Upload PAM50 registered labels from Yehuda Warszawer

spine-generic / data-multi-subject

Multi-subject data for the Spine Generic project

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Upload PAM50 registered labels from Yehuda Warszawer #160

Open mguaypaq opened 4 months ago

mguaypaq commented 4 months ago

These are the PAM50 registered labels supplied by @yw7 in #155.

I split the upload into two commits:

Some of the files are completely new, so there's no conflict.
Some of the files would overwrite existing files, by Etienne Bergeron, @valosekj, @NathanMolinier, Olivier Morinlupien, Paul Bautin, @sandrinebedard, Yassine El Bouchaibi. Which ones do we want to keep?

And some questions for Yehuda:

The zip file contained a text file called derivatives/errors.txt, which contains the single line of text, sub-pavia04_T1w_PAM50_seg.nii.gz. What does this mean?
It seems like there are a lot of .nii.gz files without a corresponding JSON sidecar.
Some of the contributed files have a JSON sidecar saying they're from Charley Gros, why is that?

sandrinebedard commented 4 months ago

This PR refractors all the naming in the data-multi-subject dataset:

https://github.com/spine-generic/data-multi-subject/pull/159

I am just missing updtaing and tested the related scripts, maybe we should address it before this PR, and afterwards we can update all the naming convention to be in sync

mguaypaq commented 4 months ago

I'm happy to wait until #159 is merged before tackling this upload. I mainly wanted to put it up on github as a PR as quickly as possible.

yw7 commented 4 months ago

The zip file contained a text file called derivatives/errors.txt, which contains the single line of text, sub-pavia04_T1w_PAM50_seg.nii.gz. What does this mean?

This is file in which the registered segmentation from PAM50 was wrong:

It seems like there are a lot of .nii.gz files without a corresponding JSON sidecar.

Some of the contributed files have a JSON sidecar saying they're from Charley Gros, why is that?

I've created the missing _PAM50_seg jsons sidecars here: data-multi-subject_PAM50_seg_sidecars_jsons.zip

Regardingthe _seg files actually only the ones with "Author": "Yehuda Warszawer" are new (when double checked, I notice I included also the original unchenged files with the original sidecars json ) Will it help If Ill recreate zip file containing only the new files?