Biology subjects

Waks, M.

Publications and source records attributed to Waks, M..

7 recordsLinked to original sources

bioRxiv2025

10.5 Tesla High-Resolution Macaque Brain MRI for Connectivity Studies

Mapping brain connectivity in primates remains a major challenge due to difficulties in resolving microscopic white matter architecture, while maintaining whole-brain coverage. Increasing imaging spatial resolution is key for disambiguating fibre configurations within smaller anatomical volumes. Here, we present novel developments that allow high-resolution diffusion MRI of the macaque brain using one of the world's highest-field human MRI scanners operating at 10.5 Tesla, allowing both in vivo and ex vivo macaque brain imaging. Our approach achieves very high spatial resolution across both tissue states, (up to 580 m)3 in vivo and (300 m)3 ex vivo, with diffusion weighting up to b = 6000 s/mm2. We detail methodological advances in data acquisition, image reconstruction, processing and whole-brain tractography that overcome critical challenges associated with ultra-high-field imaging. This work establishes a new framework for high-resolution in vivo and ex vivo neuroimaging of the NHP brain at 10.5 T using a human bore scanner, paving the way for subsequent analyses of brain connectivity across species and tissue states at unprecedented detail. The dataset, along with all processing pipelines, containerised workflows, and reusable web services, is openly shared to support reproducibility and future integration with microscopy for studying white matter microstructure and connections at the mesoscale.

neuroscience↗

bioRxiv2025

Diffusion-weighted steady-state free precession imaging in the ex vivo macaque brain on a 10.5T human MRI scanner

Diffusion MRI provides a non-invasive probe of local fibre bundles and long-range anatomical connections to characterise the structural connectome. One way to achieve very high spatial resolution diffusion MRI data for connectivity investigations is to scan ex-vivo brains over many hours or days, ideally at ultra-high field strength to boost signal levels. However, conventional diffusion MRI acquisition techniques do not generally deliver good data quality for the challenging conditions of ex-vivo tissue, characterised by reduced diffusivities and relaxation times when compared to in vivo. In this work, we investigate the potential of the diffusion-weighted steady-state free precession (DW-SSFP) sequence for ex vivo diffusion imaging of the macaque brain using a 10.5 T human MRI scanner with a conventional (Gmax = 70 mT/m) gradient set. SNR-efficiency optimisations incorporating experimental relaxation times demonstrate that the DW-SSFP sequence is predicted to achieve improved or similar SNR efficiency compared to a diffusion-weighted spin- and stimulated-echo sequence. Importantly, DW-SSFP can achieve this with the additional benefit of negligible geometric distortions, unlike conventional diffusion MRI using an echo-planar imaging readout. Using optimised DW-SSFP sequence parameters, we propose a protocol at 0.4 mm isotropic resolution using a two-shell multi-orientation protocol (effective b-values of 3200 s/mm2 and 5600 s/mm2). We fit the data using Tensor, Ball and 3-Sticks and Constrained Spherical Deconvolution signal representations. The results demonstrate high-quality diffusivity estimates across the entire brain with the ability to resolve multiple fibre populations in challenging crossing-fibre regions. The data will be made fully open source and multimodal as part of the Center for Mesoscale Connectomics, providing a resource for future connectivity investigations.

neuroscience↗

bioRxiv2025

An RF coil array system for in vivo & ex vivo non-human primate brain studies at 10.5 Tesla

