Add support for spinal rootlets segmentation

[KaterinaKrejci231054]

This draft PR adds an option to correct rootlets segmentation.

Resolves: #56

[valosekj]

You can also add rootlets into this list: https:/spinalcordtoolbox/manual-correction/blob/main/README.md?plain=1#L5-L12

[valosekj]

I added some unit tests for recently implemented get_orientation and change_orientation functions (#100) in cde0916.
The tests worked fine locally. But when triggered using the GitHub action, the tests failed on missing sct_image (which is used by get_orientation and change_orientation, e.g., here).

sct_image is missing because we do not currently install SCT for our CI. Not sure if we want to install SCT for our CI as it would increase the CI time a lot...

[valosekj]

Great work, @KaterinaKrejci231054! I tested the PR using the following command, and it worked perfectly!

python manual_correction.py -path-img ~/data/results/philadelphia-pediatric/philadelphia-pediatric_2024-06-26/data_processed -path-label ~/data/results/philadelphia-pediatric/philadelphia-pediatric_2024-06-26/derivatives/labels -change-orient RPI -path-out ~/data/results/philadelphia-pediatric/philadelphia-pediatric_2024-06-26/derivatives_corr/labels -config ~/data/results/philadelphia-pediatric/philadelphia-pediatric_2024-06-26/three_subjects_to_correct.json -fsleyes-cm jet_matplotlib

I'm pre-approving the PR.
Can you please address this comment?
I'll address the failing CI. Then, we can merge!

[valosekj]

Hey, @joshuacwnewton! I added SCT installation into the manual_correction CI in d58dfee and 56b375f, but CI still struggles to locate sct_image:

...
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/subprocess.py:1720: FileNotFoundError
=========================== short test summary info ============================
FAILED tests/test_utils.py::test_get_orientation - FileNotFoundError: [Errno 2] No such file or directory: 'sct_image'
FAILED tests/test_utils.py::test_change_orientation - FileNotFoundError: [Errno 2] No such file or directory: 'sct_image'
========================= 2 failed, 9 passed in 0.40s ==========================

Do you have any ideas on how to solve this?

[joshuacwnewton]

Thanks for the ping! I have a bit of a backlog to get through since coming back from the conference I was attending, but I'm very happy to take a look at this soon. :)

[valosekj]

@KaterinaKrejci231054, thanks for this PR, and @joshuacwnewton, thanks for fixing the CI!
LGTM now! merging