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

dcm2nii
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Wrapps MRICron's dicom to nifti converter for preprocessing.


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


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


ExtractMask
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wraps a python script that extracts masks from defaced samples.