Adding the preprocessing code back

[rohanbanerjee]

Fixes #80. Adds the removed code back to preprocess_segment.sh.

Steps to reproduce this PR:

Data: duke/temp/rohan/bids_data Config file values:

{
    "path_data": "PATH_TO_BIDS_DATA",
    "include-list": "sub-HarshmanDobby",
    "data_type": "anat",
    "contrast": "t2",
    "suffix_image": "_T2",
    "first_disc": "1",
    "last_disc": "26"
}

Run the preprocess_segment.sh using the sct_run_batch from the README of this PR.

Expected output

Running this script should create a temporary output folder with the segmentation and disc_level derivatives with the names: {SUBJECT_NAME_CONTRAST}_label-SC_mask.nii.gz {SUBJECT_NAME_CONTRAST}_labeled-discs.nii.gz