Compute image gradient in specific region

There is a binary mask representing specific region. I want to compute gradient and divergence only in this specific region. My gradient code is following:

    ux = circshift( u_bar, [0 -1]) - u_bar;
    uy = circshift( u_bar, [-1 0]) - u_bar;
    ux(:,end) = 0; uy(end,:)=0;

I know the indices for the region

    idxMask = find(R==1);