MRI2Qmap: multi-parametric quantitative mapping with MRI-driven denoising priors

Understanding the human brain requires access to its microscopic tissue architecture. Diffusion magnetic resonance imaging (MRI) provides the only noninvasive window into whole-brain microstructure in vivo, yet reliable quantitative mapping remains confined to specialized research settings requiring dense sampling and optimized acquisition protocols. To address this gap, we present a physics-informed generative microstructure network (PIGMENT) that learns a universal generative prior of human brain microstructure and adapts it zero-shot to each participant's measured data to recover subject-specific maps. Trained on 11375 scans spanning multiple sites, vendors, and field strengths, PIGMENT enabled reliable quantitative mapping for tensor, kurtosis, and NODDI models across external datasets from five independent centers. It remains effective where conventional fitting becomes unreliable, recovering meaningful maps from extremely sparse acquisitions while supporting downstream tractography and structural connectivity mapping. PIGMENT estimates demonstrated strong biological validity, preserving submillimeter cortical microarchitectural patterns and early-childhood white matter developmental trajectories from 10-fold accelerated scans. Furthermore, PIGMENT enables reliable quantitative tensor mapping on cost-efficient low-field systems and the extraction of tumor-related biomarkers using ultra-fast clinical protocols. Together, these results establish PIGMENT as a physics-informed foundation model that extends quantitative diffusion MRI into regimes traditionally too sparse, heterogeneous, or clinically constrained for reliable analysis.

Undersampled magnetic resonance imaging (MRI) reconstruction seeks to recover temporally or contrast-varying image series from incomplete multicoil k-space data while preserving state-dependent fidelity for dynamic and quantitative MRI (qMRI). Existing scan-specific implicit neural representations (INRs) often use monolithic spatiotemporal coordinate fields, explicit subspaces, motion or deformation models, calibration variables, or sequence-specific quantitative signal models. These design choices can limit flexibility in sharing spatial information while adapting image synthesis across acquisition states. Moreover, many INR-based baselines remain computationally demanding, typically requiring per-scan optimization times on the order of hundreds to thousands of seconds. We propose MoE-dqINR, a scan-specific multicoil MRI reconstruction framework that factorizes the image-domain representation into shared spatial experts and a state-conditioned routing pathway. Spatial experts encode reusable coordinate-dependent image content, whereas routing weights, conditioned on ordered acquisition states, synthesize each dynamic frame or contrast state from a common expert bank. The representation is coupled to a multicoil MRI forward model, uses the normalized state index to drive routing in both dynamic and quantitative MRI. By separating shared spatial representation from state-dependent synthesis, the framework provides an image-first architecture for dynamic and quantitative MRI while reducing scan-specific INR optimization to approximately 30 s per scan in our experiments. The proposed formulation establishes state-conditioned mixture-of-experts INR as a scan-specific multicoil MRI reconstruction prior that unifies shared spatial representation, dynamic- and qMRI-specific synthesis, and practical per-scan efficiency.

Parallel imaging techniques reduce magnetic resonance imaging (MRI) scan time but image quality degrades as the acceleration factor increases. In clinical practice, conservative acceleration factors are chosen because no mechanism exists to automatically assess the diagnostic quality of undersampled reconstructions. This work introduces a general framework for pixel-wise uncertainty quantification in parallel MRI reconstructions, enabling automatic identification of unreliable regions without access to any ground-truth reference image. Our method integrates conformal quantile regression with image reconstruction methods to estimate statistically rigorous pixel-wise uncertainty intervals. We trained and evaluated our model on Cartesian undersampled brain and knee data obtained from the fastMRI dataset using acceleration factors ranging from 2 to 10. An end-to-end Variational Network was used for image reconstruction. Quantitative experiments demonstrate strong agreement between predicted uncertainty maps and true reconstruction error. Using our method, the corresponding Pearson correlation coefficient was higher than 90% at acceleration levels at and above four-fold; whereas it dropped to less than 70% when the uncertainty was computed using a simpler a heuristic notion (magnitude of the residual). Qualitative examples further show the uncertainty maps based on quantile regression capture the magnitude and spatial distribution of reconstruction errors across acceleration factors, with regions of elevated uncertainty aligning with pathologies and artifacts. The proposed framework enables evaluation of reconstruction quality without access to fully-sampled ground-truth reference images. It represents a step toward adaptive MRI acquisition protocols that may be able to dynamically balance scan time and diagnostic reliability.