Add pmj labeling and CSA from PMJ in processing pipeline

sct-pipeline / ukbiobank-spinalcord-csa

Measure of the averaged cross-sectional area (cord CSA) between C2 and C3 of the spinal cord with UK Biobank Brain MRI dataset.

MIT License

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Closed sandrinebedard closed 3 years ago

sandrinebedard commented 3 years ago

This PR adds processing steps to compute CSA based on a distance from PMJ (see #78).

It includes:

Detect PMJ if manual label does not already exists
Call sct_process_segmentation with flag pmj at 60 mm from PMJ with default extent of 20 mm
Smooth extrapolated centerline in R-L direction (for visualization)

Closes #78