Various refactoring - Githubissues

sct-pipeline / csa-atrophy

Evaluate the sensitivity of atrophy detection with SCT

https://csa-atrophy.readthedocs.io/

MIT License

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Various refactoring #42

Closed PaulBautin closed 4 years ago

PaulBautin commented 4 years ago

After re-testing the code, minor adjustments were made to process_data.sh. @jcohenadad, these should be merged before processing the spine-generic dataset.

DONE:

add image cropping at beginning of process_data on original image
minor fixes to config files
add manual pmj detection in manual_correction.py
add reorienting and resampling to process_data.sh