Cardiac Magnetic Resonance Imaging

Chagas disease is a major cause of cardiomyopathy in Latin America. Cardiac magnetic resonance (CMR) imaging can characterize its structural abnormalities, but scanners and expert readers remain scarce in endemic regions. Electrocardiography (ECG) is inexpensive and widely available, yet structural disease must be inferred indirectly from electrical signals. We propose to transfer CMR-derived structural knowledge to ECG through contrastive pre-training. Using 63,193 paired ECG-CMR examinations from the UK Biobank, we align an ECG encoder with a clinically grounded CMR embedding space using an asymmetric InfoNCE objective. Despite seeing no Chagas cases during pre-training, the resulting representation improves ECG-based Chagas detection. Across CODE-15% and SaMi-Trop, a frozen linear probe achieves an AUROC of 0.851 and sensitivity at the top 5% of predicted risk (Top5%-TPR) of 0.427 in five-fold cross-validation, compared with 0.827 and 0.377 for an unaligned ECG-FM baseline. On the PhysioNet/CinC 2025 Challenge test set, our model obtains the highest AUROC on SaMi-Trop-3 and the best ELSA-Brasil challenge score among the three top-performing methods, indicating that imaging-supervised ECG representations can generalize to populations and settings beyond the pre-training distribution.

Reconstructing a three-dimensional left-ventricular (LV) endocardial surface from cardiac magnetic resonance (CMR) data is challenging when supervision is available on only a small number of axial slices. Through-plane geometry is weakly constrained, and automatically generated two-dimensional masks can propagate segmentation errors into the recovered shape. We present MR-RS-SDFR, a per-case implicit signed distance field (SDF) framework that reconstructs a continuous LV surface from a CMR volume and sparse axial weak masks. The method first builds a cross-slice SDF initialization from axial and longitudinal geometric cues and then refines the field using two complementary signals: MRI edge-field normal alignment, which provides an image-derived boundary cue independent of the weak masks, and differentiable reslice Dice and contour consistency, which preserve agreement with the observed planes. We evaluate three weak-mask generators -- LOO TransUNet, LOO nnU-Net, and an off-the-shelf Medical SAM3 model used without MM-WHS-specific training or fine-tuning -- and five sparsity levels from 4 to 64 axial planes. In the sparse-16 setting, final MR-RS-SDFR reconstruction reaches 0.928 Dice and 3.80mm HD95 with Medical SAM3 masks. The upstream generators do not exhibit a single common ranking across 2D and dense 3D segmentation, and nnU-Net- and Medical-SAM3-driven sparse reconstruction achieve the same mean final Dice despite different upstream error profiles. Across all three sparse-16 mask sources, MR-RS-SDFR is numerically better than protocol-matched full GHD+DVS in both Dice and HD95. Final Dice improves markedly from sparse-4 to sparse-16 and then saturates at the reported precision through sparse-64. These results support MRI-guided per-case SDF refinement as a reconstruction strategy that remains effective across weak-mask generators and supervision densities.

Cardiac magnetic resonance (CMR) imaging provides complementary information on cardiac anatomy, function, and tissue characterization across multiple sequences and views. In this work, we investigate foundation model pretraining for 2D CMR and introduce CMRVision, a CMR-specific foundation model trained using DINOv3-style self-supervised learning on a multi-center, multi-sequence cohort of 36 million CMR images. We systematically evaluate architectural and training design choices for domain-specific pretraining. CMRVision is evaluated on two downstream tasks: multi-task segmentation across cine, late gadolinium enhancement (LGE), and mapping sequences, and cine view classification. Our experiments show that CMR-specific pretraining, smaller patch sizes, and patch-level objectives consistently improve downstream performance. Across a multi-task segmentation benchmark, CMRVision achieved the strongest overall performance, outperforming prior natural-image (NI), medical-image, supervised, and CMR foundation model baselines. Improvements were modest but consistent across structures and sequences, with Dice scores ranging from 0.940-0.967 for LV and 0.855-0.905 for myocardium, and reaching 0.929 for RV, 0.920 for LA, and 0.931 for RA. The largest gains were observed for myocardium segmentation in LGE and mapping images. In a zero-shot segmentation task on unseen LGE long-axis views, the model achieved an average Dice score of 0.692, demonstrating cross-view generalization. For cine view classification, CMRVision achieved the highest average accuracy (0.906), compared to prior methods reported in the literature. These results highlight the potential of CMRVision to support robust and generalizable cardiac MRI analysis across multiple sequences and views.

Cardiac magnetic resonance imaging (CMR) produces rich sequential data such as temporal cine videos and spatial LGE/mapping stacks, yet most deep learning approaches process individual 2D slices, discarding this context. We present MR-JEPA, a self-supervised video foundation model for CMR that extends LeJEPA to 3D spatiotemporal inputs through tubelet tokenization, spatiotemporal masking augmentation, and initialization from a 2D CMR foundation model. Unlike prior CMR video models limited to cine data, MR-JEPA is pretrained on multi-sequence data (cine, LGE, mapping) from 10,505 patients across two centers without annotations. We evaluate the frozen encoder on six downstream tasks using a unified multi-view gated attention architecture: LV ejection fraction, RV ejection fraction, three myocardial strains (GLS, GCS, GRS), and four-class disease detection. MR-JEPA outperforms other compared methods on all five regression tasks, including both a domain-specific CMR model pretrained on more data with text supervision and a natural-video foundation model, achieving an LV EF MAE of 4.79% (r =0.764) and a GLS MAE of 1.87 (r=0.805), with 21-27% MAE reductions over baselines on strain tasks. For disease detection, MR-JEPA achieved a macro AUG of 0.868, remaining competitive with the domain-specific baseline despite using a fully self-supervised pretraining objective. These results demonstrate the potential of a unified video encoder for robust, multi-view utilization of diverse CMR sequences in clinical cardiac quantification and diagnosis.

Quantifying myocardial perfusion from cardiac magnetic resonance (CMR) can be achieved by fitting tracer-kinetic models to the dynamic contrast-enhanced MR data. However, fitting the observed data with multi-compartment exchange models, which describe the evolution of the contrast agent in the tissue, to estimate perfusion parameters is a challenging inverse problem that is sensitive to noise and acquisition variability. Previously, physics-informed neural networks (PINNs) have been proposed as an alternative to conventional non-linear least squares fitting methods with promising results for quantitative perfusion CMR. In this work, we extend the previously proposed PINN framework with spatiotemporal implicit neural representations (INRs) to represent the MR signal as a continuous spatiotemporal function and to improve the accuracy, smoothness, and physical consistency of the PINN model. In realistic simulated CMR datasets, our proposed PINN with INRs demonstrates improved robustness and parameter estimation accuracy over the previously established methods. The code is available at https://github.com/q-cardIA/pinn-inr.

Foundation models have shown strong transferability in cardiac MRI (CMR), but their effectiveness for heterogeneous multi-view and multi-sequence CMR analysis remains unclear. In this work, we explore the effectiveness of fine-tuning and combining different CMR foundation models for the Universal Multi-Sequence, Multi-Center and Multi-View CMR Segmentation (CMR-Multi) Challenge. CineMA was fine-tuned for cine and late gadolinium enhancement (LGE) segmentation across short-axis and long-axis views. For direct left-ventricular ejection fraction (LVEF) estimation, we used two recent frozen CMR foundation models to extract embedding vectors that were then combined using attention-based multiple-instance learning for LVEF regression. In the challenge validation set, cine segmentation achieved Dice scores of 0.862, 0.883, and 0.902 for short-axis, two-chamber and four-chamber cine MRI, respectively. LGE segmentation achieved Dice scores between 0.621 and 0.846 across views. The direct LVEF regression model achieved an MAE of 4.96 percentage points and a Pearson correlation of 0.91. These results indicate that foundation models can be effectively adapted and combined for multi-view CMR analysis, while accurate LGE scar segmentation remains a challenging task.

Tensor cross-concentrated sampling (t-CCS) bridges entrywise sampling and t-CUR slice-wise sampling by observing entries only within selected horizontal and lateral slices. Existing t-CCS completion methods, however, assume that the observations are free of gross corruption. In this work, we study robust recovery of a third-order low-tubal-rank tensor from partial t-CCS observations contaminated by sparse, arbitrarily large outliers. We propose Robust Iterative t-CUR (R-ItCUR), a tensor-native algorithm that partitions the sampled tensor cross into two exterior blocks and an intersection block, applies adaptive blockwise Welsch correction for outlier suppression, and updates the low-rank component through projected blockwise gradient descent. By operating directly on the sampled cross, R-ItCUR avoids reconstructing the full tensor throughout the iterations, resulting in substantial memory and computational savings. Experiments on synthetic tensors, cardiac MRI data, and three-dimensional seismic data demonstrate accurate recovery and strong robustness to sparse gross corruptions. The results further highlight the importance of explicitly exploiting the cross-concentrated sampling structure in robust tensor completion.

Myocardial strain analysis of cardiac magnetic resonance (CMR) images provides an important tool for evaluating cardiac function. However, current techniques require either human-adjusted post-processing with suboptimal regional accuracy, or specialized acquisitions with limited availability. In this paper, we propose to leverage the power of generative models to synthesize high-quality motion-derived strain values from routinely acquired CMR sequences. Specifically, we develop a novel Brownian bridge diffusion model in motion space to learn the probabilistic mapping between standard CMR motion estimated from widely adopted registration methods and highly accurate motion provided by advanced strain imaging techniques. To promote the fidelity of anatomical structure in the generation process, our model is conditioned on the corresponding CMR images. We validate our method on large-scale multi-center CMR datasets including subjects of paired standard cine CMR and advanced strain imaging acquisitions. Experimental results demonstrate that our framework significantly improves the accuracy of motion prediction and strain analysis from standard CMRs compared to existing learning-based approaches. Our research represents a new paradigm for potentially developing cost-effective, clinically deployable AI tools for cardiac function assessment with enhanced strain accuracy in busy clinical workflows. Our code is publicly available at https://github.com/Rishov-MIA/Brownian-Bridge-strain-analysis.

Clinical acquisition in cardiac magnetic resonance (CMR) imaging involves obtaining cross-sectional planes of the heart along the radial and longitudinal directions. Despite these planes being 2D cross-sectional images of the heart, radiologists understand the 3D spatial and continuous temporal nature of the organ being imaged. The same can not be said about the conventional deep learning architectures used to process CMR images, which rely on in-plane and grid-based operations, and are hence unable to organically integrate information from all imaging planes. This paper builds upon previous work on neural implicit segmentation functions (NISF) to overcome unaddressed challenges in cardiac function modeling in the CMR domain. For a given subject, our architecture builds a shared 3D+time representations from all available acquisition planes regardless of orientation. By design, predictions along any imaging plane orientation are cross-sections of the same 3D representation, leading to spatio-temporal consistency across all slices. Moreover, our architecture makes the rotation and translation parameters of imaging planes learnable, allowing us to correct for the commonplace respiratory and patient motion between slice acquisitions under a rigid assumption. Furthermore, interpolation of intensities and segmentation can be performed in 4D at any desired resolution. We perform our study on a 120 subject sub-cohort of CMR imaging data from the UK-Biobank. Our in-plane segmentation performance is on-par with existing CMR segmentation methods and explore how the majority of failure cases arise from limitations in the ground-truth segmentation, for which our representations make predictions with better anatomical accuracy than its original training data. We also evaluate our motion-correction capabilities, displaying quantitative and qualitative improvements in slice alignment.

Accurate estimation of left ventricular (LV) orientation is essential for cardiac magnetic resonance (CMR) imaging and downstream analysis. Existing methods typically formulate orientation recognition as discrete view classification or rely on multi-slice geometric intersection, limiting their ability to model continuous 3D orientation and generalize across arbitrary slices. This work introduces a novel paradigm: Joint LV localization and 3D orientation estimation from a single CMR slice. To investigate this setting, representative orientation-aware detection frameworks are adapted to the CMR domain, and their limitations are analyzed. Upon that, we propose the Polar-Coupled Circular (PCC) embedding that provides a continuous and unambiguous orientation representation to address the limitations. Meanwhile, a scalable benchmark is constructed through automatic slice sampling from volumetric CMR segmentation datasets. Extensive experiments on four datasets demonstrate strong performance, achieving an average mIoU of 86.18% and an average angle deviation of 3.39°. This study establishes a new task setting for single-slice LV orientation modeling and provides a geometry-consistent framework for spatially informed CMR analysis. Code is available at https://github.com/yuyi1005/cmr-3d-ood.

Aims: Cardiovascular magnetic resonance (CMR) imaging enables non-invasive assessment of myocardial structure, function, and pathology, but requires substantial experience in interpretation of CMR images that could be supported by artificial intelligence (AI)-based models. However, use of AI models for enhanced CMR reading is limited by labor-intensive data curation, suboptimal model performance, and unclear implementation pathways. Methods and results: We developed an automated data curation pipeline for CMR-based cardiovascular disease (CVD) diagnosis, integrating open-source locally-run large language models (LLMs) to extract diagnostic labels from narrative CMR reports and preprocessing multimodal imaging data, including cine and late-gadolinium-enhancement (LGE) CMR sequences. Three vision foundation models (DINO, VST, UMedPT) were fine-tuned across these modalities in a two-stage approach. The dataset comprised hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), ischemic cardiomyopathy (ICM), cardiac amyloidosis (CA), and normal controls (NOR). A total of 988 curated cases were randomly divided into 742 for training and 246 for validation. Fine-tuned AI-models achieved high discriminative diagnostic performance on an independent test set comprising 1067 patients , with individual AUC-ROC values of up to 0.937 for the correct diagnosis of HCM and 0.945 for cardiac amyloidosis. Ensemble strategies combining multiple models and modalities further improved AI-based diagnostic accuracy and robustness, achieving the highest overall diagnostic performance for HCM (AUC=0.959, CI [0.936-0.978]), CA (AUC=0.966, CI [0.939-0.986]), NOR (AUC=0.872, CI [0.852-0.894]), DCM (AUC=0.848, CI [0.808-0.885]) and ICM (AUC=0.840, CI [0.809-0.868]). All training and inference code, along with the trained model weights, are publicly available on https://github.com/sinaamirrajab/CMR_CVD.

