Welcome to brainles-preprocessing’s documentation!

PyPI version preprocessing Documentation Status tests


BrainLes preprocessing is a comprehensive tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI. It can be used to build to build modular preprocessing pipelines:

This includes normalization, co-registration, atlas registration and skulstripping / brain extraction.

BrainLes is written backend-agnostic meaning it allows to swap the registration and brain extration tools.


With a Python 3.10+ environment you can install directly from pypi.org:

pip install brainles-preprocessing


Please have a look at our Jupyter Notebook tutorials illustrating the usage of BrainLes preprocessing.


Please credit the authors by citing their work.

Atlas Reference

We provide the SRI-24 atlas from this publication. However, custom atlases can be supplied.

Brain extraction

We currently provide support for HD-BET.


We currently provide support for niftyreg.

Indices and tables