OPT: removed possibility to input transformation matrix to avoid potential conflicts with the 2-stage registration
OPT: removed possibility to input transformation matrix to avoid potential conflicts with the 2-stage registration

Former-commit-id: 87229fca4d12d74593102376db74ced2af5da456 [formerly 34755f54f6a0d1023c2adbcb782af3e5c2e7a36f]
Former-commit-id: 75940893cf7faa69e79490ac058f005bd6caeb6a
Former-commit-id: 3a93b01896c22d8acade39f2a9f7c251bd7e590b
neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox