arXiv subjects

Quentin Uhl

Publications and source records attributed to Quentin Uhl.

3 recordsLinked to original sources

arXiv2025

Reduced NEXI protocol for the quantification of human gray matter microstructure on the Connectome 2.0 scanner

Biophysical diffusion MRI models like Neurite Exchange Imaging (NEXI) are essential for probing gray matter microstructure, estimating compartment diffusivities, neurite fraction, and exchange time. However, NEXI's multi-shell, multi-diffusion-time requirements cause prohibitively long acquisitions. Leveraging the Connectome 2.0 ultra-high gradient scanner, we developed a time-efficient protocol using an Explainable AI (XAI) framework. Combining XGBoost, SHAP, and Recursive Feature Elimination trained on synthetic signals, XAI identified an optimal 8-feature subset, cutting scan time from 27 to 14 minutes. Validated in vivo in seven healthy participants, the XAI protocol was benchmarked against the full 15-feature acquisition, a Cram'er-Rao Lower Bound (CRLB) theoretical optimum, and two heuristics ("Mid-Range" and "Corner"). It robustly reproduced parameter estimates and maintained test-retest reproducibility. Remarkably, the XAI selection converged to the CRLB optimum. This validates XAI's optimality while highlighting its main advantage: achieving gold-standard optimization without complex analytical Jacobians, making it easily adaptable to numerical models or complex noise where CRLB is intractable. Furthermore, XAI showed superior in vivo robustness over heuristics: "Mid-Range" sampling yielded biased exchange time estimates from insufficient temporal diversity, while "Corner" sampling gave unstable intra-neurite diffusivity estimates (5-fold higher CV) due to noise sensitivity. Ultimately, this robust 14-minute protocol accelerates exchange-sensitive microstructural mapping, establishing a model-agnostic optimization framework adaptable to future ultra-high gradient systems and existing clinical scanners.

physics.med-ph↗

arXiv2025

Bayesian Insights into Exchange and Restriction in Gray Matter Diffusion MRI

Biophysical models in diffusion MRI (dMRI) hold promise for characterizing gray matter tissue microstructure. Yet, the reliability of their parameter estimates remains largely under-studied, especially in models that incorporate water exchange. In this study, we investigate the accuracy, precision, and presence of degeneracy of two recently proposed gray matter models, NEXI and SANDIX, using established acquisition protocols, on both simulated and \textit{in vivo} data. We employ $\mu$GUIDE, a Bayesian inference framework based on deep learning, to quantify parameter uncertainty and detect degeneracies, enabling a more interpretable assessment of model fits. Our results show that while some microstructural parameters, such as extra-cellular diffusivity and neurite signal fraction, are robustly estimated, others, including exchange time and soma radius, are often associated with high uncertainty and estimation bias, particularly under realistic noise conditions and reduced acquisition protocols. Comparison with non-linear least squares fitting highlights the critical advantage of uncertainty-aware methods: the ability to flag and filter out unreliable estimates. Together, these findings emphasize the need to report uncertainty and account for model degeneracies when interpreting model-based estimates. Our study advocates for the integration of probabilistic fitting approaches into imaging pipelines to improve reproducibility and biological interpretability.

physics.med-ph↗

arXiv2023

Quantifying human gray matter microstructure using NEXI and 300 mT/m gradients

Biophysical models of diffusion tailored to quantify gray matter microstructure are gathering increasing interest. The two-compartment Neurite EXchange Imaging ($NEXI$) model has been proposed recently to account for neurites, extra-cellular space and exchange across the cell membrane. $NEXI$ parameter estimation requires multi-shell multi-diffusion time data and has so far only been implemented experimentally on animal data collected on a preclinical MRI set-up. In this work, the first ever translation of $NEXI$ to the human cortex in vivo was achieved using a 3T Connectom MRI system with 300 mT/m gradients, that enables the acquisition of a broad range of b-values (0 - 7.5 ms/$\mu m^{2}$) with a window of diffusion times (20 - 49 ms) suitable for the expected characteristic exchange times (10 - 50 ms). Microstructure estimates of four model variants: $NEXI$, $NEXI_{dot}$ (its extension with the addition of a dot compartment) and their respective versions that correct for the Rician noise floor ($NEXI_{RM}$ and $NEXI_{dot,RM}$) that particularly impacts high b-value signal, were compared. The reliability of estimates in each model variant was evaluated in synthetic and human in vivo data. In the latter, the intra-subject (scan-rescan) vs between-subjects variability of microstructure estimates were compared in the cortex. The better performance of $NEXI_{RM}$ highlights the importance of correcting for Rician bias in the $NEXI$ model to obtain accurate estimates of microstructure parameters in the human cortex, and the sensitivity of the $NEXI$ framework to individual differences in cortical microstructure. This groundbreaking application of $NEXI$ in humans marks a pivotal moment, unlocking new avenues for studying neurodevelopment, ageing, and various neurodegenerative disorders.

physics.med-ph↗