Skip to content

Commit

Permalink
Merge pull request #11 from Hiyeri/master
Browse files Browse the repository at this point in the history 
GUI implementation of visualization improvements + plotting of seed voxel
  • Loading branch information
@arnodelorme
arnodelorme authored Jun 16, 2022
2 parents 28ac20d + 5181efb commit ad7129c
Show file tree
Hide file tree
Showing 3 changed files with 122 additions and 59 deletions.
5 changes: 3 additions & 2 deletions libs/haufe/allplots_cortex_BS.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,9 @@ function allplots_cortex_BS(cortex, data_in, colorlimits, cm, unit, smooth, prin
end
end

cortex.Vertices = cortex.Vertices(:, [2 1 3]);
cortex.Vertices(:, 1) = -cortex.Vertices(:, 1);
% coordinate transformation
% cortex.Vertices = cortex.Vertices(:, [2 1 3]);
% cortex.Vertices(:, 1) = -cortex.Vertices(:, 1);


for iatl = 1:length(cortex.Atlas)
Expand Down
172 changes: 117 additions & 55 deletions pop_roi_connectplot.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,20 +11,28 @@
% 'sourcemodel' - [string] source model file
%
% Optional inputs:
% 'measure' - ['psd'|'roipsd'|'trgc'|'crossspecimag'|'crossspecpow'|'mic'|'mim']
% 'psd' : Source power spectrum
% 'psdroi': ROI based power spectrum
% 'trgc' : Time-reversed granger causality
% 'crossspecimag': Imaginary part of coherence from cross-spectrum
% 'crossspecpow' : Average cross-spectrum power for each ROI
% 'mic' : Maximized Imaginary Coherency for each ROI
% 'mim' : Multivariate Interaction Measure for each ROI
% 'freqrange' - [min max] frequency range in Hz. Default is to plot
% broadband power.
% 'smooth' - [float] smoothing factor for cortex surface plotting
% 'plotcortex' - ['on'|'off'] plot results on smooth cortex. Default is 'on'
% 'plotmatrix' - ['on'|'off'] plot results on smooth cortex. Default is 'off'
% 'plotpsd' - ['on'|'off'] plot PSD (for 'crossspecpow' only). Default is 'off'
% 'measure' - ['psd'|'roipsd'|'trgc'|'crossspecimag'|'crossspecpow'|'mic'|'mim']
% 'psd' : Source power spectrum
% 'psdroi': ROI based power spectrum
% 'trgc' : Time-reversed granger causality
% 'gc' : Granger causality
% 'crossspecimag': Imaginary part of coherence from cross-spectrum
% 'crossspecpow' : Average cross-spectrum power for each ROI
% 'mic' : Maximized Imaginary Coherency for each ROI
% 'mim' : Multivariate Interaction Measure for each ROI
% 'freqrange' - [min max] frequency range in Hz. Default is to plot broadband power.
% 'smooth' - [float] smoothing factor for cortex surface plotting
% 'plotcortex' - ['on'|'off'] plot results on smooth cortex. Default is 'on'
% 'plotcortexparams' - [cell] ...
% 'plotcortexseedregion' - [string] plot seed voxel on cortex. Takes name of seed region as input.
% 'plot3d' - ['on'|'off'] ... Default is 'off'
% 'plot3dparams' - [cell] ...
% 'plotmatrix' - ['on'|'off'] plot results as ROI to ROI matrix. Default is 'off'
% 'plotbarplot' - ['on'|'off'] plot ROI based power spectrum as barplot. Default is 'off'
% 'hemisphere' - ['all'|'left'|'right'] hemisphere options for ROI to ROI matrix. Default is 'all'
% 'region' - ['all'|'cingulate'|'prefrontal'|'frontal'|'temporal'|'parietal'|'central'|'occipital'] region selection for ROI to ROI matrix. Default is 'all'
% 'largeplot' - ['on'|'off'] plot MIM, TRGC and Power in a single large plot. Default is 'off'
% 'plotpsd' - ['on'|'off'] plot PSD (for 'crossspecpow' only). Default is 'off'
%
% Author: Stefan Haufe and Arnaud Delorme, 2019
%
Expand Down Expand Up @@ -179,6 +187,7 @@
splot(end ).matrix = -1;
splot(end ).psd = 0;
end


if nargin < 2

Expand All @@ -195,9 +204,10 @@
' end;' ...
'end;' ...
'clear iField fieldTmp usrdat;' ];


fcregions = {'all', 'cingulate', 'prefrontal', 'frontal', 'temporal', 'parietal', 'central', 'occipital'};
plotrow = [1 1];
uigeom = { [1 1] [1 1] 1 [1 1] plotrow plotrow plotrow plotrow };
uigeom = { [1 1] [1 1] 1 [1 1] plotrow [5 3 2] [3.5 1.5 1 1] plotrow };
uilist = {{ 'style' 'text' 'string' 'Select a measure to plot' 'fontweight' 'bold'} ...
{ 'style' 'popupmenu' 'string' {splot.label} 'callback' cb_select 'value' 4 'tag' 'selection' } ...
{ 'style' 'text' 'string' 'Frequency range in Hz [min max]:'} ...
Expand All @@ -210,9 +220,13 @@
{ 'style' 'edit' 'string' '''thresholdper'', 0.8' 'tag' 'plot3dparams' } ...
...
{ 'style' 'checkbox' 'string' 'Connectivity of each area' 'tag' 'cortex' 'value' 1 } ...
{ 'style' 'text' 'string' '' 'tag' 'cortexparams' } ...
{ 'style' 'text' 'string' 'Index of seed region:' 'fontweight' 'bold' } ...
{ 'style' 'edit' 'string' '' 'tag' 'seed_region'} ...
...
{ 'style' 'checkbox' 'string' 'Matrix representation' 'tag' 'matrix' 'enable' 'off' } {} ...
{ 'style' 'checkbox' 'string' 'Matrix representation' 'tag' 'matrix' 'enable' 'off' } ...
{ 'style' 'popupmenu' 'string' fcregions 'callback' cb_select 'value' 3 'tag' 'region' } ....
{ 'style' 'checkbox' 'string' 'left' 'tag' 'hemisphere_left' 'value' 1 } ...
{ 'style' 'checkbox' 'string' 'right' 'tag' 'hemisphere_right' 'value' 1 } ...
...
{ 'style' 'checkbox' 'string' 'Power spectral density' 'tag' 'psd' 'enable' 'off' } {} ...
};
Expand All @@ -226,29 +240,40 @@
options = { options{:} 'freqrange' eval( [ '[' result{2} ']' ] ) };
options = { options{:} 'plotcortex' fastif(outs.cortex, 'on', 'off') };
options = { options{:} 'plotcortexparams' {} };
options = { options{:} 'plotcortexseedregion' str2num(result{6}) };
options = { options{:} 'plotmatrix' fastif(outs.matrix, 'on', 'off') };
options = { options{:} 'plotpsd' fastif(outs.psd , 'on', 'off') };
options = { options{:} 'plot3d' fastif(outs.plot3d, 'on', 'off') };
options = { options{:} 'plot3dparams' eval( [ '{' outs.plot3dparams '}' ] ) };
options = { options{:} 'region' fcregions{result{8}} };
% choose which hemisphere to plot
if outs.hemisphere_left == 1 && outs.hemisphere_right == 0
options = { options{:} 'hemisphere' 'left' };
elseif outs.hemisphere_left == 0 && outs.hemisphere_right == 1
options = { options{:} 'hemisphere' 'right' };
else
options = { options{:} 'hemisphere' 'all' };
end
else
options = varargin;
end

