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Merge pull request #19 from Hiyeri/dev
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merge dev into master
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@nguyen-td
nguyen-td authored Jan 31, 2023
2 parents d5c50f7 + 771b9aa commit 21f5e49
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14 changes: 8 additions & 6 deletions README.md
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Expand Up @@ -34,6 +34,8 @@ git clone https://github.com/arnodelorme/roiconnect.git
```
That's it! If you want to run the plugin, please start [EEGLAB](https://github.com/sccn/eeglab#to-use-eeglab) first. You may need to add EEGLAB to the [MATLAB path](https://de.mathworks.com/help/matlab/ref/addpath.html).

📌 `test_pipes/` includes some test pipelines which can be used to get started.

# Key features
The features of the toolbox are implemented in the following three main functions: `pop_roi_activity`, `pop_roi_connect` and `pop_roi_connectplot`.

Expand Down Expand Up @@ -66,12 +68,12 @@ The function computes all FC metrics in a frequency-resolved way, i.e., the outp
You can visualize power and FC in different modes by calling `pop_roi_connectplot`. Below, we show results of a single subject from the real data example in [[1]](#1). You can find the MATLAB code and corresponding analyses [here](https://github.com/fpellegrini/MotorImag). The plots show power or FC in left motor imagery condition. Due to the nature of the task, we show results in the 8 to 13 Hz frequency band but you are free to choose any frequency or frequency band you want.

:pushpin: If any of the images are too small for you, simply click on them, they will open in full size in another tab.<br>
:round_pushpin: Plotting is particularly optimized for PSD, MIM/MIC and GC/TRGC. The matrix plots are only available for the Desikan-Killiany atlas (68 ROIs). We are currently working on a generalized solution for all atlases.
:round_pushpin: Plotting is particularly optimized for PSD, MIM/MIC and GC/TRGC.

### Power as a region-wise bar plot
If you wish to visualize power as a barplot only, please make sure to explicitely turn `plotcortex` off because it is turned on by default.
```matlab
EEG = pop_roi_connectplot(EEG, 'measure', 'roipsd', 'plotcortex', 'off', 'plotbarplot', on, 'freqrange', [8 13]) % alpha band;
EEG = pop_roi_connectplot(EEG, 'measure', 'roipsd', 'plotcortex', 'off', 'plotbarplot', 'on', 'freqrange', [8 13]) % alpha band;
```
<p float="middle">
<img src="https://github.com/Hiyeri/roiconnect/blob/master/resources/power_barplot_left.jpg?raw=true" width="400"/>
Expand All @@ -93,7 +95,7 @@ Again, if you do not wish to see the cortex plot, you should explicitely turn `p
EEG = pop_roi_connectplot(EEG, 'measure', 'mim', 'plotcortex', 'off', 'plotmatrix', 'on', 'freqrange', [8 13]);
```
<p float="middle">
<img src="https://github.com/Hiyeri/roiconnect/blob/master/resources/FC_MIM_matrix_left.jpg?raw=true" width="400"/>
<img src="https://github.com/Hiyeri/roiconnect/blob/master/resources/FC_MIM_matrix.png?raw=true" width="400"/>
&nbsp; &nbsp;
</p>

Expand All @@ -103,17 +105,17 @@ pop_roi_connectplot(EEG, 'measure', 'mim', 'plotcortex', 'off', 'plotmatrix', 'o
```

<p float="middle">
<img src="https://github.com/Hiyeri/roiconnect/blob/master/resources/FC_MIM_matrix_groupedhems_left.jpg?raw=true" width="400"/>
<img src="https://github.com/Hiyeri/roiconnect/blob/master/resources/FC_MIM_matrix_groupedhems.png?raw=true" width="400"/>
&nbsp; &nbsp;
</p>

You can additionally filter by hemispheres and regions belonging to specific brain lobes. As an example, let us see how FC of the left hemisphere looks like.

```matlab
pop_roi_connectplot(EEG, 'measure', 'mim', 'plotcortex', 'off', 'plotmatrix', 'on', 'freqrange', [8 13], 'hemisphere', 'left') % left hemisphere, left motor imagery;
pop_roi_connectplot(EEG, 'measure', 'mim', 'plotcortex', 'off', 'plotmatrix', 'on', 'freqrange', [8 13], 'hemisphere', 'left');
```
<p float="middle">
<img src="https://github.com/Hiyeri/roiconnect/blob/master/resources/FC_MIM_matrix_lefthem_left.jpg?raw=true" width="400"/>
<img src="https://github.com/Hiyeri/roiconnect/blob/master/resources/FC_MIM_matrix_lefthem.png?raw=true" width="400"/>
&nbsp; &nbsp;
</p>

Expand Down
185 changes: 109 additions & 76 deletions pop_roi_connectplot.m
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Expand Up @@ -416,13 +416,14 @@

% plot on matrix
if strcmpi(g.plotmatrix, 'on') && ~isempty(matrix)
matrix = matrix.*seedMask;
try
roi_plotcoloredlobes(EEG, matrix, titleStr, g.measure, g.hemisphere, g.grouphemispheres, g.region);
catch
warning('Functionalities only available for the Desikan-Killiany atlas (68 ROIs).')
figure; imagesc(matrix);
end
matrix = matrix.*seedMask;
roi_plotcoloredlobes(EEG, matrix, titleStr, g.measure, g.hemisphere, g.grouphemispheres, g.region);
% try
% roi_plotcoloredlobes(EEG, matrix, titleStr, g.measure, g.hemisphere, g.grouphemispheres, g.region);
% catch
% warning('Functionalities only available for the Desikan-Killiany atlas (68 ROIs).')
% figure; imagesc(matrix);
% end
end

% plot on cortical surface
Expand All @@ -440,6 +441,8 @@
end
h = textsc(cortexTitle, 'title');
set(h, 'fontsize', 20);
elseif cortexFlag == -1
warning('EEG.roi.cortex does not contain the field "Faces" required to plot surface topographies.')
end

% plot 3D
Expand Down Expand Up @@ -477,15 +480,24 @@
end
end

function [colors, color_idxx, roi_idxx, labels_dk_cell_idx, roi_loc] = get_colored_labels(EEG)
% retrieve labels from atlas
function labels = get_labels(EEG)
% retrieve labels from atlas
labels = strings(1,length(EEG.roi.atlas.Scouts));
for i = 1:length(labels)
scout = struct2cell(EEG.roi.atlas.Scouts(i));
labels(i) = char(scout(1));
end
labels = cellstr(labels);

end

function new_labels = replace_underscores(labels)
% remove underscores in label names to avoid bug
new_labels = strrep(labels, '_', ' ');
end

function [colors, color_idxx, roi_idxx, labels_sorted, roi_loc] = get_colored_labels(EEG)
labels = get_labels(EEG);

colors = {[0,0,0]/255, [163, 107, 64]/255, [171, 163, 71]/255, [217, 37, 88]/255, [113, 15, 82]/255,[35, 103, 81]/255,[2, 45, 126]/255,};
% assign labels to colors
roi_loc ={'LT';'RT';'LL';'RL';'LF';'RF';'LO';'RO';'LT';'RT';'LPF';'RPF';'LT';'RT';'LP';'RP';'LT';'RT';'LT';'RT';'LL';'RL';'LO';'RO';'LPF';'RPF';'LO';'RO';'LPF';'RPF';'LT';'RT';'LC';'RC';'LT';'RT';'LF';'RF';'LPF';'RPF';'LF';'RF';'LO';'RO';'LC';'RC';'LL';'RL';'LC';'RC';'LP';'RP';'LL';'RL';'LF';'RF';'LF';'RF';'LP';'RP';'LT';'RT';'LP';'RP';'LT';'RT';'LT';'RT'};
Expand All @@ -502,21 +514,21 @@
roi_loc = strrep(roi_loc, 'R', '');
try
[color_idxx,roi_idxx] = sort(str2double(roi_loc));
labels_dk_cell_idx = labels(roi_idxx);
labels_sorted = labels(roi_idxx);
catch
roi_idxx = 1:length(labels);
color_idxx = mod(roi_idxx, length(colors))+1;
labels_dk_cell_idx = labels;
labels_sorted = labels;
end
end

function roi_plotpower(EEG, source_roi_power_norm_dB, titleStr)
[colors, color_idxx, roi_idxx, labels_dk_cell_idx, ~] = get_colored_labels(EEG);
n_roi_labels = size(labels_dk_cell_idx, 2);
[colors, color_idxx, roi_idxx, labels_sorted, ~] = get_colored_labels(EEG);
n_roi_labels = size(labels_sorted, 2);

barh(source_roi_power_norm_dB(roi_idxx));
set(gca, 'YDir', 'reverse');
set(gca,'ytick',[1:n_roi_labels],'yticklabel',labels_dk_cell_idx(1:end), 'fontweight','bold','fontsize', 9, 'TickLength',[0.015, 0.02], 'LineWidth',0.7);
set(gca,'ytick',[1:n_roi_labels],'yticklabel',labels_sorted(1:end), 'fontweight','bold','fontsize', 9, 'TickLength',[0.015, 0.02], 'LineWidth',0.7);
h = title([ 'ROI source power' ' (' titleStr ')' ]);
set(h, 'fontsize', 16);
ylabel('power [dB]')
Expand All @@ -542,43 +554,62 @@ function roi_plotcoloredlobes( EEG, matrix, titleStr, measure, hemisphere, group
error('Region plotting is only supported for the Desikan-Killiany atlas.');
end

% plot matrix with colored labels sorted by region according to the Desikan-Killiany atlas
% plot matrix with colored labels
load cm18
switch lower(measure)
case {'mim', 'mic', 'coh'}
cmap = cm18a;
otherwise
cmap = cm18;
end
[colors, color_idxx, roi_idxx, labels_dk_cell_idx, roi_loc] = get_colored_labels(EEG);

clim_min = min(matrix, [], 'all');
clim_max = max(matrix, [], 'all');

% assign region input to an index
[GC, GR] = groupcounts(roi_loc);
switch lower(region)
case 'cingulate'
region_idx = 1;
case 'prefrontal'
region_idx = 2;
case 'frontal'
region_idx = 3;
case 'temporal'
region_idx = 4;
case 'parietal'
region_idx = 5;
case 'central'
region_idx = 6;
case 'occipital'
region_idx = 7;
otherwise
region_idx = 99;

% hemisphere parameters to determine which labels to use
last_char = EEG.roi.atlas.Scouts(1).Label(end);
if strcmpi(hemisphere, 'left')
if strcmpi(last_char, 'R')
hem_idx = {2 2 2}; % use labels 2:2:end (first two values), only use 1/2 of the labels (3rd value)
else
hem_idx = {1 2 2}; % use labels 1:2:end (first two values), only use 1/2 of the labels (3rd value)
end
elseif strcmpi(hemisphere, 'right')
if strcmpi(last_char, 'L')
hem_idx = {1 2 2};
else
hem_idx = {2 2 2};
end
else
hem_idx = {1 1 1};
end

% sort matrix according to color scheme
% reduce matrix to only keep components corresponding to selected region
if isDKatlas == 1
[colors, color_idxx, roi_idxx, labels_sorted, roi_loc] = get_colored_labels(EEG);
labels = labels_sorted;

% assign region input to an index
[GC, ~] = groupcounts(roi_loc);
switch lower(region)
case 'cingulate'
region_idx = 1;
case 'prefrontal'
region_idx = 2;
case 'frontal'
region_idx = 3;
case 'temporal'
region_idx = 4;
case 'parietal'
region_idx = 5;
case 'central'
region_idx = 6;
case 'occipital'
region_idx = 7;
otherwise
region_idx = 99;
end

matrix = matrix(roi_idxx, roi_idxx);
if not(region_idx == 99)
if region_idx == 1
Expand All @@ -588,44 +619,40 @@ function roi_plotcoloredlobes( EEG, matrix, titleStr, measure, hemisphere, group
end
end_idx = start_idx + GC(region_idx) - 1;
matrix = matrix(start_idx:end_idx, start_idx:end_idx);
labels_dk_cell_idx = labels_dk_cell_idx(start_idx:end_idx);
labels = labels(start_idx:end_idx);
color_idxx = color_idxx(start_idx:end_idx);
end
n_roi_labels = size(matrix, 1);
end

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

% remove underscores in labels to avoid plotting bug
labels = replace_underscores(labels);

% create dummy plot and add custom legend
f = figure();
%f.WindowState = 'maximized';
hold on
n_dummy_labels = 7;
x = 1:10;
for k=1:n_dummy_labels
plot(x, x*k, '-', 'LineWidth', 9, 'Color', colors{k});
end

% labels on dummy plot for positioning
xlim([0 n_roi_labels])
ylim([0 n_roi_labels])
set(gca,'xtick',[1:n_roi_labels],'xticklabel',labels_dk_cell_idx(hem_idx{1}:hem_idx{2}:n_roi_labels));%, 'TickLabelInterpreter','none');
set(gca,'xtick',1:n_roi_labels,'xticklabel',labels(hem_idx{1}:hem_idx{2}:n_roi_labels));%, 'TickLabelInterpreter','none');
ax = gca;
for i=hem_idx{1}:hem_idx{2}:n_roi_labels
ax.XTickLabel{ceil(i/hem_idx{3})} = sprintf('\\color[rgb]{%f,%f,%f}%s', colors{color_idxx(i)}, ax.XTickLabel{ceil(i/2)});
end
xtickangle(90)
pos = get(gca, 'Position');
if isDKatlas == 1
for k=1:n_dummy_labels
plot(x, x*k, '-', 'LineWidth', 9, 'Color', colors{k});
end
for i=hem_idx{1}:hem_idx{2}:n_roi_labels
ax.XTickLabel{ceil(i/hem_idx{3})} = sprintf('\\color[rgb]{%f,%f,%f}%s', colors{color_idxx(i)}, ax.XTickLabel{ceil(i/2)});
end
legend('Cingulate', 'Prefrontal', 'Frontal', 'Temporal', 'Parietal', 'Central', 'Occipital', 'Location', 'southeastoutside'); % modify legend position
end
xtickangle(90)
pos = get(gca, 'Position');
set(gca, 'Position', pos, 'DataAspectRatio',[1 1 1], 'visible', 'off')
axes('pos', [pos(1) pos(2) pos(3) pos(4)]) % plot matrix over the dummy plot and keep the legend

Expand All @@ -640,14 +667,20 @@ function roi_plotcoloredlobes( EEG, matrix, titleStr, measure, hemisphere, group
matrix = horzcat(mat_left_col, mat_right_col); % sort columns

% sort labels
lc = {labels_dk_cell_idx; transpose(color_idxx)};
for i = 1:length(lc)
left = lc{i}(1:2:end);
right = lc{i}(2:2:end);
lc{i} = [left right];
try % if color can be assigned
lc = {labels; transpose(color_idxx)};
for i = 1:length(lc)
left = lc{i}(1:2:end);
right = lc{i}(2:2:end);
lc{i} = [left right];
end
labels = lc{1};
color_idxx = transpose(lc{2});
catch
left = labels(1:2:end);
right = labels(2:2:end);
labels = [left right];
end
labels_dk_cell_idx = lc{1};
color_idxx = transpose(lc{2});
end

% reduce matrix to keep only one hemisphere
Expand Down Expand Up @@ -677,16 +710,16 @@ function roi_plotcoloredlobes( EEG, matrix, titleStr, measure, hemisphere, group
set(gca, 'Position', pos, 'DataAspectRatio',[1 1 1], 'visible', 'on')

% add colored labels with display option
ax = gca;
set(gca,'xtick',1:n_roi_labels,'xticklabel',labels(hem_idx{1}:hem_idx{2}:n_roi_labels));
if isDKatlas == 1
set(gca,'ytick',[1:n_roi_labels],'yticklabel',labels_dk_cell_idx(hem_idx{1}:hem_idx{2}:n_roi_labels), 'fontweight','bold', 'fontsize', 9, 'TickLength',[0.015, 0.02], 'LineWidth',0.75);
set(gca,'ytick',1:n_roi_labels,'yticklabel',labels(hem_idx{1}:hem_idx{2}:n_roi_labels), 'fontsize', 9, 'TickLength',[0.015, 0.02], 'LineWidth',0.75);
for i=hem_idx{1}:hem_idx{2}:n_roi_labels
ax.XTickLabel{ceil(i/hem_idx{3})} = sprintf('\\color[rgb]{%f,%f,%f}%s', colors{color_idxx(i)}, ax.XTickLabel{ceil(i/hem_idx{3})});
ax.YTickLabel{ceil(i/hem_idx{3})} = sprintf('\\color[rgb]{%f,%f,%f}%s', colors{color_idxx(i)}, ax.YTickLabel{ceil(i/hem_idx{3})});
end
else
set(gca,'ytick',[1:n_roi_labels],'yticklabel',labels_dk_cell_idx(hem_idx{1}:hem_idx{2}:n_roi_labels), 'fontsize', 7, 'TickLength',[0.015, 0.02], 'LineWidth',0.75);
end
set(gca,'xtick',[1:n_roi_labels],'xticklabel',labels_dk_cell_idx(hem_idx{1}:hem_idx{2}:n_roi_labels));
ax = gca;
for i=hem_idx{1}:hem_idx{2}:n_roi_labels
ax.XTickLabel{ceil(i/hem_idx{3})} = sprintf('\\color[rgb]{%f,%f,%f}%s', colors{color_idxx(i)}, ax.XTickLabel{ceil(i/hem_idx{3})});
ax.YTickLabel{ceil(i/hem_idx{3})} = sprintf('\\color[rgb]{%f,%f,%f}%s', colors{color_idxx(i)}, ax.YTickLabel{ceil(i/hem_idx{3})});
set(gca,'ytick',1:n_roi_labels,'yticklabel',labels(hem_idx{1}:hem_idx{2}:n_roi_labels), 'fontsize', 7, 'TickLength',[0.015, 0.02], 'LineWidth',0.75);
end
h = title([ 'ROI to ROI ' upper(measure) ' (' titleStr ')' ]);
set(h, 'fontsize', 16);
Expand All @@ -696,8 +729,8 @@ function roi_plotcoloredlobes( EEG, matrix, titleStr, measure, hemisphere, group
function roi_largeplot(EEG, mim, trgc, roipsd, titleStr)
% plot MIM, TRGC and power (barplot) in a single large figure
load cm18
[colors, color_idxx, roi_idxx, labels_dk_cell_idx, ~] = get_colored_labels(EEG);
n_roi_labels = size(labels_dk_cell_idx, 2);
[colors, color_idxx, roi_idxx, labels_sorted, ~] = get_colored_labels(EEG);
n_roi_labels = size(labels_sorted, 2);

f = figure();
f.WindowState = 'maximized';
Expand All @@ -713,8 +746,8 @@ function roi_largeplot(EEG, mim, trgc, roipsd, titleStr)
img_sorted = img(roi_idxx, roi_idxx);
imagesc(img_sorted)

set(gca,'ytick',[1:n_roi_labels],'yticklabel',labels_dk_cell_idx(1:end), 'fontsize', 5, 'TickLength',[0.015, 0.02], 'LineWidth',0.75);
set(gca,'xtick',[1:n_roi_labels],'xticklabel',labels_dk_cell_idx(1:end));
set(gca,'ytick',[1:n_roi_labels],'yticklabel',labels_sorted(1:end), 'fontsize', 5, 'TickLength',[0.015, 0.02], 'LineWidth',0.75);
set(gca,'xtick',[1:n_roi_labels],'xticklabel',labels_sorted(1:end));
h = title([ 'ROI to ROI ' fc_names{k} ' (' titleStr ')' ]);
set(h, 'fontsize', 16);
hcb = colorbar;
Expand All @@ -735,7 +768,7 @@ function roi_largeplot(EEG, mim, trgc, roipsd, titleStr)
barh(roipsd(roi_idxx));

set(gca, 'YDir', 'reverse');
set(gca,'ytick',[1:n_roi_labels],'yticklabel',labels_dk_cell_idx(1:end), 'fontweight','bold','fontsize', 9, 'TickLength',[0.015, 0.02], 'LineWidth',0.7);
set(gca,'ytick',[1:n_roi_labels],'yticklabel',labels_sorted(1:end), 'fontsize', 9, 'TickLength',[0.015, 0.02], 'LineWidth',0.7);
h = title([ 'ROI source power' ' (' titleStr ')' ]);
set(h, 'fontsize', 16);
ylabel('power [dB]')
Expand Down
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4 changes: 1 addition & 3 deletions pipeline_connectivity.m → test_pipes/pipeline_connectivity.m
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,4 @@
tic
EEG = pop_roi_connect(EEG, 'methods', measures(iMeasure));
t(iMeasure) = toc;
end

pop_roi_connectplot(EEG, 'measure', 'MIM', 'plotmatrix', 'on', 'plotcortex', 'on');
end
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