[FieldTrip] missing anatomy in source plot of ft_sourcegrandaverage
"Jörn M. Horschig"
jm.horschig at donders.ru.nl
Mon Feb 3 13:37:44 CET 2014
Hi Joram,
the (regular) beamforming tutorial is dealing only with the single
subject case. The extended sets the stage for averaging over subjects as
well. I think all of your questions will be answered when you went
through that one. Otherwise, feel free to ask any questions that remain
open ;)
Best,
Jörn
On 2/3/2014 12:19 PM, Joram van Driel wrote:
> Hi Jörn,
>
> 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.
>
>
> With source structure you mean the result from ft_sourcegrandaverage?
> That already has a pos and dim field. Or the subject individual source
> structures, *after* ft_sourceinterpolate but *before* ft_volumenormalise?
>
> You do not have to interpolate, but then make sure that the
> dimensions of your anatomy match the dimensions of your sourcemodel.
>
>
> I'm not sure what you mean here. I did for each subject
> ft_sourceinterpolate and ft_volumenormalise. Shouldn't then
> ft_sourcegrandaverage give me something that I could plot with
> ft_sourceplot? Or am I asking too much of FieldTrip right now :)
> According to the regular beamforming tutorial this should be possible.
>
> But I will try the steps from the extended tutorial (and this one
> might be useful as well:
> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space)
> and see how far that brings me!
>
> Thanks,
> Joram
>
>
> 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>
> <mailto: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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>
>
> -- 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>
> <mailto: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>
> <tel:%2B31-%280%2924-36-68493>
>
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>
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>
>
>
> --
> Joram van Driel, MSc.
> PhD student @ University of Amsterdam
> Brain & Cognition @ Department of Psychology
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl <mailto: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 <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
>
>
> _______________________________________________
> 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
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