Merge branch 'bdl_greymatterseg' of /home/django/aroux/code/spinalcordtoolbox with conflicts.
Merge remote-tracking branch 'origin/bdl_greymatterseg' into bdl_greymatterseg
OPT: functions added to sct_checkt_atlas_integrity
OPT: added binarization in sct_dice_coefficient
REF: changed some comments
OPT: removed warping field cropping to improve results
OPT: msct_parser.py now generate usage based on the option list
OPT: msct_parser.py now generate usage based on the option list
Merge remote-tracking branch 'origin/bdl_greymatterseg' into bdl_greymatterseg
OPT: msct_parser can now generate usage
OPT: changed a few parameters for testing.
Merge branch 'bdl_greymatterseg' of https://github.com/neuropoly/spinalcordtoolbox into bdl_greymatterseg
BUG: sct_flatten_sagital nurbs issue with testing data, fixed #180
DOC: fixed spelling mistake
Merge branch 'master' into bdl_greymatterseg

Conflicts:
	scripts/msct_parser.py
	scripts/sct_segment_graymatter.py
OPT: added check folder existence to differentiate file and folder
NEW: new script for image inversion
OPT: improved parser
OPT: sct_generate_centerline: improved fitting of spline
OPT: sct_generate_centerline: added smoothness flag + added check for RPI