Preprocessing pipeline for medical imaging.
Image registration of NIfTI images, producing a rigid registration which is going to be improved by an affine registration order 0. The tool used to produce the registration is SimpleElastix.
Skull stripping using ROBEX.
N4 bias field correction algorithm for correcting low frequency intensity non-uniformity present in MRI image.
Image normalization according to Qtim deep learning tutorial. Results will have 0 mean, min intensity of around -2 and max intensity of around 2.
Refer to the main.py for an example of a single image preprocessing using all the steps listed above. There is also a structured documentation inside the resources/documentation directory.
- scikit-image -
pip install scikit-image - scikit-learn -
pip install scikit-learn - nibabel -
pip install nibabel - numpy -
pip install numpy - SimpleITK -
pip install SimpleITK