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Project description
BrainLes-Preprocessing
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
NiftyRegis 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
Installation
With a Python 3.10+ environment you can install directly from pypi.org:
pip install brainles-preprocessing
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