5764216
Visualizing Diffusion Tensor MR Images Using Streamtubes and Streamsurfaces
We present a new method for visualizing 3D volumetric diffusion tensor MR images. We distinguish between linear anisotropy and planar anisotropy and represent values in the two regimes using streamtubes and streamsurfaces, respectively. Streamtubes represent structures with primarily linear diffusion, typically fiber tracts; streamtube direction correlates with tract orientation. The cross-sectional shape and color of each streamtube represent additional information from the diffusion tensor at each point. Streamsurfaces represent structures in which diffusion is primarily planar. Our algorithm chooses a very small representative subset of the streamtubes and streamsurfaces for display. We describe the set of metrics used for the culling process, which reduces visual clutter and improves interactivity. We also generate anatomical landmarks to identify the locations of such structures as the eyes, skull surface, and ventricles. The final models are complex surface geometries that can be imported into many interactive graphics software environments. We describe a virtual environment to interact with these models. Expert feedback from doctors studying changes in white-matter structures after gamma-knife capsulotomy and preoperative planning for brain tumor surgery shows that streamtubes correlate well with major neural structures, the 2D section and geometric landmarks are important in understanding the visualization, and the stereo and interactivity from the virtual environment aid in understanding the complex geometric models.
2378459
Visualization of Topological Defects in Nematic Liquid Crystals Using Streamtubes, Streamsurfaces and Ellipsoids
Researchers in computational condensed matter physics deal with complex data sets consisting of time varying 3D tensor, vector, and scalar quantities. Particularly, in the research of topological defects in nematic liquid crystals (LC) displaying the results of the computer simulation of molecular dynamics presents a challenge. Combining existing immersive and interactive visualization methods we developed new methods that attempt to provide a clear, efficient, and intuitive way to visualize and explore LC data. In addition, the visualization of the data has presented us with a novel method of obtaining the locations of the topological defects present in a liquid crystal system.
15381284
Color Rapid Prototyping for Diffusion-Tensor MRI Visualization
We describe work toward creating color rapid prototyping (RP) plaster models as visualization tools to support scientific research in diffusion-tensor (DT) MRI analysis. We currently give surgeons and neurologists virtual-reality (VR) applications to visualize different aspects of their brain data, but having physical representations of those virtual models allows them to review the data with a very robust, natural, and fast haptic interface: their own hands. Our initial results are encouraging, and end users are excited about the possibilities of this technique. For example, using these models in conjunction with digital models on the computer screen or VR environment provides a static frame of reference that helps keep users oriented during their analysis tasks.
5623352
Toward Application of Virtual Reality to Visualization of DT-MRI Volumes
We describe a virtual reality application for visualizing tensor-valued volume data acquired with diffusion tensor magnetic resonance imaging (DT-MRI). We have prototyped a virtual environment that displays geometric representations of the volumetric 2nd-order diffusion tensor data and are developing interaction and visualization techniques for two application areas: studying changes in white-matter structures after gamma-knife capsulotomy and pre-operative planning for brain tumor surgery.
1893178
An immersive virtual environment for DT-MRI volume visualization applications: a case study
We describe a virtual reality environment for visualizing tensor-valued volumetric datasets acquired with diffusion tensor magnetic resonance imaging (DT-MRI). We have prototyped a virtual environment that displays geometric representations of the volumetric second-order diffusion tensor data and are developing interaction and visualization techniques for two application areas: studying changes in white-matter structures after gamma-knife capsulotomy and pre-operative planning for brain tumor surgery. Our feedback shows that compared to desktop displays, our system helps the user better interpret the large and complex geometric models, and facilitates communication among a group of users.
5242506
A Model for Some Subcortical DTI Planar and Linear Anisotropy
Linear anisotropy, planar anisotropy and isotropy [1] are used as metrics for different kinds of diffusion in diffusion imaging. While linear anisotropy is reported to correlate to coherent neural fiber structures, the cause for planar anisotropy remains ambiguous. We hypothesize that overlapping linear structures and partial-volume averaging generate the planar anisotropy. We identify a subcortical region containing both linear and planar anisotropy in a human volumetric diffusion tensor image (DTI), propose a model of the anatomy and of the imaging process, and calculate simulated diffusion images of the anatomical model that qualitatively agree with the human DTI. Regions of planar anisotropy are common immediately beneath the cortex. Choosing one such region as representative, we model the anatomy with isotropic regions and linearly anisotropic structures. From the possibly overlapping model structures we simulate the diffusion imaging process, generating a series of diffusion weighted images (DWIs) of the anatomical structures. We then fit the DTI from these simulated DWIs and visualize it. The visualization agrees qualitatively with the visualization of a subcortical human DTI.
3022359
CVSSearch: searching through source code using CVS comments
CVSSearch is a tool that searches for fragments of source code by using CVS comments. CVS is a version control system that is widely used in the open source community. Our search tool takes advantage of the fact that a CVS comment typically describes the lines of code involved in the commit and this description will typically hold for many future versions. In other words, CVSSearch allows one to better search the most recent version of the code by looking at previous versions to better understand the current version. In this paper we describe our algorithm for mapping CVS comments to the corresponding source code, present a search tool based on this technique, and discuss preliminary feedback.
40273501
Pattern Discovery in Probabilistic Databases
Modeling probabilistic data is one of important issues in databases due to the fact that data is often uncertainty in real-world applications. So, it is necessary to identify potentially useful patterns in probabilistic databases. Because probabilistic data in 1NF relations is redundant, previous mining techniques don't work well on probabilistic databases. For this reason, this paper proposes a new model for mining probabilistic databases. A partition is thus developed for preprocessing probabilistic data in a probabilistic databases. We evaluated the proposed technique, and the experimental results demonstrate that our approach is effective and efficient.
29457354
A novel shape matching method using biological sequence dynamic alignment
Shape description and its corresponding matching algorithm is one of the main concerns in MPEG-7. A novel dynamic shape matching algorithm is proposed. First, the conventional 8-directional chain code is exploited to describe the binary shape. A dynamic shape matching algorithm, which is derived from the solution for the biological sequence similarity analysis based on molecular evolutionary theory, is proposed to measure the similarity distance between the shapes by computing their similarity score (SS). Based on a large set of MPEG-7 binary shapes, simulation results have shown that the proposed dynamic alignment matching algorithm is fairly promising and also robust to scale changes, small non-rigid deformation, and similarity based shape matching defined in MPEG-7 core experiments.
13607587
Heavy cycles passing through some specified vertices in weighted graphs
A weighted graph is one in which every edge e is assigned a nonnegative number, called the weight of e. The sum of the weights of the edges incident with a vertex v is called the weighted degree of v. The weight of a cycle is defined as the sum of the weights of its edges. In this paper, we prove that: (1) if G is a 2-connected weighted graph such that the minimum weighted degree of G is at least d, then for every given vertices x and y, either G contains a cycle of weight at least 2d passing through both of x and y or every heaviest cycle in G is a hamiltonian cycle, and (2) if G is a 2-connected weighted graph such that the weighted degree sum of every pair of nonadjacent vertices is at least s, then for every vertex y, G contains either a cycle of weight at least s passing through y or a hamiltonian cycle. AMS classification: 05C45 05C38 05C35
1826127
On a Family-Based Haplotype Pattern Mining Method for Linkage Disequilibrium Mapping
Linkage disequilibrium mapping is an important tool in disease gene mapping. Recently, Toivonen et al. [1] introduced a haplotype mining (HPM) method that is applicable to data consisting of unrelated high-risk and normal haplotypes. The HPM method orders haplotypes by their strength of association with trait values, and uses all haplotypes exceeding a given threshold of strength of association to predict the gene location. In this study, we extend the HPM method to pedigree data by measuring the strength of association between a haplotype and quantitative traits of interest using the Quantitative Pedigree Disequilibrium Test proposed by Zhang et al. [2]. This family-based HPM (F-HPM) method can incorporate haplotype information across a set of markers and allow both missing marker data and ambiguous haplotype information. We use a simulation procedure to evaluate the statistical significance of the patterns identified from the F-HPM method. When the F-HPM method is applied to analyze the sequence data from the seven candidate genes in the simulated data sets in the 12th Genetic Analysis Workshop, the association between genes and traits can be detected with high power, and the estimated locations of the trait loci are close to the true sites.