+ 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 

Usage

see demo.ipynb for usage.

# extract centerline between 2 points given a binary 3d mask
centerline_list = extract_centerline(img,start_point,end_point)

Reference

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

wip

docker build -t wip .
docker run -it -p 8888:8888 -w $PWD -v $PWD:$PWD wip bash
jupyter notebook --ip=* --allow-root