Add PMJ detection 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

To measure CSA based on distance from pontomedullary junction (PMJ) (see this PR), we have to first detect PMJ in the processing pipeline.

[x] Add detection of PMJ in process_data.sh using sct_detect_pmj
[x] Add use of sct_process_segementation with the flag -pmj on the branch jca/sb/3063-csa-measure-from-pmj in spinalcordtoolbox
[x] Add possibilty to use manual label of PMJ