specifically, I later run into trouble with the stat.posclusterslabelmat and stat.negclusterslabelmat matrices which should apparantly contain far more values something more like 25x500 instead of 25x1. When calling<br>
neg_int = all(neg(:, m(k):m(k+1)), 2)<br>
I get the "Index exceeds matrix dimensions" error message which I assume has to do with the fact that "neg" does not have the appropriate matrix dimensions<br>
(neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )<br>
<br>
Where is the error / where should I look for the error?<br>
<br>
Some further design details:<br>
Nsubj = 24<br>
2 conditions = Correct, Incorrect<br>
Within-subject design<br>
sampling rate = 500<br>
34 channels<br>
<br>
I hope I gave enough / the necessary information for someone to help me out.<br>
<br>
Thanks in advance!<br>
<br>
Best,<br>
Anne<br>
<br>
<br>
_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><mailto:<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<br>
<br>
<br>
--<br>
Nicholas Peatfield, PhD<br>
<br>
_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><mailto:<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<br>
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<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Fri, 11 Dec 2015 12:00:39 +0530<br>
From: aishwarya selvaraj <<a href="mailto:aishwaryaselvaraj1708@gmail.com">aishwaryaselvaraj1708@gmail.com</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] filed trip<br>
Message-ID:<br>
<<a href="mailto:CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com">CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
do you still have that m file with you??<br>
could you share ??<br>
<br>
On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <<a href="mailto:mishra408@gmail.com">mishra408@gmail.com</a>><br>
wrote:<br>
<br>
> Hi Aishwarya,<br>
><br>
> I faced the similar problem. You are supposed to change your data<br>
> (.mat format) in a data structure that is read by fieldtrip. For that<br>
> you need at least following information<br>
> 1. Channel label and their location (If you don't have this file you<br>
> can use standard file available in Fieldtrip and you can include only<br>
> those electrode that you have been using in your experiment)<br>
> 2. sampling rate of the data (that you would have done while recording the<br>
> data)<br>
> 3. time vector<br>
> 4. no. of trials<br>
><br>
> You can create them in MATLAB and put them together in a structure<br>
> along with your recorded data. This worked for me.<br>
><br>
> --<br>
> Ashutosh Mishra<br>
> 5th year Integrated BS-MS student<br>
> Department of Physical Sciences<br>
> Indian Institute of Science Education and Research, Kolkata<br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
><br>
<br>
<br>
<br>
--<br>
Regards,<br>
Aishwarya Selvaraj<br>
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<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Fri, 11 Dec 2015 08:09:14 +0000<br>
From: "Pelt, S. van (Stan)" <<a href="mailto:stan.vanpelt@donders.ru.nl">stan.vanpelt@donders.ru.nl</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] filed trip<br>
Message-ID:<br>
<<a href="mailto:7CCA2706D7A4DA45931A892DF3C2894C2A2801E0@exprd03.hosting.ru.nl">7CCA2706D7A4DA45931A892DF3C2894C2A2801E0@exprd03.hosting.ru.nl</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Aishwarya,<br>
<br>
The data structure should look something like this:<br>
<br>
% 1. Load data<br>
load EEGdata.mat<br>
<br>
% 2. Make FieldTrip structure, manually<br>
data.label={'Channel1Name?,?Channel2Name?,?Channel3Name?}; %your channel names<br>
data.trial{1}=[Channel1Data; Channel2Data; Channel3Data]'; % do for each trial: channelsxtimepoints data<br>
data.fsample=500; %your recording sampling frequency<br>
data.time{1}=[Trial1Timepoints]; % for each trial: timepoints per data sample (e.g: [0 0.02 0.04 0.06 etc])<br>
<br>
Going through the Walktrough Tutorial will be the best starting point when you just started to use FieldTrip: <a href="http://www.fieldtriptoolbox.org/walkthrough" rel="noreferrer" target="_blank">http://www.fieldtriptoolbox.org/walkthrough</a><br>
After that, you may go through the other Tutorial documentation or Example Matlab scripts.<br>
<br>
Best,<br>
Stan<br>
<br>
--<br>
Stan van Pelt, PhD<br>
Donders Institute for Brain, Cognition and Behaviour<br>
Radboud University<br>
Montessorilaan 3, B.01.34<br>
6525 HR Nijmegen, the Netherlands<br>
tel: <a href="tel:%2B31%2024%203616288" value="+31243616288">+31 24 3616288</a><br>
<br>
From: <a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a> [mailto:<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>] On Behalf Of aishwarya selvaraj<br>
Sent: vrijdag 11 december 2015 7:31<br>
To: FieldTrip discussion list<br>
Subject: Re: [FieldTrip] filed trip<br>
<br>
do you still have that m file with you??<br>
could you share ??<br>
<br>
On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <<a href="mailto:mishra408@gmail.com">mishra408@gmail.com</a><mailto:<a href="mailto:mishra408@gmail.com">mishra408@gmail.com</a>>> wrote:<br>
Hi Aishwarya,<br>
<br>
I faced the similar problem. You are supposed to change your data<br>
(.mat format) in a data structure that is read by fieldtrip. For that<br>
you need at least following information<br>
1. Channel label and their location (If you don't have this file you<br>
