We consider combinatorial optimization problems arising in radiation therapy. Given a matrix I with nonnegative integer entries, we seek a decomposition of I as a weighted sum of binary matrices having the consecutive ones property, such that the total sum of the coefficients is minimized. The coefficients are restricted to be non-negative integers. Here, we investigate variants of the problem with additional constraints on the matrices used in the decomposition. Constraints appearing in the application include the interleaf motion and interleaf distance constraints. The former constraint was previously studied by Baatar et al.