Quantitative magnetic resonance imaging (qMRI) provides tissue-specific parameters vital for clinical diagnosis. Although simultaneous multi-parametric qMRI (MP-qMRI) technologies enhance imaging efficiency, robustly reconstructing qMRI from highly undersampled, high-dimensional measurements remains a significant challenge. This difficulty arises primarily because current reconstruction methods that rely solely on a single prior or physics-informed model to solve the highly ill-posed inverse problem, which often leads to suboptimal results. To overcome this limitation, we propose LoREIN, a novel unsupervised and dual-prior-integrated framework for accelerated 3D MP-qMRI reconstruction. Technically, LoREIN incorporates both low-rank prior and continuity prior via low-rank representation (LRR) and implicit neural representation (INR), respectively, to enhance reconstruction fidelity. The powerful continuous representation of INR enables the estimation of optimal spatial bases within the low-rank subspace, facilitating high-fidelity reconstruction of weighted images. Simultaneously, the predicted multi-contrast weighted images provide essential structural and quantitative guidance, further enhancing the reconstruction accuracy of quantitative parameter maps. Furthermore, our work introduces a zero-shot learning paradigm with broad potential in complex spatiotemporal and high-dimensional image reconstruction tasks, further advancing the field of medical imaging.
Quantitative magnetic resonance imaging (qMRI) requires multi-phase acqui-sition, often relying on reduced data sampling and reconstruction algorithms to accelerate scans, which inherently poses an ill-posed inverse problem. While many studies focus on measuring uncertainty during this process, few explore how to leverage it to enhance reconstruction performance. In this paper, we in-troduce PUQ, a novel approach that pioneers the use of uncertainty infor-mation for qMRI reconstruction. PUQ employs a two-stage reconstruction and parameter fitting framework, where phase-wise uncertainty is estimated during reconstruction and utilized in the fitting stage. This design allows uncertainty to reflect the reliability of different phases and guide information integration during parameter fitting. We evaluated PUQ on in vivo T1 and T2 mapping datasets from healthy subjects. Compared to existing qMRI reconstruction methods, PUQ achieved the state-of-the-art performance in parameter map-pings, demonstrating the effectiveness of uncertainty guidance. Our code is available at https://anonymous.4open.science/r/PUQ-75B2/.
Multi-contrast MRI methods acquire multiple images with different contrast weightings, which are used for the differentiation of the tissue types or quantitative mapping. However, the scan time needed to acquire multiple contrasts is prohibitively long for 3D acquisition schemes, which can offer isotropic image resolution. While deep learning-based methods have been extensively used to accelerate 2D and 2D + time problems, the high memory demand, computation time, and need for large training data sets make them challenging for large-scale volumes. To address these challenges, we generalize the plug-and-play multi-scale energy-based model (MuSE) to a regularized subspace recovery setting, where we jointly regularize the 3D multi-contrast spatial factors in a subspace formulation. The explicit energy-based formulation allows us to use variable splitting optimization methods for computationally efficient recovery.
Purpose: To propose and evaluate an accelerated $T_{1\rho}$ quantification method that combines $T_{1\rho}$-weighted fast spin echo (FSE) images and proton density (PD)-weighted anatomical FSE images, leveraging deep learning models for $T_{1\rho}$ mapping. The goal is to reduce scan time and facilitate integration into routine clinical workflows for osteoarthritis (OA) assessment. Methods: This retrospective study utilized MRI data from 40 participants (30 OA patients and 10 healthy volunteers). A volume of PD-weighted anatomical FSE images and a volume of $T_{1\rho}$-weighted images acquired at a non-zero spin-lock time were used as input to train deep learning models, including a 2D U-Net and a multi-layer perceptron (MLP). $T_{1\rho}$ maps generated by these models were compared with ground truth maps derived from a traditional non-linear least squares (NLLS) fitting method using four $T_{1\rho}$-weighted images. Evaluation metrics included mean absolute error (MAE), mean absolute percentage error (MAPE), regional error (RE), and regional percentage error (RPE). Results: Deep learning models achieved RPEs below 5% across all evaluated scenarios, outperforming NLLS methods, especially in low signal-to-noise conditions. The best results were obtained using the 2D U-Net, which effectively leveraged spatial information for accurate $T_{1\rho}$ fitting. The proposed method demonstrated compatibility with shorter TSLs, alleviating RF hardware and specific absorption rate (SAR) limitations. Conclusion: The proposed approach enables efficient $T_{1\rho}$ mapping using PD-weighted anatomical images, reducing scan time while maintaining clinical standards. This method has the potential to facilitate the integration of quantitative MRI techniques into routine clinical practice, benefiting OA diagnosis and monitoring.
This study forms the basis of a digital twin system of the knee joint, using advanced quantitative MRI (qMRI) and machine learning to advance precision health in osteoarthritis (OA) management and knee replacement (KR) prediction. We combined deep learning-based segmentation of knee joint structures with dimensionality reduction to create an embedded feature space of imaging biomarkers. Through cross-sectional cohort analysis and statistical modeling, we identified specific biomarkers, including variations in cartilage thickness and medial meniscus shape, that are significantly associated with OA incidence and KR outcomes. Integrating these findings into a comprehensive framework represents a considerable step toward personalized knee-joint digital twins, which could enhance therapeutic strategies and inform clinical decision-making in rheumatological care. This versatile and reliable infrastructure has the potential to be extended to broader clinical applications in precision health.
Self-supervised deep learning has accelerated 2D natural image analysis but remains difficult to translate into 3D MRI, where data are scarce and pre-trained 2D backbones cannot capture volumetric context. We present a sequence-invariant self-supervised framework leveraging quantitative MRI (qMRI). By simulating multiple MRI contrasts from a single 3D qMRI scan and enforcing consistent representations across these contrasts, we learn anatomy-centric rather than sequence-specific features. This yields a robust 3D encoder that performs strongly across varied tasks and protocols. Experiments on healthy brain segmentation (IXI), stroke lesion segmentation (ARC), and MRI denoising show significant gains over baseline SSL approaches, especially in low-data settings (up to +8.3% Dice, +4.2 dB PSNR). Our model also generalises effectively to unseen sites, demonstrating potential for more scalable and clinically reliable volumetric analysis. All code and trained models are publicly available.
Deep learning has proven to be a suitable alternative to least-squares (LSQ) fitting for parameter estimation in various quantitative MRI (QMRI) models. However, current deep learning implementations are not robust to changes in MR acquisition protocols. In practice, QMRI acquisition protocols differ substantially between different studies and clinical settings. The lack of generalizability and adoptability of current deep learning approaches for QMRI parameter estimation impedes the implementation of these algorithms in clinical trials and clinical practice. Neural Controlled Differential Equations (NCDEs) allow for the sampling of incomplete and irregularly sampled data with variable length, making them ideal for use in QMRI parameter estimation. In this study, we show that NCDEs can function as a generic tool for the accurate prediction of QMRI parameters, regardless of QMRI sequence length, configuration of independent variables and QMRI forward model (variable flip angle T1-mapping, intravoxel incoherent motion MRI, dynamic contrast-enhanced MRI). NCDEs achieved lower mean squared error than LSQ fitting in low-SNR simulations and in vivo in challenging anatomical regions like the abdomen and leg, but this improvement was no longer evident at high SNR. NCDEs reduce estimation error interquartile range without increasing bias, particularly under conditions of high uncertainty. These findings suggest that NCDEs offer a robust approach for reliable QMRI parameter estimation, especially in scenarios with high uncertainty or low image quality. We believe that with NCDEs, we have solved one of the main challenges for using deep learning for QMRI parameter estimation in a broader clinical and research setting.
Deep learning-based techniques have potential to optimize scan and post-processing times required for MRI-based fat quantification, but they are constrained by the lack of large training datasets. Generative models are a promising tool to perform data augmentation by synthesizing realistic datasets. However no previous methods have been specifically designed to generate datasets for quantitative MRI (q-MRI) tasks, where reference quantitative maps and large variability in scanning protocols are usually required. We propose a Physics-Informed Latent Diffusion Model (PI-LDM) to synthesize quantitative parameter maps jointly with customizable MR images by incorporating the signal generation model. We assessed the quality of PI-LDM's synthesized data using metrics such as the Fr\'echet Inception Distance (FID), obtaining comparable scores to state-of-the-art generative methods (FID: 0.0459). We also trained a U-Net for the MRI-based fat quantification task incorporating synthetic datasets. When we used a few real (10 subjects, $~200$ slices) and numerous synthetic samples ($>3000$), fat fraction at specific liver ROIs showed a low bias on data obtained using the same protocol than training data ($0.10\%$ at $\hbox{ROI}_1$, $0.12\%$ at $\hbox{ROI}_2$) and on data acquired with an alternative protocol ($0.14\%$ at $\hbox{ROI}_1$, $0.62\%$ at $\hbox{ROI}_2$). Future work will be to extend PI-LDM to other q-MRI applications.
Segmenting stroke lesions in MRI is challenging due to diverse acquisition protocols that limit model generalisability. In this work, we introduce two physics-constrained approaches to generate synthetic quantitative MRI (qMRI) images that improve segmentation robustness across heterogeneous domains. Our first method, $\texttt{qATLAS}$, trains a neural network to estimate qMRI maps from standard MPRAGE images, enabling the simulation of varied MRI sequences with realistic tissue contrasts. The second method, $\texttt{qSynth}$, synthesises qMRI maps directly from tissue labels using label-conditioned Gaussian mixture models, ensuring physical plausibility. Extensive experiments on multiple out-of-domain datasets show that both methods outperform a baseline UNet, with $\texttt{qSynth}$ notably surpassing previous synthetic data approaches. These results highlight the promise of integrating MRI physics into synthetic data generation for robust, generalisable stroke lesion segmentation. Code is available at https://github.com/liamchalcroft/qsynth
We introduce and demonstrate a new paradigm for quantitative parameter mapping in MRI. Parameter mapping techniques, such as diffusion MRI and quantitative MRI, have the potential to robustly and repeatably measure biologically-relevant tissue maps that strongly relate to underlying microstructure. Quantitative maps are calculated by fitting a model to multiple images, e.g. with least-squares or machine learning. However, the overwhelming majority of model fitting techniques assume that each voxel is independent, ignoring any co-dependencies in the data. This makes model fitting sensitive to voxelwise measurement noise, hampering reliability and repeatability. We propose a self-supervised deep variational approach that breaks the assumption of independent pixels, leveraging redundancies in the data to effectively perform data-driven regularisation of quantitative maps. We demonstrate that our approach outperforms current model fitting techniques in dMRI simulations and real data. Especially with a Gaussian mixture prior, our model enables sharper quantitative maps, revealing finer anatomical details that are not presented in the baselines. Our approach can hence support the clinical adoption of parameter mapping methods such as dMRI and qMRI.
Magnetic Resonance Fingerprinting (MRF) is a time-efficient approach to quantitative MRI, enabling the mapping of multiple tissue properties from a single, accelerated scan. However, achieving accurate reconstructions remains challenging, particularly in highly accelerated and undersampled acquisitions, which are crucial for reducing scan times. While deep learning techniques have advanced image reconstruction, the recent introduction of diffusion models offers new possibilities for imaging tasks, though their application in the medical field is still emerging. Notably, diffusion models have not yet been explored for the MRF problem. In this work, we propose for the first time a conditional diffusion probabilistic model for MRF image reconstruction. Qualitative and quantitative comparisons on in-vivo brain scan data demonstrate that the proposed approach can outperform established deep learning and compressed sensing algorithms for MRF reconstruction. Extensive ablation studies also explore strategies to improve computational efficiency of our approach.
Quantitative magnetic resonance imaging (qMRI) offers tissue-specific physical parameters with significant potential for neuroscience research and clinical practice. However, lengthy scan times for 3D multiparametric qMRI acquisition limit its clinical utility. Here, we propose SUMMIT, an innovative imaging methodology that includes data acquisition and an unsupervised reconstruction for simultaneous multiparametric qMRI. SUMMIT first encodes multiple important quantitative properties into highly undersampled k-space. It further leverages implicit neural representation incorporated with a dedicated physics model to reconstruct the desired multiparametric maps without needing external training datasets. SUMMIT delivers co-registered T1, T2, T2*, and quantitative susceptibility mapping. Extensive simulations and phantom imaging demonstrate SUMMIT's high accuracy. Additionally, the proposed unsupervised approach for qMRI reconstruction also introduces a novel zero-shot learning paradigm for multiparametric imaging applicable to various medical imaging modalities.
Quantitative magnetic resonance imaging (qMRI) is increasingly investigated for use in a variety of clinical tasks from diagnosis, through staging, to treatment monitoring. However, experiment design in qMRI, the identification of the optimal acquisition protocols, has been focused on obtaining the most precise parameter estimations, with no regard for the specific requirements of downstream tasks. Here we propose SCREENER: A general framework for task-specific experiment design in quantitative MRI. SCREENER incorporates a task-specific objective and seeks the optimal protocol with a deep-reinforcement-learning (DRL) based optimization strategy. To illustrate this framework, we employ a task of classifying the inflammation status of bone marrow using diffusion MRI data with intravoxel incoherent motion (IVIM) modelling. Results demonstrate SCREENER outperforms previous ad hoc and optimized protocols under clinical signal-to-noise ratio (SNR) conditions, achieving significant improvement, both in binary classification tasks, e.g. from 67% to 89%, and in a multi-class classification task, from 46% to 59%. Additionally, we show this improvement is robust to the SNR. Lastly, we demonstrate the advantage of DRL-based optimization strategy, enabling zero-shot discovery of near-optimal protocols for a range of SNRs not used in training. In conclusion, SCREENER has the potential to enable wider uptake of qMRI in the clinic.
Cardiac T1 mapping is a valuable quantitative MRI technique for diagnosing diffuse myocardial diseases. Traditional methods, relying on breath-hold sequences and cardiac triggering based on an ECG signal, face challenges with patient compliance, limiting their effectiveness. Image registration can enable motion-robust cardiac T1 mapping, but inherent intensity differences between time points pose a challenge. We present MBSS-T1, a subject-specific self-supervised model for motion correction in cardiac T1 mapping. Physical constraints, implemented through a loss function comparing synthesized and motion-corrected images, enforce signal decay behavior, while anatomical constraints, applied via a Dice loss, ensure realistic deformations. The unique combination of these constraints results in motion-robust cardiac T1 mapping along the longitudinal relaxation axis. In a 5-fold experiment on a public dataset of 210 patients (STONE sequence) and an internal dataset of 19 patients (MOLLI sequence), MBSS-T1 outperformed baseline deep-learning registration methods. It achieved superior model fitting quality ($R^2$: 0.975 vs. 0.941, 0.946 for STONE; 0.987 vs. 0.982, 0.965 for MOLLI free-breathing; 0.994 vs. 0.993, 0.991 for MOLLI breath-hold), anatomical alignment (Dice: 0.89 vs. 0.84, 0.88 for STONE; 0.963 vs. 0.919, 0.851 for MOLLI free-breathing; 0.954 vs. 0.924, 0.871 for MOLLI breath-hold), and visual quality (4.33 vs. 3.38, 3.66 for STONE; 4.1 vs. 3.5, 3.28 for MOLLI free-breathing; 3.79 vs. 3.15, 2.84 for MOLLI breath-hold). MBSS-T1 enables motion-robust T1 mapping for broader patient populations, overcoming challenges such as suboptimal compliance, and facilitates free-breathing cardiac T1 mapping without requiring large annotated datasets. Our code is available at https://github.com/TechnionComputationalMRILab/MBSS-T1.
Quantification of tissue parameters using MRI is emerging as a powerful tool in clinical diagnosis and research studies. The need for multiple long scans with different acquisition parameters prohibits quantitative MRI from reaching widespread adoption in routine clinical and research exams. Accelerated parameter mapping techniques leverage parallel imaging, signal modelling and deep learning to offer more practical quantitative MRI acquisitions. However, the achievable acceleration and the quality of maps are often limited. Joint MAPLE is a recent state-of-the-art multi-parametric and scan-specific parameter mapping technique with promising performance at high acceleration rates. It synergistically combines parallel imaging, model-based and machine learning approaches for joint mapping of T1, T2*, proton density and the field inhomogeneity. However, Joint MAPLE suffers from prohibitively long reconstruction time to estimate the maps from a multi-echo, multi-flip angle (MEMFA) dataset at high resolution in a scan-specific manner. In this work, we propose a faster version of Joint MAPLE which retains the mapping performance of the original version. Coil compression, random slice selection, parameter-specific learning rates and transfer learning are synergistically combined in the proposed framework. It speeds-up the reconstruction time up to 700 times than the original version and processes a whole-brain MEMFA dataset in 21 minutes on average, which originally requires ~260 hours for Joint MAPLE. The mapping performance of the proposed framework is ~2-fold better than the standard and the state-of-the-art evaluated reconstruction techniques on average in terms of the root mean squared error.
Magnetic Resonance Fingerprinting (MRF) is a time-efficient approach to quantitative MRI for multiparametric tissue mapping. The reconstruction of quantitative maps requires tailored algorithms for removing aliasing artefacts from the compressed sampled MRF acquisitions. Within approaches found in the literature, many focus solely on two-dimensional (2D) image reconstruction, neglecting the extension to volumetric (3D) scans despite their higher relevance and clinical value. A reason for this is that transitioning to 3D imaging without appropriate mitigations presents significant challenges, including increased computational cost and storage requirements, and the need for large amount of ground-truth (artefact-free) data for training. To address these issues, we introduce StoDIP, a new algorithm that extends the ground-truth-free Deep Image Prior (DIP) reconstruction to 3D MRF imaging. StoDIP employs memory-efficient stochastic updates across the multicoil MRF data, a carefully selected neural network architecture, as well as faster nonuniform FFT (NUFFT) transformations. This enables a faster convergence compared against a conventional DIP implementation without these features. Tested on a dataset of whole-brain scans from healthy volunteers, StoDIP demonstrated superior performance over the ground-truth-free reconstruction baselines, both quantitatively and qualitatively.
