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neuropoly / totalspineseg

Segmentation of vertebrae, intervertebral discs, spinal cord and CSF from MRI images.
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Missing segmentations for spinegeneric #34

Open NathanMolinier opened 3 months ago

NathanMolinier commented 3 months ago

Description

I was adding the generated segmentations to spine generic and noticed that some subject did not have any segmentations:

/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-amu05/anat/sub-amu05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-balgrist01/anat/sub-balgrist01_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-balgrist04/anat/sub-balgrist04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-beijingGE01/anat/sub-beijingGE01_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-beijingGE02/anat/sub-beijingGE02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-beijingGE03/anat/sub-beijingGE03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-beijingGE04/anat/sub-beijingGE04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-beijingPrisma04/anat/sub-beijingPrisma04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-beijingVerio03/anat/sub-beijingVerio03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-beijingVerio04/anat/sub-beijingVerio04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-brnoCeitec02/anat/sub-brnoCeitec02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-brnoCeitec03/anat/sub-brnoCeitec03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-brnoUhb02/anat/sub-brnoUhb02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-brnoUhb05/anat/sub-brnoUhb05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-cardiff01/anat/sub-cardiff01_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-cardiff04/anat/sub-cardiff04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-cardiff06/anat/sub-cardiff06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-cmrra04/anat/sub-cmrra04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-cmrra06/anat/sub-cmrra06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-cmrrb02/anat/sub-cmrrb02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-cmrrb07/anat/sub-cmrrb07_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-fslAchieva05/anat/sub-fslAchieva05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-fslPrisma01/anat/sub-fslPrisma01_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-fslPrisma02/anat/sub-fslPrisma02_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-fslPrisma03/anat/sub-fslPrisma03_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-fslPrisma04/anat/sub-fslPrisma04_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-fslPrisma05/anat/sub-fslPrisma05_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-fslPrisma06/anat/sub-fslPrisma06_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-geneva01/anat/sub-geneva01_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-geneva05/anat/sub-geneva05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-hamburg03/anat/sub-hamburg03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-hamburg06/anat/sub-hamburg06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-mgh02/anat/sub-mgh02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-mgh02/anat/sub-mgh02_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-mgh03/anat/sub-mgh03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-milan01/anat/sub-milan01_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-milan03/anat/sub-milan03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-mountSinai05/anat/sub-mountSinai05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-mountSinai06/anat/sub-mountSinai06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-mpicbs06/anat/sub-mpicbs06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-nwu03/anat/sub-nwu03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-nwu06/anat/sub-nwu06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-oxfordFmrib02/anat/sub-oxfordFmrib02_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-oxfordFmrib08/anat/sub-oxfordFmrib08_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-oxfordFmrib09/anat/sub-oxfordFmrib09_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-oxfordOhba03/anat/sub-oxfordOhba03_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-oxfordOhba05/anat/sub-oxfordOhba05_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-pavia01/anat/sub-pavia01_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-pavia06/anat/sub-pavia06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-perform02/anat/sub-perform02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-queensland02/anat/sub-queensland02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-queensland04/anat/sub-queensland04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-stanford05/anat/sub-stanford05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-strasbourg04/anat/sub-strasbourg04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-strasbourg05/anat/sub-strasbourg05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-strasbourg06/anat/sub-strasbourg06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-tokyo750w03/anat/sub-tokyo750w03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-tokyo750w04/anat/sub-tokyo750w04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-tokyo750w05/anat/sub-tokyo750w05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-tokyo750w06/anat/sub-tokyo750w06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-tokyoIngenia01/anat/sub-tokyoIngenia01_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-tokyoIngenia02/anat/sub-tokyoIngenia02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-tokyoIngenia07/anat/sub-tokyoIngenia07_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-tokyoSkyra04/anat/sub-tokyoSkyra04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ubc01/anat/sub-ubc01_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ubc06/anat/sub-ubc06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucdavis01/anat/sub-ucdavis01_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucdavis02/anat/sub-ucdavis02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucdavis05/anat/sub-ucdavis05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucdavis06/anat/sub-ucdavis06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl01/anat/sub-ucl01_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl01/anat/sub-ucl01_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl02/anat/sub-ucl02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl02/anat/sub-ucl02_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl03/anat/sub-ucl03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl03/anat/sub-ucl03_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl04/anat/sub-ucl04_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl04/anat/sub-ucl04_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl05/anat/sub-ucl05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl05/anat/sub-ucl05_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl06/anat/sub-ucl06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-ucl06/anat/sub-ucl06_T2w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-unf02/anat/sub-unf02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-vallHebron03/anat/sub-vallHebron03_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-vuiisAchieva02/anat/sub-vuiisAchieva02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-vuiisAchieva06/anat/sub-vuiisAchieva06_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-vuiisIngenia01/anat/sub-vuiisIngenia01_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-vuiisIngenia02/anat/sub-vuiisIngenia02_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-vuiisIngenia05/anat/sub-vuiisIngenia05_T1w_totalsegmri.nii.gz
/Users/nathan/Desktop/totalseg_data/multi/derivatives/labels/sub-vuiisIngenia06/anat/sub-vuiisIngenia06_T1w_totalsegmri.nii.gz

I think we could generate segmentations for these subjects to not lose any data.

yw7 commented 2 months ago

@NathanMolinier Where did you take the labels from? I think all the labels here: https://github.com/neuropoly/totalspineseg/releases/tag/labels