Pseudo-CTs from T1-weighted MRI for planning of low-intensity transcranial focused ultrasound neuromodulation: An open-source tool

Yaakub, Siti N.; White, Tristan A.; Kerfoot, Eric; Verhagen, Lennart; Hammers, Alexander; Fouragnan, Elsa

doi:10.1016/j.brs.2023.01.838

Cited by 21 publications

(21 citation statements)

References 7 publications

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“…Next, we performed transcranial simulations for the dACC and PCC for each participant in the study. We estimated the skull for each participant from a pseudo-CT derived from the participant's T1-weighted MRI using a deep learning method 36,37 . The skull was obtained from pseudo-CT images by thresholding at 300 HU and clamping values above 2000 HU.…”

Section: Acoustic Simulationsmentioning

confidence: 99%

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Transcranial focused ultrasound-mediated neurochemical and functional connectivity changes in deep cortical regions in humans

Yaakub

White

Roberts

et al. 2023

Preprint

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Low-intensity transcranial ultrasound stimulation (TUS) is an emerging non-invasive technique for focally modulating human brain function. The mechanisms and neurochemical substrates underlying TUS neuromodulation in humans and how these relate to excitation and inhibition are still poorly understood. In 24 healthy controls, we separately stimulated two deep cortical regions and investigated the effects of theta-burst TUS, a protocol shown to increase corticospinal excitability, on the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) and functional connectivity. We show for the first time in humans that theta-burst TUS selectively reduces GABA levels in the posterior cingulate, but not the dorsal anterior cingulate cortex. Functional connectivity increased following TUS in both regions. Our findings suggest that TUS changes overall excitability by reducing GABAergic inhibition, that changes in TUS-mediated neuroplasticity last at least 50 minutes after stimulation, and that these effects may be state-dependent - a mechanism increasingly recognized to influence the brain's response to neuromodulation.

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Section: Acoustic Simulationsmentioning

confidence: 99%

“…We set our simulation grid size to the size of the T1-weighted MRI with a grid spacing of 1 mm. Our acoustic simulation methods are described in further detail elsewhere 40 and the code is available online 41 .…”

Section: Acoustic Simulationsmentioning

confidence: 99%

Transcranial focused ultrasound-mediated neurochemical and functional connectivity changes in deep cortical regions in humans

Yaakub

White

Roberts

et al. 2023

Preprint

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“…However, the usage of CT scans is often constrained due to concerns about ionizing radiation exposure. To address this challenge, we used a toolbox developed by Yaakub, White, Kerfoot et al (2023). This toolbox uses deep learning convolutional neural networks (CNNs) to generate pseudo-CT images from anatomical T1-weighted MRI images, thereby aiding the planning process for TUS.…”

Section: Structural Mri and Pseudo-ctmentioning

confidence: 99%

“…We visually inspected the pseudo-CTs by comparing them with their corresponding T1-weighted images and identified no irregularities. It is important to mention that the T1 MR protocol employed in our study differed slightly from the one used in the initial development of the pseudo-CT algorithm by Yaakub, White., Kerfoot et al (2023). However, according to Yaakub, White, Roberts et al (2023), such variations in the T1 MR protocol do not significantly affect the fidelity of converting MRI to pseudo-CT images.…”

Section: Tus Simulationmentioning

confidence: 99%

Personalized depth‐specific neuromodulation of the human primary motor cortex via ultrasound

