Objective. During deep brain stimulation (DBS), it is well understood that extracellular cathodic stimulation can cause activation of passing axons. Activation can be predicted from the second derivative of the electric potential along an axon, which depends on axonal orientation with respect to the stimulation source. We hypothesize that fiber orientation influences activation thresholds and that fiber orientations can be selectively targeted with DBS waveforms. Approach. We used bioelectric field and multicompartment NEURON models to explore preferential activation based on fiber orientation during monopolar or bipolar stimulation. Preferential fiber orientation was extracted from the principal eigenvectors and eigenvalues of the Hessian matrix of the electric potential. We tested cathodic, anodic, and charge-balanced pulses to target neurons based on fiber orientation in general and clinical scenarios. Main results. Axons passing the DBS lead have positive second derivatives around a cathode, whereas orthogonal axons have positive second derivatives around an anode, as indicated by the Hessian. Multicompartment NEURON models confirm that passing fibers are activated by cathodic stimulation, and orthogonal fibers are activated by anodic stimulation. Additionally, orthogonal axons have lower thresholds compared to passing axons. In a clinical scenario, fiber pathways associated with therapeutic benefit can be targeted with anodic stimulation at 50% lower stimulation amplitudes. Significance. Fiber orientations can be selectively targeted with simple changes to the stimulus waveform. Anodic stimulation preferentially activates orthogonal fibers, approaching or leaving the electrode, at lower thresholds for similar therapeutic benefit in DBS with decreased power consumption.
C.J. Anderson, D.N. Anderson, S.M. Pulst, C.R. Butson, A.D. Dorval.
Neural Selectivity, Efficiency, and Dose Equivalence in Deep Brain Stimulation through Pulse Width Tuning and Segmented Electrodes, In bioRxiv, Cold Spring Harbor Laboratory, April, 2019.
Achieving deep brain stimulation (DBS) dose equivalence is challenging, especially with pulse width tuning and directional contacts. Further, the precise effects of pulse width tuning are unknown.
We created multicompartment neuron models for two axon diameters and used finite element modeling to determine extracellular influence from standard and segmented electrodes. We analyzed axon activation profiles and calculated volumes of tissue activated.
Long pulse widths focus the stimulation effect on small, nearby fibers, suppressing white matter tract activation (responsible for some DBS side effects) and improving battery utilization. Directional leads enable similar benefits to a greater degree. We derive equations for equivalent activation with pulse width tuning and segmented contacts.
We find agreement with classic studies and reinterpret recent articles concluding that short pulse widths focus the stimulation effect on small, nearby fibers, decrease side effects, and improve power consumption. Our field should reconsider shortened pulse widths.
We present a framework for the analysis of uncertainty in isocontour extraction. The marching squares (MS) algorithm for isocontour reconstruction generates a linear topology that is consistent with hyperbolic curves of a piecewise bilinear interpolation. The saddle points of the bilinear interpolant cause topological ambiguity in isocontour extraction. The midpoint decider and the asymptotic decider are well-known mathematical techniques for resolving topological ambiguities. The latter technique investigates the data values at the cell saddle points for ambiguity resolution. The uncertainty in data, however, leads to uncertainty in underlying bilinear interpolation functions for the MS algorithm, and hence, their saddle points. In our work, we study the behavior of the asymptotic decider when data at grid vertices is uncertain. First, we derive closed-form distributions characterizing variations in the saddle point values for uncertain bilinear interpolants. The derivation assumes uniform and nonparametric noise models, and it exploits the concept of ratio distribution for analytic formulations. Next, the probabilistic asymptotic decider is devised for ambiguity resolution in uncertain data using distributions of the saddle point values derived in the first step. Finally, the confidence in probabilistic topological decisions is visualized using a colormapping technique. We demonstrate the higher accuracy and stability of the probabilistic asymptotic decider in uncertain data with regard to existing decision frameworks, such as deciders in the mean field and the probabilistic midpoint decider, through the isocontour visualization of synthetic and real datasets.
Topological techniques have proven to be a powerful tool in the analysis and visualization of large-scale scientific data. In particular, the Morse-Smale complex and its various components provide a rich framework for robust feature definition and computation. Consequently, there now exist a number of approaches to compute Morse-Smale complexes for large-scale data in parallel. However, existing techniques are based on discrete concepts which produce the correct topological structure but are known to introduce grid artifacts in the resulting geometry. Here, we present a new approach that combines parallel streamline computation with combinatorial methods to construct a high-quality discrete Morse-Smale complex. In addition to being invariant to the orientation of the underlying grid, this algorithm allows users to selectively build a subset of features using high-quality geometry. In particular, a user may specifically select which ascending/descending manifolds are reconstructed with improved accuracy, focusing computational effort where it matters for subsequent analysis. This approach computes Morse-Smale complexes for larger data than previously feasible with significant speedups. We demonstrate and validate our approach using several examples from a variety of different scientific domains, and evaluate the performance of our method.
M. Han, I. Wald, W. Usher, Q. Wu, F. Wang, V. Pascicci, C. D. Hansen, C. R. Johnson. Ray Tracing Generalized Tube Primitives: Method and Applications, In Computer Graphics Forum, Vol. 38, No. 3, John Wiley & Sons Ltd., 2019.
We present a general high-performance technique for ray tracing generalized tube primitives. Our technique efficiently supports tube primitives with fixed and varying radii, general acyclic graph structures with bifurcations, and correct transparency with interior surface removal. Such tube primitives are widely used in scientific visualization to represent diffusion tensor imaging tractographies, neuron morphologies, and scalar or vector fields of 3D flow. We implement our approach within the OSPRay ray tracing framework, and evaluate it on a range of interactive visualization use cases of fixed- and varying-radius streamlines, pathlines, complex neuron morphologies, and brain tractographies. Our proposed approach provides interactive, high-quality rendering, with low memory overhead.
There currently exist two dominant strategies to reduce data sizes in analysis and visualization: reducing the precision of the data, e.g., through quantization, or reducing its resolution, e.g., by subsampling. Both have advantages and disadvantages and both face fundamental limits at which the reduced information ceases to be useful. The paper explores the additional gains that could be achieved by combining both strategies. In particular, we present a common framework that allows us to study the trade-off in reducing precision and/or resolution in a principled manner. We represent data reduction schemes as progressive streams of bits and study how various bit orderings such as by resolution, by precision, etc., impact the resulting approximation error across a variety of data sets as well as analysis tasks. Furthermore, we compute streams that are optimized for different tasks to serve as lower bounds on the achievable error. Scientific data management systems can use the results presented in this paper as guidance on how to store and stream data to make efficient use of the limited storage and bandwidth in practice.
J. K. Holmen, B. Peterson, A. Humphrey, D. Sunderland, O. H. Diaz-Ibarra, J. N. Thornock, M. Berzins. Portably Improving Uintah's Readiness for Exascale Systems Through the Use of Kokkos, SCI Institute, 2019.
Uncertainty and diversity in future HPC systems, including those for exascale, makes portable codebases desirable. To ease future ports, the Uintah Computational Framework has adopted the Kokkos C++ Performance Portability Library. This paper describes infrastructure advancements and performance improvements using partitioning functionality recently added to Kokkos within Uintah's MPI+Kokkos hybrid parallelism approach. Results are presented for two challenging calculations that have been refactored to support Kokkos::OpenMP and Kokkos::Cuda back-ends. These results demonstrate performance improvements up to (i) 2.66x when refactoring for portability, (ii) 81.59x when adding loop-level parallelism via Kokkos back-ends, and (iii) 2.63x when more eciently using a node. Good strong-scaling characteristics to 442,368 threads across 1728 Knights Landing processors are also shown. These improvements have been achieved with little added overhead (sub-millisecond, consuming up to 0.18% of per-timestep time). Kokkos adoption and refactoring lessons are also discussed.
