OPT: changed the script organization using several classes, add a co-registration step
OPT: changed the script organization using several classes, add a co-registration step

Former-commit-id: 6020cc31d4deb739cb2dd0fb005fe5fb7906457e [formerly 2469158b4f5142ebce78fc4426e9bfd2cc381966]
Former-commit-id: 39f0295231027b0dd2f98a54c2c2c95a2b3006e6
Former-commit-id: 340c3e5aa125b7d7de10dfcc46d327dd82ea8dbe
neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox