# 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"
```
/home/florian/flow/BrainLesion/BrainLes/preprocessing
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