BrainLes: A brain imaging toolkit beyond BraTS and lesion segmentation.

niftyreg_preprocessor

does the following

• co-registration
• atlas registration
• transformation
• skullstripping in brats-space
• apply masking
• result: 4niftis, skullstripped brats-space -> save to path

atlas

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788/

installation:

pip install -e "git+https://github.com/neuronflow/BrainLes.git@main#egg=HD_BET&subdirectory=preprocessing/brainles_preprocessing/brain_extraction/HD_BET"