BUG: adapt crop_over_mask to 2D image with shape (x,y,1)
BUG: adapt crop_over_mask to 2D image with shape (x,y,1)

Former-commit-id: 45b2508d523b6ec3ae4764ff79be08889912ca80 [formerly ec272d505503c9ba2ddd53d62cf8f814cce3c6bf]
Former-commit-id: 050658f0f482f9a9d75291c1ccc5ceb509375efb
Former-commit-id: dcbdeddc407afa40669d41f8301fc48b279d2cd1
neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox