Visualization and analysis of diffusion tensor fields

technical reportThe power of medical imaging modalities to measure and characterize biological tissue is amplified by visualization and analysis methods that help researchers to see and understand the structures within their data. Diffusion tensor magnetic resonance imaging can measure microstructural properties of biological tissue, such as the coherent linear organization of white matter of the central nervous system, or the fibrous texture of muscle tissue. This dissertation describes new methods for visualizing and analyzing the salient structure of diffusion tensor datasets. Glyphs from superquadric surfaces and textures from reactiondiffusion systems facilitate inspection of data properties and trends. Fiber tractography based on vector-tensor multiplication allows major white matter pathways to be visualized. The generalization of direct volume rendering to tensor data allows large-scale structures to be shaded and rendered. Finally, a mathematical framework for analyzing the derivatives of tensor values, in terms of shape and orientation change, enables analytical shading in volume renderings, and a method of feature detection important for feature-preserving filtering of tensor fields. Together, the combination of methods enhances the ability of diffusion tensor imaging to provide insight into the local and global structure of biological tissue

On the role of domain-specific knowledge in the visualization of technical flows

In this paper, we present an overview of a number of existing flow visualization methods, developed by the authors in the recent past, that are specifically aimed at integrating and leveraging domain-specific knowledge into the visualization process. These methods transcend the traditional divide between interactive exploration and featurebased schemes and allow a visualization user to benefit from the abstraction properties of feature extraction and topological methods while retaining intuitive and interactive control over the visual analysis process, as we demonstrate on a number of examples

Oriented tensor reconstruction: tracing neural pathways from diffusion tensor MRI

In this paper we develop a new technique for tracing anatomical fibers from 3D tensor fields. The technique extracts salient tensor features using a local regularization technique that allows the algorithm to cross noisy regions and bridge gaps in the data. We applied the method to human brain DT-MRI data and recovered identifiable anatomical structures that correspond to the white matter brain-fiber pathways. The images in this paper are derived from a dataset having 121x88x60 resolution. We were able to recover fibers with less than the voxel size resolution by applying the regularization technique, i.e., using a priori assumptions about fiber smoothness. The regularization procedure is done through a moving least squares filter directly incorporated in the tracing algorithm

Spectral, Combinatorial, and Probabilistic Methods in Analyzing and Visualizing Vector Fields and Their Associated Flows

In this thesis, we introduce several tools, each coming from a different branch of mathematics, for analyzing real vector fields and their associated flows. Beginning with a discussion about generalized vector field decompositions, that mainly have been derived from the classical Helmholtz-Hodge-decomposition, we decompose a field into a kernel and a rest respectively to an arbitrary vector-valued linear differential operator that allows us to construct decompositions of either toroidal flows or flows obeying differential equations of second (or even fractional) order and a rest. The algorithm is based on the fast Fourier transform and guarantees a rapid processing and an implementation that can be directly derived from the spectral simplifications concerning differentiation used in mathematics. Moreover, we present two combinatorial methods to process 3D steady vector fields, which both use graph algorithms to extract features from the underlying vector field. Combinatorial approaches are known to be less sensitive to noise than extracting individual trajectories. Both of the methods are extensions of an existing 2D technique to 3D fields. We observed that the first technique can generate overly coarse results and therefore we present a second method that works using the same concepts but produces more detailed results. Finally, we discuss several possibilities for categorizing the invariant sets with respect to the flow. Existing methods for analyzing separation of streamlines are often restricted to a finite time or a local area. In the frame of this work, we introduce a new method that complements them by allowing an infinite-time-evaluation of steady planar vector fields. Our algorithm unifies combinatorial and probabilistic methods and introduces the concept of separation in time-discrete Markov chains. We compute particle distributions instead of the streamlines of single particles. We encode the flow into a map and then into a transition matrix for each time direction. Finally, we compare the results of our grid-independent algorithm to the popular Finite-Time-Lyapunov-Exponents and discuss the discrepancies. Gauss\'' theorem, which relates the flow through a surface to the vector field inside the surface, is an important tool in flow visualization. We are exploiting the fact that the theorem can be further refined on polygonal cells and construct a process that encodes the particle movement through the boundary facets of these cells using transition matrices. By pure power iteration of transition matrices, various topological features, such as separation and invariant sets, can be extracted without having to rely on the classical techniques, e.g., interpolation, differentiation and numerical streamline integration

Visualization and Analysis of Flow Fields based on Clifford Convolution

Vector fields from flow visualization often containmillions of data values. It is obvious that a direct inspection of the data by the user is tedious. Therefore, an automated approach for the preselection of features is essential for a complete analysis of nontrivial flow fields. This thesis deals with automated detection, analysis, and visualization of flow features in vector fields based on techniques transfered from image processing. This work is build on rotation invariant template matching with Clifford convolution as developed in the diploma thesis of the author. A detailed analysis of the possibilities of this approach is done, and further techniques and algorithms up to a complete segmentation of vector fields are developed in the process. One of the major contributions thereby is the definition of a Clifford Fourier transform in 2D and 3D, and the proof of a corresponding convolution theorem for the Clifford convolution as well as other major theorems. This Clifford Fourier transform allows a frequency analysis of vector fields and the behavior of vectorvalued filters, as well as an acceleration of the convolution computation as a fast transform exists. The depth and precision of flow field analysis based on template matching and Clifford convolution is studied in detail for a specific application, which are flow fields measured in the wake of a helicopter rotor. Determining the features and their parameters in this data is an important step for a better understanding of the observed flow. Specific techniques dealing with subpixel accuracy and the parameters to be determined are developed on the way. To regard the flow as a superposition of simpler features is a necessity for this application as close vortices influence each other. Convolution is a linear system, so it is suited for this kind of analysis. The suitability of other flow analysis and visualization methods for this task is studied here as well. The knowledge and techniques developed for this work are brought together in the end to compute and visualize feature based segmentations of flow fields. The resulting visualizations display important structures of the flow and highlight the interesting features. Thus, a major step towards robust and automatic detection, analysis and visualization of flow fields is taken

Surface-based flow visualization

This is the author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/computers-and-graphics/.With increasing computing power, it is possible to process more complex fluid simulations. However, a gap between increasing\ud data size and our ability to visualize them still remains. Despite the great amount of progress that has been made in the field of\ud flow visualization over the last two decades, a number of challenges remain. Whilst the visualization of 2D flow has many good\ud solutions, the visualization of 3D flow still poses many problems. Challenges such as domain coverage, speed of computation, and\ud perception remain key directions for further research. Flow visualization with a focus on surface-based techniques forms the basis\ud of this literature survey, including surface construction techniques and visualization methods applied to surfaces. We detail our\ud investigation into these algorithms with discussions of their applicability and their relative strengths and drawbacks. We review the\ud most important challenges when considering such visualizations. The result is an up-to-date overview of the current state-of-the-art\ud that highlights both solved and unsolved problems in this rapidly evolving branch of research