% decode input parameters
% -----------------------
g = finputcheck(options, { 'measure' 'string' {splot.acronym} '';
'freqrange' 'real' { } [];
'smooth' 'real' { } 0.35;
'plotcortex' 'string' { 'on' 'off' } 'on';
'plotcortexparams' 'cell' { } {};
'plot3d' 'string' { 'on' 'off' } 'off';
'plot3dparams' 'cell' { } {};
'plotmatrix' 'string' { 'on' 'off' } 'off';
'plotbarplot' 'string' { 'on' 'off'} 'off';
'hemisphere' 'string' {'all' 'left' 'right'} 'all';
'region' 'string' { 'all', 'cingulate', 'prefrontal', 'frontal', 'temporal', 'parietal', 'central', 'occipital' } 'all';
'largeplot', 'string' { 'on' 'off' } 'off';
'plotpsd', 'string' { 'on' 'off' } 'off' }, 'pop_roi_connectplot');
'freqrange' 'real' { } [];
'smooth' 'real' { } 0.35;
'plotcortex' 'string' { 'on' 'off' } 'on';
'plotcortexparams' 'cell' { } {};
'plotcortexseedregion' 'integer' { } [];
'plot3d' 'string' { 'on' 'off' } 'off';
'plot3dparams' 'cell' { } {};
'plotmatrix' 'string' { 'on' 'off' } 'off';
'plotbarplot' 'string' { 'on' 'off'} 'off';
'hemisphere' 'string' {'all' 'left' 'right'} 'all';
'region' 'string' { 'all', 'cingulate', 'prefrontal', 'frontal', 'temporal', 'parietal', 'central', 'occipital' } 'all';
'largeplot', 'string' { 'on' 'off' } 'off';
'plotpsd', 'string' { 'on' 'off' } 'off' }, 'pop_roi_connectplot');
if ischar(g), error(g); end
S = EEG.roi;

Expand Down Expand Up @@ -285,7 +310,7 @@
MI = get_connect_mat( MI, S.nROI, +1);
MIM_matrix = squeeze(mean(MI(frq_inds, :, :)));

pltlarge(EEG, MIM_matrix, TRGC_matrix, source_roi_power_norm_dB, titleStr)
roi_largeplot(EEG, MIM_matrix, TRGC_matrix, source_roi_power_norm_dB, titleStr)
else
switch lower(g.measure)
case { 'psd' 'roipsd' }
Expand All @@ -307,28 +332,28 @@

if strcmpi(g.plotbarplot, 'on')
source_roi_power_norm_dB = 10*log10( mean(EEG.roi.source_roi_power(frq_inds,:)) );
pltmatrix(EEG, source_roi_power_norm_dB, titleStr, g.measure, g.hemisphere, g.region);
roi_plotcoloredlobes(EEG, source_roi_power_norm_dB, titleStr, g.measure, g.hemisphere, g.region);
end

case { 'trgc' 'gc' }
% calculation of net TRGC scores (i->j minus j->i), recommended procedure
% TRGCnet = TRGC_(:, 1:2:end)-TRGC_(:, 2:2:end);
% new way to compute net scores
if strcmpi(g.measure, 'GC')
% TRGCnet = S.GC;
% TRGCnet = S.GC;
TRGCnet = S.GC(:, :, 1) - S.GC(:, :, 2);
else
% TRGCnet = S.TRGC;
% TRGCnet = S.TRGC;
TRGCnet = S.TRGC(:, :, 1) - S.TRGC(:, :, 2);
end
% TRGCnet = TRGCnet - permute(TRGCnet, [1 3 2]);
% TRGCnet = TRGCnet(:,:);
% TRGCnet = S.GC(:, :, 1) - S.GC(:, :, 2);
% TRGCnet = S.GC(:, :, 1) - S.GC(:, :, 2);
TRGC = get_connect_mat( TRGCnet, S.nROI, -1);

if strcmpi(g.plotmatrix, 'on')
matrix = squeeze(mean(TRGC(frq_inds, :, :)));
pltmatrix(EEG, matrix, titleStr, g.measure, g.hemisphere, g.region);
roi_plotcoloredlobes(EEG, matrix, titleStr, g.measure, g.hemisphere, g.region);
end

if strcmpi(g.plot3d, 'on')
Expand All @@ -337,8 +362,16 @@
end

if strcmpi(g.plotcortex, 'on')
atrgc = mean(squeeze(mean(TRGC(frq_inds, :, :))), 2);
allplots_cortex_BS(S.cortex, atrgc, [-max(abs(atrgc)) max(abs(atrgc))], cm17, upper(g.measure), g.smooth);
if isempty(g.plotcortexseedregion)
atrgc = mean(squeeze(mean(TRGC(frq_inds, :, :))), 2);
allplots_cortex_BS(S.cortex, atrgc, [-max(abs(atrgc)) max(abs(atrgc))], cm17, upper(g.measure), g.smooth);
movegui(gcf, 'south')
else
[coordinate, seed_idx] = get_seedregion_coordinate(EEG.roi.atlas.Scouts, g.plotcortexseedregion, EEG.roi.cortex.Vertices);
atrgc = squeeze(mean(TRGC(frq_inds, seed_idx, :)));
allplots_cortex_BS(S.cortex, atrgc, [-max(abs(atrgc)) max(abs(atrgc))], cm17, upper(g.measure), g.smooth, [], {coordinate});
movegui(gcf, 'south')
end
h = textsc([ upper(g.measure) ' (' titleStr '); Red = net sender; Blue = net receiver' ], 'title');
set(h, 'fontsize', 20);
end
Expand All @@ -353,13 +386,19 @@

if strcmpi(g.plotmatrix, 'on')
matrix = squeeze(mean(MI(frq_inds, :, :)));
pltmatrix(EEG, matrix, titleStr, g.measure, g.hemisphere, g.region);
roi_plotcoloredlobes(EEG, matrix, titleStr, g.measure, g.hemisphere, g.region);
end

if strcmpi(g.plotcortex, 'on')
ami = mean(squeeze(mean(MI(frq_inds, :, :))), 2);
allplots_cortex_BS(S.cortex, ami, [min(ami) max(ami)], cm17, upper(g.measure), g.smooth);
h = textsc([ upper(g.measure) ' (' titleStr '); Red = net sender; Blue = net receiver' ], 'title');
if isempty(g.plotcortexseedregion)
ami = mean(squeeze(mean(MI(frq_inds, :, :))), 2);
allplots_cortex_BS(S.cortex, ami, [min(ami) max(ami)], cm17a, upper(g.measure), g.smooth);
else
[coordinate, seed_idx] = get_seedregion_coordinate(EEG.roi.atlas.Scouts, g.plotcortexseedregion, EEG.roi.cortex.Vertices);
ami = squeeze(mean(MI(frq_inds, seed_idx,:)));
allplots_cortex_BS(S.cortex, ami, [min(ami) max(ami)], cm17a, upper(g.measure), g.smooth, [], {coordinate});
end
h = textsc([ upper(g.measure) ' (' titleStr ') '], 'title');
set(h, 'fontsize', 20);
end

Expand Down Expand Up @@ -427,9 +466,32 @@
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)
if ~isempty(seed_idx)
% ball not visible for these regions when plotting the mean voxel
manual_region_idxs = [2, 16, 18, 25, 26, 31, 32, 45, 49, 50, 55, 56, 59, 60, 61, 64];
pos_idx = scouts(seed_idx).Vertices;
pos = vc(pos_idx,:);
if seed_idx == 1
coordinate = vc(736,:);
elseif ismember(seed_idx, manual_region_idxs)
pos_sorted = sortrows(pos, 3, 'descend'); % sort by descending Z-coordinate
coordinate = pos_sorted(1,:);
else
mid_point = mean(pos,1);
[~,closest_pos_idx] = min(eucl(mid_point, pos)); % determine mean voxel
coordinate = pos(closest_pos_idx,:);
end
else
error('Selected region not in cortex')
end
end

function pltmatrix( EEG, matrix, titleStr, measure, hemisphere, region)
% plot individual ROI to ROI matrix with colored labels (corresponding lobes/regions)
function roi_plotcoloredlobes( EEG, matrix, titleStr, measure, hemisphere, region)
% plot matrix with colored labels sorted by region according to the Desikan-Killiany atlas
load cm17
switch lower(measure)
case {'mim', 'mic', 'coh'}
Expand All @@ -438,7 +500,7 @@ function pltmatrix( EEG, matrix, titleStr, measure, hemisphere, region)
cmap = cm17;
end

% plot matrix with colored labels sorted by region according to the Desikan-Killiany atlas
% retrieve labels from atlas
labels = strings(1,length(EEG.roi.atlas.Scouts));
for i = 1:length(labels)
scout = struct2cell(EEG.roi.atlas.Scouts(i));
Expand Down Expand Up @@ -514,6 +576,15 @@ function pltmatrix( EEG, matrix, titleStr, measure, hemisphere, region)
color_idxx = color_idxx(start_idx:end_idx);
end
n_roi_labels = size(matrix, 1); % only 68 if no region is selected

% hemisphere parameters to determine which labels to use
if strcmpi(hemisphere, 'left')
hem_idx = {1 2 2}; % use labels 1:2:68 (first two values), only use 1/2 of the labels (3rd value)
elseif strcmpi(hemisphere, 'right')
hem_idx = {2 2 2}; % use labels 2:2:68 (first two values), only use 1/2 of the labels (3rd value)
else
hem_idx = {1 1 1}; % use labels 1:1:68 (first two values, all labels), use 1/1 of the labels (3rd value, all labels)
end

% create dummy plot and add custom legend
f = figure();
Expand All @@ -525,15 +596,6 @@ function pltmatrix( EEG, matrix, titleStr, measure, hemisphere, region)
plot(x, x*k, '-', 'LineWidth', 9, 'Color', colors{k});
end

% hemisphere parameters to determine which labels to use
if strcmpi(hemisphere, 'left')
hem_idx = {1 2 2}; % use labels 1:2:68 (first two values), only use 1/2 of the labels (3rd value)
elseif strcmpi(hemisphere, 'right')
hem_idx = {2 2 2}; % use labels 2:2:68 (first two values), only use 1/2 of the labels (3rd value)
else
hem_idx = {1 1 1}; % use labels 1:1:68 (first two values, all labels), use 1/1 of the labels (3rd value, all labels)
end

% labels on dummy plot for positioning
xlim([0 n_roi_labels])
ylim([0 n_roi_labels])
Expand Down Expand Up @@ -575,7 +637,7 @@ function pltmatrix( EEG, matrix, titleStr, measure, hemisphere, region)
end
end

function pltlarge(EEG, mim, trgc, roipsd, titleStr)
function roi_largeplot(EEG, mim, trgc, roipsd, titleStr)
% plot MIM, TRGC and power (barplot) in a single large figure
load cm17

Expand Down
4 changes: 2 additions & 2 deletions roi_connect.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -87,8 +87,8 @@
end
end

% MIC and MIM use a different function
if ismember(g.methods, 'MIC') || ismember(g.methods, 'MIM')
% % MIC and MIM use a different function
if any(ismember(g.methods, 'MIC')) || any(ismember(g.methods, 'MIM'))
tmpMethods = setdiff(g.methods, { 'CS' 'COH' 'PSD' 'PSDROI' 'GC' 'TRGC' 'wPLI' 'PDC' 'TRPDC' 'DTF' 'TRDTF' });
conn_mult = data2sctrgcmim(source_roi_data, EEG.srate, g.morder, 0, g.naccu, [], inds, tmpMethods);
fields = fieldnames(conn_mult);
Expand Down

0 comments on commit ad7129c

Please sign in to comment.