Alan Humphrey. Scalable Asynchronous Many-Task Runtime Solutions to Globally Coupled Problems, School of Computing, University of Utah, 2019.
Thermal radiation is an important physical process and a key mechanism in a class of challenging engineering and research problems. The principal exascale-candidate application motivating this research is a large eddy simulation (LES) aimed at predicting the performance of a commercial, 1200 MWe ultra-super critical (USC) coal boiler, with radiation as the dominant mode of heat transfer. Scalable modeling of radiation is currently one of the most challenging problems in large-scale simulations, due to the global, all-to-all physical and resulting computational connectivity. Fundamentally, radiation models impose global data dependencies, requiring each compute node in a distributed memory system to send data to, and receive data from, potentially every other node. This process can be prohibitively expensive on large distributed memory systems due to pervasive all-to-all message passing interface (MPI) communication. Correctness is also difficult to achieve when coordinating global communication of this kind. Asynchronous many-task (AMT) runtime systems are a possible leading alternative to mitigate programming challenges at the runtime system-level, sheltering the application developer from the complexities introduced by future architectures. However, large-scale parallel applications with complex global data dependencies, such as in radiation modeling, pose significant scalability challenges themselves, even for a highly tuned AMT runtime. The principal aims of this research are to demonstrate how the Uintah AMT runtime can be adapted, making it possible for complex multiphysics applications with radiation to scale on current petascale and emerging exascale architectures. For Uintah, which uses a directed acyclic graph to represent the computation and associated data dependencies, these aims are achieved through: 1) the use of an AMT runtime; 2) adapting and leveraging Uintah’s adaptive mesh refinement support to dramatically reduce computation, communication volume, and nodal memory footprint for radiation calculations; and 3) automating the all-to-all communication at the runtime level through a task graph dependency analysis phase designed to efficiently manage data dependencies inherent in globally coupled problems.
G. S. Smith, K. A. Mills, G. M. Pontone, W. S. Anderson, K. M. Perepezko, J. Brasic, Y. Zhou, J. Brandt, C. R. Butson, D. P. Holt, W. B. Mathews, R. F. Dannals, D. F. Wong, Z. Mari. Effect of STN DBS on vesicular monoamine transporter 2 and glucose metabolism in Parkinson's disease, In Parkinsonism and Related Disorders, Elsevier, 2019.
Deep brain stimulation (DBS) is an established treatment Parkinson's Disease (PD). Despite the improvement of motor symptoms in most patients by sub-thalamic nucleus (STN) DBS and its widespread use, the neurobiological mechanisms are not completely understood. The objective of the present study was to elucidate the effects of STN DBS in PD on the dopamine system and neural circuitry employing high-resolution positron emission tomography (PET) imaging. The hypotheses tested were that STN DBS would decrease striatal VMAT2, secondary to an increase in dopamine concentrations, and would decrease striatal cerebral metabolism and increase cortical metabolism.
W. Usher, I. Wald, J. Amstutz, J. Gunther, C. Brownlee, V. Pascucci. Scalable Ray Tracing Using the Distributed FrameBuffer, In Eurographics Conference on Visualization (EuroVis) 2019, Vol. 38, No. 3, 2019.
Image- and data-parallel rendering across multiple nodes on high-performance computing systems is widely used in visualization to provide higher frame rates, support large data sets, and render data in situ. Specifically for in situ visualization, reducing bottlenecks incurred by the visualization and compositing is of key concern to reduce the overall simulation runtime. Moreover, prior algorithms have been designed to support either image- or data-parallel rendering and impose restrictions on the data distribution, requiring different implementations for each configuration. In this paper, we introduce the Distributed FrameBuffer, an asynchronous image-processing framework for multi-node rendering. We demonstrate that our approach achieves performance superior to the state of the art for common use cases, while providing the flexibility to support a wide range of parallel rendering algorithms and data distributions. By building on this framework, we extend the open-source ray tracing library OSPRay with a data-distributed API, enabling its use in data-distributed and in situ visualization applications.
