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
A minimal example can be found following these badges:
For further information please have a look at our Jupyter Notebook tutorials illustrating the usage of BrainLes preprocessing.
We provide a (WIP) documentation. Have a look here
Please credit the authors by citing their work.
We provide the SRI-24 atlas from this publication. However, custom atlases can be supplied.
We currently provide support for HD-BET.
We currently provide support for ANTs (default), Niftyreg (Linux), eReg (experimental)