NEW: option to specify the name of the output folder containing the template
NEW: option to specify the name of the output folder containing the template

Former-commit-id: 364802c473abcb6200c34f9ba9e03da79cef1d27 [formerly 6eeacd3262b7b661d54d9be744a52b545c8a1350]
Former-commit-id: 3fc87c0263ad060d16b09846132e17869acafef7
Former-commit-id: 34ec51fb8fc464d8623e72847fdd4923d4c9becb
neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox