[FieldTrip] ft_sourcestatistics cannot find field 'pos'

Joram van Driel joramvandriel at gmail.com
Fri Jan 24 12:16:26 CET 2014


Hi Nietzsche,

Thanks for the suggestion, but unfortunately that's not what's going wrong.
My input data is a subject-by-condition array, so if I fill in
sourcedat{:,1} and sourcedat{:,2}, that would be equivalent to having two
separate variables and do source_condition1{:},source_condition2{:}. I
tried that but I get the same error "??? Reference to non-existent field
'pos'."

In fact, the error is I think a bug of the newest fieldtrip version,
because when I tried an older version (fieldtrip-20131031), it works
(although it later crashes on a design array issue, but that's something I
have to figure out myself ;)).

The 'pos' field is a field that is present in the output of
ft_sourceanalysis; according to the help it's a N-by-3 matrix of the x-y-z
position of all the sources, where N is the sum of the length of the
'inside' and 'outside' fields.
This 'pos' field is removed in further steps (ft_sourceinterpolate). When
calling ft_sourceanalysis in version fieldtrip-20140109, the function
statistics_wrapper searches for this field (line 228) and can't find it.

Chrs,

- Joram



On Fri, Jan 24, 2014 at 9:55 AM, Lam, Nietzsche <n.lam at fcdonders.ru.nl>wrote:

> Hi Joram,
>
> I'm not entirely sure if this is the solution, but when you call
> ft_sourcestatistics, you can try this:
>
> <stat = ft_sourcestatistics(cfg,sourceDiffNorm{:}, sourceDiffNorm{:})>
>
> FieldTrip statistics functions understands that you want to use the data
> from all subjects when you use {:}, so there's no need to call individual
> columns with {:,X}.
>
> Best,
> Nietzsche
>
>
>
> ----- Original Message -----
> > From: "Joram van Driel" <joramvandriel at gmail.com>
> > To: "FieldTrip discussion list" <fieldtrip at science.ru.nl>
> > Sent: Friday, 24 January, 2014 8:54:24 AM
> > Subject: [FieldTrip] ft_sourcestatistics cannot find field 'pos'
> > Hi all,
> >
> >
> > I'm getting stuck with ft_sourcestatistics.
> > I want to do a simple two-condition contrast on neuromag MEG data,
> > where I did frequency beamforming on a pre vs. post tf-window.
> >
> >
> > I followed the instructions of the tutorial, so for each subject and
> > condition:
> >
> >
> > 1) ft_sourceanalysis with subject-specific vol and grid structures,
> > where I did the pre vs post contrast as follows:
> >
> >
> >
> > sourceAll = ft_sourceanalysis(cfg, freqAll(condi));
> >
> > cfg.grid.filter = sourceAll.avg.filter;
> > sourcePre_con = ft_sourceanalysis(cfg, freqPre(condi) );
> > sourcePost_con = ft_sourceanalysis(cfg, freqPost(condi));
> >
> >
> >
> > sourceDiff(condi) = sourcePost_con;
> > sourceDiff(condi).avg.pow = (sourcePost_con.avg.pow -
> > sourcePre_con.avg.pow) ./ sourcePre_con.avg.pow;
> >
> >
> > 2) ft_sourceinterpolate with the subject-specific mri
> > 3) ft_volumenormalize to MNI with coordsys 'neuromag'.
> > 4) The output is stored in a subject-by-condition cell array, which I
> > put into ft_sourcestatistics with the following cfg:
> >
> >
> >
> > cfg = [];
> > cfg.parameter = 'avg.pow';
> > cfg.method = 'analytic';
> > cfg.statistic = 'depsamplesT';
> > cfg.correctm = 'no';
> > cfg.alpha = 0.05;
> >
> >
> > Nsub = 10;
> > cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)];
> > cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub];
> > cfg.tail = 0; % number, -1, 1 or 0 (default = 0)
> > cfg.ivar = 1; % number or list with indices, independent variable(s)
> > cfg.uvar = 2; % number or list with indices, unit variable(s)
> >
> >
> > stat = ft_sourcestatistics(cfg,sourceDiffNorm{:,1},
> > sourceDiffNorm{:,2});
> >
> >
> >
> >
> > This results in the error that it cannot find the field 'pos'; however
> > this field is only present in the result from ft_sourceanalysis (and
> > differs for each subject), but disappears as soon as
> > ft_sourceinterpolate is applied. I tried to put the result from
> > ft_sourceanalysis straight into ft_sourcestatistics (which according
> > to the help should be possible), but this doesn't recognize the input
> > as volume data (and apart from that, the subjects aren't spatially
> > aligned this way).
> >
> >
> > I hope someone can help me with this; any help is much appreciated!
> >
> >
> > 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
>
> --
> Nietzsche H.L. Lam, MSc
> PhD Candidate
>
> Max Planck Institute for Psycholinguistics
> Wundtlaan 1, 6525 XD Nijmegen, The Netherlands
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Kapittelweg 29, 6525EN Nijmegen, The Netherlands
>
> n.lam at fcdonders.ru.nl
> +31-24-3668219
>
>
> neurobiologyoflanguage.com
> _______________________________________________
> fieldtrip mailing list
> 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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