REF: updated flags (-i -->  -mt0, -j -->  -mt1 )
REF: updated flags (-i -->  -mt0, -j -->  -mt1 )

Former-commit-id: 05ca80a96b0df59109450de5a487748776a89489
Former-commit-id: 9acaa8e5785c3e55c54b39ead0b4a98023003696
3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox