Manual correction/segmentation of M12 MS lesions from model prediction

[plbenveniste]

In this issue, we describe the work done to manually segment MS lesions in the spinal cord on PSIR and STIR contrasts.
This work is pushed on branch plb/m12_lesion_seg

The segmentation predictions were done using the model stored in this release r20240125.

The lesion segmentations were then manually corrected by either Catherine Spino or Pierre-Louis Benveniste

[plbenveniste]

The following list of subjects were manually segmented by Michelle Chen (because we thought they were M0 data at first and they ended up being M12 data). More info can be found in issue 39.

Subject segmented by Michelle Chen:

• sub-edm054
• sub-tor029
• sub-mon002
• sub-mon005
• sub-mon003
• sub-edm065
• sub-edm035
• sub-edm031
• sub-mon006
• sub-tor051
• sub-edm088
• sub-tor036
• sub-mon009 (image is problematic)
• sub-tor016
• sub-mon032 (image is problematic)
• sub-tor043
• sub-tor010
• sub-mon007
• sub-mon060
• sub-tor039
• sub-tor044
• sub-mon011
• sub-mon041
• sub-tor012
• sub-mon014
• sub-edm005
• sub-tor038
• sub-mon031
• sub-mon010
• sub-mon052
• sub-tor021

This was pushed in the main branch (during final merge of branches, we need to check that no file is overwritten. Normally, all files should be newly created)

I verified that the model prediction for ms lesion segmentation were not included in branch plb/m12_lesion_seg (in order to have no conflict when merging).

[plbenveniste]

The following subject were manually corrected by Catherine Spino.

Subject manually corrected:

• sub-cal056_ses-M12_STIR.nii.gz
• sub-cal072_ses-M12_STIR.nii.gz
• sub-edm011_ses-M12_PSIR.nii.gz
• sub-edm013_ses-M12_PSIR.nii.gz
• sub-mon001_ses-M12_PSIR.nii.gz
• sub-mon004_ses-M12_PSIR.nii.gz
• sub-tor006_ses-M12_PSIR.nii.gz
• sub-tor007_ses-M12_PSIR.nii.gz
• sub-van005_ses-M12_PSIR.nii.gz
• sub-van010_ses-M12_PSIR.nii.gz

The QC is stored at duke/temp/plben/CANPROCO_PROJECT/manual_correction_ms_lesion_m12/qc_catherine_spino.zip