Refactored the sct_create_mask
Refactored the sct_create_mask

Removed most of the `sct.run` functions and moved towards using the native
functions. Clean up some unused variables and make the code pep8 style
compliant.


Former-commit-id: e45aa45d097a49a3c6988d9c78ebdeea7382c0ed
neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox