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Full-Text Articles in Physical Sciences and Mathematics
Comparison Of Physics-Based Deformable Registration Methods For Image-Guided Neurosurgery, Nikos Chrisochoides, Yixun Liu, Fotis Drakopoulos, Andriy Kot, Panos Foteinos, Christos Tsolakis, Emmanuel Billias, Olivier Clatz, Nicholas Ayache, Andrey Fedorov, Alex Golby, Peter Black, Ron Kikinis
Comparison Of Physics-Based Deformable Registration Methods For Image-Guided Neurosurgery, Nikos Chrisochoides, Yixun Liu, Fotis Drakopoulos, Andriy Kot, Panos Foteinos, Christos Tsolakis, Emmanuel Billias, Olivier Clatz, Nicholas Ayache, Andrey Fedorov, Alex Golby, Peter Black, Ron Kikinis
Computer Science Faculty Publications
This paper compares three finite element-based methods used in a physics-based non-rigid registration approach and reports on the progress made over the last 15 years. Large brain shifts caused by brain tumor removal affect registration accuracy by creating point and element outliers. A combination of approximation- and geometry-based point and element outlier rejection improves the rigid registration error by 2.5 mm and meets the real-time constraints (4 min). In addition, the paper raises several questions and presents two open problems for the robust estimation and improvement of registration error in the presence of outliers due to sparse, noisy, and incomplete …
A Unified Framework For Parallel Anisotropic Mesh Adaptation, Christos Tsolakis
A Unified Framework For Parallel Anisotropic Mesh Adaptation, Christos Tsolakis
Computer Science Theses & Dissertations
Finite-element methods are a critical component of the design and analysis procedures of many (bio-)engineering applications. Mesh adaptation is one of the most crucial components since it discretizes the physics of the application at a relatively low cost to the solver. Highly scalable parallel mesh adaptation methods for High-Performance Computing (HPC) are essential to meet the ever-growing demand for higher fidelity simulations. Moreover, the continuous growth of the complexity of the HPC systems requires a systematic approach to exploit their full potential. Anisotropic mesh adaptation captures features of the solution at multiple scales while, minimizing the required number of elements. …
Adaptive Physics-Based Non-Rigid Registration For Immersive Image-Guided Neuronavigation Systems, Fotis Drakopoulos, Christos Tsolakis, Angelos Angelopoulos, Yixun Liu, Chengjun Yao, Kyriaki Rafailia Kavazidi, Nikolaos Foroglou, Andrey Fedorov, Sarah Frisken, Ron Kikinis, Alexandra Golby, Nikos Chrisochoides
Adaptive Physics-Based Non-Rigid Registration For Immersive Image-Guided Neuronavigation Systems, Fotis Drakopoulos, Christos Tsolakis, Angelos Angelopoulos, Yixun Liu, Chengjun Yao, Kyriaki Rafailia Kavazidi, Nikolaos Foroglou, Andrey Fedorov, Sarah Frisken, Ron Kikinis, Alexandra Golby, Nikos Chrisochoides
Computer Science Faculty Publications
Objective: In image-guided neurosurgery, co-registered preoperative anatomical, functional, and diffusion tensor imaging can be used to facilitate a safe resection of brain tumors in eloquent areas of the brain. However, the brain deforms during surgery, particularly in the presence of tumor resection. Non-Rigid Registration (NRR) of the preoperative image data can be used to create a registered image that captures the deformation in the intraoperative image while maintaining the quality of the preoperative image. Using clinical data, this paper reports the results of a comparison of the accuracy and performance among several non-rigid registration methods for handling brain deformation. A …
Parallel Anisotropic Unstructured Grid Adaptation, Christos Tsolakis, Nikos Chrisochoides, Michael A. Park, Adrien Loseille, Todd Michal
Parallel Anisotropic Unstructured Grid Adaptation, Christos Tsolakis, Nikos Chrisochoides, Michael A. Park, Adrien Loseille, Todd Michal
Computer Science Faculty Publications
Computational fluid dynamics (CFD) has become critical to the design and analysis of aerospace vehicles. Parallel grid adaptation that resolves multiple scales with anisotropy is identified as one of the challenges in the CFD Vision 2030 Study to increase the capacity and capability of CFD simulation. The study also cautions that computer architectures are undergoing a radical change, and dramatic increases in algorithm concurrency will be required to exploit full performance. This paper reviews four different methods to parallel anisotropic grid adaptation. They cover both ends of the spectrum: 1) using existing state-of-the-art software optimized for a single core and …
Automatic Linear And Curvilinear Mesh Generation Driven By Validity Fidelity And Topological Guarantees, Jing Xu
Computer Science Theses & Dissertations
Image-based geometric modeling and mesh generation play a critical role in computational biology and medicine. In this dissertation, a comprehensive computational framework for both guaranteed quality linear and high-order automatic mesh generation is presented. Starting from segmented images, a quality 2D/3D linear mesh is constructed. The boundary of the constructed mesh is proved to be homeomorphic to the object surface. In addition, a guaranteed dihedral angle bound of up to 19:47o for the output tetrahedra is provided. Moreover, user-specified guaranteed bounds on the distance between the boundaries of the mesh and the boundaries of the materials are allowed. The …
Watertight And 2-Manifold Surface Meshes Using Dual Contouring With Tetrahedral Decomposition Of Grid Cubes, Tanweer Rashid, Sharmin Sultana, Michel A. Audette
Watertight And 2-Manifold Surface Meshes Using Dual Contouring With Tetrahedral Decomposition Of Grid Cubes, Tanweer Rashid, Sharmin Sultana, Michel A. Audette
Computational Modeling & Simulation Engineering Faculty Publications
The Dual Contouring algorithm (DC) is a grid-based process used to generate surface meshes from volumetric data. The advantage of DC is that it can reproduce sharp features by inserting vertices anywhere inside the grid cube, as opposed to the Marching Cubes (MC) algorithm that can insert vertices only on the grid edges. However, DC is unable to guarantee 2-manifold and watertight meshes due to the fact that it produces only one vertex for each grid cube. We present a modified Dual Contouring algorithm that is capable of overcoming this limitation. Our method decomposes an ambiguous grid cube into a …
Tetrahedral Image-To-Mesh Conversion Software For Anatomic Modeling Of Arteriovenous Malformations, Fotis Drakopoulos, Ricardo Ortiz, Andinet Enquobahrie, Deanna Sasaki-Adams, Nikos Chrisochoides
Tetrahedral Image-To-Mesh Conversion Software For Anatomic Modeling Of Arteriovenous Malformations, Fotis Drakopoulos, Ricardo Ortiz, Andinet Enquobahrie, Deanna Sasaki-Adams, Nikos Chrisochoides
Computer Science Faculty Publications
We describe a new implementation of an adaptive multi-tissue tetrahedral mesh generator targeting anatomic modeling of Arteriovenous Malformation (AVM) for surgical simulations. Our method, initially constructs an adaptive Body-Centered Cubic (BCC) mesh of high quality elements. Then, it deforms the mesh surfaces to their corresponding physical image boundaries, hence, improving the mesh fidelity and smoothness. Our deformation scheme, which builds upon the ITK toolkit, is based on the concept of energy minimization, and relies on a multi-material point-based registration. It uses non-connectivity patterns to implicitly control the number of the extracted feature points needed for the registration, and thus, adjusts …
Automatic Curvilinear Quality Mesh Generation Driven By Smooth Boundary And Guaranteed Fidelity, Jing Xu, Andrey N. Chernikov
Automatic Curvilinear Quality Mesh Generation Driven By Smooth Boundary And Guaranteed Fidelity, Jing Xu, Andrey N. Chernikov
Computer Science Faculty Publications
The development of robust high-order finite element methods requires the construction of valid high-order meshes for complex geometries without user intervention. This paper presents a novel approach for automatically generating a high-order mesh with two main features: first, the boundary of the mesh is globally smooth; second, the mesh boundary satisfies a required fidelity tolerance. Invalid elements are eliminated. Example meshes demonstrate the features of the algorithm.
Generalized Insertion Region Guides For Delaunay Mesh Refinement, Andrey Chernikov, Nikos Chrisochoides
Generalized Insertion Region Guides For Delaunay Mesh Refinement, Andrey Chernikov, Nikos Chrisochoides
Computer Science Faculty Publications
Mesh generation by Delaunay refinement is a widely used technique for constructing guaranteed quality triangular and tetrahedral meshes. The quality guarantees are usually provided in terms of the bounds on circumradius-to-shortest-edge ratio and on the grading of the resulting mesh. Traditionally circumcenters of skinny elements and middle points of boundary faces and edges are used for the positions of inserted points. However, recently variations of the traditional algorithms are being proposed that are designed to achieve certain optimization objectives by inserting new points in neighborhoods of the center points. In this paper we propose a general approach to the selection …
Fully Generalized Two-Dimensional Constrained Delaunay Mesh Refinement, Panagiotis A. Foteinos, Andrey N. Chernikov, Nikos P. Chrisochoides
Fully Generalized Two-Dimensional Constrained Delaunay Mesh Refinement, Panagiotis A. Foteinos, Andrey N. Chernikov, Nikos P. Chrisochoides
Computer Science Faculty Publications
Traditional refinement algorithms insert a Steiner point from a few possible choices at each step. Our algorithm, on the contrary, defines regions from where a Steiner point can be selected and thus inserts a Steiner point among an infinite number of choices. Our algorithm significantly extends existing generalized algorithms by increasing the number and the size of these regions. The lower bound for newly created angles can be arbitrarily close to $30^{\circ}$. Both termination and good grading are guaranteed. It is the first Delaunay refinement algorithm with a $30^{\circ}$ angle bound and with grading guarantees. Experimental evaluation of our algorithm …