Department of Computer Systems

Large-Scale Simulations of the Ultrasound Wave Propagation in the Human Brain

Czech title:Simulace ąíření ultrazvukových vln v lidském mozku
Reseach leader:Jaroą Jiří
Team leaders:Dvořák Václav
Agency:South Moravian Centre for International Mobility
Keywords:Brain research, Oncology, Acoustics, Computational physics, Modelling tools, Computer science.
The simulation of ultrasound wave propagation through biological tissue has a wide range of practical applications. Recently, high intensity focused ultrasound has been applied to functional neurosurgery as an alternative, non-invasive treatment of various brain disorders such as brain tumours, cerebral haemorrhage, essential tremor, and Parkinsons disease. The technique works by sending a focused beam of ultrasound into the tissue, typically using a large transducer. At the focus, the acoustic energy is sufficient to cause cell death in a localised region while the surrounding tissue is left unharmed. The major challenge is to ensure the focus is accurately placed at the desired target within the brain because the skull can significantly distort it. The accurate ultrasound simulations thus gain importance in providing patient specific treatment plans. However, existing simulation tools are unable to cope with the extreme scale and physical complexity of realistic simulations in the brain.
The aim of this project is to develop, validate and apply new computer models to simulate how ultrasound waves travel through the intact skull and inside the brain. These models will be based on innovative advances in theoretical acoustic and numerical methods, and will use the state-of-the-art computing facilities that have only recently become available. They will allow to accurately predict the position of the focus in the brain during the treatment for the first time. This will allow physicians to carefully plan and optimise the treatment parameters to increase the effectiveness of the focused ultrasound surgery, reduce the time it takes to treat patients and extend the range and location of cancers that are eligible for treatment.


2016CUDA implementation of the k-Wave Toolbox version 1.1, software, 2016
Authors: Jaroą Jiří, Treeby Bradley E.
2014C++ implementation of the k-Wave Toolbox version 1.1, software, 2014
Authors: Jaroą Jiří, Treeby Bradley E., Cox Ben T.


2017GEORGIOU Panyiotis, JARO© Jiří, PAYNE Heather, ALLEN Clare, GIBSON Eli, BARRATT Dean and TREEBY Bradley E. Beam Distortion Due to Gold Fiducial Markers During Salvage High-Intensity Focused Ultrasound in the Prostate. Journal of Medical Physics. 111 River St., Hoboken, NJ 07030-5774: American Association of Physicists in Medicine, 2017, vol. 44, no. 2, pp. 679-693. ISSN 0094-2405.
 ROBERTSON James L., COX Ben T., JARO© Jiří and TREEBY Bradley E. Accurate simulation of transcranial ultrasound propagation for ultrasonic neuromodulation and stimulation. The Journal of the Acoustical Society of America. 2017, vol. 141, no. 3, pp. 1726-1738. ISSN 1520-8524.
 SUOMI Visa, JARO© Jiří, TREEBY Bradley E. and CLEVELAND Robin. Full modelling of high-intensity focused ultrasound and thermal heating in the kidney of realistic patient models. IEEE Transactions on Biomedical Engineering. 2017, vol. 2017, no. 66, pp. 1-12. ISSN 0018-9294.
2016BROWN Michael D., JARO© Jiří, COX Ben T. and TREEBY Bradley E. Control of Broadband Optically Generated Ultrasound Pulses Using Binary Amplitude Holograms. The Journal of the Acoustical Society of America. 2016, vol. 139, no. 4, pp. 1637-1647. ISSN 1520-8524.
 JARO© Jiří, RENDELL Alistair P. and TREEBY Bradley E. Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound. The International Journal of High Performance Computing Applications. 2455 Teller Road Thousand Oaks, CA 91320: SAGE Publications, 2016, vol. 2016, no. 2, pp. 137-155. ISSN 1741-2846.
 JARO© Jiří, VAVERKA Filip and TREEBY Bradley E. Spectral Domain Decomposition Using Local Fourier Basis: Application to Ultrasound Simulation on a Cluster of GPUs. International Journal of Supercomputing Frontiers and Innovations. South Ural State University (Chelyabinsk, Russia): Association for Computing Machinery, 2016, vol. 3, no. 3, pp. 39-54. ISSN 2313-8734.
 MERTA Michal, ZAPLETAL Jan and JARO© Jiří. Many Core Acceleration of the Boundary Element Method. In: Proceedings of High Performance Computing in Science and Engineering. Basel: Springer International Publishing, 2016, pp. 116-125. ISBN 978-3-319-40360-1.
 SUOMI Visa, JARO© Jiří, TREEBY Bradley E. and CLEVELAND Robin. Nonlinear 3-D simulation of high-intensity focused ultrasound therapy in the kidney. In: 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). Orlando: Institute of Electrical and Electronics Engineers, 2016, pp. 5648-5651. ISBN 978-1-4577-0220-4.
 TREEBY Bradley E., JARO© Jiří and COX Ben T. Advanced photoacoustic image reconstruction using the k-Wave toolbox. In: SPIE Proceedings Vol. 9708: Photons Plus Ultrasound: Imaging and Sensing 2016. San Francisco: SPIE - the international society for optics and photonics, 2016, pp. 1-14. ISBN 978-1-62841-942-9.
2015JARO© Jiří, DOHNAL Matěj and TREEBY Bradley E. Large-scale Ultrasound Simulations with Local Fourier Basis Decomposition. The International Conference for High Performance Computing, Networking, Storage Analysis, SC15. Austin, 2015.
 JARO© Jiří, NIKL Vojtěch and TREEBY Bradley E. Large-scale Ultrasound Simulations Using the Hybrid OpenMP/MPI Decomposition. In: Proceedings of the 3rd International Conference on Exascale Applications and Software. Edinburgh: Association for Computing Machinery, 2015, pp. 115-119. ISBN 978-0-9926615-1-9.
2014NIKL Vojtěch and JARO© Jiří. Parallelisation of the 3D Fast Fourier Transform Using the Hybrid OpenMP/MPI Decomposition. In: Mathematical and Engineering Methods in Computer Science. Heidelberg: Springer International Publishing, 2014, pp. 100-112. ISBN 978-3-319-14895-3.
 TREEBY Bradley E., JARO© Jiří, ROHRBACH Daniel and COX Ben T. Modelling Elastic Wave Propagation Using the k-Wave MATLAB Toolbox. In: 2014 IEEE International Ultrasonics Symposium (IUS). Chicago, IL: Institute of Electrical and Electronics Engineers, 2014, pp. 146-149. ISBN 978-1-4799-7049-0.

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