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

Johanna Zumer johanna.zumer at donders.ru.nl
Wed Jun 12 16:03:16 CEST 2013

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.


2013/6/12 Nicolai Mersebak <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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