can use standard file available in Fieldtrip and you can include only<br>
those electrode that you have been using in your experiment)<br>
2. sampling rate of the data (that you would have done while recording the data)<br>
3. time vector<br>
4. no. of trials<br>
<br>
You can create them in MATLAB and put them together in a structure<br>
along with your recorded data. This worked for me.<br>
<br>
--<br>
Ashutosh Mishra<br>
5th year Integrated BS-MS student<br>
Department of Physical Sciences<br>
Indian Institute of Science Education and Research, Kolkata<br>
_______________________________________________<br>
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Message: 6<br>
Date: Fri, 11 Dec 2015 11:43:05 +0100<br>
From: Juan <<a href="mailto:juangpc@gmail.com">juangpc@gmail.com</a>><br>
To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
Subject: [FieldTrip] possible bug in tutorial code for creating<br>
sourcemodel<br>
Message-ID:<br>
<CAPO7YL+ufEwMRmBZk=<a href="mailto:XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com">XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Community,<br>
<br>
My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.<br>
Currently I am learning to do beamforming source analysis using Fieldtrip.<br>
<br>
While following the tutorial: "Creating a sourcemodel for<br>
source-reconstruction of MEG or EEG data <<a href="http://goog_2124598831" rel="noreferrer" target="_blank">http://goog_2124598831</a>><br>
?"<br>
??<br>
<br>
? ?when I reach "<br>
Subject-specific grids that are equivalent across subjects in normalized<br>
space<br>
?" procedure , there is an example code. This code throws an error when I<br>
execute it with a version of Fieldtrip I downloaded yesterday. I think I<br>
have downloaded correctly all the required info (Subject01.zip).<br>
<br>
?Code:<br>
<br>
% NOTE: the path to the template file is user-specific<br>
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');<br>
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret<br>
the coordinate system<br>
% segment the template brain and construct a volume conduction model<br>
(i.e. head model): % this is needed to describe the boundary that<br>
define which dipole locations are 'inside' the brain.<br>
cfg = [];<br>
template_seg = ft_volumesegment(cfg, template);<br>
<br>
cfg = [];<br>
cfg.method = 'singleshell';<br>
template_headmodel = ft_prepare_headmodel(cfg, template_seg);<br>
template_headmodel = ft_convert_units(template_headmodel, 'cm'); %<br>
Convert the vol to cm, because the CTF convenction is to express<br>
everything in cm.<br>
% construct the dipole grid in the template brain coordinates% the<br>
negative inwardshift means an outward shift of the brain surface for<br>
inside/outside detection<br>
cfg = [];<br>
cfg.grid <<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html" rel="noreferrer" target="_blank">http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html</a>>.resolution<br>
= 1;<br>
cfg.grid <<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html" rel="noreferrer" target="_blank">http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html</a>>.tight<br>
= 'yes';<br>
cfg.inwardshift = -1.5;<br>
??<br>
cfg.headmodel = template_headmodel;<br>
<br>
The problem occurs when I execute ?this line:<br>
<br>
?<br>
?<br>
?<br>
?<br>
template_grid = ft_prepare_sourcemodel(cfg);<br>
<br>
Matlab's output:<br>
?<br>
>> template_grid = ft_prepare_sourcemodel(cfg);<br>
creating dipole grid based on automatic 3D grid with specified resolution<br>
Error using ft_prepare_sourcemodel (line 317)<br>
creating a 3D-grid sourcemodel this way requires sensor position<br>
information to estimate the extent of the brain<br>
?<br>
<br>
<br>
I have managed to look around and found that you can specify the required<br>
"sensor position information" by executing this code just before<br>
(considering the folder with the information downloaded for this subject is<br>
located just there:<br>
<br>
?cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';<br>
<br>
Then the rest of the sample code in the tutorial can be executed with no<br>
issues.<br>
<br>
template_grid = ft_prepare_sourcemodel(cfg);<br>
% make a figure with the template head model and dipole gridfigure<br>
<<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html" rel="noreferrer" target="_blank">http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html</a>>hold<br>
<<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html" rel="noreferrer" target="_blank">http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html</a>><br>
on<br>
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',<br>
'none');alpha 0.5; camlight<br>
<<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html" rel="noreferrer" target="_blank">http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html</a>>;<br>
ft_plot_mesh(template_grid.pos(template_grid.inside,:));<br>
<br>
<br>
My questions:<br>
<br>
?Is there a better solution for this problem? Maybe I can learn a little<br>
bit more about the toolbox with your answers.<br>
<br>
I didn't want to correct the wiki because? my solution depends on where one<br>
is placing the downloaded subject's data, and it is platform dependent.<br>
Should I add something to the tutorial anyway?<br>
? I figure this can be interesting to other people.?<br>
