Scilpy is the main library supporting research and development at the Sherbrooke Connectivity Imaging Lab (SCIL).
Scilpy mainly comprises tools and utilities to quickly work with diffusion MRI. Most of the tools are based on or are wrappers of the DIPY library, and most of them will eventually be migrated to DIPY. Those tools implement the recommended workflows and parameters used in the lab.
The library's structure is mostly aligned on that of DIPY. The library and scripts can be installed locally by using:
pip install -e .
On Linux, most likely you will have to install libraries for COMMIT/AMICO
sudo apt install libblas-dev liblapack-dev
On Ubuntu-20.04, you will have to install libraries for matplotlib
sudo apt install libfreetype6-dev
While on MacOS you will have to use (most likely)
brew install openblas lapack
Note that using this technique will make it harder to remove the scripts when changing versions. We highly recommend working in a Python Virtual Environment.
Scilpy documentation is available: https://scilpy.readthedocs.io/en/latest/