[FieldTrip] Source statistics on spatio-temporal source reconstruction data (MNE)

"Jörn M. Horschig" jm.horschig at donders.ru.nl
Wed Jun 12 16:20:29 CEST 2013


it might be a good way, at least I am doing it that way :) But think 
about defining neighbouring voxels beforehands (easily doable for a 
decent programmer, hard for a not-so-experienced programmer). In the 
upcoming months/years there will be something changing on the 
source-front anyway, so maybe it is best to use the temporary solution 
with ft_timelockXXX until then. Note that my personal opinion does not 
necessarily reflect the opinion of the core dev team ;)


On 6/12/2013 4:03 PM, Johanna Zumer wrote:
> Dear Nicolai,
> Good timing, I have just last week filed a 'bug' for this code 
> modification request: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2185
> You may add yourself to the CC list if you wish to receive updates on 
> the bug progress.
> I would be interested to hear if anyone else has thoughts on your 
> suggestion to 'hack' it as a timelock structure with channels.
> Best,
> Johanna
> 2013/6/12 Nicolai Mersebak <nicolai at mersebak.dk 
> <mailto:nicolai at mersebak.dk>>
>     Dear all,
>     I have a question concerning the usage of ft_sourcegrandaverage
>     and ft_sourcestatistics.
>     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.
>     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:
>     Error in ft_sourcegrandaverage (line 158)
>       dat(:,i) = tmp(:);
>     Looking into the code:
>     for i=1:Nsubject
>       tmp = getsubfield(varargin{i}, parameterselection(cfg.parameter,
>     varargin{i}));
>       dat(:,i) = tmp(:);
>       tmp = getsubfield(varargin{i}, 'inside');
>       inside(tmp,i) = 1;
>     end
>     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].
>     I seached the mailing list for similar issues and found this thread:
>     http://mailman.science.ru.nl/pipermail/fieldtrip/2010-September/003122.html
>     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 ?
>     Or if any have succeeded in using the cluster-based permutation
>     test on source level also including the temporal dimension ?
>     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".
>     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 ?
>     I know this is a work around solution, but have anyone tried or
>     have any experience using such an approach ?
>     Best,
>     Nicolai
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Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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