Multidimensional MRI Core Publications

O'Donnell LJ, Golby AJ, Westin C-F. Fiber Clustering versus the Parcellation-based Connectome. Neuroimage. 2013;80 :283-9.Abstract
We compare two strategies for modeling the connections of the brain's white matter: fiber clustering and the parcellation-based connectome. Both methods analyze diffusion magnetic resonance imaging fiber tractography to produce a quantitative description of the brain's connections. Fiber clustering is designed to reconstruct anatomically-defined white matter tracts, while the parcellation-based white matter segmentation enables the study of the brain as a network. From the perspective of white matter segmentation, we compare and contrast the goals and methods of the parcellation-based and clustering approaches, with special focus on reviewing the field of fiber clustering. We also propose a third category of new hybrid methods that combine the aspects of parcellation and clustering, for joint analysis of connection structure and anatomy or function. We conclude that these different approaches for segmentation and modeling of the white matter can advance the neuroscientific study of the brain's connectivity in complementary ways.
Savadjiev P, Rathi Y, Bouix S, Smith AR, Schultz RT, Verma R, Westin C-F. Combining Surface and Fiber Geometry: An Integrated Approach to Brain Morphology. Med Image Comput Comput Assist Interv. 2013;16 (Pt 1) :50-7.Abstract
Despite the fact that several theories link cortical development and function to the development of white matter and its geometrical structure, the relationship between gray and white matter morphology has not been widely researched. In this paper, we propose a novel framework for investigating this relationship. Given a set of fiber tracts which connect to a particular cortical region, the key idea is to compute two scalar fields that represent geometrical characteristics of the white matter and of the surface of the cortical region. The distributions of these scalar values are then linked via Mutual Information, which results in a quantitative marker that can be used in the study of normal and pathological brain structure and development. We apply this framework to a population study on autism spectrum disorder in children.
Wassermann D, Makris N, Rathi Y, Shenton M, Kikinis R, Kubicki M, Westin C-F. On Describing Human White Matter Anatomy: The White Matter Query Language. Med Image Comput Comput Assist Interv. 2013;16 (Pt 1) :647-54.Abstract

The main contribution of this work is the careful syntactical definition of major white matter tracts in the human brain based on a neuroanatomist's expert knowledge. We present a technique to formally describe white matter tracts and to automatically extract them from diffusion MRI data. The framework is based on a novel query language with a near-to-English textual syntax. This query language allows us to construct a dictionary of anatomical definitions describing white matter tracts. The definitions include adjacent gray and white matter regions, and rules for spatial relations. This enables automated coherent labeling of white matter anatomy across subjects. We use our method to encode anatomical knowledge in human white matter describing 10 association and 8 projection tracts per hemisphere and 7 commissural tracts. The technique is shown to be comparable in accuracy to manual labeling. We present results applying this framework to create a white matter atlas from 77 healthy subjects, and we use this atlas in a proof-of-concept study to detect tract changes specific to schizophrenia.

Wassermann D, Ross J, Washko G, Westin C-F, San José Estépar R. Diffeomorphic Point Set Registration using Non-Stationary Mixture Models. Proc IEEE Int Symp Biomed Imaging. 2013.Abstract

This paper investigates a diffeomorphic point-set registration based on non-stationary mixture models. The goal is to improve the non-linear registration of anatomical structures by representing each point as a general non-stationary kernel that provides information about the shape of that point. Our framework generalizes work done by others that use stationary models. We achieve this by integrating the shape at each point when calculating the point-set similarity and transforming it according to the calculated deformation. We also restrict the non-rigid transform to the space of symmetric diffeomorphisms. Our algorithm is validated in synthetic and human datasets in two different applications: fiber bundle and lung airways registration. Our results shows that non-stationary mixture models are superior to Gaussian mixture models and methods that do not take into account the shape of each point.

Knutsson H, Westin C-F. Tensor Metrics and Charged Containers for 3D Q-space Sample Distribution. Med Image Comput Comput Assist Interv. 2013;16 (Pt 1) :679-86.Abstract
This paper extends Jones' popular electrostatic repulsion based algorithm for distribution of single-shell Q-space samples in two fundamental ways. The first alleviates the single-shell requirement enabling full Q-space sampling. Such an extension is not immediately obvious since it requires distributing samples evenly in 3 dimensions. The extension is as elegant as it is simple: Add a container volume of the desired shape having a constant charge density and a total charge equal to the negative of the sum of the moving point charges. Results for spherical and cubic charge containers are given. The second extension concerns the way distances between sample point are measured. The Q-space samples represent orientation, rather than direction and it would seem appropriate to use a metric that reflects this fact, e.g. a tensor metric. To this end we present a means to employ a generalized metric in the optimization. Minimizing the energy will result in a 3-dimensional distribution of point charges that is uniform in the terms of the specified metric. The radically different distributions generated using different metrics pinpoints a fundamental question: Is there an inherent optimal metric for Q-space sampling? Our work provides a versatile tool to explore the role of different metrics and we believe it will be an important contribution to further the continuing debate and research on the matter.
Rathi Y, Gagoski B, Setsompop K, Michailovich O, Grant EP, Westin C-F. Diffusion Propagator Estimation from Sparse Measurements in a Tractography Framework. Med Image Comput Comput Assist Interv. 2013;16 (Pt 3) :510-7.Abstract
Estimation of the diffusion propagator from a sparse set of diffusion MRI (dMRI) measurements is a field of active research. Sparse reconstruction methods propose to reduce scan time and are particularly suitable for scanning un-coperative patients. Recent work on reconstructing the diffusion signal from very few measurements using compressed sensing based techniques has focussed on propagator (or signal) estimation at each voxel independently. However, the goal of many neuroscience studies is to use tractography to study the pathology in white matter fiber tracts. Thus, in this work, we propose a joint framework for robust estimation of the diffusion propagator from sparse measurements while simultaneously tracing the white matter tracts. We propose to use a novel multi-tensor model of diffusion which incorporates the biexponential radial decay of the signal. Our preliminary results on in-vivo data show that the proposed method produces consistent and reliable fiber tracts from very few gradient directions while simultaneously estimating the bi-exponential decay of the diffusion propagator.
Lemaire J-J, Golby A, Wells III WM, Pujol S, Tie Y, Rigolo L, Yarmarkovich A, Pieper S, Westin C-F, Jolesz FA, et al. Extended Broca's Area in the Functional Connectome of Language in Adults: Combined Cortical and Subcortical Single-subject Analysis using fMRI and DTI Tractography. Brain Topogr. 2013;26 (3) :428-41.Abstract

Traditional models of the human language circuitry encompass three cortical areas, Broca's, Geschwind's and Wernicke's, and their connectivity through white matter fascicles. The neural connectivity deep to these cortical areas remains poorly understood, as does the macroscopic functional organization of the cortico-subcortical language circuitry. In an effort to expand current knowledge, we combined functional MRI (fMRI) and diffusion tensor imaging to explore subject-specific structural and functional macroscopic connectivity, focusing on Broca's area. Fascicles were studied using diffusion tensor imaging fiber tracking seeded from volumes placed manually within the white matter. White matter fascicles and fMRI-derived clusters (antonym-generation task) of positive and negative blood-oxygen-level-dependent (BOLD) signal were co-registered with 3-D renderings of the brain in 12 healthy subjects. Fascicles connecting BOLD-derived clusters were analyzed within specific cortical areas: Broca's, with the pars triangularis, the pars opercularis, and the pars orbitaris; Geschwind's and Wernicke's; the premotor cortex, the dorsal supplementary motor area, the middle temporal gyrus, the dorsal prefrontal cortex and the frontopolar region. We found a functional connectome divisible into three systems-anterior, superior and inferior-around the insula, more complex than previously thought, particularly with respect to a new extended Broca's area. The extended Broca's area involves two new fascicles: the operculo-premotor fascicle comprised of well-organized U-shaped fibers that connect the pars opercularis with the premotor region; and (2) the triangulo-orbitaris system comprised of intermingled U-shaped fibers that connect the pars triangularis with the pars orbitaris. The findings enhance our understanding of language function.

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