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: 6f84735ef221817209cb2ebabfea26814c76a1af
Former-commit-id: ddb5e5482d59585c2dc1353246823abcdd9251c8
3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox