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neuropoly / data-management

Repo that deals with datalad aspects for internal use
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Add total segmentator data to whole-spine #308

Closed NathanMolinier closed 5 months ago

NathanMolinier commented 5 months ago

Description

I just pushed a new branch nm/add_totalseg_segmentations to the whole-spine dataset with spine segmentations and new SC segmentations.

I also ran this following command to make sure that segmentations are stored as uint8:

for file in  */*/*label-*.nii.gz;do sct_image -i "$file" -type uint8;done

The branch is then ready for review.

I used these codes:

Related issue

https://github.com/neuropoly/data-management/issues/306

NathanMolinier commented 5 months ago

I still need to change something before merging

NathanMolinier commented 5 months ago

I erased SC and CSF segmentation from label-spine_dseg and saved them as single files. I also removed single sacrum masks and added them to label-spine_dseg.

The branch is now ready for review !

mguaypaq commented 5 months ago

Git-annex and bids-validator look fine, merged in https://data.neuro.polymtl.ca/datasets/whole-spine/pulls/1.