Hi Max,
To create a 3D binary mask and compare two volumes using the Dice metric, you have already made progress by extracting points and calculating the volume of the convex hull. The next step is to create a binary mask for each volume. You can use the 'inpolyhedron' function available on File Exchange to obtain the binary mask: https://www.mathworks.com/matlabcentral/fileexchange/37856-inpolyhedron-are-points-inside-a-triangulated-volume
Based on the provided code and the sample files, you can refer the following code to calculate the "Sørensen–Dice" coefficient:
fileID_1 = fopen('Seg1.txt', 'r');
fileID_2 = fopen('Seg2.txt', 'r');
formatSpec = '%f %f %f';
data_1 = textscan(fileID_1, formatSpec);
data_2 = textscan(fileID_2, formatSpec);
fclose(fileID_1);
fclose(fileID_2);
unique_points_1 = [data_1{1}, data_1{2}, data_1{3}];
unique_points_2 = [data_2{1}, data_2{2}, data_2{3}];
[k1, volume1] = convhull(unique_points_1(:,1), unique_points_1(:,2), unique_points_1(:,3));
[k2, volume2] = convhull(unique_points_2(:,1), unique_points_2(:,2), unique_points_2(:,3));
% Plotting the convex hulls
figure;
trisurf(k1, unique_points_1(:,1), unique_points_1(:,2), unique_points_1(:,3), 'FaceColor', 'red', 'FaceAlpha', 0.5);
hold on;
trisurf(k2, unique_points_2(:,1), unique_points_2(:,2), unique_points_2(:,3), 'FaceColor', 'blue', 'FaceAlpha', 0.5);
hold off;
all_points = [unique_points_1; unique_points_2];
% Define the 3D grid bounds (you need to define gridX, gridY, gridZ)
% For example, you can use the min and max of the combined points
gridX = linspace(min(all_points(:,1)), max(all_points(:,1)), 100);
gridY = linspace(min(all_points(:,2)), max(all_points(:,2)), 100);
gridZ = linspace(min(all_points(:,3)), max(all_points(:,3)), 100);
binary_mask_1 = inpolyhedron(k1, unique_points_1, gridX, gridY, gridZ);
binary_mask_2 = inpolyhedron(k2, unique_points_2, gridX, gridY, gridZ);
intersection = binary_mask_1 & binary_mask_2;
dice_metric = 2 * nnz(intersection) / (nnz(binary_mask_1) + nnz(binary_mask_2));
disp(['Dice metric: ', num2str(dice_metric)]);
The grid resolution ("gridX", "gridY", "gridZ") is set to 100 in the sample code can be adjusted based on the input data. A higher resolution will provide a more detailed mask but will require more computation.
Hope this helps!