PurposeWe aimed to develop an innovative RF coil toolset for high resolution in vivo and ex vivo non-human primate neuroimaging applications at 10.5T MRI. The main goal was to improve our multimodal neural connectivity pipeline through the improved SNR, CNR, and spatial resolution that result from utilizing high-density RF coil arrays in combination with ultra-high field MRI. MethodsTwo RF coil arrays, both comprising 8 transmit and 40 receive channels, were designed and built for in vivo and ex vivo NHP imaging at 10.5 T. Experimental data was collected on multiple in vivo and ex vivo specimens, showing the utility UHF MRI for NHP neuroscience. ResultsExperimental results demonstrate uniform whole-brain coverage within both in vivo--which included the cerebellar, and spinal cord regions--and ex vivo specimens. High spatial resolutions (in vivo: 0.1x0.1x0.5 mm, ex vivo: 120 micron isotropic) were achieved, revealing detailed anatomical structures throughout. High temporal stability allowed for EPI and dMRI applications. ConclusionAn RF coil toolset comprising two 8ch transmit/40ch receive arrays was successfully designed for both in vivo and ex vivo NHP brain applications at 10.5 T. Both high-density RF coil arrays coupled with the SNR and CNR benefits available at UHF supported unmatched anatomical, functional, and diffusion applications at some of the highest spatial resolutions to date. Additionally, the combined capability of both in vivo and ex vivo MRI with the same brain specimen allows for tighter control for experimental-paradigm multistage studies examining translation between in vivo and ex vivo methodologies.

neuroscience↗

bioRxiv2025

A Numerical Alternative to MR Thermometry for Safety Validation of Multi-Channel RF Transmit Coils

PurposeThis study proposes an alternative approach to MR thermometry (MRT) for the safety validation of multi-channel RF transmit coils and demonstrates its use to enable human studies at 10.5T. MethodsTo ensure patient safety, specific absorption rate (SAR) limits established under international guidelines must not be exceeded. Predicting SAR on state-of-the-art parallel transmit systems relies on electromagnetic simulations, which require extensive experimental validation. Despite a well-established validation workflow, SAR prediction errors are unavoidable and must be quantified as a safety margin. While MRT tests are commonly used for this purpose, their technical challenges necessitate an alternative. The proposed technique propagates the error between experimentally and numerically acquired B+distributions to the uncertainty in simulated peak local SAR using Monte-Carlo simulations without the need for MRT. This method was validated using a 16-channel transceiver coil for imaging the human torso (henceforth referred to as a "body" coil) at 10.5T with two excitation scenarios, as well as an 8-channel 10.5T head coil with four excitation scenarios. ResultsThe proposed numerical technique proved more conservative than existing MRT-based SAR error quantification methods across all tested scenarios. Its application to validate three state-of-the-art head coils (16Tx/32Rx, 16Tx/80Rx, and 16Tx/128Rx) led to regulatory approval for human head imaging and high-quality functional as well as diffusion MRI results at 10.5T. ConclusionA numerical alternative to MRT requires only the experimental acquisition of B+ maps for comparison with simulations, enabling the quantification of uncertainty in SAR prediction. This technique was applied to three 16-channel transmit arrays, each used in conjunction with high-channel-count receive arrays for in vivo imaging.

neuroscience↗

bioRxiv2025

Mesoscopic whole-brain T2*-weighted and associated quantitative MRI in healthy humans at 10.5 T

PurposeTo demonstrate the feasibility and performance of mesoscopic whole brain T2*-weighted (T2*w) MRI at 10.5 T by combining a motion-robust multi-echo gradient-echo (GRE) method with high-density RF receive arrays. MethodsMulti-echo GRE data were collected in healthy adults at isotropic 0.5 mm resolution using a custom-built 16-channel transmit/80-channel receive (16Tx/80Rx) RF coil. Whole brain images were reconstructed with navigator-guided joint motion and field correction and were used for quantitative R2* and susceptibility ({chi}) mapping. Intrinsic signal-to-noise ratio (iSNR) and quantification precision for R2* and{chi} were also estimated. The results were compared with those obtained in the same subjects with matched resolution at 7 T using the commercial Nova 1Tx/32Rx coil, to demonstrate the iSNR and quantification precision gains at 10.5 T. G-factors were also calculated at each field strength to evaluate parallel imaging performances. To demonstrate the benefit of increased parallel imaging performances at 10.5 T, whole brain images with higher acceleration were also obtained using a custom-built 16Tx/128Rx coil. Resultsthe utilized motion robust GRE sequence and reconstruction effectively reduced artifacts from motion and field changes during scans, producing high-quality whole-brain T2*w images and multi-parametric maps at 10.5 T with delineation of fine-scale brain structures. Compared to 7 T, the 10.5 T approach led to gains in both iSNR and quantification precision of R2* and{chi} . Quantitatively, iSNR estimated in the peripheral cortical gray matter increased by 42%. Parallel imaging performances were also improved at 10.5 T owing to the utilized high-density coils compared to the commonly used commercially available coil at 7 T, allowing high-quality images with up to 12-fold combined acceleration when using the 128Rx coil. ConclusionIt is feasible to perform motion-robust whole-brain mesoscopic multi-echo gradient echo imaging of the human brain at 10.5 T. Intrinsic SNR and quantification precision of R2* and{chi} were estimated and compared with 7 T results. The results presented here may shed light on future optimal implementation of anatomic T2*w brain MRI at ultrahigh field beyond 7 T.

