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roi_connstats.m
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roi_connstats.m
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% roi_connstats() - Compute connectivity between ROIs and run statistics.
%
% Usage:
% EEG = roi_connstats(EEG, fcomb, nshuf);
%
% Inputs:
% EEG - EEGLAB dataset with ROI activity computed.
%
% Optional inputs:
% 'methods' - [cell] Cell of strings corresponding to methods.
% 'CS' : Cross spectrum
% 'aCOH' : Coherence
% 'cCOH' : (complex-valued) coherency
% 'iCOH' : absolute value of the imaginary part of coherency
% 'wPLI' : Weighted Phase Lag Index
% 'MIM' : Multivariate Interaction Measure for each ROI
% 'MIC' : Maximized Imaginary Coherency for each ROI
% 'nshuf' - [integer] Number of shuffles for statistical significance testing. The first shuffle is the true value. Default is 1001.
% 'roi_selection' - [cell array of integers] Cell array of ROI indices {1, 2, 3, ...} indicating for which regions (ROIs) connectivity should be computed.
% Default is all (set to EEG.roi.nROI).
% 'freqresolution' - [integer] Desired frequency resolution (in number of frequencies). If
% specified, the signal is zero padded accordingly.
% Default is 0 (means no padding).
% 'poolsize' - [integer] Number of workers in the parallel pool (check parpool documentation) for parallel computing
function EEG = roi_connstats(EEG, varargin)
if nargin < 2
help roi_connstats;
% TODO: open GUI as in roi_connect.m
return
end
if ~isfield(EEG, 'roi') || ~isfield(EEG.roi, 'source_roi_data')
error('Cannot find ROI data - compute ROI data first');
else
data = EEG.roi.source_roi_data;
end
% decode input parameters
% Add fcomb in parameter list
g = finputcheck(varargin, { ...
'methods' 'cell' { } { };
'nshuf' 'integer' { } 1001;
'freqresolution' 'integer' { } 0;
'roi_selection' 'cell' { } { }; ...
'poolsize' 'integer' { } 1 ; ...
'fcomb' 'struct' { } struct; ...
},'roi_connstats');
if ischar(g), error(g); end
if ~isempty(intersect(g.methods, {'COH'}))
warning("'COH' is not supported anymore and will be replaced with aCOH (coherence). " + ...
"Please double-check with the documentation if this is what you want.")
coh_idx = strcmpi(g.methods, 'COH');
g.methods{coh_idx} = 'aCOH';
end
methodset1 = { 'CS' 'MIM' 'MIC' 'wPLI' 'cCOH' 'aCOH' 'iCOH' }; % GC/TRGC, PDC/TRPDC, DTF/TRDTF not included (yet)
methodset2 = {'PAC'} ;
tmpMethods1 = intersect(g.methods, methodset1);
tmpMethods2 = intersect(g.methods, methodset2);
if ~isempty(tmpMethods1)
npcs = repmat(EEG.roi.nPCA, 1, EEG.roi.nROI);
conn = shuffle_CS(data, npcs, tmpMethods1, g.nshuf, 'freqresolution', g.freqresolution, 'roi_selection', g.roi_selection, 'poolsize', g.poolsize); % (nfreq, nROI, nROI, nshuf)
for iMethod = 1:length(tmpMethods1)
EEG.roi.(tmpMethods1{iMethod}) = conn.(tmpMethods1{iMethod});
if strcmpi(tmpMethods1{iMethod}, 'MIM') || strcmpi(tmpMethods1{iMethod}, 'MIC')
EEG.roi.inds = conn.inds;
end
end
end
%
if ~isempty(tmpMethods2)
npcs = repmat(EEG.roi.nPCA, 1, EEG.roi.nROI);
% Add parameter
conn = shuffle_BS(data, npcs, tmpMethods2, g.nshuf, 'freqresolution', g.freqresolution, 'roi_selection', g.roi_selection, 'poolsize', g.poolsize, 'fcomb', g.fcomb);
for iMethod = 1:length(tmpMethods2)
EEG.roi.(tmpMethods2{iMethod}) = conn.(tmpMethods2{iMethod});
%if strcmpi(tmpMethods2{iMethod}, 'PAC')
% EEG.roi.inds = conn.inds;
end
end
end