Project Details
Large-Scale Ultrasound Propagation Simulations in the Human Brain
Project Period: 1. 1. 2014 - 31. 12. 2016
Project Type: grant
Code: SoMoPro-II-2013-IG
Agency: South Moravian Centre for International Mobility
Program:
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.
Dvořák Václav, prof. Ing., DrSc. (UPSY FIT VUT) , team leader
2018
- SUOMI Visa, JAROŠ 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, vol. 65, no. 11, 2018, pp. 2660-2670. ISSN 0018-9294. Detail
2017
- ROBERTSON James L., COX Ben T., JAROŠ Jiří and TREEBY Bradley E. Accurate simulation of transcranial ultrasound propagation for ultrasonic neuromodulation and stimulation. Journal of the Acoustical Society of America, vol. 141, no. 3, 2017, pp. 1726-1738. ISSN 1520-8524. Detail
- AHMED Hashim U., SHAH Taimur T., GEORGIOU Panayiotis, JAROŠ 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. Medical Physics, vol. 44, no. 2, 2017, pp. 679-693. ISSN 0094-2405. Detail
2016
- TREEBY Bradley E., JAROŠ Jiří and COX Ben T. 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, vol. 9708. San Francisco: SPIE - the international society for optics and photonics, 2016, pp. 1-14. ISBN 978-1-62841-942-9. Detail
- BROWN Michael D., JAROŠ Jiří, COX Ben T. and TREEBY Bradley E. Control of Broadband Optically Generated Ultrasound Pulses Using Binary Amplitude Holograms. Journal of the Acoustical Society of America, vol. 139, no. 4, 2016, pp. 1637-1647. ISSN 1520-8524. Detail
- JAROŠ Jiří, RENDELL Alistair P. and TREEBY Bradley E. Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound. International Journal of High Performance Computing Applications, vol. 30, no. 2, 2016, pp. 137-155. ISSN 1741-2846. Detail
- MERTA Michal, ZAPLETAL Jan and JAROŠ Jiří. Many Core Acceleration of the Boundary Element Method. In: Proceedings of High Performance Computing in Science and Engineering. Lecture Notes in Computer Science, vol. 9611. Basel: Springer International Publishing, 2016, pp. 116-125. ISBN 978-3-319-40360-1. Detail
- SUOMI Visa, JAROŠ 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). Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. Orlando: Institute of Electrical and Electronics Engineers, 2016, pp. 5648-5651. ISBN 978-1-4577-0220-4. Detail
- JAROŠ Jiří, VAVERKA Filip and TREEBY Bradley E. Spectral Domain Decomposition Using Local Fourier Basis: Application to Ultrasound Simulation on a Cluster of GPUs. Supercomputing Frontiers and Innovations, vol. 3, no. 3, 2016, pp. 40-55. ISSN 2313-8734. Detail
- JAROŠ Jiří, VAVERKA Filip and TREEBY Bradley E. Spectral Domain Decomposition Using Local Fourier Basis: Application to Ultrasound Simulation on a Cluster of GPUs. Salt Lake City, 2016. Detail
2015
- JAROŠ 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. Detail
- JAROŠ 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. Detail
2014
- TREEBY Bradley E., JAROŠ Jiří, ROHRBACH Daniel and COX Ben T. 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, pp. 146-149. ISBN 978-1-4799-7049-0. Detail
- NIKL Vojtěch and JAROŠ Jiří. 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, vol. 8934. Heidelberg: Springer International Publishing, 2014, pp. 100-112. ISBN 978-3-319-14895-3. Detail