Scilpy

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 is now built for Python 3.10 so be sure to create a virtual environnement for Python 3.10. If this version is not installed on your computer:

sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt-get install python3.10 python3.10-dev python3.10-venv python3.10-minimal python3.10-tk

Make sure your pip is up-to-date before trying to install:

pip install --upgrade pip

The library's structure is mostly aligned on that of DIPY.

The library and scripts can be installed locally by using:

export SETUPTOOLS_USE_DISTUTILS=stdlib
pip install -e .

If you don't want to install legacy scripts:

export SCILPY_LEGACY='False'
pip install -e .

(Then, without the legacy scripts, if you want to use pytest, use:)

pytest --ignore=scripts/legacy

On Linux, most likely you will have to install libraries for COMMIT/AMICO

sudo apt install libblas-dev liblapack-dev

While on MacOS you will have to use (most likely)

brew install openblas lapack

On Ubuntu >=20.04, you will have to install libraries for matplotlib

sudo apt install libfreetype6-dev

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/

License

frheault/scilpy

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