Preprocessing for extracting the spinal cord ROI via centerline estimation.

[uzaymacar]

The added script get_sc_roi_via_centerline.sh extracts the spinal cord ROI via centerline estimation using SCT's sct_get_centerline command.

To run this preprocessing, use:

sct_run_batch -path-data PATH_TO_SPINE_GENERIC_PROCESSED -path-output spine-generic-processed_sc_roi -script get_sc_roi_via_centerline.sh

To-dos:

• [ ] Add a file check command to see if all expected files are there.
• [ ] Decide if you need to apply any dilation.
• [ ] Run a full QC on all subjects.

[uzaymacar]

Here is a visualization of this current preprocessing pipeline for subject sub-amu01:

[uzaymacar]

The latest commit 957debf dilates the GT mask and crops the images as discussed last week. Data exploration shows that after cropping via the current preprocessing script in this PR and resampling to 1 mm^3:

• T1w images have a maximum shape of (44, 102, 278)
• T2w images have a maximum shape of (38, 176, 248)
• T2star images have a maximum shape of (29, 30, 120)

We'll use these values to inform the selection of center-crop, length, and stride parameters.

NOTE: This PR will NOT be merged and we'll incorporate the preprocessing done here in a unified preprocessing script.