Fix path confusion when using manual_correction.py

[NathanMolinier]

Description

This PR addresses several issues related to path use with manual correction script

To avoid future confusions regarding the different use cases of the script manual_correction.py, this PR allows the user to directly specify:

• the folder where images are stored using -path-img
• the folder where labels are stored using -path-label
• the folder where corrected labels will be stored using -path-out

Some additions to code were also done to improve robustness regarding the use of the "-manual" suffix and more, see related issues.

Related issues

#51
#47
#41
#40
#32

[NathanMolinier]

The PR is not ready for merging, some testing need to be added

[valosekj]

Thanks for this initiative!

The PR is not ready for merging, some testing need to be added

Okay, I have converted the PR to draft.

[valosekj]

The PR is now ready to use! We will test it. If it works, then we will merge.

[valosekj]

Tested for creating SCI lesions from scratch. Working fine!

python manual_correction.py -config /Users/valosek/data/spineimage.ca/site_012/lesions_to_correct.yml -path-img /Users/valosek/data/spineimage.ca/site_012 -load-other-contrast acq-STIRsag_T2w

Also tested during correction of SC seg produced by sct_deepseg_sc:

python manual_correction.py -config /Users/valosek/data/spineimage.ca/site_012/sc_seg_to_correct.yml -path-img /Users/valosek/data/results/site_012_2023-06-27/data_processed -path-out /Users/valosek/data/spineimage.ca/site_012/derivatives/labels -suffix-files-seg _label-SC_mask
Enter your name (Firstname Lastname). It will be used to generate a json sidecar with each corrected file: Jan Valosek
FILES_SEG:   0%|                                                                                                                                                                             | 0/16 [00:00<?, ?file/s]
Copying: /Users/valosek/data/results/site_012_2023-06-27/data_processed/sub-hal001/anat/sub-hal001_acq-sag_T2w_label-SC_mask.nii.gz to /Users/valosek/data/spineimage.ca/site_012/derivatives/labels/sub-hal001/anat/sub-hal001_acq-sag_T2w_label-SC_mask-manual.nii.gz

[valosekj]

I tested the latest commit f6af1aa with the following commands. With both, the script worked well!

Correct SC seg created using sct_run_batch located under data_processed and save them to the final git-annex dataset (specified by -path-out flag):

python manual_correction.py -config sci-paris_sc_seg_2023-07-12/qc_fail_sc.yml -path-img sci-paris_sc_seg_2023-07-12/data_processed -path-label sci-paris_sc_seg_2023-07-12/data_processed -path-out data/data.neuro.polymtl.ca/sci-paris/derivatives/labels

Add automatically generated and visually QCed SC seg (using -add-seg-only flag) to the final git-annex dataset (specified by -path-out flag):

python manual_correction.py -config sci-paris_sc_seg_2023-07-12/qc_fail_sc.yml -path-img sci-paris_sc_seg_2023-07-12/data_processed -path-label sci-paris_sc_seg_2023-07-12/data_processed -path-out data/data.neuro.polymtl.ca/sci-paris/derivatives/labels -add-seg-only

[valosekj]

@NathanMolinier thanks a lot for this great contribution! 🚀