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README.md

Option-1

Run the notebook on Binder: Binder

Option-2

Use Docker!

Warning: Pulled image (3.5GB) expands to 14GB, be careful about this option if your disk space is low.

  • Pull the Docker image

docker pull agahkarakuzu/elastixmrb

The Dockerfile used to build agahkarakuzu/elastixmrb is available at Docker folder.

  • Run the Docker image

docker run -it --rm -p 8888:8888 agahkarakuzu/elastixmrb

  • Go to your web browser and visit localhost:8888, which will be asking for a password. This password is the hash displayed on the terminal. Copy the hash that follows ?token= expression, and paste it to the password section on your browser.

http://127.0.0.1:8888/?token=b47gjhjrt465tuewadhy4tw546fsjtwy

Option-3

Hi! To (locally) run the hands-on session of the SimpleElastix workshop at the OpenMR Benelux 2020, there are a couple of requirements that should be installed previous to the start of the session:

  • Jupyter Notebook
  • Python>3
  • torch 1.3
  • SimpleElastix - Python binding
  • nibabel
  • h5py
  • scipy
  • matplotlib
  • ipywidgets

If you are having any problems installing any of the packages, especially SimpleElastix, which have some known issues with MacOS, please contact me via our Slack channel, or DM me there, I will be happy to give you some support!

Slack: OpenMR2020 - Workshop Help Center

Cheers!

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