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

Czech title

Simulace šíření ultrazvukových vln v lidském mozku

Type

grant

Keywords

Brain research, Oncology, Acoustics, Computational physics, Modelling tools, Computer science.

Abstract

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.

Team members

Jaroš Jiří, doc. Ing., Ph.D. (DCSY) – research leader
Dvořák Václav, prof. Ing., DrSc.

Publications

2018

SUOMI, V.; JAROŠ, J.; TREEBY, B.; CLEVELAND, R. Full modelling of high-intensity focused ultrasound and thermal heating in the kidney of realistic patient models. IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, 2018, vol. 65, no. 11, p. 2660-2670. ISSN: 0018-9294. Detail

2017

AHMED, H.; SHAH, T.; GEORGIOU, P.; JAROŠ, J.; PAYNE, H.; ALLEN, C.; GIBSON, E.; BARRATT, D.; TREEBY, B. Beam Distortion Due to Gold Fiducial Markers During Salvage High-Intensity Focused Ultrasound in the Prostate. MEDICAL PHYSICS, 2017, vol. 44, no. 2, p. 679-693. ISSN: 0094-2405. Detail
ROBERTSON, J.; COX, B.; JAROŠ, J.; TREEBY, B. Accurate simulation of transcranial ultrasound propagation for ultrasonic neuromodulation and stimulation. Journal of the Acoustical Society of America, 2017, vol. 141, no. 3, p. 1726-1738. ISSN: 1520-8524. Detail

2016

BROWN, M.; JAROŠ, J.; COX, B.; TREEBY, B. Control of Broadband Optically Generated Ultrasound Pulses Using Binary Amplitude Holograms. Journal of the Acoustical Society of America, 2016, vol. 139, no. 4, p. 1637-1647. ISSN: 1520-8524. Detail
JAROŠ, J.; RENDELL, A.; TREEBY, B. Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound. International Journal of High Performance Computing Applications, 2016, vol. 30, no. 2, p. 137-155. ISSN: 1741-2846. Detail
JAROŠ, J.; VAVERKA, F.; TREEBY, B. Spectral Domain Decomposition Using Local Fourier Basis: Application to Ultrasound Simulation on a Cluster of GPUs. Salt Lake City: 2016. p. 1 (1 s.). Detail
JAROŠ, J.; VAVERKA, F.; TREEBY, B. Spectral Domain Decomposition Using Local Fourier Basis: Application to Ultrasound Simulation on a Cluster of GPUs. International Journal of Supercomputing Frontiers and Innovations, 2016, vol. 3, no. 3, p. 40-55. ISSN: 2313-8734. Detail
MERTA, M.; ZAPLETAL, J.; JAROŠ, J. Many Core Acceleration of the Boundary Element Method. In Proceedings of High Performance Computing in Science and Engineering. Lecture Notes in Computer Science. Basel: Springer International Publishing, 2016. p. 116-125. ISBN: 978-3-319-40360-1. Detail
SUOMI, V.; JAROŠ, J.; TREEBY, B.; CLEVELAND, R. 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). Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. Orlando: Institute of Electrical and Electronics Engineers, 2016. p. 5648-5651. ISBN: 978-1-4577-0220-4. Detail
TREEBY, B.; JAROŠ, J.; COX, B. Advanced photoacoustic image reconstruction using the k-Wave toolbox. In Progress in Biomedical Optics and Imaging - Proceedings of SPIE. Progress in Biomedical Optics and Imaging - Proceedings of SPIE. San Francisco: SPIE - the international society for optics and photonics, 2016. p. 1-14. ISBN: 978-1-62841-942-9. Detail

2015

JAROŠ, J.; DOHNAL, M.; TREEBY, B. Large-scale Ultrasound Simulations with Local Fourier Basis Decomposition. The International Conference for High Performance Computing, Networking, Storage Analysis, SC15. Austin: 2015. p. 0-0. Detail
JAROŠ, J.; NIKL, V.; TREEBY, B. Large-scale Ultrasound Simulations Using the Hybrid OpenMP/MPI Decomposition. Proceedings of the 3rd International Conference on Exascale Applications and Software. Edinburgh: Association for Computing Machinery, 2015. p. 115-119. ISBN: 978-0-9926615-1-9. Detail

2014

NIKL, V.; JAROŠ, J. Parallelisation of the 3D Fast Fourier Transform Using the Hybrid OpenMP/MPI Decomposition. In Mathematical and Engineering Methods in Computer Science. Lecture Notes in Computer Science. Heidelberg: Springer International Publishing, 2014. p. 100-112. ISBN: 978-3-319-14895-3. Detail
TREEBY, B.; JAROŠ, J.; ROHRBACH, D.; COX, B. Modelling Elastic Wave Propagation Using the k-Wave MATLAB Toolbox. In IEEE International Ultrasonics Symposium, IUS. Chicago, IL: Institute of Electrical and Electronics Engineers, 2014. p. 146-149. ISBN: 978-1-4799-7049-0. Detail