REF: harmonized flags. Added parser. Related to #669
REF: harmonized flags. Added parser. Related to #669

Former-commit-id: 0facd08c20b6f548f8678c6a0dffc68ea46827ee
Former-commit-id: bff405d132214b72e969f755bf511afa10f63b0c
3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox,3324fr/spinalcordtoolbox