Magnetic Resonance Imaging

Perineural invasion (PNI) is associated with poor prognosis in cholangiocarcinoma (CCA). However, its detection from 3D MRI remains challenging due to the subtle and spatially heterogeneous imaging signatures at the tumor periphery. Capturing such spatially sparse cues necessitates volumetric analysis of 3D MRI, but existing deep learning approaches incur prohibitive computational costs on volumetric medical images, limiting their clinical deployment. We propose Dual Sparsity Spikformer (SpikeDS), a spiking neural network architecture that jointly exploits activation sparsity from binary spike communication and spatial sparsity from window pruning based on firing rates. SpikeDS introduces Dual Sparsity Spiking Attention (DSSA), which combines two complementary mechanisms. The first is Window-based Expert Mixture Spiking Attention (W-EMSA), which selectively applies attention only to salient windows identified by their firing rates. The second is Cross-Window Spiking Self-Attention (CW-SSA), which enables global context exchange through an asymmetric scheme in which pruned windows still contribute as key-value sources. Evaluated on a clinical cohort of 139 CCA patients via 5-fold cross-validation, SpikeDS achieves an AUC of 0.753 while consuming only 14.4 mJ, surpassing the best baseline in both AUC and energy efficiency. These results suggest that dual sparsity provides an effective hardware-aware strategy for improving the efficiency of 3D spiking transformers without compromising diagnostic performance.

Diffusion-weighted imaging (DWI) is acquired as part of bi-parametric prostate MRI, but suffers from artifacts that degrade downstream quantitative and diagnostic performance. While DWI preprocessing is standard in brain imaging, its adoption in prostate imaging remains limited and lacks standardized pipelines. This study investigated the effect of different DWI preprocessing strategies on apparent diffusion coefficient (ADC) estimation and automatic Prostate Imaging Reporting and Data System (PI-RADS) classification. 268 cases were derived from the fastMRI prostate cohort by sequentially applying denoising, Gibbs-ringing correction, and diffeomorphic registration for susceptibility distortion correction. ADC maps were compared using linear least squares (LLS) and iteratively-weighted LLS (IWLLS). A 3-class DenseNet classifier was trained to predict PI-RADS scores from multi-channel MRI inputs. ADC analysis revealed statistically significant differences across preprocessing pipelines, with LLS and IWLLS producing numerically equivalent maps. Linear relationships between ADC values were preserved across most datasets (PCC ~0.99), while distortion correction realigned DWI to T2w anatomy and altered ADC values accordingly (PCC ~0.90). Classification showed the best AUROC and sensitivity for high-risk PI-RADS classes in the fully processed dataset. False-negative analysis revealed this dataset produced the least overconfident incorrect predictions on high-risk classes, which is a desirable property for clinical triage. DWI preprocessing, particularly distortion correction, enhances both ADC map quality and the predictive power of deep learning models for PI-RADS classification, supporting the need for optimized preprocessing pipelines in prostate MRI.

Biomedical imaging data exhibit substantial acquisition variability, where identical biological structures can appear markedly different due to differences in imaging devices, acquisition protocols, sites, and reconstruction settings. Consequently, learned representations often entangle underlying biological information with acquisition-dependent appearance, limiting interpretability, generalisation, and clinical deployment. We show that these sources of variation can be disentangled by jointly modelling medical images and acquisition metadata. Using large-scale clinical brain MRI data as a case study, we learn representations that disentangle anatomical structure from contrast-dependent appearance. The resulting framework enables the organisation of heterogeneous imaging protocols, sequence understanding, the detection of image-metadata inconsistencies and imaging artifacts, while preserving biologically relevant anatomical features across diverse acquisitions. Building on these disentangled representations, it further supports generative and translational capabilities, performing both metadata-conditioned synthesis of realistic 3D brain MRIs and anatomy-preserving harmonisation for cross-modality and cross-site adaptation. Our findings demonstrate that acquisition variability is a structured component of the imaging process that can be modeled, audited, synthesised, and controlled, establishing a foundation for acquisition-aware representation learning in large-scale biomedical imaging.

Perineural invasion (PNI) is a clinically relevant indicator of tumor aggressiveness and can influence surgical decision-making, motivating interest in reliable preoperative assessment. The subtle MRI features of PNI, however, often resemble nearby anatomy, complicating noninvasive prediction. These fine perineural cues are easily attenuated by routine downsampling or overly global feature aggregation, reducing the effectiveness of conventional volumetric models. We present LoSA-Net, a localized and scale-adaptive architecture for boundary-sensitive PNI prediction in 3D MRI. Talking Neighborhood Attention (TNA) preserves nerve-aligned detail through localized self-attention with head-wise mixing, and Scale-Adaptive Feature Mixing (SAFM) modulates the receptive field using multi-scale depthwise processing. Cross-Scale Refinement and Alignment (CSRA) maintains consistency between semantic context and high-resolution boundaries across stages. In contrast-enhanced MRI scans from 168 patients with cholangiocarcinoma, LoSA-Net achieves an AUC of 0.7567 and outperforms representative convolutional and transformer baselines under matched preprocessing and optimization settings.

Perineural invasion (PNI) is a critical prognostic factor in cholangiocarcinoma. Non-invasive prediction from 3D MRI is challenging, demanding models that efficiently capture both fine-grained details and global context. We propose the Multi-window Mixture-of-Head Attention Transformer (MMA-Former), a novel end-to-end 3D architecture featuring a Coarse-Fine Transformer (CFT) structure for parallel multi-scale feature extraction. We advance this structure by integrating a novel Window-Specific Mixture-of-Head attention (WS-MoH) mechanism. Unlike standard Multi-Head Self Attention (MSA), WS-MoH generates a representation for each 3D window and dynamically routes the entire window to specialized or common attention heads. This enables spatially adaptive feature extraction tailored to the local context of each window, enhancing specialization and reducing redundancy without increasing parameters. Evaluated on a retrospective dataset of 168 T1-weighted MRI scans, MMA-Former achieved an AUC of 0.752, outperforming other 3D architectures, including the best CNN (AUC of 0.708) and Transformer baselines (AUC of 0.681).

Self-supervised learning offers a compelling approach for medical imaging, where labeled data are scarce and acquisition costs are high. We present COJEPA, a self-supervised framework for volumetric brain MRI that combines a joint-embedding predictive architecture (JEPA) with a contrastive loss (CO), targeting two complementary properties: local predictivity and global discriminability. The model is trained without labels on T1-weighted structural MRI from two cohorts (HCP-YA and AABC, $N{=}2286$, ages 22 to 90), extending I-JEPA to 3D with foreground-aware block masking, a hierarchical convolutional patch embedding, and world-space sinusoidal positional encodings. We evaluate all three objectives across zero-shot twin retrieval, brain tumor segmentation (BraTS 2024), and age regression (OpenBHB). COJEPA achieves the best monozygotic twin recall at rank@1 (0.84), the best finetuning age MAE (2.55 years on OpenBHB 3.0T), and matches CO on BraTS whole-tumor Dice, demonstrating that the combined objective yields representations that are simultaneously discriminative and locally structured.

Forecasting the future anatomy of slow-evolving neurodegenerative diseases could enable earlier, more targeted intervention and improve clinical trial design, but it remains challenging because true progression signals are subtle in longitudinal MRI. In this low-signal regime, transferring modern generative sequence models directly is unreliable: training is dominated by stable baseline anatomy and confounded by dense, sample-specific nuisance variation. We first provide a theoretical analysis that explains these failures through two modes. Identity collapse occurs when optimization is driven toward reproducing the current anatomy, which prevents the model from learning faint temporal change. The continuous interpolation trap arises when standard smooth networks cannot separate localized biological drift from pervasive noise, which leads to spurious changes that diffuse across the volume. To address both issues, we propose Latent Drift, a progressive generative framework that learns change in a compressed semantic representation rather than synthesizing full-resolution anatomy. This design removes pixel-level identity from the prediction target and concentrates model capacity on progression-relevant dynamics. We further apply Finite Scalar Quantization to the learned change representation, which suppresses small, high-frequency nuisance fluctuations while preserving consistent structural drift. Experiments on longitudinal 3D brain MRI show that Latent Drift improves patient-specific neuro-forecasting over diffusion and autoregressive transformer baselines across generative fidelity and clinically relevant evaluation metrics. Project page: \href{https://cutepkq.github.io/latent-drift}{https://cutepkq.github.io/latent-drift}.

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.

