Biology subjects

Auerbach, E. J.

Publications and source records attributed to Auerbach, E. J..

4 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

Precision functional imaging in infants using multi-echo fMRI at 7T

Personalized functional brain developmental trajectories can be studied with Precision Functional Mapping (PFM). Our previous work has demonstrated that PFM can be achieved in infants despite rapid brain growth. However, even with extensive data collection (up to 1 hour of fMRI), the reliability and precision of these maps remain lower than those observed in youth and adults - particularly within subcortical structures. In this work we demonstrate the utility of high-field 7T MRI compared to 3T MRI for facilitating PFM in infants. We showcase data from multi-echo fMRI acquisitions in the same infants at both 7T and 3T and demonstrate that 7T imaging in infants is safe and feasible with our subject-specific safety workflow. Moreover, we demonstrate that the use of a higher magnetic field strength affords a spatial resolution more appropriately matched to infants smaller head and brain sizes, yielding notable improvements in data quality, especially for PFM. The increase in both spatial precision and reliability also suggests that 7T MRI can reduce the amount of data required for PFM. Last, we show how ultra-high field imaging can help us study the development of subcortical-to-cortical connectivity patterns, crucial for understanding brain development during this developmental window. 7T MRI is a promising new avenue for developmental cognitive neuroscience.

neuroscience↗

bioRxiv2020

Ultra-high field (10.5 T) resting state fMRI in the macaque

Resting state functional connectivity refers to the temporal correlations between spontaneous hemodynamic signals obtained using functional magnetic resonance imaging. This technique has demonstrated that the structure and dynamics of identifiable networks are altered in psychiatric and neurological disease states. Thus, resting state network organizations can be used as a diagnostic, or prognostic recovery indicator. However, much about the physiological basis of this technique is unknown. Thus, providing a translational bridge to an optimal animal model, the macaque, in which invasive circuit manipulations are possible, is of utmost importance. Current approaches to resting state measurements in macaques face unique challenges associated with signal-to-noise, the need for invasive contrast agents, and within-subject designs. These limitations can, in principle, be overcome through ultra-high magnetic fields. However, ultra-high field imaging has yet to be adapted for fMRI in macaques. Here, we demonstrate that the combination of high channel count transmitter and receiver arrays, optimized pulse sequences, and careful anesthesia regimens, allows for detailed within-subject resting state analysis at ultra-high resolutions. In this study, we uncover thirty spatially detailed resting state components that are highly robust across individual macaques and closely resemble the quality and findings of connectomes from large human datasets. This detailed map of the rsfMRI macaque connectome will be the basis for future neurobiological circuit manipulation work, providing valuable biological insights into human connectomics.

neuroscience↗