implement ways to compute normalized compression measure

[jcohenadad]

things to do:

# per subject
sct_process_segmentation -i SEG -vert 2:3 -o csa_C2C3.csv
sct_process_segmentation -i SEG -vert 8:9 -o csa_T1T2.csv
# fetch the value LEVEL_CONTINUOUS corresponding to the slice number in this file: PAM50_levels_continuous.nii.gz. 
# fetch in the $SCT_DIR/PAM50_level_continuous.nii.gz file the Z value that corresponds to LEVEL_CONTINUOUS
sct_process_segmentation -i $SCT_DIR/data/PAM50/PAM50_cord.nii.gz -z Z -o csa_PAM50Z.csv
# extract C2C3 and T1T2 from PAM50
sct_process_segmentation -i $SCT_DIR/data/PAM50/PAM50_cord.nii.gz -vert 2:3 -o csa_PAM50_C2C3.csv
sct_process_segmentation -i $SCT_DIR/data/PAM50/PAM50_cord.nii.gz -vert 8:9 -o csa_PAM50_T1T2.csv
# compute a scaling factor that is the average of the scaling between C2C3 and T1T2
# use that scaling factor to scale the PAM50 at the level of the injury