REF: added parser, changed flags (-b --> -bvec, -p --> -param, -t --> -thr,  -o --> -ofolder)
REF: added parser, changed flags (-b --> -bvec, -p --> -param, -t --> -thr,  -o --> -ofolder)

Former-commit-id: d6b958bec72650f2b6d2f8f5de2da7cb56fa0b20 [formerly 29a627d63e2a7744da4b7543e4c94ca1ed79b36d]
Former-commit-id: 047a29c72cf682516f219f256b502925b7b5bd8a
Former-commit-id: f66faca14c88ec33f3e7a0d3594cac74f41351c8
neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox