BUG: fixed pipeline for taking manual set of sc and not csf
BUG: fixed pipeline for taking manual set of sc and not csf

Former-commit-id: cec45e3c0fabddfa7a50f9ff3bb7cc1b056ae9a4 [formerly 6f84735ef221817209cb2ebabfea26814c76a1af]
Former-commit-id: ddb5e5482d59585c2dc1353246823abcdd9251c8
Former-commit-id: 2871ea756b1514618f48edafc3cde503de619819
neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox