P. T. Bremer, D. Maljovec, A. Saha, Bei Wang, J. Gaffney, B. K. Spears, V. Pascucci. ND2AV: N-Dimensional Data Analysis and Visualization -- Analysis for the National Ignition Campaign, In Computing and Visualization in Science, 2015.
T. Bregman, R. Reznikov, M. Diwan, R. Raymond, C. R.Butson, J. N.Nobrega, C. Hamani. Antidepressant-like Effects of Medial Forebrain Bundle Deep Brain Stimulation in Rats are not Associated With Accumbens Dopamine Release, In Brain Stimulation, Vol. 8, No. 4, pp. 708--713. 2015.
Medial forebrain bundle (MFB) deep brain stimulation (DBS) is currently being investigated in patients with treatment-resistant depression. Striking features of this therapy are the large number of patients who respond to treatment and the rapid nature of the antidepressant response.
To study antidepressant-like behavioral responses, changes in regional brain activity, and monoamine release in rats receiving MFB DBS.
Antidepressant-like effects of MFB stimulation at 100 μA, 90 μs and either 130 Hz or 20 Hz were characterized in the forced swim test (FST). Changes in the expression of the immediate early gene (IEG) zif268 were measured with in situ hybridization and used as an index of regional brain activity. Microdialysis was used to measure DBS-induced dopamine and serotonin release in the nucleus accumbens.
Stimulation at parameters that approximated those used in clinical practice, but not at lower frequencies, induced a significant antidepressant-like response in the FST. In animals receiving MFB DBS at high frequency, increases in zif268 expression were observed in the piriform cortex, prelimbic cortex, nucleus accumbens shell, anterior regions of the caudate/putamen and the ventral tegmental area. These structures are involved in the neurocircuitry of reward and are also connected to other brain areas via the MFB. At settings used during behavioral tests, stimulation did not induce either dopamine or serotonin release in the nucleus accumbens.
These results suggest that MFB DBS induces an antidepressant-like effect in rats and recruits structures involved in the neurocircuitry of reward without affecting dopamine release in the nucleus accumbens.
H. Carr, Z. Geng, J. Tierny, A. Chattophadhyay,, A. Knoll. Fiber Surfaces: Generalizing Isosurfaces to Bivariate Data, In Computer Graphics Forum, Vol. 34, No. 3, pp. 241-250. 2015.
CIBC. Note: Data Sets: NCRR Center for Integrative Biomedical Computing (CIBC) data set archive. Download from: http://www.sci.utah.edu/cibc/software.html, 2015.
CIBC. Note: Cleaver: A MultiMaterial Tetrahedral Meshing Library and Application. Scientific Computing and Imaging Institute (SCI), Download from: http://www.sci.utah.edu/cibc/software.html, 2015.
Performance of an Efficient Image-registration Algorithm in Processing MR Renography Data, In J Magnetic Resonance Imaging, July, 2015.
To evaluate the performance of an edge-based registration technique in correcting for respiratory motion artifacts in magnetic resonance renographic (MRR) data and to examine the efficiency of a semiautomatic software package in processing renographic data from a cohort of clinical patients.
MATERIALS AND METHODS:
The developed software incorporates an image-registration algorithm based on the generalized Hough transform of edge maps. It was used to estimate glomerular filtration rate (GFR), renal plasma flow (RPF), and mean transit time (MTT) from 36 patients who underwent free-breathing MRR at 3T using saturation-recovery turbo-FLASH. The processing time required for each patient was recorded. Renal parameter estimates and model-fitting residues from the software were compared to those from a previously reported technique. Interreader variability in the software was quantified by the standard deviation of parameter estimates among three readers. GFR estimates from our software were also compared to a reference standard from nuclear medicine.
The time taken to process one patient's data with the software averaged 12 ± 4 minutes. The applied image registration effectively reduced motion artifacts in dynamic images by providing renal tracer-retention curves with significantly smaller fitting residues (P < 0.01) than unregistered data or data registered by the previously reported technique. Interreader variability was less than 10% for all parameters. GFR estimates from the proposed method showed greater concordance with reference values (P < 0.05).
These results suggest that the proposed software can process MRR data efficiently and accurately. Its incorporated registration technique based on the generalized Hough transform effectively reduces respiratory motion artifacts in free-breathing renographic acquisitions. J. Magn. Reson. Imaging 2015.
Spatio-temporal Image Analysis for Longitudinal and Time-Series Image Data, In Proceedings of the Third International Workshop, STIA 2014, Image Processing, Computer Vision, Pattern Recognition, and Graphics, Vol. 8682, Springer LNCS, 2015.
This book constitutes the thoroughly refereed post-conference proceedings of the Third
International Workshop on Spatio-temporal Image Analysis for Longitudinal and Time-
Series Image Data, STIA 2014, held in conjunction with MICCAI 2014 in Boston, MA, USA, in
The 7 papers presented in this volume were carefully reviewed and selected from 15
submissions. They are organized in topical sections named: longitudinal registration and
shape modeling, longitudinal modeling, reconstruction from longitudinal data, and 4D
J. Edwards, E. Daniel, V. Pascucci, C. Bajaj.
Approximating the Generalized Voronoi Diagram of Closely Spaced Objects, In Computer Graphics Forum, Vol. 34, No. 2, Wiley-Blackwell, pp. 299-309. May, 2015.
Generalized Voronoi Diagrams (GVDs) have far-reaching applications in robotics, visualization, graphics, and simulation. However, while the ordinary Voronoi Diagram has mature and efficient algorithms for its computation, the GVD is difficult to compute in general, and in fact, has only approximation algorithms for anything but the simplest of datasets. Our work is focused on developing algorithms to compute the GVD efficiently and with bounded error on the most difficult of datasets -- those with objects that are extremely close to each other.
