Added sc seg for MS patient in canproco and sct-testing-large

plbenveniste commented 4 months ago

Related to this comment.

Canproco modifications :

Pushed 33 SC segmentations made with the CanProCo region-based model (release). I then also manually corrected them (QC here)

Sct-testing-large modifications :

Pushed 186 SC segmentations made with SCT v6.2 (contrast-agnostic-sc-seg model). I then also manually corrected them (QC is stored in /duke/temp/plben/ms-lesion-agnostic

mguaypaq commented 4 months ago

For canproco: git-annex is happy, and the json syntax is valid. Merged into master.

For sct-testing-large: git-annex is happy, and the json syntax is valid. But I noticed that some files had "Author": "Pierre-Louis Benveniste " (with a trailing space), which is evil, so I added a commit to remove the trailing spaces. Merged into master.

Before closing this issue, does someone need to look at the QC?

plbenveniste commented 4 months ago

I think we can move forward on this. I only included the QC in this issue because it was automatically generated by the manual correction script

mguaypaq commented 4 months ago

Alright, it's already merged into master, so I'll just close this issue.

plbenveniste commented 4 months ago

~~I just realized that I had something weird happening on my computer. I pushed everything last week, but it seems that the last commit wasn't pushed.~~

Nevermind, all good !

NathanMolinier commented 3 months ago

Hey @plbenveniste ! I was looking at the spinal cord segmentations in the canproco dataset and I noticed that some segmentations were missing for some T2w image of the session ses-M0, is it a known issue ?

Here are the files that doesn't exist:

ValueError: missing files:
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-edm005/ses-M0/anat/sub-edm005_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-edm031/ses-M0/anat/sub-edm031_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-edm035/ses-M0/anat/sub-edm035_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-edm054/ses-M0/anat/sub-edm054_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-edm065/ses-M0/anat/sub-edm065_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-edm088/ses-M0/anat/sub-edm088_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon002/ses-M0/anat/sub-mon002_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon003/ses-M0/anat/sub-mon003_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon005/ses-M0/anat/sub-mon005_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon006/ses-M0/anat/sub-mon006_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon007/ses-M0/anat/sub-mon007_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon009/ses-M0/anat/sub-mon009_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon010/ses-M0/anat/sub-mon010_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon011/ses-M0/anat/sub-mon011_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon014/ses-M0/anat/sub-mon014_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon031/ses-M0/anat/sub-mon031_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon032/ses-M0/anat/sub-mon032_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon041/ses-M0/anat/sub-mon041_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon052/ses-M0/anat/sub-mon052_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-mon060/ses-M0/anat/sub-mon060_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor010/ses-M0/anat/sub-tor010_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor012/ses-M0/anat/sub-tor012_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor014/ses-M0/anat/sub-tor014_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor016/ses-M0/anat/sub-tor016_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor021/ses-M0/anat/sub-tor021_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor029/ses-M0/anat/sub-tor029_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor036/ses-M0/anat/sub-tor036_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor038/ses-M0/anat/sub-tor038_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor039/ses-M0/anat/sub-tor039_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor043/ses-M0/anat/sub-tor043_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor044/ses-M0/anat/sub-tor044_ses-M0_T2w_seg-manual.nii.gz
/home/GRAMES.POLYMTL.CA/p118739/data_nvme_p118739/data/datasets/canproco/derivatives/labels/sub-tor051/ses-M0/anat/sub-tor051_ses-M0_T2w_seg-manual.nii.gz

Also, maybe I'm a bit picky about this (I'm sorry) but I think we would all benefit from following our new data naming convention also regarding the JSON content.

valosekj commented 3 months ago

Hey @plbenveniste ! I was looking at the spinal cord segmentations in the canproco dataset and I noticed that some segmentations were missing for some T2w image of the session ses-M0, is it a known issue ?

This might be related to https://github.com/neuropoly/data-management/issues/296 which moved SC segmentations for some subjects from M0 to M12.

plbenveniste commented 3 months ago

Thanks @NathanMolinier for your message. Those files are missing a SC segmentation as they were recently added with the new Erin data (issue #39. I did not segment the SC as I am not using T2w images.

Also, regarding the convention, the newly added files don't follow the new conventions so that the conventions used in the dataset are homogeneous. The entirety of the dataset will be reformatted soon.

neuropoly / data-management

Added sc seg for MS patient in canproco and sct-testing-large #303