Novel toolbox for planning transcranial ultrasound stimulation studies in humans

Brain Stimulation Lab
Simulated focused ultrasound beam (red/blue) and location of magnetic resonance spectroscopy measurement (white square) overlaid on a structural magnetic resonance image (MRI)
Pseudo-CTs from T1-weighted MRI for planning of low-intensity transcranial focused ultrasound neuromodulation: An open-source tool
Led by University of Plymouth: Siti Nurbaya Yaakub, Tristan A. White, Professor Elsa Fouragnan
 
Partners: Kings College London; Radboud University Nijmegen, Netherlands
 
2023
Aimed for use by other researchers, we created a novel toolbox to generate computed tomography (CT) images from anatomical T1-weighted magnetic resonance (MR) images for use in planning transcranial ultrasound stimulation (TUS) studies in humans. This software is used across many labs (UK, Europe, US and China; 41 users).
 
Alternative methods to CT scans
As the skulls accounts for the bulk of transcranial ultrasound attenuation and aberration, individualised skull models of bone density and geometry are an essential part of planning TUS studies safely, precisely and efficiently. CT images are considered the gold standard for skull imaging, but obtaining CT images for research participants can be prohibitive as it includes exposure to radiation and they are not always readily available. 
Alternative methods to estimate the skull include short echo time (TE) MR imaging sequences and deep learning convolutional neural networks (CNNs) for translating MR to CT images. Its use in TUS research is also low as these methods are not freely available or easily implemented.
Open-source toolbox aims to facilitate reproducibility and best practice in TUS
This method generates pseudo-CT which can be used to produce accurate acoustic stimulations with focal pressures statistically equivalent to stimulations based on reference CTs.

Toolbox: https://github.com/sitiny/mr-to-pct
Code to run k-Wave-based transcranial simulations of the ultrasound acoustic field and temperature as described in the Supplementary Methods: https://github.com/sitiny/BRIC_TUS_Simulation_Tools
Publication
Yaakub SN, White TA, Kerfoot E, Verhagen L, Hammers A & Fouragnan EF (2023) 'Pseudo-CTs from T1-weighted MRI for planning of low-intensity transcranial focused ultrasound neuromodulation: An open-source tool' Brain Stimulation 16, (1) 75-78 , DOI Open access
Leading the way in transcranial ultrasound stimulation
The University of Plymouth's pioneering research in transcranial ultrasound stimulation has the potential to improve the lives of millions of people with mental health conditions as well as neurological disorders like Parkinson’s disease.
Professor Elsa Fouragnan is a leading authority on transcranial ultrasound stimulation research in the UK, and is recognised internationally. Her lab is one of the few in the UK to apply TUS in humans.
This research is hosted at the University’s Brain Research & Imaging Centre (BRIC) – the most advanced multi-modal brain research facility in the South West.
Dr. Elsa Fouragnan