title: Software-based Diffusion MR Human Brain Phantom for Evaluating Fiber-tracking Algorithms.
abstract: Fiber tracking provides insights into the brain white matter network and has become more and more popular in diffusion MR imaging. Hardware or software phantom provides an essential platform to investigate, validate and compare various tractography algorithms towards a "gold standard". Software phantoms excel due to their flexibility in varying imaging parameters, such as tissue composition, SNR, as well as potential to model various anatomies and pathologies. This paper describes a novel method in generating diffusion MR images with various imaging parameters from realistically appearing, individually varying brain anatomy based on predefined fiber tracts within a high-resolution human brain atlas. Specifically, joint, high resolution DWI and structural MRI brain atlases were constructed with images acquired from 6 healthy subjects (age 22-26) for the DWI data and 56 healthy subject (age 18-59) for the structural MRI data. Full brain fiber tracking was performed with filtered, two-tensor tractography in atlas space. A deformation field based principal component model from the structural MRI as well as unbiased atlas building was then employed to generate synthetic structural brain MR images that are individually varying. Atlas fiber tracts were accordingly warped into each synthetic brain anatomy. Diffusion MR images were finally computed from these warped tracts via a composite hindered and restricted model of diffusion with various imaging parameters for gradient directions, image resolution and SNR. Furthermore, an open-source program was developed to evaluate the fiber tracking results both qualitatively and quantitatively based on various similarity measures.
authors.affiliation: Department of Psychiatry, University of North Carolina at Chapel Hill.
authors.forename: Yundi
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Department of Psychiatry, University of North Carolina at Chapel Hill.
authors.forename: Gwendoline
authors.initials: G
authors.lastname: Roger
authors.affiliation: Department of Psychiatry, University of North Carolina at Chapel Hill.
authors.forename: Clement
authors.initials: C
authors.lastname: Vachet
authors.affiliation: Department of Psychiatry, University of North Carolina at Chapel Hill.
authors.forename: Francois
authors.initials: F
authors.lastname: Budin
authors.affiliation: Department of Psychiatry, University of North Carolina at Chapel Hill.
authors.forename: Eric
authors.initials: E
authors.lastname: Maltbie
authors.affiliation: Department of Psychiatry, University of North Carolina at Chapel Hill.
authors.forename: Audrey
authors.initials: A
authors.lastname: Verde
authors.affiliation: Department of Psychiatry, University of North Carolina at Chapel Hill.
authors.forename: Marion
authors.initials: M
authors.lastname: Hoogstoel
authors.affiliation: Department of Psychiatry, University of North Carolina at Chapel Hill.
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Berger
authors.affiliation: Department of Psychiatry, University of North Carolina at Chapel Hill ; Department of Computer Science, University of North Carolina at Chapel Hill.
authors.forename: Martin
authors.initials: M
authors.lastname: Styner
keywords: Atlas; Diffusion-weighted MRI; Fiber tracking; Phantom; Tractography; Validation