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StdDTIPreprocessing Pipeline

Pipeline: StdDTIPreprocessing

Type: DTI

Description: Pipeline to preprocess DTI scan types

Source: Xue Wang, NU Department of Radiology, Todd Parrish group

Estimation of Diffusion Tensor with FSL's Diffusion Toolbox (FDT), Generates FA and MD maps, eigenvalues and eigenvectors.

Steps (all FSL except for rotbvecs, which is custom)
1. (optional) fslmerge
2. fslroi (get the no diffusion volume)
3. bet (get the brain mask based on the no diffusion volume)
4. eddy_correct (eddy current correction)
5. rotbvecs (rotate bvecs)
6. dtifit (fit the diffusion model to get MD, FA maps etc)