<div dir="ltr"><div><div>Hi everyone,<br><br>I recently tried <a href="http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space">http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space</a> and noticed some inconsistencies between the example code and the results; I updated the code on the wiki but I wanted to send a message to the list to double-check whether my changes are ok. Firstly, I had to add a call to ft_convert_units, because otherwise the vol was expressed in mm and the grid in cm, causing the grid to be much smaller than the volume conductor (see <a href="http://i.imgur.com/gzct9Dm.png">http://i.imgur.com/gzct9Dm.png</a>). Is this change ok?<br>
<br></div>The result I get is still not quite consistent with the examples shown on that page, though; in my result, the grid is a cube (<a href="http://i.imgur.com/NSgCFpg.png">http://i.imgur.com/NSgCFpg.png</a>), whereas in the example the grid is brain-shaped. I used the same Fieldtrip brain template and the same code from the example (except for the change above), so I'm not sure if the difference is due to different plot settings, a change in the Fieldtrip code since this example was made, or a change in the sample brain included in Fieldtrip since the example was made.<br>
<br></div>Best,<br>Steve<br><div><div><div><br><br>On Thu, Jun 13, 2013 at 5:05 AM, <<a href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a>> wrote:<br>><br>> Send fieldtrip mailing list submissions to<br>
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><br>><br>> Today's Topics:<br>><br>> 1. Re: Source statistics on spatio-temporal source<br>> reconstruction data (MNE) (Nicolai Mersebak)<br>><br>><br>> ----------------------------------------------------------------------<br>
><br>> Message: 1<br>> Date: Thu, 13 Jun 2013 12:04:34 +0200<br>> From: Nicolai Mersebak <<a href="mailto:nicolai@mersebak.dk">nicolai@mersebak.dk</a>><br>> To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
> Subject: Re: [FieldTrip] Source statistics on spatio-temporal source<br>> reconstruction data (MNE)<br>> Message-ID: <<a href="mailto:6F3697BB-194F-422F-A1BF-EBBB132F805B@mersebak.dk">6F3697BB-194F-422F-A1BF-EBBB132F805B@mersebak.dk</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>><br>> Thanks to all of you for your comments and ideas - they are very helpful!<br>><br>> I ( off course :) ) have some follow up questions.<br>
><br>> I have created an ERP structure for my MNE source, so the only think which I need and that is not straight forward is the neighbour structure.<br>><br>> I am using the standard bem template (fieldtrip-20130124/template/headmodel/standard_bem.mat) as a head model and use the following code to get a grid for all subjects as I don't have any subject specific information regarding the anatomy.<br>
><br>> cfg = [];<br>> cfg.grid.xgrid = -100:10:100;<br>> cfg.grid.ygrid = -100:10:100;<br>> cfg.grid.zgrid = -100:10:100;<br>> cfg.grid.tight = 'yes';<br>> cfg.grid.unit = hdm.unit; % unit: mm<br>
> cfg.vol = hdm;<br>> grid = ft_prepare_sourcemodel(cfg);<br>><br>><br>> @Jan-Mathijs and Stephan: I guess making a subject specific grid based on a warped template requires anatomic information for each subject, e.g. a MRI image like this tutorial shows:<br>
> <a href="http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s%5B">http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s%5B</a><br>
><br>> The final grid output in the tutorial - does it have this 3D grid which can be used as a neighbour structure ?<br>><br>> I am not sure how to go from my cortical sheet [vertices x coordinates(x,y,z)] to a 3D grid, which I can use as a neighbour structure ?<br>
><br>> A second thing I would like to know is, if any of you have tried to use an atlas (e.g ALL template atlas) where the regions now are channels in the permutation test? Going from source points to atlas regions can be done through ft_sourcestatistics, but I am still interested in keeping the temporal dimension. The reason to use atlas regions instead of source points is to decrease the computation time.<br>
><br>> Best,<br>><br>> Nicolai<br>><br>></div></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jun 13, 2013 at 5:05 AM, <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. Re: Source statistics on spatio-temporal source<br>
reconstruction data (MNE) (Nicolai Mersebak)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 13 Jun 2013 12:04:34 +0200<br>
From: Nicolai Mersebak <<a href="mailto:nicolai@mersebak.dk">nicolai@mersebak.dk</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] Source statistics on spatio-temporal source<br>