bioengineering↗

bioRxiv2024

A 128-channel receive array with enhanced SNR performance for 10.5 tesla brain imaging

PurposeTo develop and characterize the performance of a 128-channel head array for brain imaging at 10.5 tesla and evaluate the potential of brain imaging at this unique, >10 tesla magnetic field. MethodsThe coil is composed of a 16-channel self-decoupled loop transmit/receive array with a 112-loop receive-only (Rx) insert. Interactions between the outer transmitter and the inner 112Rx insert were mitigated using coaxial cable traps placed every 1/16 of a wavelength on each feed cable, locating most preamplifier boards outside the transmitter field and miniaturizing those placed directly on individual coils. ResultsThe 128-channel array described herein achieved 77% of ultimate intrinsic SNR in the center of the brain. Transmit field maps obtained experimentally on a phantom with and without the receive array were similar and matched EM simulations, leading to FDA approval for human imaging. Anatomical and functional data, including with power demanding sequences, were acquired successfully on human volunteers. ConclusionsCounterintuitive to expectations based on magnetic fields [≤]7T, the higher channel counts provided SNR gains centrally, capturing [~]80% uiSNR. Fraction of uiSNR achieved centrally in 64Rx, 80Rx, and 128Rx arrays suggested that a plateau was being reached at 80%. At this plateau, linear to approximately quadratic B0 dependent SNR gains for the periphery and the center, respectively, were observed for 10.5T relative 7T.

neuroscience↗

bioRxiv2024

RF coil design strategies for improving SNR at theultrahigh magnetic field of 10.5 Tesla

PurposeTo develop multichannel transmit and receive arrays towards capturing the ultimate-intrinsic-SNR (uiSNR) at 10.5 Tesla (T) and to demonstrate the feasibility and potential of whole-brain, high-resolution human brain imaging at this high field strength. MethodsA dual row 16-channel self-decoupled transmit (Tx) array was converted to a 16Tx/Rx transceiver using custom transmit/receive switches. A 64-channel receive-only (64Rx) array was built to fit into the 16Tx/Rx array. Electromagnetic modeling and experiments were employed to define safe operation limits of the resulting 16Tx/80Rx array and obtain FDA approval for human use. ResultsThe 64Rx array alone captured approximately 50% of the central uiSNR at 10.5T while the identical 7T 64Rx array captured [~]76% of uiSNR at this lower field strength. The 16Tx/80Rx configuration brought the fraction of uiSNR captured at 10.5T to levels comparable to the performance of the 64Rx array at 7T. SNR data obtained at the two field strengths with these arrays displayed [Formula] dependent increases over a large central region. Whole-brain high resolution T2* and T1 weighted anatomical and gradient-recalled echo EPI BOLD fMRI images were obtained at 10.5T for the first time with such an advanced array, illustrating the promise of >10T fields in studying the human brain. ConclusionWe demonstrated the ability to approach the uiSNR at 10.5T over the human brain with a novel, high channel count array, achieving large SNR gains over 7T, currently the most commonly employed ultrahigh field platform, and demonstrate high resolution and high contrast anatomical and functional imaging at 10.5T.

neuroscience↗