Clinical cardiac MRI is commonly acquired with high in-plane resolution but coarse through-plane resolution to reduce scan time and accommodate breath-hold and cardiac-motion constraints, which limits 3D analysis and diagnostic accuracy. We propose STRMSR, a reference- and memory-guided through-plane super-resolution (SR) framework that reconstructs high-resolution (HR) cardiac volumes by leveraging HR reference views acquired from the same subject and intermediate SR results as the memory. Our method uses coarse-to-fine contextual matching to establish robust correspondence between low-resolution target and reference/memory images under spatial misalignment. A learnable patch-wise dynamic feature aggregation module predicts content-adaptive mixture weights for each local patch, effectively fusing dynamic information while suppressing unreliable feature transfers. The intermediate SR results stored in the memory bank ensure slice-to-slice consistency for the super-resolved 3D volume. Experiments on the WHS cardiac MRI dataset under two reference protocols, orthogonal-plane views and long-axis chamber views, demonstrate consistent improvements over baselines at 4x and 8x upsampling factors.

We propose Bi-PT, a pipeline for reconstructing 3D four-chamber human heart meshes from clinical sparsely sampled cardiac magnetic resonance imaging (CMR) data. This work addresses the error-prone generation of 3D cardiac shape from a sparse point cloud (SPC) extracted from 2D long-axis and short-axis views used in routine clinical CMR protocols. Bi-PT enables accurate inference of the four-chamber heart mesh from the SPC by learning robust point features via bidirectional point cross-attention between an atlas and the SPC, together with per-point semantic labels that improve correspondence estimation. We formulate the deformation field as a Neural Ordinary Differential Equation (NODE) parameterized by a per-point affine transformation and translation to deform the atlas toward the target heart shape. By learning such a NODE, we can guarantee the deformation field to be a locally affine diffeomorphic deformation. We also integrate a semantic label loss into the Chamfer distance to encourage label-consistent correspondences and add a smoothness regularization to stabilize and improve the learning of the deformation field. Extensive experiments demonstrate that Bi-PT achieves accurate and robust performance compared to baselines.

Real-time cardiac cine MRI enables visualization of the beating heart during free breathing, but severe undersampling and motion make reconstruction highly challenging. A central challenge for reconstruction is incorporating powerful priors of cardiac anatomy while remaining computationally efficient. We propose Piecewise Dynamic Diffusion Regularization (PDDR), a reconstruction method that integrates a spatiotemporal diffusion model as a generative prior within a variational reconstruction framework for cine MRI. The model employs dedicated spatial layers to encode anatomical structure and temporal layers to capture cardiac motion learned from gated cine data. PDDR leverages the dynamic prior in a piecewise manner, enabling the efficient use of spatiotemporal diffusion models for processing of long real-time sequences. Experiments on retrospectively accelerated and prospective real-time cine MRI demonstrate that PDDR outperforms classical, unsupervised, and diffusion-based methods, delivering high-quality reconstructions with substantially reduced computation time compared to state-of-the-art baselines. These results highlight PDDR as a practical and scalable solution for free-breathing, real-time cardiac MRI. Code is available at https://github.com/MLI-lab/pddr.

Implicit neural representations (INRs) are well suited to cardiac motion estimation, providing continuous, compact representations of motion fields. However, fitting an INR to each image sequence is time-consuming and sensitive to the optimisation trajectory. Learned priors can help guide optimisation towards plausible motion fields and enable faster adaptation, but learning priors for cardiac motion INRs remains under-explored. In this work, we compare four strategies for learning cardiac motion priors, including a population prior learned by joint optimisation, a consensus prior obtained by weight averaging, auto-decoders, and meta-learning. Using short-axis tagged cardiac magnetic resonance images from the UK Biobank, we evaluate their impact on tracking accuracy, motion behaviour, and adaptation trajectory. All learned priors substantially improved early adaptation performance compared with random initialisation. While the simple consensus prior was effective, auto-decoders recovered large deformations faster during early adaptation. Meta-learning achieved strong early performance and maintained the best adaptation trajectory over 50 iterations.

Cardiac magnetic resonance imaging (CMR) routinely records structured acquisition metadata, yet most CMR foundation models rely primarily on image-only pre-training and leave this naturally available source of weak semantic supervision largely underexplored. We propose MetaCLIP-CMR, a metadata-driven framework based on Contrastive Language--Image Pre-training (CLIP), which converts imaging modality, anatomical view, scanner vendor, field strength, and scanner model into textual supervision for CMR representation learning. The pretrained image encoder is evaluated on imaging modality classification, cine view classification, and cardiac segmentation. MetaCLIP-CMR achieves 86.8% modality accuracy and 86.5% cine view accuracy, clearly outperforming ImageNet and masked reconstruction initialisations. For downstream cardiac segmentation, MetaCLIP-CMR consistently obtains the highest Dice score across the evaluated ACDC and M&Ms cine short-axis (SAX) settings under both full-data and 20% fine-tuning regimes. Compared with recent image-focused large-scale CMR pre-training models, MetaCLIP-CMR achieves comparable ACDC segmentation performance, while requiring less than 1% of their pre-training image scale. These results suggest that metadata learning offers a natural and easy-to-use strategy for transforming routinely recorded acquisition information into effective supervision for foundation-level CMR representation learning, highlighting the promise of metadata-driven multimodal pre-training.

Developing robust artificial intelligence models for 4D (3D + time) medical imaging is constrained by limited annotated data, inter-device domain shifts, and privacy restrictions. To address this, we propose a 4D controllable generative framework for anatomically consistent data augmentation. A semi-supervised variational autoencoder learns a compact latent representation of anatomical volumes while jointly predicting aligned segmentation masks in a unified framework. Anatomical structure is then disentangled from temporal dynamics through a cascaded latent diffusion model (LDM). A static LDM generates subject-specific anatomy conditioned on clinical priors (diagnosis and volumes measures) and a subsequent motion LDM estimates residual latent motions, ensuring strict temporal coherence across the 4D sequence. The proposed approach was evaluated on cine cardiac MRI as a representative 4D imaging application. Experiments across multiple datasets demonstrate high controllability of static anatomy (Pearson r > 0.8) and strong temporal coherence (FVD = 288.08). In cross-vendor generalization experiments, augmenting training sets with synthetic 4D sequences significantly improves downstream segmentation performance. Using nnU-Net, the proposed augmentation strategy improves the average Dice score by 1.4% and reduces the Hausdorff Distance by 3.0mm compared to training on real data alone, for the left ventricle, Dice improves by 2.8% with a 5.4mm reduction in boundary error. Overall, this framework provides a scalable and controllable solution for 4D medical image synthesis, supporting the development of more robust models with limited annotations and cross-vendor variability. Code available on https://github.com/cyiheng/4DCardiacMRISynthesis.

Cardiac magnetic resonance imaging (CMR) captures rich spatiotemporal information about ventricular structure and motion, but conventional risk models use only a few image-derived indices from selected cardiac phases. We present a latent dynamical model that encodes bi-ventricular anatomy and full-cycle cine motion as a continuous latent trajectory, using heart-rate-aware neural ordinary differential equation (ODE) dynamics and a graph-based mesh autoencoder to reconstruct anatomically consistent 3D+t ventricular motion. A covariate-conditioned prior defines the expected end-diastolic latent state, and a Cox proportional hazards model tests whether deviations from this prior predict incident heart failure. We studied 72,386 UK Biobank participants without baseline cardiovascular disease, including 367 incident heart failure events. In a held-out evaluation subset, adding the latent score to refitted pooled cohort equations improved the stratified C-index from 0.704 to 0.785, compared with 0.764 for seven established cardiac markers. Compared with non-graph and non-ODE approaches, the proposed model gave the best trade-off between reconstruction fidelity, generative realism, and downstream prognostic performance. These results suggest that continuous full-cycle modeling of ventricular motion provides informative cardiac phenotypes beyond conventional CMR summaries, while external validation in more representative patient cohorts is required before clinical risk-prediction use.

Correspondence is fundamentally relational: it seeks the unknown transformation between two observations of a common scene, not the content of either. Yet the dominant learning-based methods do not represent the transformation as a first-class object in the architecture. They encode each image independently and let a learned similarity function or a deep decoder discover the mapping implicitly. Phase correlation is the canonical exception, measuring the inter-image relationship directly in the Fourier domain, but the rigidity of its fixed basis confines it to global translation. We introduce a learned generalization of phase correlation that lifts this restriction by learning the basis on which the transformation decomposes. The same algebraic primitive extends to dense non-rigid deformations and to unitary dynamics. On the ACDC cardiac-MRI benchmark the framework matches or exceeds prior published baselines on both registration directions. On CAMUS echocardiography it matches state-of-the-art without auxiliary scoring or adaptive-smoothness mechanisms. Applied to time-evolved wavefunction pairs of the 1-D quantum harmonic oscillator, the same framework recovers the Hermite-function eigenstates and the quantized energy levels of the unknown Hamiltonian from observation pairs alone.

