Merge branch 'master' of https://github.com/arnodelorme/roiconnect

sccn · Oct 21, 2022 · 6b4006d · 6b4006d
2 parents 614c3bd + 3d947be
commit 6b4006d
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diff --git a/pipeline_connectivity.m b/pipeline_connectivity.m
@@ -35,6 +35,7 @@
 measures = { 'CS' 'COH' 'DTF'  'wPLI'  'PDC'  'MIM'  'MIC' 'GC' };
 measures = { 'CS' 'COH' 'wPLI'  'PDC'  'MIM'  'MIC' 'GC' };
 measures = { 'CS' 'COH' 'MIM' 'GC' };
+measures = { 'CS' 'COH' 'MIM' };
 
 EEG_no_connect = EEG;
 EEG = pop_roi_connect(EEG_no_connect, 'methods', {'MIM'});

diff --git a/pop_roi_connectplot.m b/pop_roi_connectplot.m
@@ -357,10 +357,6 @@
 %                     TRGCnet = S.TRGC(:, :, 1) - S.TRGC(:, :, 2);
                     TRGC = S.TRGC;
                 end
-%                 TRGCnet = TRGCnet - permute(TRGCnet, [1 3 2]); 
-%                 TRGCnet = TRGCnet(:,:); 
-%                 TRGCnet = S.GC(:, :, 1) - S.GC(:, :, 2);
-%                 TRGC = get_connect_mat( TRGCnet, S.nROI, -1);
                 matrix = squeeze(mean(TRGC(frq_inds, :, :)));
                 cortexPlot  = mean(matrix, 2);
                 cortexTitle = [ upper(g.measure) ' (' titleStr '); Red = net sender; Blue = net receiver' ];
@@ -373,27 +369,23 @@
 %                     MI = S.MIM(:, :);
                     MI = S.MIM;
                 end
-%                 MI = get_connect_mat( MI, S.nROI, +1);
                 matrix = squeeze(mean(MI(frq_inds, :, :)));
                 cortexPlot = mean(matrix, 2);
 
             case { 'crossspecpow' 'coh' 'crossspecimag' }
                 if strcmpi(g.measure, 'coh')
                     PS = abs(S.COH); % do not know what to do here
-                    PS = squeeze(mean(mean(reshape(PS, S.srate+1, S.nPCA, S.nROI, S.nPCA, S.nROI), 2), 4));
                     PSarea2area = squeeze(mean(PS(frq_inds, :, :)));
                     cortexPlot = mean(PSarea2area, 2);
                 elseif strcmpi(g.measure, 'crossspecimag')
                     PS = abs(imag(cs2coh(S.CS)));
-                    PS = squeeze(mean(mean(reshape(PS, S.srate+1, S.nPCA, S.nROI, S.nPCA, S.nROI), 2), 4));
                     PSarea2area = squeeze(mean(PS(frq_inds, :, :)));
                     cortexPlot = mean(PSarea2area, 2);
                 else
                     PS = cs2psd(S.CS);
-                    PS2 = squeeze(mean(mean(reshape(PS, S.srate+1, S.nPCA, S.nROI, S.nPCA, S.nROI), 2), 4));
-                    PSarea2area = squeeze(mean(PS2(frq_inds, :, :),1));
-                    apow = squeeze(sum(sum(reshape(PS(frq_inds, :), [], S.nPCA, S.nROI), 1), 2)).*S.source_roi_power_norm';
+                    apow = squeeze(sum(sum(reshape(PS(frq_inds, :), [], S.nROI), 1), 2)).*S.source_roi_power_norm';
                     cortexPlot = 10*log10(apow);
+                    PSarea2area = [];
                 end
                 plotPSDFreq = S.freqs(frq_inds);
                 plotPSD     = PS(frq_inds, :);
@@ -451,20 +443,6 @@
     end
 end
 
-function measure = get_connect_mat( measureOri, nROI, signVal)
-    % create a ROI x ROI connectivity matrix, if needed
-    % TRGCmat(f, ii, jj) is net TRGC from jj to ii
-    measure = [];
-    iinds = 0;
-    for iroi = 1:nROI
-        for jroi = (iroi+1):nROI
-            iinds = iinds + 1;
-            measure(:, iroi, jroi) = signVal * measureOri(:, iinds);
-            measure(:, jroi, iroi) = measureOri(:, iinds);
-        end
-    end
-end
-
 function [coordinate, seed_idx] = get_seedregion_coordinate(scouts, seed_idx, vc)
     % determine voxel of selected seed region, if needed
     % assign region index to selected seed region (passed as index)