I've never worked with 3-D data, but it seems like you might be doing something sorta similar to me. One way you can do it is to use regionprops. It takes two matrices and calculates things for the things in common with them.
stats = regionprops(Islands,Labels, 'Centroid');
You can also look into the intersect function in matlab or ismember. Its possible that youtube tutorials for watershedding and finding centroids with bwlabel will also be helpful
I'm not a pro at matlab but I hope this helped a little.