Cine cardiac magnetic resonance is the gold standard for assessing cardiac function, but the scarcity of public datasets limits the development of advanced data-driven models. To address this limitation, we propose a generative method for synthesizing temporally coherent and anatomically consistent cardiac sequences. Our text-to-video framework decouples cardiac spatial structure from temporal motion. First, a fine-tuned diffusion model synthesizes an initial frame from a clinical text prompt, controlling anatomical features. Then, a latent flow model conditioned on a cardiac phase embedding generates the complete cardiac motion, ensuring spatial consistency and temporal control. Our model generates anatomically and pathologically diverse sequences with high temporal coherence and strong fidelity to input prompts, achieving a FID of 31.68 for image realism and a CLIP score of 31.04 for text-image alignment. These experimental results highlight its potential to produce high-fidelity, on-demand medical data, offering a scalable solution to data scarcity.

Multi-view cardiac magnetic resonance (CMR) imaging provides complementary anatomical information and is widely used for noninvasive disease assessment. Recent transformer-based models have demonstrated strong representation learning capabilities for CMR analysis; however, they typically learn unified latent embeddings that entangle view-specific anatomical variations with disease-related features. Such entanglement biases classifiers toward structural attributes rather than view-invariant pathological patterns. This issue is exacerbated in low-data regimes, particularly for underrepresented cardiac conditions, where limited samples increase the susceptibility to shortcut learning and view-dependent decision boundaries. To address this, we propose a Motion-Guided View--Disease Disentanglement framework MoViD built upon a ViT-MAE backbone. The model explicitly factorizes latent representations into view-specific and disease-discriminative components using dual-branch supervised contrastive objectives and a gradient-reversal adversarial constraint that minimizes disease leakage into the view embedding. Additionally, an annotation-free temporal motion feature, derived from inter-frame difference maps, is introduced to localize the beating heart region and suppress background artifacts. A focal reweighting mechanism is incorporated into the contrastive loss to mitigate class imbalance. We evaluate the framework on a private clinical venous thrombosis dataset and two public benchmarks (M&Ms, M&Ms2). Across disease classification and cardiac segmentation tasks, our approach consistently outperforms standard transformer baselines and demonstrates competitive performance against large-scale pretrained foundation models, validating the efficacy of structural disentanglement in medical image analysis.

Multimodal Large Language Models (MLLMs) have shown strong performance on public medical benchmarks, yet existing evaluations often remain weak proxies for clinical use, relying on isolated inputs and simplified recognition-style tasks. We introduce CardioLens, a leakage-resistant evaluation testbed for multi-sequence Cardiovascular Magnetic Resonance (CMR), constructed from private hospital archives through a rigorous report-to-QA construction and verification pipeline. CardioLens contains 473,896 slices and 13,494 verified QA pairs across 4D Cine, LGE, perfusion, and T2-weighted imaging, and evaluates three stages of CMR interpretation: image understanding, report generation, and disease diagnosis. Across 24 state-of-the-art MLLMs, CardioLens reveals a substantial clinical reality gap: models perform poorly overall, with performance degrading along the real CMR workflow. Confusion analysis further shows a category-collapse failure mode, where models default to frequent abnormal categories rather than distinguishing clinically distinct findings. To rule out MLLM-compatible input construction as the primary cause, we compare random, clinically motivated, and data-driven slice selection protocols under different slice budgets; performance changes only marginally, typically by about 1%. Explicit reasoning prompts also fail to rescue performance, often making models more conservative rather than improving visual evidence use. These results show that current MLLMs remain far from reliable CMR interpretation, where clinical decisions require integrating distributed evidence across sequences, views, and temporal phases. CardioLens provides a clinically grounded testbed for developing next-generation MLLMs toward real-world clinical deployment.

Vision Transformer (ViT) models, utilizing self-attention mechanisms, have demonstrated robust generalization capabilities across various vision tasks, including image classification. However, these models, typically pretrained on general public datasets, often lack the specialized domain knowledge necessary for medical imaging applications. In this study, we investigate the adaptation of ViT models, specifically for cardiac magnetic resonance (MR) images, using an in-house dataset. We found that pretrained ViT features do not effectively transfer to the cardiac MR domain. To overcome this limitation, we introduce an adaptation strategy that utilizes image-based self-supervised contrastive learning, demonstrating superior performance compared to traditional supervised training approaches. Moreover, our adapted ViT model exhibits strong generalization to external MR datasets such as BraTS and ADNI. Through ablation studies, we further investigate the impact of batch size and dataset scale on performance. Ultimately, our adapted model achieves classification AUC exceeding 0.75 across the four most common cardiac MR sequences.

