[FieldTrip] missing anatomy in source plot of ft_sourcegrandaverage

[Joram van Driel]

Hi Jörn,
Not a stupid question at all, because indeed there isn't. I thought that
was the problem too; I already tried putting the .anatomy field of one of
the (normalized) subjects into the grandavg structure, but that resulted in
a bunch of errors due to an error in the cornerpoints function.
This is how the grandavg structure looks like after ft_sourcegrandaverage
(fieldtrip version 20140127):

        pos: [7109137x3 double]
        dim: [181 217 181]
        avg: [1x1 struct]
        var: [1x1 struct]
     dimord: 'voxel'
     inside: [1550519x1 double]
    outside: [5558618x1 double]
         df: [7109137x1 double]
        cfg: [1x1 struct]

This my cfg:

grandavg = cell(1,2);
cfg = [];
cfg.parameter = 'avg.pow';
cfg.keepindividual = 'no';
grandavg{1} = ft_sourcegrandaverage(cfg,sourceDiffAll{:,1}); % condition 1
grandavg{2} = ft_sourcegrandaverage(cfg,sourceDiffAll{:,2}); % condition 2

Hope you can find out what the problem is..!

Thanks a lot,
Joram



On Mon, Feb 3, 2014 at 9:10 AM, "Jörn M. Horschig" <
jm.horschig at donders.ru.nl> wrote:

> Hi Joram,
>
> this might be a stupid question, but is there a grandavg{1}.anatomy field
> at all?
>
> Best,
> Jörn
>
>
> On 1/31/2014 12:44 PM, Joram van Driel wrote:
>
>> Hi all,
>>
>> I'm trying to plot the grand average of a source analysis. However no
>> matter what I try, the result of ft_sourcegrandaverage keeps giving me only
>> the functional data, no anatomy.
>>
>> My cfg for ft_sourceplot is:
>>
>> cfg = [];
>> cfg.method        = 'ortho';
>> cfg.interactive   = 'no';
>> cfg.funparameter  = 'avg.pow';
>> cfg.maskparameter = cfg.funparameter;
>> cfg.funcolorlim   = [0 0.2];
>> cfg.opacitylim    = [0 0.2];
>> cfg.opacitymap    = 'rampup';
>>
>> ft_sourceplot(cfg,grandavg{1})
>>
>> I thus created my own grandaverage, like this (where sourceDiffAll{:,:}
>> is a subject-by-condition cell structure):
>>
>> temp = zeros([length(nsubjects) size(sourceDiffAll{1,1}.avg.pow)]);
>> for s=1:length(nsubjects)
>>     temp(s,:,:,:) = sourceDiffAll{s,2}.avg.pow -
>> sourceDiffAll{s,1}.avg.pow; % create condition contrast
>> end
>> customavg = sourceDiffAll{1,1}; % just copy one subject one condition
>> customavg.avg.pow = squeeze(mean(temp,1)); % and replace power with the
>> grand average power condition-contrast
>>
>> Now using ft_sourceplot on customavg works just fine.
>> Any idea of what's going wrong with ft_sourceplot on
>> ft_sourcegrandaverage?
>> Thanks!
>>
>> - Joram
>>
>>
>> --
>> Joram van Driel, MSc.
>> PhD student @ University of Amsterdam
>> Brain & Cognition @ Department of Psychology
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> --
> 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
>
> Contact:
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> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
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>
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>



-- 
Joram van Driel, MSc.
PhD student @ University of Amsterdam
Brain & Cognition @ Department of Psychology
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