Welcome to brainles-preprocessing’s documentation!

PyPI version panoptica Documentation Status


BrainLes-Preprocessing is a comprehensive tool tailored for preprocessing tasks in medical imaging, with a current focus on brain MRIs. Here’s what it can currently do:

  • Co-registration using NiftyReg: Aligning two images or series of images. While NiftyReg is the current tool used for co-registration, our architecture allows for potential extensions with other tools in the future.

  • Atlas Registration: Maps images to a standard atlas for consistent spatial referencing.

  • Transformation: Adjusts the image based on certain parameters.

  • Skull-stripping in BRATS-space: Removes non-brain tissue from MRI data.

  • Apply Masking: Applies a mask to an image, highlighting or hiding specific parts of it.

The outcome of this processing sequence is a set of 4 NIFTI images, skull-stripped in BRATS-space. These results are then saved to the provided path.

Atlas Reference

We use the SRI-24 atlas from this publication


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

pip install brainles-preprocessing

Indices and tables