Removal of hard-coded `configuration` file in `preprocess_segment.sh` script and extraction of `include_list` from the `configuration` file directly

[rohanbanerjee]

This PR solves the issues #72 and #73

What this PR solves:

• In the preprocess_segment.sh, the configuration.json file was hard-coded which meant whatever we pass as a value the -config flag, it will read only the configuration.json from the script. This PR takes the configuration.json from the sct_run_batch command rather than a hard-coded value.
• We are also passing the values to --include-list while running the preprocessing.sh using sct_run_batch even when the values are already mentioned in the include-list in the configuration.json. This PR helps the sct_run_batch to take this value directly from the configuration.json file.

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