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Planning for Transcranial Focused Ultrasound Neuromodulation


One of the aspects of safely and accurately targeting brain regions with transcranial focused ultrasound is estimating the trajectory and intensity of the ultrasound waves through the skull. Our projects in this theme include synthesising individual skull maps for each study participant and using computer simulations to estimate the acoustic field through the skull. Our methods are described below. For more details, see our paper:

Estimating individual skull geometry

Individual skull models of bone density and geometry are important when planning the expected transcranial ultrasound acoustic field and estimating mechanical and thermal safety in low-intensity transcranial ultrasound stimulation (TUS) studies. Computed tomography (CT) images have typically been used to estimate skull acoustic properties. However, obtaining CT images in research participants may be prohibitive due to exposure to ionising radiation and limited access to CT scanners within research groups.


We present a validated open-source tool for researchers to obtain individual skull estimates from T1-weighted magnetic resonance (MR) images, for use in acoustic simulations. We refined a previously trained and validated 3D convolutional neural network (CNN) to generate 100 keV pseudo-CTs. The network was pretrained on 110 individuals and refined and tested on a database of 37 healthy control individuals. Compared with reference CTs, our CNN produced pseudo-CTs with a mean absolute error of 109.8 ± 13.0 HU across the whole head.

Our toolbox is available on GitHub:


Clockwise from top left: Structural T1-weighted MR image, actual CT image, pseudo-CT image synthesised from T1-weighted MRI, difference image between pseudo-CT and real CT.

Acoustic simulations


We can estimate and visualise the path of the acoustic pressure wave generated by the ultrasound transducer through the skull using computer simulations. We use a Matlab-based toolbox, k-Wave (Treeby and Cox, 2010), to perform acoustic simulations based on individual skull anatomy and transducer positions to get a better picture of where the ultrasound wave is going and how much pressure is being applied.

We compared simulations based on reference CTs to simulations based on our pseudo-CTs and binary skull masks, a common alternative in the absence of CT. The focal pressure was statistically equivalent for simulations based on reference CT and pseudo-CT (0.48 +/- 0.04 MPa and 0.50 +/- 0.04 MPa respectively) but not for binary skull masks (0.28 +/- 0.05 MPa). We show that our network can produce pseudo-CT comparable to reference CTs in healthy individuals, and that these can be used in acoustic simulations.

Our code for performing acoustic simulations is available on GitHub:

Feel free to contact us if you are interested in using our method to go from T1-weighted MR images to pseudo-CT and using these for your acoustic simulations!


Left to right: Structural T1-weighted MR image, CT image, simulated ultrasound focus in the dorsal anterior cingulate cortex (in colour) on the structural MR image.

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