Bring metrics in PAM50 anatomical dimensions in sct_process_segmentation

[sandrinebedard]

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Description

This PR adresses #3733 . The concept is to bring metrics generated in sct_process_segmentation to the PAM50 anatomical space in order to do slicewise comparison. The metrics need to be computed slicewise and the vertfile needs to be specified. 2 .csv files will be output.

• Adds the option -normalize PAM50 in sct_process_segmentation
• Brings the metrics in the PAM50 anatomical dimensions in metrics_to_PAM50.py
  • Interpolates metrics perlevel, except the first and last where scaling is applied
• Aggregates metrics and save in a second .csv file.

To run the script:

sct_process_segmentation -i <segmentation> -perslice 1 -vertfile <labeled segmentation> -normalize-PAM50 1

Linked issues

Fixes #3733. (We should reopen the issue after this PR is merged, as there are other ideas in the issue.)

[jcohenadad]

for the SUM(length) column, put n/a instead

[sandrinebedard]

TODO: change the output csv file with _PAM50 only!

[joshuacwnewton]

The new changes LGTM! But, as a result of the newest changes, we now have test failures.

[joshuacwnewton]

I think I'm just about ready to approve this? It mostly LGTM! I just had one last question (and one more task for myself).

[joshuacwnewton]

Assuming the tests pass with the new dataset release, this LGTM! I'd say it's ready to merge.

Links to next steps:

• Incorporating changes into Add new CLI script to compute normalized metric ratios (MSCC, etc.) for compressed levels #4003
• Centralize metric-related modules in a new metrics submodule #4019 and