A Retrospective Evaluation of Automated Optimization of Deep Brain Stimulation Settings, In Brain Stimulation, Vol. 12, No. 2, Elsevier, pp. e54--e55. March, 2019.
Influence of head tissue conductivity uncertainties on EEG dipole reconstruction, In Frontiers in Neuroscience, 2019.
Reliable EEG source analysis depends on sufficiently detailed and accurate head models. In this study, we investigate how uncertainties inherent to the experimentally determined conductivity values of the different conductive compartments influence the results of EEG source analysis. In a single source scenario, the superficial and focal somatosensory P20/N20 component, we analyze the influence of varying conductivities on dipole reconstructions using a generalized polynomial chaos (gPC) approach. We find that in particular the conductivity uncertainties for skin and skull have a significant influence on the EEG inverse solution, leading to variations in source localization by several centimeters. The conductivity uncertainties for gray and white matter were found to have little influence on the source localization, but a strong influence on the strength and orientation of the reconstructed source, respectively. As the CSF conductivity is most accurately determined of all conductivities in a realistic head model, CSF conductivity uncertainties had a negligible influence on the source reconstruction. This small uncertainty is a further benefit of distinguishing the CSF in realistic volume conductor models.
Adaptive mesh refinement (AMR) is a key technology for large-scale simulations that allows for adaptively changing the simulation mesh resolution, resulting in significant computational and storage savings. However, visualizing such AMR data poses a significant challenge due to the difficulties introduced by the hierarchical representation when reconstructing continuous field values. In this paper, we detail a comprehensive solution for interactive isosurface rendering of block-structured AMR data. We contribute a novel reconstruction strategy—the octant method—which is continuous, adaptive and simple to implement. Furthermore, we present a generally applicable hybrid implicit isosurface ray-tracing method, which provides better rendering quality and performance than the built-in sampling-based approach in OSPRay. Finally, we integrate our octant method and hybrid isosurface geometry into OSPRay as a module, providing the ability to create high-quality interactive visualizations combining volume and isosurface representations of BS-AMR data. We evaluate the rendering performance, memory consumption and quality of our method on two gigascale block-structured AMR datasets.
A. Warner, J. Tate, B. Burton,, C.R. Johnson.
A High-Resolution Head and Brain Computer Model for Forward and Inverse EEG Simulation, In bioRxiv, Cold Spring Harbor Laboratory, Feb, 2019.
To conduct computational forward and inverse EEG studies of brain electrical activity, researchers must construct realistic head and brain computer models, which is both challenging and time consuming. The availability of realistic head models and corresponding imaging data is limited in terms of imaging modalities and patient diversity. In this paper, we describe a detailed head modeling pipeline and provide a high-resolution, multimodal, open-source, female head and brain model. The modeling pipeline specifically outlines image acquisition, preprocessing, registration, and segmentation; three-dimensional tetrahedral mesh generation; finite element EEG simulations; and visualization of the model and simulation results. The dataset includes both functional and structural images and EEG recordings from two high-resolution electrode configurations. The intermediate results and software components are also included in the dataset to facilitate modifications to the pipeline. This project will contribute to neuroscience research by providing a high-quality dataset that can be used for a variety of applications and a computational pipeline that may help researchers construct new head models more efficiently.
O. Abdullah, L. Dai, J. Tippetts, B. Zimmerman, A. Van Hoek, S. Joshi, E. Hsu.
High resolution and high field diffusion MRI in the visual system of primates (P3.086), In Neurology, Vol. 90, No. 15 Supplement, Wolters Kluwer Health, Inc, 2018.
Objective: Establishing a primate multiscale genetic brain network linking key microstructural brain components to social behavior remains an elusive goal.
Background: Diffusion MRI, which quantifies the magnitude and anisotropy of water diffusion in brain tissues, offers unparalleled opportunity to link the macroconnectome (resolution of ~0.5mm) to histological-based microconnectome at synaptic resolution.
Design/Methods: We tested the hypothesis that the simplest (and most clinically-used) reconstruction technique (known as diffusion tensor imaging, DTI) will yield similar brain connectivity patterns in the visual system (from optic chiasm to visual cortex) compared to more sophisticated and accurate reconstruction methods including diffusion spectrum imaging (DSI), q-ball imaging (QBI), and generalized q-sampling imaging. We obtained high resolution diffusion MRI data on ex vivo brain from Macaca fascicularis: MRI 7T, resolution 0.5 mm isotropic, 515 diffusion volumes up to b-value (aka diffusion sensitivity) of 40,000 s/mm2 with scan time ~100 hrs.
Results: Tractography results show that despite the limited ability of DTI to resolve crossing fibers at the optic chiasm, DTI-based tracts mapped to the known projections of layers in lateral geniculate nucleus and to the primary visual cortex. The other reconstructions were superior in localized regions for resolving crossing regions.
Conclusions: In conclusion, despite its simplifying assumptions, DTI-based fiber tractography can be used to generate accurate brain connectivity maps that conform to established neuroanatomical features in the visual system.
K. A. Aiello, S. P. Ponnapalli, O. Alter.
Mathematically universal and biologically consistent astrocytoma genotype encodes for transformation and predicts survival phenotype, In APL Bioengineering, Vol. 2, No. 3, AIP Publishing, pp. 031909. September, 2018.
DNA alterations have been observed in astrocytoma for decades. A copy-number genotype predictive of a survival phenotype was only discovered by using the generalized singular value decomposition (GSVD) formulated as a comparative spectral decomposition. Here, we use the GSVD to compare whole-genome sequencing (WGS) profiles of patient-matched astrocytoma and normal DNA. First, the GSVD uncovers a genome-wide pattern of copy-number alterations, which is bounded by patterns recently uncovered by the GSVDs of microarray-profiled patient-matched glioblastoma (GBM) and, separately, lower-grade astrocytoma and normal genomes. Like the microarray patterns, the WGS pattern is correlated with an approximately one-year median survival time. By filling in gaps in the microarray patterns, the WGS pattern reveals that this biologically consistent genotype encodes for transformation via the Notch together with the Ras and Shh pathways. Second, like the GSVDs of the microarray profiles, the GSVD of the WGS profiles separates the tumor-exclusive pattern from normal copy-number variations and experimental inconsistencies. These include the WGS technology-specific effects of guanine-cytosine content variations across the genomes that are correlated with experimental batches. Third, by identifying the biologically consistent phenotype among the WGS-profiled tumors, the GBM pattern proves to be a technology-independent predictor of survival and response to chemotherapy and radiation, statistically better than the patient's age and tumor's grade, the best other indicators, and MGMT promoter methylation and IDH1 mutation. We conclude that by using the complex structure of the data, comparative spectral decompositions underlie a mathematically universal description of the genotype-phenotype relations in cancer that other methods miss.
D. N. Anderson, B. Osting, J. Vorwerk, A. D Dorval, C. R Butson. Optimized programming algorithm for cylindrical and directional deep brain stimulation electrodes, In Journal of Neural Engineering, Vol. 15, No. 2, pp. 026005. 2018.
