Reconstruction of the human cerebral cortex from magnetic resonance images
Reconstructing the geometry of the human cerebral cortex from MR images is an important step in both brain mapping and surgical path planning applications. Difficulties with imaging noise, partial volume averaging, image intensity inhomogeneities, convoluted cortical structures, and the requirement to preserve anatomical topology make the development of accurate automated algorithms particularly challenging. Here the authors address each of these problems and describe a systematic method for obtaining a surface representation of the geometric central layer of the human cerebral cortex. Using fuzzy segmentation, an isosurface algorithm, and a deformable surface model, the method reconstructs the entire cortex with the correct topology, including deep convoluted sulci and gyri. The method is largely automated and its results are robust to imaging noise, partial volume averaging, and image intensity inhomogeneities. The performance of this method is demonstrated, both qualitatively and quantitatively, and the results of its application to six subjects and one simulated MR brain volume are presented.

title: A 2D moving grid geometric deformable model
abstract: Geometric deformable models based on the level set method have become very popular. To overcome an inherent limitation in accuracy while maintaining computational efficiency, adaptive grid techniques using local grid refinement have been developed for use with these models. However, this strategy requires a very complex data structure, yields large numbers of contour points, and is inconsistent with our previously presented topology-preserving geometric deformable model (TGDM). In this paper, we incorporate an alternative adaptive grid technique called the moving grid method into the geometric deformable model framework. We find that it is simpler to implement than grid refinement, requiring no large, complex, hierarchical data structures. It also limits the number of contour vertices in the final contour and supports the incorporation of the topology-preserving constraint of TGDM. After presenting the algorithm, we demonstrate its performance using both simulated and real images.

title: Reconstruction of the Central Layer of the Human Cerebral Cortex from MR Images
abstract: Reconstruction of the human cerebral cortex from MR images is a fundamental step in human brain mapping and in applications such as surgical path planning. In a previous paper, we described a method for obtaining a surface representation of the central layer of the human cerebral cortex using fuzzy segmentation and a deformable surface model. This method, however, suffers from several problems. In this paper, we significantly improve upon the previous method by using a fuzzy segmentation algorithm robust to intensity inhomogeneities, and using a deformable surface model specifically designed for capturing convoluted sulci or gyri. We demonstrate the improvement over the previous method both qualitatively and quantitatively, and show the result of its application to six subjects. We also experimentally validate the convergence of the deformable surface initialization algorithm.

title: Snakes, shapes, and gradient vector flow
abstract: Snakes, or active contours, are used extensively in computer vision and image processing applications, particularly to locate object boundaries. Problems associated with initialization and poor convergence to boundary concavities, however, have limited their utility. This paper presents a new external force for active contours, largely solving both problems. This external force, which we call gradient vector flow (GVF), is computed as a diffusion of the gradient vectors of a gray-level or binary edge map derived from the image. It differs fundamentally from traditional snake external forces in that it cannot be written as the negative gradient of a potential function, and the corresponding snake is formulated directly from a force balance condition rather than a variational formulation. Using several two-dimensional (2-D) examples and one three-dimensional (3-D) example, we show that GVF has a large capture range and is able to move snakes into boundary concavities.

title: Finding the Brain Cortex Using Fuzzy Segmentation, Isosurfaces, and Deformable Surface Models
abstract: A method for finding the cortical surface of the brain from magnetic resonance images using a combination of fuzzy segmentation, isosurface extraction, and a deformable surface is presented. After MR images are acquired and preprocessed to remove extracranial tissue, fuzzy membership functions for gray matter, white matter, and cerebrospinal fluid are computed. An iterative procedure using isosurfaces of filtered white matter membership functions is then used to obtain a topologically correct estimate of the cortical surface. This estimate forms the initialization of a deformable surface, which is then allowed to converge to peaks of the gray matter membership function. We demonstrate the results of each step and show the final parameterized map of the medial layer of the cortex.

title: A topology preserving deformable model using level sets
abstract: Active contour and surface models, also known as deformable models, constitute a class of powerful segmentation techniques. Geometric deformable models implemented via level-set methods have advantages over parametric ones due to their intrinsic behavior, parameterization independence, and ease of implementation. However, a long claimed advantage of geometric deformable models, the ability to automatically handle topology changes, turns out to be a liability in applications where the objects to be segmented have a known topology that must be preserved. In this paper, we present a geometric deformable model that preserves topology using the simple point concept from digital topology. This algorithm maintains the other advantages of standard geometric deformable models including sub-pixel accuracy and production of nonintersecting curves (or surfaces). Several experiments on simulated and real data are provided to demonstrate the performance of the proposed algorithm.

