This PR addresses the issue https://github.com/sct-pipeline/ukbiobank-spinalcord-csa/issues/51. It includes the modification of manual_correction.py to add an option to add the segmentations not in the -config list to the derivatives folder, add suffix -manual and create json sidecar.
Notes:
This option is only available for segmentations and not for vertebral lableing because we don't create automatically C1-2, C2-3 and C3-4 disc labeling (which we do for manual labeling).
T2w segmentations will also be added if they are available. This will only be the case for the first 350 subjects (T2w segmentations are already manually qc-ed).
More precisely:
Adds the flag -add-seg-only tomanual_correction.py
Gets the list of filenames that have segmentations
Excludes the files in -config list from the files to add to derivatives
Copies source file, adds suffix -manualand creates json sidecar (as for normal usage of manual_correction.py for segmentations) but no interactive window is open
The function remove_suffix was added to utils.py to remove the suffix _seg to get a list of files as we have in -config flag in manual_correction.py (this way the same loop can be used)
The instructions to use this option were added to README
Description
This PR addresses the issue https://github.com/sct-pipeline/ukbiobank-spinalcord-csa/issues/51. It includes the modification of
manual_correction.pyto add an option to add the segmentations not in the-configlist to the derivatives folder, add suffix-manualand create json sidecar.Notes:
More precisely:
-add-seg-onlytomanual_correction.py-configlist from the files to add to derivatives-manualand creates json sidecar (as for normal usage ofmanual_correction.pyfor segmentations) but no interactive window is openremove_suffixwas added toutils.pyto remove the suffix_segto get a list of files as we have in-configflag inmanual_correction.py(this way the same loop can be used)READMELinked issue
Closes #51