+ 3d centerline extraction demo using geodesic distance transform in Python
see extract_centerline.py
+ Extract oblique 2d slice (or 3d slab) from volume with SimpleITK
see extract_slice.py
see demo.ipynb for usage.
# extract centerline between 2 points given a binary 3d mask
centerline_list = extract_centerline(img,start_point,end_point)
Teng, Pang-yu, Ahmet Murat Bagci, and Noam Alperin. "Automated prescription of an optimal imaging plane for measurement of cerebral blood flow by phase contrast magnetic resonance imaging." IEEE Transactions on Biomedical Engineering 58.9 (2011): 2566-2573. https://www.ncbi.nlm.nih.gov/pubmed/21672671
docker build -t wip .
docker run -it -p 8888:8888 -w $PWD -v $PWD:$PWD wip bash
jupyter notebook --ip=* --allow-root