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You don't need to create zero-filled Mats to store stuff, this is not MatLab, you should make use of openCV's advantages! First, to assign values to a matrix you should use the setTo method.

Mat A, B;
A = stuff;
B = other stuff;

A.setTo(255, B);

This code sets in A all non-zero elements in B to 255.

To get difference between Mat use the absdiff function.

Mat A, B, diff;

A = stuff;
B = other stuff;
absdiff(A, B, diff);

Just make sure A and B are of the same type.