T. Etiene, R.M. Kirby, C. Silva. An Introduction to Verification of Visualization Techniques, Morgan & Claypool Publishers, 2015.
SCI Institute. Note: FluoRender: An interactive rendering tool for confocal microscopy data visualization. Scientific Computing and Imaging Institute (SCI) Download from: http://www.fluorender.org, 2015.
Note: FusionView: Problem Solving Environment for MHD Visualization. Scientific Computing and Imaging Institute (SCI), Download from: http://www.scirun.org, 2015.
Y. Gao, L. Zhu, J. Cates, R. S. MacLeod, S. Bouix,, A. Tannenbaum.
A Kalman Filtering Perspective for Multiatlas Segmentation, In SIAM J. Imaging Sciences, Vol. 8, No. 2, pp. 1007-1029. 2015.
K. Gillette, J.D. Tate, B. Kindall, P. Van Dam, E. Kholmovski, R.S. MacLeod. Generation of Combined-Modality Tetrahedral Meshes, In Computing in Cardiology, 2015.
Registering and combining anatomical components from different image modalities, like MRI and CT that have different tissue contrast, could result in patient-specific models that more closely represent underlying anatomical structures.
In this study, we combined a pair of CT and MRI scans of a pig thorax to make a tetrahedral mesh and compared different registration techniques including rigid, affine, thin plate spline morphing (TPSM), and iterative closest point (ICP), to superimpose the segmented bones from the CT scan on the soft tissues segmented from the MRI. The TPSM and affine-registered bones remained close to, but not overlapping, important soft tissue.
Simulation models, including an ECG forward model and a defibrillation model, were computed on generated multi-modality meshes after TPSM and affine registration and compared to those based on the original torso mesh.
B. D. Goodwin, C. R. Butson.
Subject-Specific Multiscale Modeling to Investigate Effects of Transcranial Magnetic Stimulation, In Neuromodulation: Technology at the Neural Interface, Vol. 18, No. 8, Wiley-Blackwell, pp. 694--704. May, 2015.
Transcranial magnetic stimulation (TMS) is an effective intervention in noninvasive neuromodulation used to treat a number of neurophysiological disorders. Predicting the spatial extent to which neural tissue is affected by TMS remains a challenge. The goal of this study was to develop a computational model to predict specific locations of neural tissue that are activated during TMS. Using this approach, we assessed the effects of changing TMS coil orientation and waveform.
MATERIALS AND METHODS:
We integrated novel techniques to develop a subject-specific computational model, which contains three main components: 1) a figure-8 coil (Magstim, Magstim Company Limited, Carmarthenshire, UK); 2) an electromagnetic, time-dependent, nonhomogeneous, finite element model of the whole head; and 3) an adaptation of a previously published pyramidal cell neuron model. We then used our modeling approach to quantify the spatial extent of affected neural tissue for changes in TMS coil rotation and waveform.
We found that our model shows more detailed predictions than previously published models, which underestimate the spatial extent of neural activation. Our results suggest that fortuitous sites of neural activation occur for all tested coil orientations. Additionally, our model predictions show that excitability of individual neural elements changes with a coil rotation of ±15°.
Our results indicate that the extent of neuromodulation is more widespread than previous published models suggest. Additionally, both specific locations in cortex and the extent of stimulation in cortex depend on coil orientation to within ±15° at a minimum. Lastly, through computational means, we are able to provide insight into the effects of TMS at a cellular level, which is currently unachievable by imaging modalities.
Proceedings of the IV International Conference on Particle-Based Methods - Fundamentals and Applications, Barcelona, Spain, Edited by E. Onate and M. Bischoff and D.R.J. Owen and P. Wriggers and T. Zohdi, CIMNE, pp. 202-213. September, 2015.
While particle-in-cell type methods, such as MPM, have been very successful in providing solutions to many challenging problems there are some important issues that remain to be resolved with regard to their analysis. One such challenge relates to the difference in dimensionality between the particles and the grid points to which they are mapped. There exists a non-trivial null space of the linear operator that maps particles values onto nodal values. In other words, there are non-zero particle values values that when mapped to the nodes are zero there. Given positive mapping weights such null space values are oscillatory in nature. The null space may be viewed as a more general form of the ringing instability identified by Brackbill for PIC methods. It will be shown that it is possible to remove these null-space values from the solution and so to improve the accuracy of PIC methods, using a matrix SVD approach. The expense of doing this is prohibitive for real problems and so a local method is developed for doing this.
A. V. P. Grosset, M. Prasad, C. Christensen, A. Knoll, C. Hansen. TOD-Tree: Task-Overlapped Direct send Tree Image Compositing for Hybrid MPI Parallelism, In Eurographics Symposium on Parallel Graphics and Visualization (2015), Edited by C. Dachsbacher, P. Navrátil, 2015.
The proceedings of the 2nd Annual Deep Brain Stimulation Think Tank summarize the most contemporary clinical, electrophysiological, and computational work on DBS for the treatment of neurological and neuropsychiatric disease and represent the insights of a unique multidisciplinary ensemble of expert neurologists, neurosurgeons, neuropsychologists, psychiatrists, scientists, engineers and members of industry. Presentations and discussions covered a broad range of topics, including advocacy for DBS, improving clinical outcomes, innovations in computational models of DBS, understanding of the neurophysiology of Parkinson's disease (PD) and Tourette syndrome (TS) and evolving sensor and device technologies.
Morse-Smale Analysis of Ion Diffusion for DFT Battery Materials Simulations, In Topology-Based Methods in Visualization (TopoInVis), 2015.A. Gyulassy, A. Knoll, K. C. Lau, Bei Wang, P. T. Bremer, M. E. Papka, L. A. Curtiss, V. Pascucci.
Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrodinger's equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ion diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.