Upload PAM50 registered labels from Yehuda Warszawer

[mguaypaq]

These are the PAM50 registered labels supplied by @yw7 in #31.

I split the upload into two commits:

1. Some of the files are completely new, so there's no conflict.
2. Some of the files would overwrite others that were provided by @sandrinebedard in Fix MTS and add T1w disc labels #30. Which ones do we want to keep?

[mguaypaq]

If it's useful, we can also have both sets of images available, one on master, and another:

1. in the history of master, so that others can refer to a specific commit ID; or
2. in the history of master, and make a release of the dataset to easily refer to that version; or
3. on a separate branch, and optionally turn it into a release of the dataset.

[sandrinebedard]

Some of the files would overwrite others that were provided by @sandrinebedard in #30. Which ones do we want to keep?

Looks like we both did the same manual disc labeling... I don't know what we should keep... It is fine to keep yehuda's

I don't think sub-chiba750_T1w_PAM50_seg.nii.gz is an appropriate name, what is it exaclty?

Is it the segmentation of the vertebrae warped from the PAM50 template, is it only 0 and 1?? if so I would suggest:

sub-chiba750_T1w_PAM50_seg.nii.gz --> sub-chiba750_T1w_label-vertebrae_desc-PAM50_seg.nii.gz (or dseg if not 0 and 1 only)

[sandrinebedard]

I don't see any json sidecars with : _PAM50_seg.nii.gz?

[yw7]

2. Some of the files would overwrite others that were provided by @sandrinebedard in Fix MTS and add T1w disc labels #30. Which ones do we want to keep?

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

what is it exaclty?
the '_PAM50_seg' files are the vertebrae+discs+sc+csf registered from the PAM50 template the labels classes are like in https://github.com/neuropoly/totalsegmentator-mri?tab=readme-ov-file#list-of-class.

So maybe dseg is better. For me it is ok as you suggested, I'm not that familiar with all the lab naming conventionד.

I don't see any json sidecars with : _PAM50_seg.nii.gz?

Regarding the json sidecars, I've created them here: data-single-subject_PAM50_seg_sidecars_jsons.zip

[mguaypaq]

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

Ok, good to know. With this information I should be able to include only the files for "Yehuda Warszawer". No need to make a new zip file.

So maybe dseg is better. For me it is ok as you suggested, I'm not that familiar with all the lab naming conventions.

I'll consult with our resident BIDS expert and rename the files.

I don't see any json sidecars with : _PAM50_seg.nii.gz?

Regarding the json sidecars, I've created them here: data-single-subject_PAM50_seg_sidecars_jsons.zip

Thanks! I was able to download the zip file.