SCIENTIFIC COMPUTING AND IMAGING INSTITUTE
at the University of Utah

An internationally recognized leader in visualization, scientific computing, and image analysis

SCI Publications

2011


F. Shi, D. Shen, P.-T. Yap, Y. Fan, J.-Z. Cheng, H. An, L.L. Wald, G. Gerig, J.H. Gilmore, W. Lin. “CENTS: Cortical Enhanced Neonatal Tissue Segmentation,” In Human Brain Mapping HBM, Vol. 32, No. 3, Note: ePub 5 Aug 2010, pp. 382--396. March, 2011.
DOI: 10.1002/hbm.21023
PubMed ID: 20690143



M. Steinberger, M. Waldner, M. Streit, A. Lex, D. Schmalstieg. “Context-Preserving Visual Links,” In IEEE Transactions on Visualization and Computer Graphics (InfoVis '11), Vol. 17, No. 12, 2011.

ABSTRACT

Evaluating, comparing, and interpreting related pieces of information are tasks that are commonly performed during visual data analysis and in many kinds of information-intensive work. Synchronized visual highlighting of related elements is a well-known technique used to assist this task. An alternative approach, which is more invasive but also more expressive is visual linking in which line connections are rendered between related elements. In this work, we present context-preserving visual links as a new method for generating visual links. The method specifically aims to fulfill the following two goals: first, visual links should minimize the occlusion of important information; second, links should visually stand out from surrounding information by minimizing visual interference. We employ an image-based analysis of visual saliency to determine the important regions in the original representation. A consequence of the image-based approach is that our technique is application-independent and can be employed in a large number of visual data analysis scenarios in which the underlying content cannot or should not be altered. We conducted a controlled experiment that indicates that users can find linked elements in complex visualizations more quickly and with greater subjective satisfaction than in complex visualizations in which plain highlighting is used. Context-preserving visual links were perceived as visually more attractive than traditional visual links that do not account for the context information.



B. Summa, G. Scorzelli, M. Jiang, P.-T. Bremer, V. Pascucci. “Interactive Editing of Massive Imagery Made Simple: Turning Atlanta into Atlantis,” In ACM Transactions on Graphics, Vol. 30, No. 2, pp. 7:1--7:13. April, 2011.
DOI: 10.1145/1944846.1944847

ABSTRACT

This article presents a simple framework for progressive processing of high-resolution images with minimal resources. We demonstrate this framework's effectiveness by implementing an adaptive, multi-resolution solver for gradient-based image processing that, for the first time, is capable of handling gigapixel imagery in real time. With our system, artists can use commodity hardware to interactively edit massive imagery and apply complex operators, such as seamless cloning, panorama stitching, and tone mapping.

We introduce a progressive Poisson solver that processes images in a purely coarse-to-fine manner, providing near instantaneous global approximations for interactive display (see Figure 1). We also allow for data-driven adaptive refinements to locally emulate the effects of a global solution. These techniques, combined with a fast, cache-friendly data access mechanism, allow the user to interactively explore and edit massive imagery, with the illusion of having a full solution at hand. In particular, we demonstrate the interactive modification of gigapixel panoramas that previously required extensive offline processing. Even with massive satellite images surpassing a hundred gigapixels in size, we enable repeated interactive editing in a dynamically changing environment. Images at these scales are significantly beyond the purview of previous methods yet are processed interactively using our techniques. Finally our system provides a robust and scalable out-of-core solver that consistently offers high-quality solutions while maintaining strict control over system resources.



