REF: adding parser and changing options. Related to #669
REF: adding parser and changing options. Related to #669

Former-commit-id: fb141084d46a3e34b1529508cdc864a2ad1d1a59
Former-commit-id: c501695d6ee3315b2574a9ded1180843a7dae9c5
3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox