OPT: add option to remove tmp folder and correct output file type
OPT: add option to remove tmp folder and correct output file type

Former-commit-id: 732998691336748957138bc236f86f68ff19e03d
neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox