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: ec272d505503c9ba2ddd53d62cf8f814cce3c6bf
Former-commit-id: 050658f0f482f9a9d75291c1ccc5ceb509375efb
3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox