2023 SCT Course example

[valosekj]

This issue summarizes changes between the manual_correction.py script used during previous SCT courses (see issue here) and the current manual_correction.py (r20231101) script located within this repository.

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The following section describes an example from the SCT 6.1 course, slide 147:

Considering the following folder (produced by sct_run_batch):

$ cd output/data_processed/
$ tree
.
└── sub-03
    └── anat
        ├── sub-03_T2w.nii.gz
        └── sub-03_T2w_seg.nii.gz

And the following qc_fail.yml config file listing images to correct:

FILES_SEG:
- sub-03_T2w.nii.gz

The manual_correction.py command is:

python manual_correction.py -config qc_fail.yml -path-img output/data_processed -path-label output/data_processed -path-out data/derivatives/labels

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Notable changes compared to the manual_correction.py script used during previous SCT courses:

• -path-in has been renamed to -path-img
• path-label has to be provided. In this particular example, paths for both -path-img and -path-label are the same (because both the images and the labels are in the same data_processed folder). If -path-label is not provided, the script assumes that the labels are located under derivatives/labels.
• no -manual suffix is used - to be in line with our convention, we do not use the -manual suffix anymore -- the information about the label provenance is stored in the JSON sidecar
• the script tracks corrected files -- after running the manual_correction.py command, the qc_fail.yml config file is updated with the CORR_SEG flag (in order to track the corrected files):

CORR_SEG:
- sub-03_T2w.nii.gz
FILES_SEG: []