Full modelling of high-intensity focused ultrasound and thermal heating in the kidney using realistic patient models

Objective: High-intensity focused ultrasound (HIFU) therapy can be used for non-invasive treatment of kidney (renal) cancer, but the clinical outcomes have been variable. In this study, the efficacy of renal HIFU therapy was studied using nonlinear acoustic and thermal simulations in three patients. Methods: The acoustic simulations were conducted with and without refraction in order to investigate its effect on the shape, size and pressure distribution at the focus. The values for the attenuation, sound speed, perfusion and thermal conductivity of the kidney were varied over the reported ranges to determine the effect of variability on heating. Furthermore, the phase aberration was studied in order to quantify the underlying phase shifts using a second order polynomial function. Results: The ultrasound field intensity was found to drop on average 11.1 dB with refraction and 6.4 dB without refraction. Reflection at tissue interfaces was found to result in a loss less than 0.1 dB. Focal point splitting due to refraction significantly reduced the heating efficacy. Perfusion did not have a large effect on heating during short sonication durations. Small changes in temperature were seen with varying attenuation and thermal conductivity, but no visible changes were present with sound speed variations. The aberration study revealed an underlying trend in the spatial distribution of the phase shifts. Conclusion: The results show that the efficacy of HIFU therapy in the kidney could be improved with aberration correction. Significance: A method is proposed by which patient specific pre-treatment calculations could be used to overcome the aberration and therefore make ultrasound treatment possible.Comment: Journal paper, IEEE Transactions on Biomedical Engineering (2018

Performance Evaluation of Pseudospectral Ultrasound Simulations on a Cluster of Xeon Phi Accelerators

The rapid development of novel procedures in medical ultrasonics, including treatment planning in therapeutic ultrasound and image reconstruction in photoacoustic tomography, leads to increasing demand for large-scale ultrasound simulations. However, routine execution of such simulations using traditional methods, e.g., finite difference time domain, is expensive and often considered intractable due to the computational and memory requirements. The k-space corrected pseudospectral time domain method used by the k-Wave toolbox allows for significant reductions in spatial and temporal grid resolution. These improvements are achieved at the cost of all-to-all communication, which are inherent to the multi-dimensional fast Fourier transforms. To improve data locality, reduce communication and allow efficient use of accelerators, we recently implemented a domain decomposition technique based on a local Fourier basis. In this paper, we investigate whether it is feasible to run the distributed k-Wave implementation on the Salomon cluster equipped with 864 Intel Xeon Phi (Knight’s Corner) accelerators. The results show the immaturity of the KNC platform with issues ranging from limited support of Infiniband and LustreFS in Intel MPI on this platform to poor performance of 3D FFTs achieved by Intel MKL on the KNC architecture. Yet, we show that it is possible to achieve strong and weak scaling comparable to CPU-only platforms albeit with the runtime 1.8× to 4.3× longer. However, the accounting policy for Salomon’s accelerators is far more favorable and thus their employment reduces the computational cost significantly

Eulerian-Lagrangian method for simulation of cloud cavitation

We present a coupled Eulerian-Lagrangian method to simulate cloud cavitation in a compressible liquid. The method is designed to capture the strong, volumetric oscillations of each bubble and the bubble-scattered acoustics. The dynamics of the bubbly mixture is formulated using volume-averaged equations of motion. The continuous phase is discretized on an Eulerian grid and integrated using a high-order, finite-volume weighted essentially non-oscillatory (WENO) scheme, while the gas phase is modeled as spherical, Lagrangian point-bubbles at the sub-grid scale, each of whose radial evolution is tracked by solving the Keller-Miksis equation. The volume of bubbles is mapped onto the Eulerian grid as the void fraction by using a regularization (smearing) kernel. In the most general case, where the bubble distribution is arbitrary, three-dimensional Cartesian grids are used for spatial discretization. In order to reduce the computational cost for problems possessing translational or rotational homogeneities, we spatially average the governing equations along the direction of symmetry and discretize the continuous phase on two-dimensional or axi-symmetric grids, respectively. We specify a regularization kernel that maps the three-dimensional distribution of bubbles onto the field of an averaged two-dimensional or axi-symmetric void fraction. A closure is developed to model the pressure fluctuations at the sub-grid scale as synthetic noise. For the examples considered here, modeling the sub-grid pressure fluctuations as white noise agrees a priori with computed distributions from three-dimensional simulations, and suffices, a posteriori, to accurately reproduce the statistics of the bubble dynamics. The numerical method and its verification are described by considering test cases of the dynamics of a single bubble and cloud cavitaiton induced by ultrasound fields.Comment: 28 pages, 16 figure