reconstruction data (MNE)<br>
Message-ID: <<a href="mailto:6F3697BB-194F-422F-A1BF-EBBB132F805B@mersebak.dk">6F3697BB-194F-422F-A1BF-EBBB132F805B@mersebak.dk</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Thanks to all of you for your comments and ideas - they are very helpful!<br>
<br>
I ( off course :) ) have some follow up questions.<br>
<br>
I have created an ERP structure for my MNE source, so the only think which I need and that is not straight forward is the neighbour structure.<br>
<br>
I am using the standard bem template (fieldtrip-20130124/template/headmodel/standard_bem.mat) as a head model and use the following code to get a grid for all subjects as I don't have any subject specific information regarding the anatomy.<br>
<br>
cfg = [];<br>
cfg.grid.xgrid = -100:10:100;<br>
cfg.grid.ygrid = -100:10:100;<br>
cfg.grid.zgrid = -100:10:100;<br>
cfg.grid.tight = 'yes';<br>
cfg.grid.unit = hdm.unit; % unit: mm<br>
cfg.vol = hdm;<br>
grid = ft_prepare_sourcemodel(cfg);<br>
<br>
<br>
@Jan-Mathijs and Stephan: I guess making a subject specific grid based on a warped template requires anatomic information for each subject, e.g. a MRI image like this tutorial shows:<br>
<a href="http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s%5B" target="_blank">http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s%5B</a><br>
<br>
The final grid output in the tutorial - does it have this 3D grid which can be used as a neighbour structure ?<br>
<br>
I am not sure how to go from my cortical sheet [vertices x coordinates(x,y,z)] to a 3D grid, which I can use as a neighbour structure ?<br>
<br>
A second thing I would like to know is, if any of you have tried to use an atlas (e.g ALL template atlas) where the regions now are channels in the permutation test? Going from source points to atlas regions can be done through ft_sourcestatistics, but I am still interested in keeping the temporal dimension. The reason to use atlas regions instead of source points is to decrease the computation time.<br>
<br>
Best,<br>
<br>
Nicolai<br>
<br>
<br>
Den 12/06/2013 kl. 18.58 skrev "<a href="mailto:smoratti@psi.ucm.es">smoratti@psi.ucm.es</a>" <<a href="mailto:smoratti@psi.ucm.es">smoratti@psi.ucm.es</a>>:<br>
<br>
><br>
> I think Jan.Mathijs alternative suggestion is quite attractive. With the neighbors on a cortical sheet I also had the problems that sometimes the vertices do not have the same distance and then clustering may be biased to smaller or bigger clusters as the number of neighbors does not guarantee same cluster sizes. With the interpolation onto a 3D grid, you won't have that problem.<br>
><br>
> best,<br>
><br>
> Stephan<br>
><br>
><br>
> ________________________________________________________<br>
> Stephan Moratti, PhD<br>
><br>
> see also: <a href="http://web.me.com/smoratti/" target="_blank">http://web.me.com/smoratti/</a><br>
><br>
> Universidad Complutense de Madrid<br>
> Facultad de Psicolog?a<br>
> Departamento de Psicolog?a B?sica I<br>
> Campus de Somosaguas<br>
> 28223 Pozuelo de Alarc?n (Madrid)<br>
> Spain<br>
><br>
> and<br>
><br>
> Center for Biomedical Technology<br>
> Laboratory for Cognitive and Computational Neuroscience<br>
> Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de Madrid<br>
> Campus Montegancedo<br>
> 28223 Pozuelo de Alarc?n (Madrid)<br>
> Spain<br>
><br>
><br>
> email: <a href="mailto:smoratti@psi.ucm.es">smoratti@psi.ucm.es</a><br>
> Tel.: <a href="tel:%2B34%20679219982" value="+34679219982">+34 679219982</a><br>
><br>
> El 12/06/2013, a las 18:00, jan-mathijs schoffelen escribi?:<br>
><br>
>> An alternative would be to interpolate the cortical sheet to a 3D grid (where the grid is defined for each subject based on a warped template grid defined in a standard space), and then do clustering using a regular 3D spatial neighbourhood structure. The rationale being that two vertices on the sheet may appear as disconnected (e.g. being on two sides of a sulcus) whereas, given the poor spatial resolution, they belong to the same spatial blob.<br>
>><br>
>> Best,<br>
>> Jan-Mathijs<br>
>><br>
>> On Jun 12, 2013, at 5:44 PM, <a href="mailto:smoratti@psi.ucm.es">smoratti@psi.ucm.es</a> wrote:<br>
>><br>
>>> Dear Nicolai,<br>
>>><br>
>>> Indeed I have used ft_timelockstatistics for minimum norm source data. The trick is to put the source level data into a ERF structure. Determining the neighbors of a source surface with vertices is not trivial. However I used tess_vertconn.m from the BrainStorm toolbox to get the connectivity matrix that tells you who is a neighbor. This you can feed into timelockstats.<br>
>>><br>
>>> Hope that helps,<br>
>>><br>
