brainles-preprocessing 0.0.11

TODO.

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 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

The atlas employed in our workflow is based on the following publication: Link to the Atlas Article

Installation

1. Directly from the GitHub Repository: Using pip, you can directly install the preprocessing tool:

   pip install git+https://github.com/BrainLesion/preprocessing.git
   

2. Clone and Install Locally: For a local installation, you can clone the repository and then install it:

   git clone https://github.com/BrainLesion/preprocessing.git
   cd preprocessing
   pip install .
   

Directory Reference

/home/florian/flow/BrainLesion/BrainLes/preprocessing