Estimation of Execution Parameters for k-Wave Simulations

Estimation of execution parameters takes centre stage in automatic offloading of complex biomedical workflows to cloud and high performance facilities. Since ordinary users have no or very limited knowledge of the performance characteristics of particular tasks in the workflow, the scheduling system has to have the capabilities to select appropriate amount of compute resources, e.g., compute nodes, GPUs, or processor cores and estimate the execution time and cost. The presented approach considers a fixed set of executables that can be used to create custom workflows, and collects performance data of successfully computed tasks. Since the workflows may differ in the structure and size of the input data, the execution parameters can only be obtained by searching the performance database and interpolating between similar tasks. This paper shows it is possible to predict the execution time and cost with a high confidence. If the task parameters are found in the performance database, the mean interpolation error stays below 2.29%. If only similar tasks are found, the mean interpolation error may grow up to 15%. Nevertheless, this is still an acceptable error since the cluster performance may vary on order of percent as well

Simulating Focused Ultrasound Transducers using Discrete Sources on Regular Cartesian Grids

Accurately representing the behaviour of acoustic sources is an important part of ultrasound simulation. This is particularly challenging in ultrasound therapy where multielement arrays are often used. Typically, sources are defined as a boundary condition over a 2D plane within the computational model. However, this approach can become difficult to apply to arrays with multiple elements distributed over a non-planar surface. In this work, a grid-based discrete source model for single and multi-element bowl-shaped transducers is developed to model the source geometry explicitly within a regular Cartesian grid. For each element, the source model is defined as a symmetric, simply-connected surface with a single grid point thickness. Simulations using the source model with the opensource k-Wave toolbox are validated using the Rayleigh integral, O'Neil's solution, and experimental measurements of a focused bowl transducer under both quasi continuous wave and pulsed excitation. Close agreement is shown between the discrete bowl model and the axial pressure predicted by O'Neil's solution for a uniform curved radiator, even at very low grid resolutions. Excellent agreement is also shown between the discrete bowl model and experimental measurements. To accurately reproduce the near-field pressure measured experimentally, it is necessary to derive the drive signal at each grid point of the bowl model directly using holography. However, good agreement is also obtained in the focal region using uniformly radiating monopole sources distributed over the bowl surface. This allows the response of multi-element transducers to be modelled, even where measurement of an input plane is not possible

Wave Propagation

A wave is one of the basic physics phenomena observed by mankind since ancient time. The wave is also one of the most-studied physics phenomena that can be well described by mathematics. The study may be the best illustration of what is “science”, which approximates the laws of nature by using human defined symbols, operators, and languages. Having a good understanding of waves and wave propagation can help us to improve the quality of life and provide a pathway for future explorations of the nature and universe. This book introduces some exciting applications and theories to those who have general interests in waves and wave propagations, and provides insights and references to those who are specialized in the areas presented in the book

Evaluation of the Suitability of Intel Xeon Phi Clusters for the Simulation of Ultrasound Wave Propagation Using Pseudospectral Methods

The ability to perform large-scale ultrasound simulations using Fourier pseudospectral methods has generated significant interest in medical ultrasonics, including for treatment planning in therapeutic ultrasound and image reconstruction in photoacoustic tomography. However, the routine execution of such simulations is computationally very challenging. Nowadays, the trend in parallel computing is towards the use of accelerated clusters where computationally intensive parts are offloaded from processors to accelerators. During last five years, Intel has released two generations of Xeon Phi accelerators. The goal of this paper is to investigate the performance on both architectures with respect to current processors, and evaluate the suitability of accelerated clusters for the distributed simulation of ultrasound propagation using Fourier-based methods. The paper reveals that the former version of Xeon Phis, the Knight’s Corner architecture, suffers from several flaws that reduce the performance far below the Haswell processors. On the other hand, the second generation called Knight’s Landing shows very promising performance comparable with current processors