Comparison of Distances for Supervised Segmentation of White Matter Tractography

Tractograms are mathematical representations of the main paths of axons within the white matter of the brain, from diffusion MRI data. Such representations are in the form of polylines, called streamlines, and one streamline approximates the common path of tens of thousands of axons. The analysis of tractograms is a task of interest in multiple fields, like neurosurgery and neurology. A basic building block of many pipelines of analysis is the definition of a distance function between streamlines. Multiple distance functions have been proposed in the literature, and different authors use different distances, usually without a specific reason other than invoking the "common practice". To this end, in this work we want to test such common practices, in order to obtain factual reasons for choosing one distance over another. For these reasons, in this work we compare many streamline distance functions available in the literature. We focus on the common task of automatic bundle segmentation and we adopt the recent approach of supervised segmentation from expert-based examples. Using the HCP dataset, we compare several distances obtaining guidelines on the choice of which distance function one should use for supervised bundle segmentation

Autotract: Automatic cleaning and tracking of fibers

We propose a new tool named Autotract to automate fiber tracking in diffusion tensor imaging (DTI). Autotract uses prior knowledge from a source DTI and a set of corresponding fiber bundles to extract new fibers for a target DTI. Autotract starts by aligning both DTIs and uses the source fibers as seed points to initialize a tractography algorithm. We enforce similarity between the propagated source fibers and automatically traced fibers by computing metrics such as fiber length and fiber distance between the bundles. By analyzing these metrics, individual fiber tracts can be pruned. As a result, we show that both bundles have similar characteristics. Additionally, we compare the automatically traced fibers against bundles previously generated and validated in the target DTI by an expert. This work is motivated by medical applications in which known bundles of fiber tracts in the human brain need to be analyzed for multiple datasets

Mapping Topographic Structure in White Matter Pathways with Level Set Trees

Fiber tractography on diffusion imaging data offers rich potential for describing white matter pathways in the human brain, but characterizing the spatial organization in these large and complex data sets remains a challenge. We show that level set trees---which provide a concise representation of the hierarchical mode structure of probability density functions---offer a statistically-principled framework for visualizing and analyzing topography in fiber streamlines. Using diffusion spectrum imaging data collected on neurologically healthy controls (N=30), we mapped white matter pathways from the cortex into the striatum using a deterministic tractography algorithm that estimates fiber bundles as dimensionless streamlines. Level set trees were used for interactive exploration of patterns in the endpoint distributions of the mapped fiber tracks and an efficient segmentation of the tracks that has empirical accuracy comparable to standard nonparametric clustering methods. We show that level set trees can also be generalized to model pseudo-density functions in order to analyze a broader array of data types, including entire fiber streamlines. Finally, resampling methods show the reliability of the level set tree as a descriptive measure of topographic structure, illustrating its potential as a statistical descriptor in brain imaging analysis. These results highlight the broad applicability of level set trees for visualizing and analyzing high-dimensional data like fiber tractography output

EXTRACTING FLOW FEATURES USING BAG-OF-FEATURES AND SUPERVISED LEARNING TECHNIQUES

Measuring the similarity between two streamlines is fundamental to many important flow data analysis and visualization tasks such as feature detection, pattern querying and streamline clustering. This dissertation presents a novel streamline similarity measure inspired by the bag-of-features concept from computer vision. Different from other streamline similarity measures, the proposed one considers both the distribution of and the distances among features along a streamline. The proposed measure is tested in two common tasks in vector field exploration: streamline similarity query and streamline clustering. Compared with a recent streamline similarity measure, the proposed measure allows users to see the interesting features more clearly in a complicated vector field. In addition to focusing on similar streamlines through streamline similarity query or clustering, users sometimes want to group and see similar features from different streamlines. For example, it is useful to find all the spirals contained in different streamlines and present them to users. To this end, this dissertation proposes to segment each streamline into different features. This problem has not been studied extensively in flow visualization. For instance, many flow feature extraction techniques segment streamline based on simple heuristics such as accumulative curvature or arc length, and, as a result, the segments they found usually do not directly correspond to complete flow features. This dissertation proposes a machine learning-based streamline segmentation algorithm to segment each streamline into distinct features. It is shown that the proposed method can locate interesting features (e.g., a spiral in a streamline) more accurately than some other flow feature extraction methods. Since streamlines are space curves, the proposed method also serves as a general curve segmentation method and may be applied in other fields such as computer vision. Besides flow visualization, a pedagogical visualization tool DTEvisual for teaching access control is also discussed in this dissertation. Domain Type Enforcement (DTE) is a powerful abstraction for teaching students about modern models of access control in operating systems. With DTEvisual, students have an environment for visualizing a DTE-based policy using graphs, visually modifying the policy, and animating the common DTE queries in real time. A user study of DTEvisual suggests that the tool is helpful for students to understand DTE

MODELING AND QUANTITATIVE ANALYSIS OF WHITE MATTER FIBER TRACTS IN DIFFUSION TENSOR IMAGING

Diffusion tensor imaging (DTI) is a structural magnetic resonance imaging (MRI) technique to record incoherent motion of water molecules and has been used to detect micro structural white matter alterations in clinical studies to explore certain brain disorders. A variety of DTI based techniques for detecting brain disorders and facilitating clinical group analysis have been developed in the past few years. However, there are two crucial issues that have great impacts on the performance of those algorithms. One is that brain neural pathways appear in complicated 3D structures which are inappropriate and inaccurate to be approximated by simple 2D structures, while the other involves the computational efficiency in classifying white matter tracts. The first key area that this dissertation focuses on is to implement a novel computing scheme for estimating regional white matter alterations along neural pathways in 3D space. The mechanism of the proposed method relies on white matter tractography and geodesic distance mapping. We propose a mask scheme to overcome the difficulty to reconstruct thin tract bundles. Real DTI data are employed to demonstrate the performance of the pro- posed technique. Experimental results show that the proposed method bears great potential to provide a sensitive approach for determining the white matter integrity in human brain. Another core objective of this work is to develop a class of new modeling and clustering techniques with improved performance and noise resistance for separating reconstructed white matter tracts to facilitate clinical group analysis. Different strategies are presented to handle different scenarios. For whole brain tractography reconstructed white matter tracts, a Fourier descriptor model and a clustering algorithm based on multivariate Gaussian mixture model and expectation maximization are proposed. Outliers are easily handled in this framework. Real DTI data experimental results show that the proposed algorithm is relatively effective and may offer an alternative for existing white matter fiber clustering methods. For a small amount of white matter fibers, a modeling and clustering algorithm with the capability of handling white matter fibers with unequal length and sharing no common starting region is also proposed and evaluated with real DTI data

Segmentation des fibres de la matière blanche

Ce mémoire porte sur la segmentation des fibres de la matière blanche et sur le développement d'outils visuels permettant d'interagir avec les résultats. Pour y parvenir, une métrique innovatrice permettant de quantifier la différence entre deux fibres de la matière blanche est créée. Cette mesure fait appel à des notions de multirésolution, de courbure, de torsion afin de caractériser la forme géométrique d'une fibre. Elle regroupe également des mesures plus simples telles la distance du cosinus, la distance euclidienne entre les centres de masse et la différence des longueurs d'arc pour capter respectivement l'orientation, la translation et la taille d'une fibre. Ensuite, une nouvelle technique de segmentation permettant de gérer des quantités importantes de données est développée. Finalement, ces nouvelles méthodes sont validées sur différents jeux de données