D.J. Swenson, S.E. Geneser, J.G. Stinstra, R.M. Kirby, R.S. MacLeod. “Cardiac Position Sensitivity Study in the Electrocardiographic Forward Problem Using Stochastic Collocation and Boundary Element Methods,” In Annals of Biomedical Engineering, Vol. 39, No. 12, pp. 2900--2910. 2011.
DOI: 10.1007/s10439-011-0391-5
PubMed ID: 21909818
PubMed Central ID: PMC336204

ABSTRACT

The electrocardiogram (ECG) is ubiquitously employed as a diagnostic and monitoring tool for patients experiencing cardiac distress and/or disease. It is widely known that changes in heart position resulting from, for example, posture of the patient (sitting, standing, lying) and respiration significantly affect the body-surface potentials; however, few studies have quantitatively and systematically evaluated the effects of heart displacement on the ECG. The goal of this study was to evaluate the impact of positional changes of the heart on the ECG in the specific clinical setting of myocardial ischemia. To carry out the necessary comprehensive sensitivity analysis, we applied a relatively novel and highly efficient statistical approach, the generalized polynomial chaos-stochastic collocation method, to a boundary element formulation of the electrocardiographic forward problem, and we drove these simulations with measured epicardial potentials from whole-heart experiments. Results of the analysis identified regions on the body-surface where the potentials were especially sensitive to realistic heart motion. The standard deviation (STD) of ST-segment voltage changes caused by the apex of a normal heart, swinging forward and backward or side-to-side was approximately 0.2 mV. Variations were even larger, 0.3 mV, for a heart exhibiting elevated ischemic potentials. These variations could be large enough to mask or to mimic signs of ischemia in the ECG. Our results suggest possible modifications to ECG protocols that could reduce the diagnostic error related to postural changes in patients possibly suffering from myocardial ischemia.



M. Szegedi, J. Hinkle, S. Joshi, V. Sarkar, P. Rassiah-Szegedi, B. Wang, B. Salter. “WE-E-BRC-05: Voxel Based Four Dimensional Tissue Deformation Reconstruction (4DTDR) Validation Using a Real Tissue Phantom,” In Medical Physics, Vol. 38, pp. 3819. 2011.



G. Tamm, A. Schiewe, J. Krüger. “ZAPP – A management framework for distributed visualization systems,” In Proceedings of CGVCVIP 2011 : IADIS International Conference on Computer Graphics, Visualization, Computer Vision And Image Processing, pp. (accepted). 2011.



J.D. Tate, J.G. Stinstra, T. Pilcher, A. Poursaid, E. Saarel, R.S. MacLeod. “Measuring Defibrillator Surface Potentials for Simulation Verification,” In Proceedings of the IEEE Engineering in Medicine and Biology Society EMBS 33rd Annual International Conference, pp. 239 - 242. 2011.
ISSN: 1557-170X
DOI: 10.1109/IEMBS.2011.6090045
PubMed ID: 22254294

ABSTRACT

Though implantable cardioverter defibrillators (ICDs) are increasing in use in both adults and children, little progress has been devoted to optimizing device and electrode placement. To facilitate effective ICD placement, especially in pediatric cases, we have developed a predictive model that evaluates the efficacy of a delivered shock. We have also developed an experimental validation approach based on measurements from clinical cases. The approach involves obtaining body surface potential maps of ICD discharges during implantation surgery using a limited lead selection and body surface estimation algorithm. Comparison of the simulated and measured potentials yielded very similar patterns and a typical correlation greater than 0.93, suggesting that the predictive simulation generates realistic potential values. This validation approach provides confidence in application of the simulation pipeline and offers areas to focus future improvements.

Keywords: Electric potential, Electric shock, Electrodes;Estimation, Lead;Surface reconstruction, Torso, Algorithms, Body Surface Potential Mapping, Computer Simulation, Defibrillators, Implantable, Humans, Models, Cardiovascular, Therapy, Computer-Assisted



J.D. Tate, J.G. Stinstra, T.A. Pilcher, R.S. MacLeod. “Measurement of Defibrillator Surface Potentials for Simulation Verification,” In Computing in Cardiology, In 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, IEEE, pp. 853--856. Aug, 2011.
DOI: 10.1109/iembs.2011.6090045



D. Thompson, J.A. Levine, J.C. Bennett, P.-T. Bremer, A. Gyulassy, V. Pascucci, P.P. Pebay. “Analysis of Large-Scale Scalar Data Using Hixels,” In Proceedings of the 2011 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV), Providence, RI, pp. 23--30. 2011.
DOI: 10.1109/LDAV.2011.6092313



L.T. Tran, M. Berzins. “IMPICE Method for Compressible Flow Problems in Uintah,” In International Journal For Numerical Methods In Fluids, Note: Published online 20 July, 2011.



L.T. Tran, M. Berzins. “Defect Sampling in Global Error Estimation for ODEs and Method-Of-Lines PDEs Using Adjoint Methods,” SCI Technical Report, No. UUSCI-2011-006, SCI Institute, University of Utah, 2011.



X. Tricoche, C. Garth, A. Sanderson. “Visualization of topological structures in area-preserving maps,” In IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 17, No. 12, pp. 1765--1774. Dec, 2011.
DOI: 10.1109/TVCG.2011.254
PubMed ID: 22034293

ABSTRACT

Area-preserving maps are found across a wide range of scientific and engineering problems. Their study is made challenging by the significant computational effort typically required for their inspection but more fundamentally by the fractal complexity of salient structures. The visual inspection of these maps reveals a remarkable topological picture consisting of fixed (or periodic) points embedded in so-called island chains, invariant manifolds, and regions of ergodic behavior. This paper is concerned with the effective visualization and precise topological analysis of area-preserving maps with two degrees of freedom from numerical or analytical data. Specifically, a method is presented for the automatic extraction and characterization of fixed points and the computation of their invariant manifolds, also known as separatrices, to yield a complete picture of the structures present within the scale and complexity bounds selected by the user. This general approach offers a significant improvement over the visual representations that are so far available for area-preserving maps. The technique is demonstrated on a numerical simulation of magnetic confinement in a fusion reactor.



P. Tsuji, D. Xiu, L. Ying. “A Fast Method for High-frequency Acoustic Scattering from Random Scatterers,” In International Journal for Uncertainty Quantification, Vol. 1, No. 2, pp. 99--117. 2011.
DOI: 10.1615/IntJUncertaintyQuantification.v1.i2.10

ABSTRACT

This paper is concerned with the uncertainty quantification of high-frequency acoustic scattering from objects with random shape in two-dimensional space. Several new methods are introduced to efficiently estimate the mean and variance of the random radar cross section in all directions. In the physical domain, the scattering problem is solved using the boundary integral formulation and Nystrom discretization; recently developed fast algorithms are adapted to accelerate the computation of the integral operator and the evaluation of the radar cross section. In the random domain, it is discovered that due to the highly oscillatory nature of the solution, the stochastic collocation method based on sparse grids does not perform well. For this particular problem, satisfactory results are obtained by using quasi-Monte Carlo methods. Numerical results are given for several test cases to illustrate the properties of the proposed approach.

Keywords: acoustic scattering, random domains, uncertainty quantification, boundary integral equations, fast algorithms, quasi-Monte Carlo methods



N.J. Tustison, S.P. Awate, G. Song, T.S. Cook, J.C. Gee. “Point Set Registration Using Havrda–Charvat–Tsallis Entropy Measures,” In IEEE Transactions on Medical Imaging, Vol. 30, No. 2, pp. 451--460. 2011.



G.R. Vergara, S. Vijayakumar, E.G. Kholmovski, J.J. Blauer, M.A. Guttman, C. Gloschat, G. Payne, K. Vij, N.W. Akoum, M. Daccarett, C.J. McGann, R.S. Macleod, N.F. Marrouche. “Real-time magnetic resonance imaging-guided radiofrequency atrial ablation and visualization of lesion formation at 3 Tesla,” In Heart Rhythm, Vol. 8, No. 2, pp. 295--303. 2011.
PubMed ID: 21034854



H.T. Vo, J. Bronson, B. Summa, J.L.D. Comba, J. Freire, B. Howe, V. Pascucci, C.T. Silva. “Parallel Visualization on Large Clusters using MapReduce,” SCI Technical Report, No. UUSCI-2011-002, SCI Institute, University of Utah, 2011.



