[FieldTrip] Using Atlas ROIs in EEG Source Statistics (ft_sourcestatistics)

[Roey Schurr]

Hello again,

Sorry, it seems like the older version (with ft_volumelookup) is just our
mistake.
However the problem is still relevant, for the function volumelookup is
still undefinded in our case.

Hopefully someone might know what we did wrong.

Thank you once again!
Aia and Roey


On Tue, Oct 8, 2013 at 12:54 AM, Roey Schurr <roeysc at gmail.com> wrote:

> Hello all,
>
> We are having some problems defining atlas-based ROIs using
> ft_sourcestatistics on two source structures obtained via ft_sourceanalysis
> (whose grid is later changed according to a precalculated MNI-warped grid).
>
> It seems like the function "statistics_wrapper" has changed between
> "fieldtrip-20130822" and "fieldtrip-20131007": line 136 now calls
> "volumelookup" and not "ft_volumelookup", so we get the following error:
>
>       ??? Undefined function or method 'volumelookup' for input
>       arguments of type 'struct'.
>
>       Error in ==> statistics_wrapper at 136
>               tmp = volumelookup(tmpcfg, varargin{1});
>
> Using the older fieldtrip vesion we get this error:
>     ??? Subscript indices must either be real positive integers or
>     logicals.
>
>       Error in ==> statistics_wrapper at 213
>             tmp(i,:) = mean(dat(roi,:), 1);
>
>       Error in ==> ft_sourcestatistics at 107
>           [stat, cfg] = statistics_wrapper(cfg, varargin{:});
>
> So it seems like we didn't define the ROIs correctly, however we are not
> sure why.
>
> Any suggestions would be greatly appreciated!
> The relevant pieceof code is attached.
>
> Thank you all,
> Aia and Roey
>
>
>
> Relevant code
> ============
> % Convert sources units to mm, to fit the atlas's units
> sourceCondition1 = ft_convert_units(sourceCondition1, 'mm');
> sourceCondition2 = ft_convert_units(sourceCondition2, '
> design = [ ones(1,length(sourceCondition1.trial)),
> 2*ones(1,length(sourceCondition2.trial)) ];
>
> cfg = [];
> cfg.dim = sourceCondition1.dim;
> cfg.method = 'montecarlo';
> cfg.statistic = 'indepsamplesT';
> cfg.parameter = 'pow';
> cfg.correctm = 'cluster';
> cfg.numrandomization = 1000;
> cfg.alpha = 0.01;
> cfg.tail = 0;
> cfg.design(1,:) = design;
> cfg.ivar = 1;
>
> % Load the Atlas
> templateDir = which('ft_defaults'); % use a known function (ft_defaults)
> to find FieldTrip's directory
> backslashIndices = find(templateDir=='\');
> templateDir(backslashIndices(end)+1:end) = [];      clear backslashIndices;
> cfg.atlas = [templateDir, 'template\atlas\aal\ROI_MNI_V4.nii'];
>
>
> cfg.roi = AAL_names; % This is a cell array of the atlas's ROIs:
> "Precentral_L", "Precentral_R", etc/
>
> cfg.avgoverroi   = 'yes';
> cfg.hemisphere   = 'both';
> cfg.inputcoord   = 'mni';
>
> stat = ft_sourcestatistics(cfg, sourceCondition1, sourceCondition2);
>
>
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