Quantitative MRI (qMRI) offers significant advantages over weighted images by providing objective parameters related to tissue properties. Deep learning-based methods have demonstrated effectiveness in estimating quantitative maps from series of weighted images. In this study, we present qMRI Diffuser, a novel approach to qMRI utilising deep generative models. Specifically, we implemented denoising diffusion probabilistic models (DDPM) for T1 quantification in the brain, framing the estimation of quantitative maps as a conditional generation task. The proposed method is compared with the residual neural network (ResNet) and the recurrent inference machine (RIM) on both phantom and in vivo data. The results indicate that our method achieves improved accuracy and precision in parameter estimation, along with superior visual performance. Moreover, our method inherently incorporates stochasticity, enabling straightforward quantification of uncertainty. Hence, the proposed method holds significant promise for quantitative MR mapping.
Quantitative MRI enables direct quantification of contrast agent concentrations in contrast-enhanced scans. However, the lengthy scan times required by conventional methods are inadequate for tracking contrast agent transport dynamically in mouse brain. We developed a 3D MR fingerprinting (MRF) method for simultaneous T1 and T2 mapping across the whole mouse brain with 4.3-min temporal resolution. We designed a 3D MRF sequence with variable acquisition segment lengths and magnetization preparations on a 9.4T preclinical MRI scanner. Model-based reconstruction approaches were employed to improve the accuracy and speed of MRF acquisition. The method's accuracy for T1 and T2 measurements was validated in vitro, while its repeatability of T1 and T2 measurements was evaluated in vivo (n=3). The utility of the 3D MRF sequence for dynamic tracking of intracisternally infused Gd-DTPA in the whole mouse brain was demonstrated (n=5). Phantom studies confirmed accurate T1 and T2 measurements by 3D MRF with an undersampling factor up to 48. Dynamic contrast-enhanced (DCE) MRF scans achieved a spatial resolution of 192 x 192 x 500 um3 and a temporal resolution of 4.3 min, allowing for the analysis and comparison of dynamic changes in concentration and transport kinetics of intracisternally infused Gd-DTPA across brain regions. The sequence also enabled highly repeatable, high-resolution T1 and T2 mapping of the whole mouse brain (192 x 192 x 250 um3) in 30 min. We present the first dynamic and multi-parametric approach for quantitatively tracking contrast agent transport in the mouse brain using 3D MRF.
We propose PHIMO, a physics-informed learning-based motion correction method tailored to quantitative MRI. PHIMO leverages information from the signal evolution to exclude motion-corrupted k-space lines from a data-consistent reconstruction. We demonstrate the potential of PHIMO for the application of T2* quantification from gradient echo MRI, which is particularly sensitive to motion due to its sensitivity to magnetic field inhomogeneities. A state-of-the-art technique for motion correction requires redundant acquisition of the k-space center, prolonging the acquisition. We show that PHIMO can detect and exclude intra-scan motion events and, thus, correct for severe motion artifacts. PHIMO approaches the performance of the state-of-the-art motion correction method, while substantially reducing the acquisition time by over 40%, facilitating clinical applicability. Our code is available at https://github.com/HannahEichhorn/PHIMO.
Deep learning-based methods have achieved prestigious performance for magnetic resonance imaging (MRI) reconstruction, enabling fast imaging for many clinical applications. Previous methods employ convolutional networks to learn the image prior as the regularization term. In quantitative MRI, the physical model of nuclear magnetic resonance relaxometry is known, providing additional prior knowledge for image reconstruction. However, traditional reconstruction networks are limited to learning the spatial domain prior knowledge, ignoring the relaxometry prior. Therefore, we propose a relaxometry-guided quantitative MRI reconstruction framework to learn the spatial prior from data and the relaxometry prior from MRI physics. Additionally, we also evaluated the performance of two popular reconstruction backbones, namely, recurrent variational networks (RVN) and variational networks (VN) with U- Net. Experiments demonstrate that the proposed method achieves highly promising results in quantitative MRI reconstruction.