title: eQoS: Provisioning of Client-Perceived End-to-End QoS Guarantees in Web Servers
abstract: It is important to guarantee client-perceived end-to-end quality of service (QoS) under heavy load conditions. Existing work focuses on network transfer time or server-side request processing time. In this paper, we propose a novel framework, eQoS, to monitor and control client-perceived response time in heavy loaded Web servers. The response time is measured with respect to Web pages that contain multiple embedded objects. Within the framework, we propose an adaptive fuzzy controller, STFC, to allocate server resources. The controller assumes no knowledge of the pageview traffic model. It deals with the effect of process delay in resource allocation by its two-level self-tuning capabilities. We also prove the stability of the STFC. We implement a prototype of eQoS in Linux and conduct comprehensive experiments across wide-range server workload conditions on PlanetLab and simulated networks. Experimental results demonstrate the effectiveness of the framework: it controls the deviation of client-perceived pageview response time to be within 20 percent of a predefined target with both synthetic and real Web traffics. We also compare the STFC with other controllers, including static fuzzy, linear proportional integral (PI), and adaptive PI controllers. Experimental results show that, although the STFC works slightly worse than the static fuzzy controller in the environment where the static fuzzy controller is best tuned, because of its self-tuning capabilities, it has better performance in all other test cases by around 25 percent on average in terms of the deviation from the target response time. In addition, due to its model independence, the STFC outperforms the linear PI and adaptive PI controllers by 50 percent and 75 percent on average, respectively

title: Relaxed Implementation of Spectral Methods for Graph Partitioning
abstract: This paper presents a fast implementation of the recursive spectral bisection method for p-way partitioning. It is known that recursive bisections for p-way partitioning using optimal strategies at each step may not lead to a good overall solution. The relaxed implementation accelerates the partitioning process by relaxing the accuracy requirement of spectral bisection (SB) method. Considering the solution quality of a SB method on a graph is primarily determined by the accuracy of its Fiedler vector, we propose to set a tight iteration number bound and a loose residual tolerance for Lanczos algorithms to compute the Fiedler vector. The relaxed SB was tested on eight representative meshes from different applications. Experimental results show that the relaxed SB on six meshes produces approximately equivalent quality solutions as the Chaco SB while gaining 10% to 35% improvements in execution time. On the other two meshes, the relaxed SB approaches the Chaco SB in quality as p increases and reduces the execution time by 40% to 70%. Coupled with the Kernighan-Lin local refinement algorithm, the relaxed SB is able to yield high quality solutions in all test cases as p goes beyond 32. Multilevel and spectral quadrisection algorithms benefit from relaxed implementations, as well.

title: Design and evaluation of an environment APE for automatic parallelization of programs
abstract: In this paper, we present the design and evaluation of a compiler system, called APE, for automatic parallelization of scientific and engineering applications on distributed memory computers. APE is built on top of SUIF compiler. It extends SUIF with capabilities in parallelizing loops with non-uniform cross-iteration dependencies, and in handling loops that have indirect access patterns. We have evaluated the effectiveness of SUIF with several CFD test codes, and found that SUIF handles uniform loops over dense and regular data structures very well. For non-uniform loops, an innovative and efficient parallelization approach based on convex theory have been proposed and is being implemented. We have also presented a class of scalable algorithms for parallel distribution and redistribution of unstructured data structures during parallelizing irregular loops.

title: Time-stamping algorithms for parallelization of loops at run-time
abstract: In this paper we present two new run-time algorithms for the parallelization of loops that have indirect access patterns. The algorithms can handle any type of loop-carried dependencies. They follow the INSPECTOR/EXECUTOR scheme and improve upon previous algorithms with the same generality by allowing concurrent reads of the same location and by increasing the overlap of dependent iterations. The algorithms are based on time-stamping rules and implemented using multithreading tools. The experimental results on an SMP server with four processors show that our schemes are efficient and outperform their competitors consistently in all test cases. The difference between the two proposed algorithms is that one allows partially concurrent reads without causing extra overhead in its inspector while the other allows fully concurrent reads at a slight overhead in the dependence analysis. The algorithm allowing fully concurrent reads obtains up to an 80% improvement over its competitor.

title: An analytical comparison of nearest neighbor algorithms for load balancing in parallel computers
abstract: With nearest neighbor load balancing algorithms, a processor makes balancing decisions based on its local information and manages work load migrations within its neighborhood. This paper compares a couple of fairly well-known nearest neighbor algorithms, the dimension exchange and the diffusion methods and their variants in terms of their performances in both one-port and all-port communication architectures. It turns out that the dimension exchange method outperforms the diffusion method in the one-port communication model, and that the strength of the diffusion method is in asynchronous implementations in the all-port communication model. The underlying communication networks considered assume the most popular topologies, the mesh and the torus and their special cases: the hypercube and the k-ary n-cube.<<ETX>>