H.T. Vo, J. Bronson, B. Summa, J.L.D. Comba, J. Freire, B. Howe, V. Pascucci, C.T. Silva. “Parallel Visualization on Large Clusters using MapReduce,” In Proceedings of the 2011 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV), pp. 81--88. 2011.

ABSTRACT

Large-scale visualization systems are typically designed to efficiently \"push\" datasets through the graphics hardware. However, exploratory visualization systems are increasingly expected to support scalable data manipulation, restructuring, and querying capabilities in addition to core visualization algorithms. We posit that new emerging abstractions for parallel data processing, in particular computing clouds, can be leveraged to support large-scale data exploration through visualization. In this paper, we take a first step in evaluating the suitability of the MapReduce framework to implement large-scale visualization techniques. MapReduce is a lightweight, scalable, general-purpose parallel data processing framework increasingly popular in the context of cloud computing. Specifically, we implement and evaluate a representative suite of visualization tasks (mesh rendering, isosurface extraction, and mesh simplification) as MapReduce programs, and report quantitative performance results applying these algorithms to realistic datasets. For example, we perform isosurface extraction of up to l6 isovalues for volumes composed of 27 billion voxels, simplification of meshes with 30GBs of data and subsequent rendering with image resolutions up to 800002 pixels. Our results indicate that the parallel scalability, ease of use, ease of access to computing resources, and fault-tolerance of MapReduce offer a promising foundation for a combined data manipulation and data visualization system deployed in a public cloud or a local commodity cluster.

Keywords: MapReduce, Hadoop, cloud computing, large meshes, volume rendering, gigapixels



H.T. Vo, C.T. Silva, L.F. Scheidegger, V. Pascucci. “Simple and Efficient Mesh Layout with Space-Filling Curves,” In Journal of Graphics, GPU, and Game Tools, pp. 25--39. 2011.
ISSN: 2151-237X



Y. Wang, A. Gupta, Z. Liu, H. Zhang, M.L. Escolar, J.H. Gilmore, S. Gouttard, P. Fillard, E. Maltbie, G. Gerig, M. Styner. “DTI registration in atlas based fiber analysis of infantile Krabbe disease,” In Neuroimage, pp. (in print). 2011.
PubMed ID: 21256236



D. Wang, R.M. Kirby, C.R. Johnson. “Finite Element Based Discretization and Regularization Strategies for 3D Inverse Electrocardiography,” In IEEE Transactions for Biomedical Engineering, Vol. 58, No. 6, pp. 1827--1838. 2011.
PubMed ID: 21382763
PubMed Central ID: PMC3109267

ABSTRACT

We consider the inverse electrocardiographic problem of computing epicardial potentials from a body-surface potential map. We study how to improve numerical approximation of the inverse problem when the finite-element method is used. Being ill-posed, the inverse problem requires different discretization strategies from its corresponding forward problem. We propose refinement guidelines that specifically address the ill-posedness of the problem. The resulting guidelines necessitate the use of hybrid finite elements composed of tetrahedra and prism elements. Also, in order to maintain consistent numerical quality when the inverse problem is discretized into different scales, we propose a new family of regularizers using the variational principle underlying finite-element methods. These variational-formed regularizers serve as an alternative to the traditional Tikhonov regularizers, but preserves the L2 norm and thereby achieves consistent regularization in multiscale simulations. The variational formulation also enables a simple construction of the discrete gradient operator over irregular meshes, which is difficult to define in traditional discretization schemes. We validated our hybrid element technique and the variational regularizers by simulations on a realistic 3-D torso/heart model with empirical heart data. Results show that discretization based on our proposed strategies mitigates the ill-conditioning and improves the inverse solution, and that the variational formulation may benefit a broader range of potential-based bioelectric problems.