Measure CSA based on distance from pontomedullary junction (PMJ)

[sandrinebedard]

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Description

This PR addressed #3063. The goal is to measure CSA based on a distance from pontomedullary junction (PMJ) To take into account the curvature of the spinal cord, we use linear interpolation between PMJ and centerline. We can after measure the distance along the centerline.

This PR adds the API csa_pmj.py and intergrates the method in sct_process_segmentation and aggregate_slicewise.py.
It also adds QC report for this method.

Note: we will need to update the documentation

Linked issues

Resolves #3063 and closes #3431

[sandrinebedard]

I've cleaned up and added some comments to the code, I think it would be ready to merge! We also discussed that we need to update the documentation with this new feature, do we want to address that soon? (I can also open an issue for this)

[joshuacwnewton]

Sorry for not giving this feedback sooner... I probably should have looked at this much earlier, before the QC PR. 😅

[jcohenadad]

Amazing contribution @sandrinebedard !!

[joshuacwnewton]

I have a few nitpicky suggestions, but for the most part, this LGTM!

I'd say feel free to merge after this! 🙂