[FieldTrip] ft_sourcestatistics cannot find field 'pos'

[Joram van Driel]

Sorry, this should have been:
This 'pos' field is removed in further steps (ft_sourceinterpolate). When
calling *ft_sourcestatistics* in version fieldtrip-20140109, the function
statistics_wrapper searches for this field (line 228) and can't find it.


On Fri, Jan 24, 2014 at 12:16 PM, Joram van Driel
<joramvandriel at gmail.com>wrote:

> 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
>



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