?<br>
?<br>
<br>
Best,<br>
<br>
<br>
Juan<br>
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Message: 7<br>
Date: Fri, 11 Dec 2015 10:54:54 +0000<br>
From: "Schoffelen, J.M. (Jan Mathijs)" <<a href="mailto:jan.schoffelen@donders.ru.nl">jan.schoffelen@donders.ru.nl</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] possible bug in tutorial code for creating<br>
sourcemodel<br>
Message-ID: <<a href="mailto:93DA3667-0D6E-45A6-8387-1C01B51D7925@fcdonders.ru.nl">93DA3667-0D6E-45A6-8387-1C01B51D7925@fcdonders.ru.nl</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Juan,<br>
<br>
We?ll look into this specific issue soon, it should work without specifying sensor positions. However, for now and in general I would recommend just using a pre-cooked template grid. These can be found in fieldtrip/template/sourcemodel. This is mentioned in the tutorial, and I will make this more explicit shortly.<br>
<br>
Best,<br>
<br>
Jan-Mathijs<br>
<br>
On Dec 11, 2015, at 11:43 AM, Juan <<a href="mailto:juangpc@gmail.com">juangpc@gmail.com</a><mailto:<a href="mailto:juangpc@gmail.com">juangpc@gmail.com</a>>> wrote:<br>
<br>
Dear Community,<br>
<br>
My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab. Currently I am learning to do beamforming source analysis using Fieldtrip.<br>
<br>
While following the tutorial: "Creating a sourcemodel for source-reconstruction of MEG or EEG data<<a href="http://goog_2124598831/" rel="noreferrer" target="_blank">http://goog_2124598831/</a>><br>
?<http:/>"<br>
??<br>
<br>
? ?when I reach "<br>
Subject-specific grids that are equivalent across subjects in normalized space<br>
?" procedure , there is an example code. This code throws an error when I execute it with a version of Fieldtrip I downloaded yesterday. I think I have downloaded correctly all the required info (Subject01.zip).<br>
<br>
?Code:<br>
<br>
<br>
% NOTE: the path to the template file is user-specific<br>
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');<br>
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the coordinate system<br>
<br>
% segment the template brain and construct a volume conduction model (i.e. head model):<br>
% this is needed to describe the boundary that define which dipole locations are 'inside' the brain.<br>
cfg = [];<br>
template_seg = ft_volumesegment(cfg, template);<br>
<br>
cfg = [];<br>
cfg.method = 'singleshell';<br>
template_headmodel = ft_prepare_headmodel(cfg, template_seg);<br>
template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.<br>
<br>
% construct the dipole grid in the template brain coordinates<br>
% the negative inwardshift means an outward shift of the brain surface for inside/outside detection<br>
cfg = [];<br>
cfg.grid<<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html" rel="noreferrer" target="_blank">http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html</a>>.resolution = 1;<br>
cfg.grid<<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html" rel="noreferrer" target="_blank">http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html</a>>.tight = 'yes';<br>
cfg.inwardshift = -1.5;<br>
<br>
??<br>
cfg.headmodel = template_headmodel;<br>
<br>
<br>
The problem occurs when I execute ?this line:<br>
<br>
<br>
?<br>
?<br>
?<br>
?<br>
template_grid = ft_prepare_sourcemodel(cfg);<br>
<br>
Matlab's output:<br>
?<br>
>> template_grid = ft_prepare_sourcemodel(cfg);<br>
creating dipole grid based on automatic 3D grid with specified resolution<br>
Error using ft_prepare_sourcemodel (line 317)<br>
creating a 3D-grid sourcemodel this way requires sensor position information to estimate the extent of the brain<br>
?<br>
<br>
<br>
I have managed to look around and found that you can specify the required "sensor position information" by executing this code just before (considering the folder with the information downloaded for this subject is located just there:<br>
<br>
<br>
?cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';<br>
<br>
<br>
<br>
Then the rest of the sample code in the tutorial can be executed with no issues.<br>
<br>
<br>
template_grid = ft_prepare_sourcemodel(cfg);<br>
<br>
% make a figure with the template head model and dipole grid<br>
figure<<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html" rel="noreferrer" target="_blank">http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html</a>><br>
hold<<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html" rel="noreferrer" target="_blank">http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html</a>> on<br>
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor', 'none');alpha 0.5; camlight<<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html" rel="noreferrer" target="_blank">http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html</a>>;<br>
ft_plot_mesh(template_grid.pos(template_grid.inside,:));<br>
<br>
My questions:<br>
<br>
?Is there a better solution for this problem? Maybe I can learn a little bit more about the toolbox with your answers.<br>
<br>
I didn't want to correct the wiki because? my solution depends on where one is placing the downloaded subject's data, and it is platform dependent. Should I add something to the tutorial anyway?<br>
? I figure this can be interesting to other people.?<br>
?<br>
?<br>
<br>
Best,<br>
<br>
<br>
Juan<br>
<br>
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