BUG: forgot to use affine registered image for 1-step reg
BUG: forgot to use affine registered image for 1-step reg

Former-commit-id: 09e4c0df393a1039c3cfdf9d04cdc66c8f63a4f4
Former-commit-id: 4a99010921e35f840a3adf720fd3219ed4a014dd
3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox