add function to plot full matrice for DTI data

Aswendt-Lab · May 22, 2023 · b77d1a6 · b77d1a6
1 parent fe03994
commit b77d1a6
Showing 1 changed file with 107 additions and 0 deletions.
diff --git a/DTI/plotFullMatrcies.m b/DTI/plotFullMatrcies.m
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+%% plotCorrelationMatrices
+% This script displays scatter plots of the correlation of selected
+% regions (figure 1) and their mean values and standard deviation (figure
+% 2). Please adjust the parameters in lines 8 - 10 and hit 'Run'.
+
+%% Specifications
+
+filename =  "C:\Users\marc\Documents\UniklinikArbeit\Projekt_AIDAconnect\AIDAconnect_output_dti\Control\Baseline.mat"; % path to a processed MAT-File
+min = 0;
+max = 1000;
+clims = [min, max]; % dynamic range of plot, e.g.: [0, 1] -> correlations between 0 and 1 can be displayed with different colors
+binarize_thresh = 100;
+
+%% Do not modify the following lines
+
+P = load(filename);
+infoDTI = P.infoDTI;
+
+load('../Tools/infoData/acronyms_splitted.mat');
+numberOfSubjects = size(infoDTI.names,1);
+
+% Determine number of subplots
+plotSize = sqrt(numberOfSubjects);
+plotSize_compare = floor(plotSize)+0.5;
+if plotSize < plotSize_compare
+    plot_x = floor(plotSize);
+    plot_y = ceil(plotSize);
+else
+    plot_x = ceil(plotSize);
+    plot_y = plot_x;
+end
+
+listWithSubjectIndices = zeros(1,numberOfSubjects);
+for jj = 1:numberOfSubjects
+    listWithSubjectIndices(jj) = jj; % (e.g. = [1,2,3,4,5])
+end
+
+figure('Name', 'Mean Correlation Matrix and STD')
+subplot(1,4,1)
+imagesc(mean(infoDTI.matrix(:, :, listWithSubjectIndices), 3), clims);
+c = colorbar;
+c.Label.String = "Correlation";
+caxis(clims)
+axis square;
+set(gca, 'XTick', [1,25,50,75,98], ... % Change the axes tick marks
+    'XTickLabel', [1,25,50,75,98], ... % and tick labels
+    'XTickLabelRotation', 90, ...
+    'YTick', [1,25,50,75,98], ...
+    'YTickLabel', [1,25,50,75,98]); 
+title('Mean')
+
+subplot(1,4,2)
+imagesc(std(infoDTI.matrix(:, :, listWithSubjectIndices), 0, 3), clims./2);
+c = colorbar;
+c.Label.String = "Correlation";
+caxis(clims)
+axis square;
+set(gca, 'XTick', [1,25,50,75,98], ... % Change the axes tick marks
+    'XTickLabel', [1,25,50,75,98], ... % and tick labels
+    'XTickLabelRotation', 90, ...
+    'YTick', [1,25,50,75,98], ...
+    'YTickLabel', [1,25,50,75,98]); 
+title('Std')
+
+
+mean_matrix = mean(infoDTI.matrix,3);
+binarized_matrix = mean_matrix;
+[rows, cols, depth] = size(mean_matrix);
+for ii=1:depth
+    for jj=1:rows
+        for hh=1:cols
+            if mean_matrix(jj,hh,ii) < binarize_thresh
+                mean_matrix(jj,hh,ii) = min;
+                binarized_matrix(jj,hh,ii) = min;
+            else 
+                binarized_matrix(jj,hh,ii) = max;
+            end
+        end
+    end
+end
+
+subplot(1,4,3)
+imagesc(mean_matrix, clims);
+c = colorbar;
+c.Label.String = "Correlation";
+caxis(clims)
+axis square;
+set(gca, 'XTick', [1,25,50,75,98], ... % Change the axes tick marks
+    'XTickLabel', [1,25,50,75,98], ... % and tick labels
+    'XTickLabelRotation', 90, ...
+    'YTick', [1,25,50,75,98], ...
+    'YTickLabel', [1,25,50,75,98]); 
+title("w > " + binarize_thresh)
+
+subplot(1,4,4)
+imagesc(binarized_matrix, clims);
+c = colorbar;
+c.Label.String = "Correlation";
+caxis(clims)
+axis square;
+set(gca, 'XTick', [1,25,50,75,98], ... % Change the axes tick marks
+    'XTickLabel', [1,25,50,75,98], ... % and tick labels
+    'XTickLabelRotation', 90, ...
+    'YTick', [1,25,50,75,98], ...
+    'YTickLabel', [1,25,50,75,98]); 
+title_str = "w > " + binarize_thresh + " binarized";
+title(title_str)