Objective. Deep brain stimulation (DBS) is a growing treatment option for movement and psychiatric disorders. As DBS technology moves toward directional leads with increased numbers of smaller electrode contacts, trial-and-error methods of manual DBS programming are becoming too time-consuming for clinical feasibility. We propose an algorithm to automate DBS programming in near real-time for a wide range of DBS lead designs. Approach. Magnetic resonance imaging and diffusion tensor imaging are used to build finite element models that include anisotropic conductivity. The algorithm maximizes activation of target tissue and utilizes the Hessian matrix of the electric potential to approximate activation of neurons in all directions. We demonstrate our algorithm's ability in an example programming case that targets the subthalamic nucleus (STN) for the treatment of Parkinson's disease for three lead designs: the Medtronic 3389 (four cylindrical contacts), the direct STNAcute (two cylindrical contacts, six directional contacts), and the Medtronic-Sapiens lead (40 directional contacts). Main results. The optimization algorithm returns patient-specific contact configurations in near real-time—less than 10 s for even the most complex leads. When the lead was placed centrally in the target STN, the directional leads were able to activate over 50% of the region, whereas the Medtronic 3389 could activate only 40%. When the lead was placed 2 mm lateral to the target, the directional leads performed as well as they did in the central position, but the Medtronic 3389 activated only 2.9% of the STN. Significance. This DBS programming algorithm can be applied to cylindrical electrodes as well as novel directional leads that are too complex with modern technology to be manually programmed. This algorithm may reduce clinical programming time and encourage the use of directional leads, since they activate a larger volume of the target area than cylindrical electrodes in central and off-target lead placements.
Objective: During deep brain stimulation (DBS), it is well understood that extracellular cathodic stimulation can cause activation of passing axons. Activation can be predicted from the second derivative of the electric potential along an axon, which depends on axonal orientation with respect to the stimulation source. We hypothesize that fiber orientation influences activation thresholds and that fiber orientations can be selectively targeted with DBS waveforms. Approach: We used bioelectric field and multicompartment NEURON models to explore preferential activation based on fiber orientation during monopolar or bipolar stimulation. Preferential fiber orientation was extracted from the principal eigenvectors and eigenvalues of the Hessian matrix of the electric potential. We tested cathodic, anodic, and charge-balanced pulses to target neurons based on fiber orientation in general and clinical scenarios. Main Results: Axons passing the DBS lead have positive second derivatives around a cathode, whereas orthogonal axons have positive second derivatives around an anode, as indicated by the Hessian. Multicompartment NEURON models confirm that passing fibers are activated by cathodic stimulation, and orthogonal fibers are activated by anodic stimulation. Additionally, orthogonal axons have lower thresholds compared to passing axons. In a clinical scenario, fiber pathways associated with therapeutic benefit can be targeted with anodic stimulation at 50% lower stimulation amplitudes. Significance: Fiber orientations can be selectively targeted with simple changes to the stimulus waveform. Anodic stimulation preferentially activates orthogonal fibers, approaching or leaving the electrode, at lower thresholds for similar therapeutic benefit in DBS with decreased power consumption.
Finite Element Framework for Computational Fluid Dynamics in FEBio, In Journal of Biomechanical Engineering, Vol. 140, No. 2, ASME International, pp. 021001. Jan, 2018.
The mechanics of biological fluids is an important topic in biomechanics, often requiring the use of computational tools to analyze problems with realistic geometries and material properties. This study describes the formulation and implementation of a finite element framework for computational fluid dynamics (CFD) in FEBio, a free software designed to meet the computational needs of the biomechanics and biophysics communities. This formulation models nearly incompressible flow with a compressible isothermal formulation that uses a physically realistic value for the fluid bulk modulus. It employs fluid velocity and dilatation as essential variables: The virtual work integral enforces the balance of linear momentum and the kinematic constraint between fluid velocity and dilatation, while fluid density varies with dilatation as prescribed by the axiom of mass balance. Using this approach, equal-order interpolations may be used for both essential variables over each element, contrary to traditional mixed formulations that must explicitly satisfy the inf-sup condition. The formulation accommodates Newtonian and non-Newtonian viscous responses as well as inviscid fluids. The efficiency of numerical solutions is enhanced using Broyden's quasi-Newton method. The results of finite element simulations were verified using well-documented benchmark problems as well as comparisons with other free and commercial codes. These analyses demonstrated that the novel formulation introduced in FEBio could successfully reproduce the results of other codes. The analogy between this CFD formulation and standard finite element formulations for solid mechanics makes it suitable for future extension to fluid–structure interactions (FSIs).