Conventional cardiac cine MRI relies on breath-hold Cartesian acquisitions, which are vulnerable to motion artifacts and can be uncomfortable or infeasible, particularly for pediatric and other noncompliant patients who cannot reliably hold their breath. Free-breathing radial acquisitions can alleviate these limitations, but robust reconstruction at high acceleration remains challenging due to prominent streak artifacts. To address these limitations, we propose Cine-DL, a clinically oriented framework that couples targeted k-space preprocessing with fast, model-based deep reconstruction. In this pipeline, raw free-breathing radial data undergo retrospective cardiac binning and respiratory gating to resolve cardiac phases and discard motion-corrupted spokes. We then introduce Streak Optimized Coil Compression (SOC), which explicitly preserves cardiac signals while suppressing peripheral interference that typically drives the streak artifacts. The resulting 2D+t cine series is reconstructed with an unrolled network that alternates a ResNet proximal operator with physics-based data consistency updates solved via conjugate gradient. We further employ a memory-efficient training strategy that reduces peak memory usage. We evaluate Cine-DL on free-breathing volunteer data against established baselines (k-t SENSE and iGRASP) and demonstrate clinical translation via hospital deployment on newly acquired patient data. Our experiments show that Cine-DL consistently improves quantitative metrics and visual fidelity, supporting a practical route toward routine, time-sensitive clinical adoption of free-breathing cine MRI.

Purpose: Real-time (RT) bSSFP MRI enables fast free-breathing cardiovascular imaging but requires 10-16 slices for functional assessment, resulting in prolonged scan times. Simultaneous multi-slice (SMS) imaging can reduce acquisition time but when combined with non-Cartesian trajectories, it relies on iterative reconstructions that preclude online use. This study investigates deep artifact suppression to facilitate rapid, online reconstruction of RT-SMS. Methods: A spiral bSSFP SMS RT sequence with two simultaneously acquired slices was implemented at 1.5 T. Reconstruction used slice separation in k-space, followed by deep artifact suppression in image space using a 3D U-Net. Ten healthy volunteers were imaged. RT-SMS image quality and reconstruction time were compared between deep artifact suppression and compressed sensing (CS) reconstructions. Left (LV) and right (RV) ventricular volumes at end diastole (EDV) and end systole (ESV) and LV mass (LVM) were compared between RT-SMS with deep artifact suppression and reference-standard breath-hold (BH) imaging. Results: The RT-SMS acquisition was ~13x faster than BH imaging (15 s vs 3 min 15 s). RT-SMS reconstruction using deep artifact suppression was ~50x faster than CS (30 s vs 24 min 55 s). Deep artifact suppression consistently outperformed CS in quantitative and qualitative image quality (p<0.001). Functional agreement between BH and RT-SMS with deep artifact suppression was good (LVEDV: -7.5 +/- 6.8 ml, LVESV: -0.9 +/- 4.2 ml, RVEDV: -6.4 +/- 8.4 ml, RVESV: 0.2 +/- 10.7 ml, LVM: -10.3 +/- 11.0 g). Conclusion: Online deep artifact suppression reconstruction for RT-SMS bSSFP CMR enables free-breathing short-axis coverage with a substantial reduction in acquisition and reconstruction time while maintaining diagnostic image quality.

Quantitative cardiac magnetic resonance imaging (MRI) enables non-invasive myocardial tissue characterization but relies on robust motion correction within these variable-length, variable-contrast image sequences. Groupwise registration, which simultaneously aligns all images, has shown greater robustness than pairwise registration for motion correction. However, current deep-learning-based groupwise registration methods cannot generalize across MRI sequences: the architecture typically encodes input data as a fixed-length channel stack, which rigidly couples network design to protocol-specific sequence length, input ordering, and contrast dynamics. At inference time, any change in imaging protocols will render the network unusable. In this work, we introduce \emph{\AnyTwoReg}, a new set-based groupwise registration framework that takes a quantitative MRI sequence as an unordered set. This set formulation fundamentally decouples network design from sequence length and input ordering. By utilizing a shared encoder and correlation-guided feature aggregation, \emph{\AnyTwoReg} constructs a permutation-invariant canonical reference for registration, and learns a permutation-equivariant mapping from images to deformation fields. Additionally, we extract contrast-insensitive image features from an existing foundation model to handle extreme contrast variations. Trained exclusively on a single public $T_1$ mapping dataset (STONE, sequence length $L=11$), \AnyTwoReg generalizes to two unseen quantitative MRI datasets (MOLLI, ASL) with variable lengths ($L \in [11, 60]$) and different contrast dynamics. It achieves strong cross-protocol generalization in a zero-shot manner, and consistently improves downstream quantitative mapping quality. Notably, while designed for quantitative MRI sequences, our framework is directly applicable to Cine MRI sequences for inter-cardiac-phase registration.

Converting free-text cardiac magnetic resonance (CMR) reports into auditable structured data remains a bottleneck for cohort assembly, longitudinal curation, and clinical decision support. We present CMR-EXTR, a lightweight framework that converts free-text CMR reports into structured data and assigns per-field confidence for quality control. A teacher-student distillation pipeline enables fully offline inference while limiting manual annotation. Uncertainty integrates three complementary principles -- distribution plausibility, sampling stability, and cross-field consistency -- to triage human review. Experiments show that CMR-EXTR achieves 99.65% variable-level accuracy, demonstrating both reliable extraction and informative confidence scores. To our knowledge, this is the first CMR-specific extraction system with integrated confidence estimation. The code is available at https://github.com/yuyi1005/CMR-EXTR.

