Clean up processing and repository

[sandrinebedard]

Description

This PR adds:

• Remove crop for data in data_processed_clean
• Add a config file to use with sct_process_segmentation with the exclude list included inside

Remaining todo:

• [x] Merge analysis with nnUnet

Related issues

Fixes #63

[valosekj]

Hey! If you plan to rerun the process_data.sh script, we could also investigate issue https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/issues/63.

[sandrinebedard]

@valosekj

I modified the script to use the T1w discs labels in git-annex, results are /duke/projects/ivadomed/contrast-agnostic-seg/data_processed_sg_2023-08-08_NO_CROP/

Here is the updated result:

(base) sebeda@joplin:~/duke/projects/ivadomed/contrast-agnostic-seg/data_processed_sg_2023-08-08_NO_CROP/data_processed/sub-brnoUhb04/anat$ sct_label_utils -i sub-brnoUhb04_T1w_seg_labeled_discs.nii.gz -display

--
Spinal Cord Toolbox (git-sb/3733-bring-metrics-to-pam50-add_mscc-108c962d02dfda28548986301d67d7ed80a5cf4c)

sct_label_utils -i sub-brnoUhb04_T1w_seg_labeled_discs.nii.gz -display
--

Position=(102,130,159) -- Value= 1.0
Position=(104,130,132) -- Value= 2.0
Position=(104,131,120) -- Value= 3.0
Position=(104,130,102) -- Value= 4.0
Position=(103,129,84) -- Value= 5.0
Position=(103,126,66) -- Value= 6.0
Position=(103,120,49) -- Value= 7.0
Position=(104,111,33) -- Value= 8.0
Position=(104,100,16) -- Value= 9.0
All labels (useful syntax):
102,130,159,1.0:104,130,132,2.0:104,131,120,3.0:104,130,102,4.0:103,129,84,5.0:103,126,66,6.0:103,120,49,7.0:104,111,33,8.0:104,100,16,9.0