[FieldTrip] NaNs as output of ft_sourceanalysis (DICS)

[Andreas Sauer]

Dear Eelke and Jörn,

thanks for the super quick responses! And sorry for the double post...

I tried Eelke's suggestion and that holds. So, I have only NaNs in the
fields for the dipole locations outside the brain.
However, if I continue and calculate the contrast between pre and post and
plot it I don't see any activation.

I will try your suggestion, Jörn, as well and see whether it has to do with
the re-definition.

Thanks again for your suggestions!

Best,

Andreas


2013/6/4 Eelke Spaak <eelke.spaak at donders.ru.nl>

> Dear Andreas,
>
> How many NaNs do you get exactly and in which field? If it is some
> NaNs in source.avg.pow, then it is quite normal: the estimates for
> dipole locations which were flagged as outside the brain are always
> NaN, as they are not scanned. The following should hold:
>
> sum(isnan(source.avg.pow)) == numel(source.outside)
> &&
> sum(~isnan(source.avg.pow)) == numel(source.inside)
>
> Best,
> Eelke
>
> On 4 June 2013 11:42, Andreas Sauer <sauer.mpih at googlemail.com> wrote:
> > Dear all,
> >
> > I would like to analyze sources with the beamforming approach using the
> DICS
> > method. I followed the steps in the tutorial and everything works well.
> > However, the output of ft_sourceanalysis contains only NaNs.
> >
> > I checked the TF data that I calculated in the step before but that looks
> > fine, so I assume the error happens somewhere during ft_sourceanalysis.
> >
> > That's how I calculate the TFRs:
> >
> >         cfg = [];
> >         cfg.toilim = [-0.5 -0.3]; % baseline activity
> >         eval(['dataPre =
> > ft_redefinetrial(cfg,Cond_',num2str(cond(j)),');']);
> >         cfg.toilim = [0.1 1.0]; % task-related activity
> >         eval(['dataPost =
> > ft_redefinetrial(cfg,Cond_',num2str(cond(j)),');']);
> >
> >         % Combine the two datasets...
> >         data = appenddata(cfg, dataPre, dataPost);
> >         trialdesign = [ones(1,length(dataPost.trial))
> > ones(1,length(dataPre.trial))*2];
> >
> >         % ... and compute the CSD matrices...
> >         cfg = [];
> >         cfg.output     = 'powandcsd';
> >         cfg.channel    = Channel.meg;
> >         cfg.method     = 'mtmfft';
> >         cfg.taper      = 'dpss';
> >         cfg.foilim     = [75 75];
> >         cfg.tapsmofrq  = 15; % amount of spectral smoothing = +/- 15 Hz
> >         cfg.channelcmb = {Channel.meg Channel.meg};
> >
> >         % ... for the baseline and task part separately...
> >         eval(['freqPre.Cond_',num2str(cond(j)), ' =
> > ft_freqanalysis(cfg,dataPre);']);
> >         eval(['freqPost.Cond_',num2str(cond(j)), ' =
> > ft_freqanalysis(cfg,dataPost);']);
> >
> >         % ... and for the whole trial
> >         eval(['freqAll.Cond_',num2str(cond(j)), ' =
> > ft_freqanalysis(cfg,data);']);
> >         eval(['freqAll.Cond_',num2str(cond(j)), '.trialdesign =
> > trialdesign;']); % pre and post info
> >
> > And that's how I calculate the sources:
> >
> >         cfg               = [];
> >         cfg.frequency     = 75;
> >         cfg.method        = 'dics';
> >         cfg.grid          = grid; % Here it gives .pos, .inside,
> .outside to
> > the structure
> >         cfg.vol           = vol;
> >         cfg.dim           = template_grid.dim; % Here I give the
> dimension
> > of the template grid
> >         cfg.grad          = Cond_101.hdr.grad;
> >         cfg.lambda        = '5%';
> >         cfg.reducerank    = 'no';
> >         cfg.projectnoise  = 'yes';
> >         cfg.realfilter    = 'yes';
> >         cfg.keepfilter    = 'yes'; % the output saves the computed
> inverse
> > filter
> >
> >         eval(['SourceAll = ft_sourceanalysis(cfg,
> > freqAll.Cond_',num2str(cond(k)),');'])
> >
> >         % use the common filter here
> >         cfg.grid.filter = SourceAll.avg.filter;
> >         eval(['sourcePre_con = ft_sourceanalysis(cfg,
> > freqPre.Cond_',num2str(cond(k)),');'])
> >         eval(['sourcePost_con = ft_sourceanalysis(cfg,
> > freqPost.Cond_',num2str(cond(k)),');'])
> >
> >
> >
> > I would really appreciate any help with that! Thanks a lot!
> >
> > Best,
> >
> > Andreas
> >
> > --
> > Andreas Sauer
> > Max Planck Institute for Brain Research
> > Deutschordenstr. 46
> > 60528 Frankfurt am Main
> > Germany
> >
> > T: +49 69 96769 278
> > F: +49 69 96769 327
> > Email: andreas.sauer at brain.mpg.de
> > www.brain.mpg.de
> >
> > _______________________________________________
> > 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
>



-- 
Dipl.-Psych. Andreas Sauer
Max Planck Institute for Brain Research
Deutschordenstraße 46
60528 Frankfurt am Main
Germany

T: +49 69 96769 278
F: +49 69 96769 327
Email: sauer.mpih at gmail.com
www.brain.mpg.de
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130604/4e664044/attachment-0002.html>