See my demo, which handles negative values which will occur. -1 = red, 0 = black, and +1 = blue.
workspace; % Make sure the workspace panel is showing.
% Create two sample images.
fontSize = 22;
binaryImageA = false(200, 300);
binaryImageB = false(200, 300);
% Make two regions that overlap.
binaryImageA(60:140, 100:200) = true;
binaryImageB(100:150, 150:250) = true;
% Display the sample images.
subplot(2, 2, 1);
imshow(binaryImageA);
title('Binary Image A', 'FontSize', fontSize);
grid on;
% Enlarge figure to full screen.
set(gcf, 'units','normalized','outerposition',[0 0 1 1]);
subplot(2, 2, 2);
imshow(binaryImageB);
title('Binary Image B', 'FontSize', fontSize);
grid on;
% Subtract the two sample images
differenceImage = int32(binaryImageA) - int32(binaryImageB);
% Display the difference image.
figure;
imshow(differenceImage, []);
title('Difference Image: A - B', 'FontSize', fontSize);
grid on;
% Make colormap: red for negative, 0 for 0, blue for positive.
cmap = [1 0 0; 0 0 0; 0 0 1];
% Apply colormap
colormap(cmap);
colorbar;