Bao,

Kim,

Shettigar

et al. 2024

The Journal of Physiology

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Non‐invasive brain stimulation has the potential to boost neuronal plasticity in the primary motor cortex (M1), but it remains unclear whether the stimulation of both superficial and deep layers of the human motor cortex can effectively promote M1 plasticity. Here, we leveraged transcranial ultrasound stimulation (TUS) to precisely target M1 circuits at depths of approximately 5 mm and 16 mm from the cortical surface. Initially, we generated computed tomography images from each participant's individual anatomical magnetic resonance images (MRI), which allowed for the generation of accurate acoustic simulations. This process ensured that personalized TUS was administered exactly to the targeted depths within M1 for each participant. Using long‐term depression and long‐term potentiation (LTD/LTP) theta‐burst stimulation paradigms, we examined whether TUS over distinct depths of M1 could induce LTD/LTP plasticity. Our findings indicated that continuous theta‐burst TUS‐induced LTD‐like plasticity with both superficial and deep M1 stimulation, persisting for at least 30 min. In comparison, sham TUS did not significantly alter M1 excitability. Moreover, intermittent theta‐burst TUS did not result in the induction of LTP‐ or LTD‐like plasticity with either superficial or deep M1 stimulation. These findings suggest that the induction of M1 plasticity can be achieved with ultrasound stimulation targeting distinct depths of M1, which is contingent on the characteristics of TUS. imageKey points The study integrated personalized transcranial ultrasound stimulation (TUS) with electrophysiology to determine whether TUS targeting superficial and deep layers of the human motor cortex (M1) could elicit long‐term depression (LTD) or long‐term potentiation (LTP) plastic changes. Utilizing acoustic simulations derived from individualized pseudo‐computed tomography scans, we ensured the precision of TUS delivery to the intended M1 depths for each participant. Continuous theta‐burst TUS targeting both the superficial and deep layers of M1 resulted in the emergence of LTD‐like plasticity, lasting for at least 30 min. Administering intermittent theta‐burst TUS to both the superficial and deep layers of M1 did not lead to the induction of LTP‐ or LTD‐like plastic changes. We suggest that theta‐burst TUS targeting distinct depths of M1 can induce plasticity, but this effect is dependent on specific TUS parameters.

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“…A method based on normalizing the ZTE signal has the advantage of requiring training. However, as ML methods continue to improve [11,26,40,41], there is a potential of reducing the need for training data from CT scans for studies with limited access to them.…”

Section: Current Limitations Of Zte-based Processingmentioning

confidence: 99%

BabelBrain: An Open-Source Application for Prospective Modeling of Transcranial Focused Ultrasound for Neuromodulation Applications

Pichardo¹

2023

Preprint

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BabelBrain is an open-source standalone graphic-user-interface application designed for studies of neuromodulation using transcranial focused ultrasound. It calculates the transmitted acoustic field in the brain tissue, taking into account the distortion effects caused by the skull barrier. The simulation is prepared using scans from magnetic resonance imaging (MRI) and, if available, computed tomography and zero-echo time MRI scans. It also calculates the thermal effects based on a given ultrasound regime, such as the total duration of exposure, the duty cycle, and acoustic intensity. The tool is designed to work in tandem with neuronavigation and visualization software, such as 3DSlicer. It uses image processing to prepare domains for ultrasound simulation and uses the Ba-belViscoFDTD library for transcranial modeling calculations. BabelBrain supports multiple GPU backends, including Metal, OpenCL, and CUDA, and works on all major operating systems including Linux, MacOS, and Windows. This tool is particularly optimized for Apple ARM64 systems, which are common in brain imaging research. The paper presents the modeling pipeline used in BabelBrain and a numerical study where different methods of acoustic properties mapping were tested to select the best method that can reproduce the transcranial pressure transmission efficiency reported in the literature.

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Pseudo-CTs from T1-weighted MRI for planning of low-intensity transcranial focused ultrasound neuromodulation: An open-source tool

Cited by 21 publications

References 7 publications

Transcranial focused ultrasound-mediated neurochemical and functional connectivity changes in deep cortical regions in humans

Transcranial focused ultrasound-mediated neurochemical and functional connectivity changes in deep cortical regions in humans

Personalized depth‐specific neuromodulation of the human primary motor cortex via ultrasound

BabelBrain: An Open-Source Application for Prospective Modeling of Transcranial Focused Ultrasound for Neuromodulation Applications

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