>>> Stephan<br>
>>><br>
>>> ________________________________________________________<br>
>>> Stephan Moratti, PhD<br>
>>><br>
>>> see also: <a href="http://web.me.com/smoratti/" target="_blank">http://web.me.com/smoratti/</a><br>
>>><br>
>>> Universidad Complutense de Madrid<br>
>>> Facultad de Psicolog?a<br>
>>> Departamento de Psicolog?a B?sica I<br>
>>> Campus de Somosaguas<br>
>>> 28223 Pozuelo de Alarc?n (Madrid)<br>
>>> Spain<br>
>>><br>
>>> and<br>
>>><br>
>>> Center for Biomedical Technology<br>
>>> Laboratory for Cognitive and Computational Neuroscience<br>
>>> Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de Madrid<br>
>>> Campus Montegancedo<br>
>>> 28223 Pozuelo de Alarc?n (Madrid)<br>
>>> Spain<br>
>>><br>
>>><br>
>>> email: <a href="mailto:smoratti@psi.ucm.es">smoratti@psi.ucm.es</a><br>
>>> Tel.: <a href="tel:%2B34%20679219982" value="+34679219982">+34 679219982</a><br>
>>><br>
>>> El 12/06/2013, a las 15:44, Nicolai Mersebak escribi?:<br>
>>><br>
>>>> Dear all,<br>
>>>><br>
>>>> I have a question concerning the usage of ft_sourcegrandaverage and ft_sourcestatistics.<br>
>>>><br>
>>>> After using ft_sourceanalysis (method: MNE), I get spatio-temporal source reconstructed data in source.avg.pow (4050 x 897): 4050 sources and 897 time points.<br>
>>>><br>
>>>> Now I would like to use the cluster-based permutation test on my source reconstructed data. However it seems like ft_sourcegrandaverage and ft_sourcestatistics don't support source level time courses. E.g when I am using ft_sourcegrandaverage I am getting the following error:<br>
>>>><br>
>>>> Error in ft_sourcegrandaverage (line 158)<br>
>>>> dat(:,i) = tmp(:);<br>
>>>><br>
>>>> Looking into the code:<br>
>>>><br>
>>>> for i=1:Nsubject<br>
>>>> tmp = getsubfield(varargin{i}, parameterselection(cfg.parameter, varargin{i}));<br>
>>>> dat(:,i) = tmp(:);<br>
>>>> tmp = getsubfield(varargin{i}, 'inside');<br>
>>>> inside(tmp,i) = 1;<br>
>>>> end<br>
>>>><br>
>>>> I see that "tmp" are getting the structure [N_sources x timepoints] from source.avg.pow for one subject, where "dat" requires the structure [N_sources x 1].<br>
>>>><br>
>>>> I seached the mailing list for similar issues and found this thread:<br>
>>>><br>
>>>> <a href="http://mailman.science.ru.nl/pipermail/fieldtrip/2010-September/003122.html" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/2010-September/003122.html</a><br>
>>>><br>
>>>> Since I am interested in using the temporal dimension in my statistics, I would like to know if it is still not possible to use spatio-temporal source reconstructed data in ft_sourcestatistics and ft_sourcegrandaverage ?<br>
>>>><br>
>>>> Or if any have succeeded in using the cluster-based permutation test on source level also including the temporal dimension ?<br>
>>>><br>
>>>> Alternative I was thinking that I might could use ft_timelockstatistics, where I substituted the channels with sources, e.g instead of having 64 channels, I would now have 4050 "channels".<br>
>>>> If so I need to calculate a label structure and an appropriate neighbor structure, which I guess is possible as I have all the 3D coordinates for each source, e.g in leadfield.pos ?<br>
>>>> I know this is a work around solution, but have anyone tried or have any experience using such an approach ?<br>
>>>><br>
>>>> Best,<br>
>>>><br>
>>>> Nicolai<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" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><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" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
>><br>
>> Jan-Mathijs Schoffelen, MD PhD<br>
>><br>
>> Donders Institute for Brain, Cognition and Behaviour,<br>
>> Centre for Cognitive Neuroimaging,<br>
>> Radboud University Nijmegen, The Netherlands<br>
>><br>
>> Max Planck Institute for Psycholinguistics,<br>
>> Nijmegen, The Netherlands<br>
>><br>
>> <a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a><br>
>> Telephone: <a href="tel:%2B31-24-3614793" value="+31243614793">+31-24-3614793</a><br>
>><br>
>> <a href="http://www.hettaligebrein.nl" target="_blank">http://www.hettaligebrein.nl</a><br>
>><br>
>> _______________________________________________<br>
>> fieldtrip mailing list<br>
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><br>
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End of fieldtrip Digest, Vol 31, Issue 27<br>
*****************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>Stephen Politzer-Ahles<br>University of Kansas<br>Linguistics Department<br><a href="http://people.ku.edu/~sjpa/" target="_blank">http://people.ku.edu/~sjpa/</a>
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