BrainSuite Diffusion Pipeline (BDP): Processing tools for diffusion-MRI

Diffusion weighted MRI has uniquely enabled the study of in vivo brain micro-architecture. However, accurate inferences from diffusion weighted images (DWI) require specialized processing. BrainSuite Diffusion Pipeline (BDP) offers an end-to-end processing pipeline for diffusion MRI that includes implementations of established as well as novel processing methods. It allows essential processing steps to correct localized susceptibility-induced geometric distortions, co-register DWI and T1 weighted MRI (T1w-MRI), estimate white matter orientations for tractography and estimate microstructure related quantitative maps. It also includes novel methods including registration-based distortion correction, INVERSION (Inverse contrast Normalization for Very Simple Registration)[2] based T1w-MRI/DWI co-registration and orientation distribution function (ODF) estimators called Funk-Radon and cosine transform (FRACT)[3] and EAP response function optimized (ERFO)[8] ODF, for improved tracking. In addition, BDP seamlessly integrates with BrainSuite's anatomical processing and image analysis tools, namely, Cortical Surface Extraction (CSE), Surface and Volume Registration (SVReg), BrainSuite Statistics toolbox in R (bssr) and graphical interface for visualization. BDP is available as an opensource software for Windows, Linux, MacOS, and is included as part of the BrainSuite BIDS App.[5] An interface is also provided for NiPype.[4]