ENABLING TECHNIQUES FOR EXPRESSIVE FLOW FIELD VISUALIZATION AND EXPLORATION

Flow visualization plays an important role in many scientific and engineering disciplines such as climate modeling, turbulent combustion, and automobile design. The most common method for flow visualization is to display integral flow lines such as streamlines computed from particle tracing. Effective streamline visualization should capture flow patterns and display them with appropriate density, so that critical flow information can be visually acquired. In this dissertation, we present several approaches that facilitate expressive flow field visualization and exploration. First, we design a unified information-theoretic framework to model streamline selection and viewpoint selection as symmetric problems. Two interrelated information channels are constructed between a pool of candidate streamlines and a set of sample viewpoints. Based on these information channels, we define streamline information and viewpoint information to select best streamlines and viewpoints, respectively. Second, we present a focus+context framework to magnify small features and reduce occlusion around them while compacting the context region in a full view. This framework parititions the volume into blocks and deforms them to guide streamline repositioning. The desired deformation is formulated into energy terms and achieved by minimizing the energy function. Third, measuring the similarity of integral curves is fundamental to many tasks such as feature detection, pattern querying, streamline clustering and hierarchical exploration. We introduce FlowString that extracts shape invariant features from streamlines to form an alphabet of characters, and encodes each streamline into a string. The similarity of two streamline segments then becomes a specially designed edit distance between two strings. Leveraging the suffix tree, FlowString provides a string-based method for exploratory streamline analysis and visualization. A universal alphabet is learned from multiple data sets to capture basic flow patterns that exist in a variety of flow fields. This allows easy comparison and efficient query across data sets. Fourth, for exploration of vascular data sets, which contain a series of vector fields together with multiple scalar fields, we design a web-based approach for users to investigate the relationship among different properties guided by histograms. The vessel structure is mapped from the 3D volume space to a 2D graph, which allow more efficient interaction and effective visualization on websites. A segmentation scheme is proposed to divide the vessel structure based on a user specified property to further explore the distribution of that property over space

Learning motion patterns using hierarchical Bayesian models

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.Cataloged from PDF version of thesis.Includes bibliographical references (p. 163-179).In far-field visual surveillance, one of the key tasks is to monitor activities in the scene. Through learning motion patterns of objects, computers can help people understand typical activities, detect abnormal activities, and learn the models of semantically meaningful scene structures, such as paths commonly taken by objects. In medical imaging, some issues similar to learning motion patterns arise. Diffusion Tensor Magnetic Resonance Imaging (DT-MRI) is one of the first methods to visualize and quantify the organization of white matter in the brain in vivo. Using methods of tractography segmentation, one can connect local diffusion measurements to create global fiber trajectories, which can then be clustered into anatomically meaningful bundles. This is similar to clustering trajectories of objects in visual surveillance. In this thesis, we develop several unsupervised frameworks to learn motion patterns from complicated and large scale data sets using hierarchical Bayesian models. We explore their applications to activity analysis in far-field visual surveillance and tractography segmentation in medical imaging. Many existing activity analysis approaches in visual surveillance are ad hoc, relying on predefined rules or simple probabilistic models, which prohibits them from modeling complicated activities. Our hierarchical Bayesian models can structure dependency among a large number of variables to model complicated activities. Various constraints and knowledge can be nicely added into a Bayesian framework as priors. When the number of clusters is not well defined in advance, our nonparametric Bayesian models can learn it driven by data with Dirichlet Processes priors.(cont.) In this work, several hierarchical Bayesian models are proposed considering different types of scenes and different settings of cameras. If the scenes are crowded, it is difficult to track objects because of frequent occlusions and difficult to separate different types of co-occurring activities. We jointly model simple activities and complicated global behaviors at different hierarchical levels directly from moving pixels without tracking objects. If the scene is sparse and there is only a single camera view, we first track objects and then cluster trajectories into different activity categories. In the meanwhile, we learn the models of paths commonly taken by objects. Under the Bayesian framework, using the models of activities learned from historical data as priors, the models of activities can be dynamically updated over time. When multiple camera views are used to monitor a large area, by adding a smoothness constraint as a prior, our hierarchical Bayesian model clusters trajectories in multiple camera views without tracking objects across camera views. The topology of multiple camera views is assumed to be unknown and arbitrary. In tractography segmentation, our approach can cluster much larger scale data sets than existing approaches and automatically learn the number of bundles from data. We demonstrate the effectiveness of our approaches on multiple visual surveillance and medical imaging data sets.by Xiaogang Wang.Ph.D