[FieldTrip] Sourcestatistics - Problem

[Martin Winkels]

Hello Stephan,

thanks for the answer. It helps, but only a little bit. Do you have any
more suggestions?

Thanks,

Martin

On Fri, Jan 27, 2012 at 8:59 PM, smoratti at psi.ucm.es <smoratti at psi.ucm.es>wrote:

> Hi Martin,
>
> Sometimes it might be useful to decrease the cluster alpha p value (e.g.
> 0.01). This prevents too much clustering and favors your strong effects.
> Maybe this helps.
>
> Best,
>
> Stephan
>
> ________________________________________________________
> Stephan Moratti, PhD
>
> see also: http://web.me.com/smoratti/
>
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
> and
>
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
>
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
>
> El 27/01/2012, a las 16:42, Martin Winkels escribió:
>
> Hello,
>
> we are working with the ft_sourcestatistics function and we are facing
> some problems.
>
>
> We got some very well known data, our subjects just have been stimulated
> left and right hand. We are calculating right vs left hand data. The
> calculated GrandAVG-data looks very good, you can see this in the attached
> files. (GAVG_LEFT and GAVG_RIGHT). We got activity in the left and right
> brain hemisphere, localized at single spot.
>
> Now I wanted to calculate a statistic for this subject and I got some
> weird results. If you look up the file statplot.jpg you can see that the
> positive cluster looks quite okay but the negative cluster only looks good
> in the upper right corner but then it is distributed all over the brain
> till the lower left corner.
>
> Based on the GAVG-results this cant be. I also attached the data itself
> and a script to show the GAVG data as well as the script to calculate the
> data.
>
> I would be very very pleased if somebody could help me with that issue,
> I've been working on this for a while now.
>
>
>
> I have uploaded the data to the recommended filehoster:
>
> http://www.sendspace.com/filegroup/sJhI%2F5uBRdJI6JGXUjWtPA
>
> There are two files that belong together, you can extract them and there
> will be a .mat structure, the m-files and three pictures.
>
>
>
> Thanks, Martin
>
> I post the code as an attachment to this email:
>
> function calc_stat( ~ )
> %%UNTITLED2 Summary of this function goes here
> %   Detailed explanation goes here
>
> %path to grandAVG mat-file
> load
> ('/media/sonja1/MatlabAnalysis/Martin/SEF/sourcestatistics/GrandAVG/grandAVG.mat');
>
> sourcePost = GA_RIGHT;
> sourcePre = GA_LEFT;
>
> %%
> % configfile for calculating the statistics
> cfg = [];
> cfg.channel = {'MEG'};
> cfg.latency = [0 1];
>
> cfg.parameter   = 'pow';
> cfg.dim         =  sourcePre.dim;
>
> cfg_neighb.method = 'template';
> cfg.template =  'CTF275_neighb.mat';
> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, GA_RIGHT.nei);
>
> cfg.method = 'montecarlo';
> cfg.statistic = 'depsamplesT';
> cfg.correctm = 'cluster';
>
> cfg.tail = 0;                     % -1, 1 or 0 (default = 0); one-sided or
> two-sided test
> cfg.clusteralpha = 0.05;         % alpha level of the sample-specific test
> statistic that will be used for thresholding
> cfg.clusterstatistic = 'maxsum'; % test statistic that will be evaluated
> under the permutation distribution.
> cfg.minnbchan = 2;               % minimum number of neighborhood channels
> that is required for a selected
> cfg.clustertail = 0;
> cfg.alpha = 0.025;               % alpha level of the permutation test
> cfg.numrandomization = 100;      % number of draws from the permutation
> distribution
>
>
> nsubj=length(sourcePre.trial);
> cfg.design(1,:) = [1:nsubj 1:nsubj];
> cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2];
> cfg.uvar        = 1; % row of design matrix that contains unit variable
> (in this case: subjects)
> cfg.ivar        = 2; % row of design matrix that contains independent
> variable (the conditions)
>
> stat = ft_sourcestatistics(cfg, sourcePost, sourcePre);
>
> %%
> %Plot the statistics
> cfg = [];
> cfg.method        = 'ortho';
> cfg.interactive   = 'yes';
> cfg.funparameter = 'stat';
> %stat.mask = ones(stat.dim);
> cfg.maskparameter = 'mask';
> %cfg.maskparameter = 'mask';
> cfg.funcolorlim   = [-10 10];
>
> cfg.opacitymap    = 'vdown';
> cfg.opacitylim    = 'maxabs';
>
>
> cfg.anatomy = GA_RIGHT.anatomy;
> stat.anatomy = GA_RIGHT.anatomy;
>
> figure
> ft_sourceplot(cfg, stat)
>
> end
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120128/d9246b76/attachment-0002.html>