Fastr_tools

The pipelines uses fastr to create wrappers around executables and python scripts.

dcm2nii

Wrapps MRICron’s dicom to nifti converter for preprocessing.

deface

wraps Free Surfer’s deface tool to deface T1 (or T1 registered) samples pulled from xnat.

elastix

wraps elastix tool for registration of non-T1 samples to T1.

ExtractMask

wraps a python script that extracts masks from defaced samples.