[FieldTrip] missing anatomy in source plot of ft_sourcegrandaverage

["Jörn M. Horschig"]

Hi Joram,

you probably need to interpolate to a template and then put the pos and 
dim field from the template you used in the source structure. You do not 
have to interpolate, but then make sure that the dimensions of your 
anatomy match the dimensions of your sourcemodel.

Not sure if you followed any tutorial, but this is a good one:
http://fieldtrip.fcdonders.nl/tutorial/beamformingextended

Best,
Jörn


On 2/3/2014 9:59 AM, Joram van Driel wrote:
> 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 <mailto: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
>
>
>         _______________________________________________
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>         fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
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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
>
>     Contact:
>     E-Mail: jm.horschig at donders.ru.nl <mailto:jm.horschig at donders.ru.nl>
>     Tel: +31-(0)24-36-68493 <tel:%2B31-%280%2924-36-68493>
>     Web: http://www.ru.nl/donders
>
>     Visiting address:
>     Trigon, room 2.30
>     Kapittelweg 29
>     NL-6525 EN Nijmegen
>     The Netherlands
>
>     _______________________________________________
>     fieldtrip mailing list
>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> -- 
> Joram van Driel, MSc.
> PhD student @ University of Amsterdam
> Brain & Cognition @ Department of Psychology
>
>
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> 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:
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