dcm-oklahoma - new data

[valosekj]

We recently received new data and labels for dcm-oklahoma.

Before pushing the new files to git-annex, I went through them to check their consistency with the already existing dcm-oklahoma dataset, and I noticed the following:

1. our current git-annex dataset has a structure sub-/anat; the newly shared data also contains ses- directories:

sub-CSM137
└── ses-spinalcord
    └── anat
        ├── sub-CSM137_ses-spinalcord_T2star.nii.gz
        ├── sub-CSM137_ses-spinalcord_T2w.nii.gz

There is no other session, so maybe we can remove ses-spinalcord.

2. T2w labels (SC seg and compression label) have a different orientation than the source T2w image, for example:

function orientation { sct_image -i ${1} -header | grep -E qform_[xyz] | awk '{printf "%s", substr($2, 1, 1)}' }
$ cd sub-CSM137/ses-spinalcord/anat
$ orientation sub-CSM137_ses-spinalcord_T2w.nii.gz
RPI
$ orientation sub-CSM137_ses-spinalcord_T2w_seg.nii.gz
ASR
$ orientation sub-CSM137_ses-spinalcord_T2w_label-compression-manual.nii.gz
ASR

This can be fixed by sct_image -setorient RPI

3. T2w_seg has missing parts for some slices, e.g., sub-CSM137_ses-spinalcord_T2w_seg.nii.gz:

[valosekj]

Okay, I addressed the points 1 and 2 and pushed the data; details: https://data.neuro.polymtl.ca/datasets/dcm-oklahoma/pulls/2