Scilpy is closely related to DIPY: it follows the same organization. But it also contains work that has been developped by our lab and that is not included yet into Dipy. We have a public version of Scilpy on Github, with work that has been tested and that we want to share with the community, and a private version on Bitbucket (you have to ask for access) with our work that is either not tested, still being developped or not converted into python 3.

For each script, you can use the -h option for explanations on how to use it. Ex: -h

If you don’t know the name of a script, you may look for all scripts matching some keywords with: keyword

Finally, for a html version of the help, you will find the description of all scripts and modules, as well as some tutorials, on scilpy’s official documentation.

Installing scilpy

Scilpy currently supports python versions 3.8 to 3.10. There are many ways to install a python version on your system. We refer the reader to section Installing Python for one such method. Once your python distribution is correctly installed, Scilpy can be installed by following the procedure outlined below.

  • Users: you can follow the instructions on the Github page or follow these instructions :

git clone
cd scilpy
pip install -e .
  • Developpers: instead, you should try python develop


Before installing anything, please read the Virtual Environment page!