spine-generic - the original version - contains correction for SC seg, GM seg, and disc labels
sct_tutorial_data - contains -add-seg-only and contains correction for SC seg, PMJ , and disc labels
ukbiobank-spinalcord-csa - contains -add-seg-only flag, uses ITK-snap instead of FSLeyes for SC seg corrections, and contains correction for SC seg, PMJ , and disc labels
Also, be aware of copy_files_to_derivatives.py script used to copy manually corrected files (segmentations, vertebral labeling, etc.) from the source preprocessed dataset to the git-annex BIDS dataset's derivatives folder
Summary of
manual_correction.pyversions:spine-generic- the original version - contains correction for SC seg, GM seg, and disc labelssct_tutorial_data- contains-add-seg-onlyand contains correction for SC seg, PMJ , and disc labelsukbiobank-spinalcord-csa- contains-add-seg-onlyflag, usesITK-snapinstead ofFSLeyesfor SC seg corrections, and contains correction for SC seg, PMJ , and disc labelscanproco- similar toukbiobank-spinalcord-csadcm_metri_normalization- similar toukbiobank-spinalcord-csaAlso be aware of the bash script for MS lesion corrections and this comment
Summary of
package_for_correction.pyversions:spine-generic- the original versionukbiobank-spinalcord-csacanprococanproco/jv_make_get_subject_and_get_ses_more_robust- contains-suffix-files-segflagAlso, be aware of copy_files_to_derivatives.py script used to copy manually corrected files (segmentations, vertebral labeling, etc.) from the source preprocessed dataset to the git-annex BIDS dataset's derivatives folder