ntatsisk/brats-reg-elastix

BraTS-Reg registration challenge using Elastix

• The challenge: https://www.med.upenn.edu/cbica/brats-reg-challenge/
• ITKElastix: https://github.com/InsightSoftwareConsortium/ITKElastix

File explanation

1. brats-reg-analysis.py: Runs the registration for each subject and saves the results. Make sure to speficy the correct filepaths in fileconfig.py first.
2. calculate-point-distance.py: Transforms the landmarks based on the previous registration, and calculates the median point distance (metric specified by the challenge) before and after registration per subject.
3. landmark-reader: Contains a napari plugin that loads and visualizes the landmarks to aid visual inspection. To use, run pip install elastix-napari and then pip install -e . inside the landmark-reader directory.