Canproco - adding discs labels for session M12

NathanMolinier commented 1 year ago

Description

Discs labels for the session M12 were generated using the hourglass network however some manual corrections need to be done before merging.

The new branch is nm/add_discs-labels_ses-M12

plbenveniste commented 1 year ago

QC of disc labels of M12 subjects

The QC is available here : duke.neuro.polymtl.ca/temp/plben/generate_qc_vert_levels_M12. QC was obtained using generate_qc.py which is in the same folder.

QC was performed over the 340 images.

Identified 50 problematic subjects:

- /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-tor035_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon032_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van182_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-tor061_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-tor092_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van177_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon005_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-edm118_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-edm127_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van124_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-cal104_ses-M12_STIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van201_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-tor141_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van208_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-cal134_ses-M12_STIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon185_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon149_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-cal194_ses-M12_STIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van213_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon198_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon138_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon199_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-cal143_ses-M12_STIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van155_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon072_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-edm161_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van198_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-edm113_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-tor098_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-tor053_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-edm114_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon096_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon065_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon009_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van175_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-tor090_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van174_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van189_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-cal165_ses-M12_STIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-edm005_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van055_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon172_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon121_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon132_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon168_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-cal176_ses-M12_STIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van216_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-mon160_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van194_ses-M12_PSIR.nii.gz - /Users/plbenveniste/Desktop/generate_qc_vert_levels_M12/sub-van135_ses-M12_PSIR.nii.gz

Disc label segmentation were manually corrected using the script : manual_correction.py.

The following file was removed :

sub-mon032_ses-M12_PSIR_label-discs.nii.gz (poor quality image: label disc file empty)

The following files were kept because some lesions are visible, even though the quality is not great :

sub-mon005_ses-M12_PSIR_label-discs.nii.g : poor image quality
sub-van201_ses-M12_PSIR_label-discs.nii.gz : poor image quality
sub-tor141_ses-M12_PSIR_label-discs.nii.gz : poor image quality
sub-cal134_ses-M12_STIR_label-discs.nii.gz : poor image quality
sub-mon072_ses-M12_PSIR_label-discs.nii.gz : poor image quality
sub-mon096_ses-M12_PSIR_label-discs.nii.gz : poor image quality
sub-mon009_ses-M12_PSIR_label-discs.nii.gz : poor image quality

The corrections were pushed to the same branch and the file sub-mon032_ses-M12_PSIR_label-discs.nii.gz was deleted in the branch as well.

Ready to review.

mguaypaq commented 1 year ago

git annex get derivatives/labels/ is happy, for all the new commits on the branch.
bids-validator is irrelevant, since this PR only makes changes under derivatives/.
I shortened the second "Author" field in the JSON sidecars, which contained redundant information.
I standardized file names from label-discs to labels-disc (there were some of each).

Merged into master, and deleted the branch nm/add_discs-labels_ses-M12.

neuropoly / data-management

Canproco - adding discs labels for session M12 #275

Description