Conventional MRI reconstruction methods treat images and coil sensitivities as discrete objects, leading to high memory demands and limited structural awareness that hamper effective regularization. These limitations hinder accurate reconstruction in highly undersampled scenarios, such as dynamic 3D cardiac magnetic resonance (CMR). We introduce a discretization-free, memory-efficient, model-based framework for dynamic 2D and 3D MRI reconstruction from highly undersampled data. We represent magnetization and coil sensitivities as continuous objects -- differentiable functions -- using tensor products of univariate neural fields. This tensor product structure enables scalable optimization in high-dimensional spatiotemporal settings. Our method outperforms state-of-the-art model-based reconstructions in dynamic 2D and 3D MR settings, preserving structure and motion even under aggressive undersampling (e.g., acceleration factor 16).

The emergence of large-scale pretrained foundation models has transformed computer vision, enabling strong performance across diverse downstream tasks. However, their potential for physics-based inverse problems, such as accelerated cardiac MRI reconstruction, remains largely underexplored. In this work, we investigate whether natural-domain foundation models can serve as effective image priors for accelerated cardiac MRI reconstruction, and compare the performance obtained against domain-specific counterparts such as BiomedCLIP. We propose an unrolled reconstruction framework that incorporates pretrained, frozen visual encoders, such as CLIP, DINOv2, and BiomedCLIP, within each cascade to guide the reconstruction process. Through extensive experiments, we show that while task-specific state-of-the-art reconstruction models such as E2E-VarNet achieve superior performance in standard in-distribution settings, foundation-model-based approaches remain competitive. More importantly, in challenging cross-domain scenarios, where models are trained on cardiac MRI and evaluated on anatomically distinct knee and brain datasets--foundation models exhibit improved robustness, particularly under high acceleration factors and limited low-frequency sampling. We further observe that natural-image-pretrained models, such as CLIP, learn highly transferable structural representations, while domain-specific pretraining (BiomedCLIP) provides modest additional gains in more ill-posed regimes. Overall, our results suggest that pretrained foundation models offer a promising source of transferable priors, enabling improved robustness and generalization in accelerated MRI reconstruction.

Cardiac Magnetic Resonance (CMR) imaging provides a comprehensive assessment of cardiac structure and function but remains constrained by high acquisition costs and reliance on expert annotations, limiting the availability of large-scale labeled datasets. In contrast, electrocardiograms (ECGs) are inexpensive, widely accessible, and offer a promising modality for conditioning the generative synthesis of cine CMR. To this end, we propose ECGFlowCMR, a novel ECG-to-CMR generative framework that integrates a Phase-Aware Masked Autoencoder (PA-MAE) and an Anatomy-Motion Disentangled Flow (AMDF) to address two fundamental challenges: (1) the cross-modal temporal mismatch between multi-beat ECG recordings and single-cycle CMR sequences, and (2) the anatomical observability gap due to the limited structural information inherent in ECGs. Extensive experiments on the UK Biobank and a proprietary clinical dataset demonstrate that ECGFlowCMR can generate realistic cine CMR sequences from ECG inputs, enabling scalable pretraining and improving performance on downstream cardiac disease classification and phenotype prediction tasks.

Reconstructing cardiac motion from CMR sequences is critical for diagnosis, prognosis, and intervention. Existing methods rely on complete CMR stacks to infer full heart motion, limiting their applicability during intervention when only sparse observations are available. We present TetHeart, the first end-to-end framework for unified 4D heart mesh recovery from both offline full-stack and intra-procedural sparse-slice observations. Our method leverages deformable tetrahedra to capture shape and motion in a coherent space shared across cardiac structures. Before a procedure, it initializes detailed, patient-specific heart meshes from high-quality full stacks, which can then be updated using whatever slices can be obtained in real-time, down to a single one during the procedure. TetHeart incorporates several key innovations: (i) an attentive slice-adaptive 2D-3D feature assembly mechanism that integrates information from arbitrary numbers of slices at any position; (ii) a distillation strategy to ensure accurate reconstruction under extreme sparsity; and (iii) a weakly supervised motion learning scheme requiring annotations only at keyframes, such as the end-diastolic and end-systolic phases. Trained and validated on three large public datasets and evaluated zero-shot on additional private interventional and public datasets without retraining, TetHeart achieves state-of-the-art accuracy and strong generalization in both pre- and intra-procedural settings. Code and dataset is available at https://github.com/Scalsol/TetHeart.