Beyond Crossing Fibers: Bootstrap Probabilistic Tractography Using Complex Subvoxel Fiber Geometries

Diffusion magnetic resonance imaging fiber tractography is a powerful tool for investigating human white matter connectivity in vivo. However, it is prone to false positive and false negative results, making interpretation of the tractography result difficult. Optimal tractography must begin with an accurate description of the subvoxel white matter fiber structure, includes quantification of the uncertainty in the fiber directions obtained, and quantifies the confidence in each reconstructed fiber tract. This paper presents a novel and comprehensive pipeline for fiber tractography that meets the above requirements. The subvoxel fiber geometry is described in detail using a technique that allows not only for straight crossing fibers but for fibers that curve and splay. This technique is repeatedly performed within a residual bootstrap statistical process in order to efficiently quantify the uncertainty in the subvoxel geometries obtained. A robust connectivity index is defined to quantify the confidence in the reconstructed connections. The tractography pipeline is demonstrated in the human brain

Local white matter geometry from diffusion tensor gradients

We introduce a mathematical framework for computing geometrical properties of white matter fibres directly from diffusion tensor fields. The key idea is to isolate the portion of the gradient of the tensor field corresponding to local variation in tensor orientation, and to project it onto a coordinate frame of tensor eigenvectors. The resulting eigenframe-centered representation then makes it possible to define scalar indices (or measures) that describe the local white matter geometry directly from the diffusion tensor field and its gradient, without requiring prior tractography. We derive new scalar indices of (1) fibre dispersion and (2) fibre curving, and we demonstrate them on synthetic and in vivo data. Finally, we illustrate their applicability to a group study on schizophrenia

Structural connectivity of cytoarchitectonically distinct human left temporal pole subregions: a diffusion MRI tractography study

The temporal pole (TP) is considered one of the major paralimbic cortical regions, and is involved in a variety of functions such as sensory perception, emotion, semantic processing, and social cognition. Based on differences in cytoarchitecture, the TP can be further subdivided into smaller regions (dorsal, ventrolateral and ventromedial), each forming key nodes of distinct functional networks. However, the brain structural connectivity profile of TP subregions is not fully clarified. Using diffusion MRI data in a set of 31 healthy subjects, we aimed to elucidate the comprehensive structural connectivity of three cytoarchitectonically distinct TP subregions. Diffusion tensor imaging (DTI) analysis suggested that major association fiber pathways such as the inferior longitudinal, middle longitudinal, arcuate, and uncinate fasciculi provide structural connectivity to the TP. Further analysis suggested partially overlapping yet still distinct structural connectivity patterns across the TP subregions. Specifically, the dorsal subregion is strongly connected with wide areas in the parietal lobe, the ventrolateral subregion with areas including constituents of the default-semantic network, and the ventromedial subregion with limbic and paralimbic areas. Our results suggest the involvement of the TP in a set of extensive but distinct networks of cortical regions, consistent with its functional roles

Localized abnormalities in the cingulum bundle in patients with schizophrenia: A Diffusion Tensor tractography study

The cingulum bundle (CB) connects gray matter structures of the limbic system and as such has been implicated in the etiology of schizophrenia. There is growing evidence to suggest that the CB is actually comprised of a conglomeration of discrete sub-connections. The present study aimed to use Diffusion Tensor tractography to subdivide the CB into its constituent sub-connections, and to investigate the structural integrity of these sub-connections in patients with schizophrenia and matched healthy controls. Diffusion Tensor Imaging scans were acquired from 24 patients diagnosed with chronic schizophrenia and 26 matched healthy controls. Deterministic tractography was used in conjunction with FreeSurfer-based regions-of-interest to subdivide the CB into 5 sub-connections (I1 to I5). The patients with schizophrenia exhibited subnormal levels of FA in two cingulum sub-connections, specifically the fibers connecting the rostral and caudal anterior cingulate gyrus (I1) and the fibers connecting the isthmus of the cingulate with the parahippocampal cortex (I4). Furthermore, while FA in the I1 sub-connection was correlated with the severity of patients' positive symptoms (specifically hallucinations and delusions), FA in the I4 sub-connection was correlated with the severity of patients' negative symptoms (specifically affective flattening and anhedonia/asociality). These results support the notion that the CB is a conglomeration of structurally interconnected yet functionally distinct sub-connections, of which only a subset are abnormal in patients with schizophrenia. Furthermore, while acknowledging the fact that the present study only investigated the CB, these results suggest that the positive and negative symptoms of schizophrenia may have distinct neurobiological underpinnings

Gray matter alterations in early aging: A diffusion magnetic resonance imaging study

Many studies have observed altered neurofunctional and structural organization in the aging brain. These observations from functional neuroimaging studies show a shift in brain activity from the posterior to the anterior regions with aging (PASA model), as well as a decrease in cortical thickness, which is more pronounced in the frontal lobe followed by the parietal, occipital, and temporal lobes (retrogenesis model). However, very little work has been done using diffusion MRI (dMRI) with respect to examining the structural tissue alterations underlying these neurofunctional changes in the gray matter. Thus, for the first time, we propose to examine gray matter changes using diffusion MRI in the context of aging. In this work, we propose a novel dMRI based measure of gray matter “heterogeneity” that elucidates these functional and structural models (PASA and retrogenesis) of aging from the viewpoint of diffusion MRI. In a cohort of 85 subjects (all males, ages 15–55 years), we show very high correlation between age and “heterogeneity” (a measure of structural layout of tissue in a region-of-interest) in specific brain regions. We examine gray matter alterations by grouping brain regions into anatomical lobes as well as functional zones. Our findings from dMRI data connects the functional and structural domains and confirms the “retrogenesis” hypothesis of gray matter alterations while lending support to the neurofunctional PASA model of aging in addition to showing the preservation of paralimbic areas during healthy aging

Surface recovery from three-dimensional point data

The reconstruction of 3D surface models from incomplete data is a fundamental problem in computer vision, and has been investigated for years. The goal of the research presented in this thesis is to examine novel ways of solving the problem of surface reconstruction from 3D point data sets. The approach to surface recovery presented here combines two different philosophies, that of a parametric reconstruction approach, and that of a geometric flow reconstruction approach. Many algorithms for surface recovery are based on either one of the two types of approaches, but few have attempted to bring the two together in order to combine their advantages.This thesis introduces a novel hybrid algorithm for surface recovery. The motivation is to demonstrate that the inclusion of structural information through the use of local data parameterization can improve the behaviour of flow-based algorithms for surface reconstruction. The key ideas are to tailor a curvature consistency algorithm to the case of a set of points in 3D and to then incorporate a flux maximizing geometric flow for surface reconstruction. This hybrid method is specifically designed to preserve discontinuities in 3D, to be robust to noise, and to reconstruct objects with arbitrary topologies. The approach is illustrated with experimental results on a variety of data sets

On the Differential Geometry of 3D Flow Patterns: Generalized Helicoids and Diffusion MRI Analysis

Configurations of dense locally parallel 3D curves occur in medical imaging, computer vision and graphics. Examples include white matter fibre tracts, textures, fur and hair. We develop a differential geometric characterization of such structures by considering the local behaviour of the associated 3D frame field, leading to the associated tangential, normal and bi-normal curvature functions. Using results from the theory of generalized minimal surfaces we adopt a generalized helicoid model as an osculating object and develop the connection between its parameters and these curvature functions. These developments allow for the construction of parametrized 3D vector fields (sampled osculating objects) to locally approximate these patterns. We apply these results to the analysis of diffusion MRI data via a type of 3D streamline flow. Experimental results on data from a human brain demonstrate the advantages of incorporating the full differential geometry. 1

DECT-CLUST: Dual-Energy CT Image Clustering and Application to Head and Neck Squamous Cell Carcinoma Segmentation

Dual-energy computed tomography (DECT) is an advanced CT computed tomography scanning technique enabling material characterization not possible with conventional CT scans. It allows the reconstruction of energy decay curves at each 3D image voxel, representing varied image attenuation at different effective scanning energy levels. In this paper, we develop novel unsupervised learning techniques based on mixture models and functional data analysis models to the clustering of DECT images. We design functional mixture models that integrate spatial image context in mixture weights, with mixture component densities being constructed upon the DECT energy decay curves as functional observations. We develop dedicated expectation–maximization algorithms for the maximum likelihood estimation of the model parameters. To our knowledge, this is the first article to develop statistical functional data analysis and model-based clustering techniques to take advantage of the full spectral information provided by DECT. We evaluate the application of DECT to head and neck squamous cell carcinoma. Current image-based evaluation of these tumors in clinical practice is largely qualitative, based on a visual assessment of tumor anatomic extent and basic one- or two-dimensional tumor size measurements. We evaluate our methods on 91 head and neck cancer DECT scans and compare our unsupervised clustering results to tumor contours traced manually by radiologists, as well as to several baseline algorithms. Given the inter-rater variability even among experts at delineating head and neck tumors, and given the potential importance of tissue reactions surrounding the tumor itself, our proposed methodology has the potential to add value in downstream machine learning applications for clinical outcome prediction based on DECT data in head and neck cancer

Insights into the Brain: Neuroimaging of Brain Development and Maturation

The study of how the human brain develops has always been a challenge and an interest to the scientific community. In recent years, new evidence has suggested that many neuropsychiatric disorders may originate from aberrations early in development. This discovery necessitates the application of methodologies that make possible the investigation of human brain development in vivo and across the lifespan. In this commentary, we present evidence that the advent of structural neuroimaging has specifically and significantly contributed critical information about the developmental trajectories of postnatal human brain development that would otherwise not have been possible. We believe that this is particularly relevant to present day research as it has become increasingly clear that growth trajectories within the brain might serve as an endophenotype for a number of factors, ranging from IQ to psychiatric illness. We highlight seminal early works that helped to jumpstart the field of developmental neuroimaging and which inspired incredible new advances in neuroimaging methodologies that are being developed and applied in the field today