Accurate tumour localization and diagnosis is a critical component of clinical care for brain cancers. Magnetic Resonance Imaging (MRI) is the most commonly used imaging modality due to its superior soft-tissue contrast. However, standard MRI often exhibits limited contrast and imaging artifacts, which necessitates the use of contrast agents to enhance lesion visibility. The administration of chemical contrast agents is not always feasible and may be contraindicated in patients with renal impairment or other health conditions. As a result, developing accurate and non-invasive contrast enhanced MRI (CEMRI) synthesis methods has clinical importance. In recent years, numerous approaches for CEMRI synthesis have been proposed, predominantly relying on generative artificial intelligence models. While these methods demonstrate promising performance, their dependence on implicit feature learning often limits their ability to preserve anatomical boundaries and tumour-specific fine structures. To address these challenges, we propose an anatomically aware frequency-and-structure-guided vision transformer (AA-ViT), for CEMRI synthesis using pre-contrast MRI modalities (T1, T2, and FLAIR). Experiments on the BraTS 2021 dataset demonstrate that the proposed method preserves anatomical and lesion boundaries, achieving higher PSNR and SSIM than state-of-the-art approaches. Clinical evaluation by three neuroradiologists and a neurosurgeon on 19 randomly selected cases across diverse gliomas yielded a mean score of 3.94/5, providing preliminary clinical validation rarely seen in prior studies. Synthetic post-contrast scans from our model could lower scanning costs, shorten imaging time, and avoid the potential risks of using gadolinium-based contrast agents.

Alzheimer's disease (AD) is a common neurodegenerative disorder, and early diagnosis is of great significance for delaying disease progression and enabling timely intervention. Mild cognitive impairment (MCI), which represents an intermediate clinical stage between cognitively normal aging and AD. Structural magnetic resonance imaging (sMRI) provides detailed characterization of anatomical structures and plays an important role in AD-related brain analysis. However, existing sMRI-based brain network methods typically rely on a single graph construction strategy, limiting their ability to jointly capture spatial relationships and morphological similarities between brain regions. To address these issues, this paper proposes an sMRI-based multi-view masked graph neural network model (MVMGNN) for AD diagnosis. A joint node-edge masking mechanism is proposed to simultaneously select radiomics feature dimensions and structural connections, reducing redundancy during graph learning. Furthermore, a patient-level cross-view gated fusion mechanism is proposed to integrate multi-view representations. Experimental results on the ADNI dataset demonstrate that MVMGNN outperforms several competing approaches in AD classification. Interpretability analysis further demonstrates that MVMGNN is able to identify key brain regions associated with AD, providing useful insights into discriminative patterns in sMRI-based brain networks.Our implementation is publicly available at https://github.com/chenzhao2023/MVMGNN_AD

In longitudinal Alzheimer's disease (AD) diagnosis support, clinical and imaging information is often collected at irregular visits. Integrating these multimodal observations may improve diagnostic assessment, but naive fusion can degrade performance when MRI is noisy or intermittently unavailable. We propose AT-Attn, a temporal-aware multimodal framework that combines Change-and-Time encoding, time-biased asymmetric cross-attention, and gated fusion to integrate MRI with longitudinal clinical information. We evaluate AT-Attn on an MRI-retained ADNI cohort of 1,520 patients using structural MRI, six cognitive-scale trajectories, and seven static clinical variables under patient-level five-fold cross-validation. The main asymmetric AT-Attn model achieves accuracy 0.719+/-0.024, macro F1 0.721+/-0.023, ROC-AUC 0.873+/-0.013, and PR-AUC 0.783+/-0.018, outperforming unimodal and naive multimodal fusion baselines while remaining competitive with strong tabular baselines. These results suggest that a temporal-aware and constrained fusion strategy can help structural MRI contribute clinically relevant complementary information for patient-level AD diagnosis support.

Magnetic resonance imaging (MRI) super-resolution is vital for improving diagnostic accessibility, yet most methods treat it as a deterministic mapping from a fixed low-resolution input to a high-resolution target. This overlooks a key property of MRI acquisition physics: spatial resolution and signal-to-noise ratio (SNR) are inherently coupled, making any given low-resolution scan merely one of many possible realizations under varying acquisition trade-offs. We rethink MRI super-resolution as a physics-aware reconstruction problem, in which the goal is to identify the optimal resolution-SNR configuration and then super-resolve it to obtain high-quality MRI results. A key implication of this formulation is that MRI resolution becomes dynamic rather than fixed. To handle such resolution-heterogeneous inputs, we adapt 2D Gaussian Splatting (2D GS) to MRI by formulating reconstruction as a coordinate-based, resolution-agnostic rendering problem. To further enhance fidelity, we introduce three innovations: (1) a prior-aware Gaussian representation that combines an Anatomical Structure Prior for tissue-specific kernel initialization with an Imaging System Prior that captures hardware characteristics via a covariance dictionary; (2) a physics-constrained signal modeling scheme that predicts intrinsic tissue parameters (proton density rho and effective relaxation rate R2) and synthesizes intensities through governing physical equations, ensuring biophysically plausible contrast; and (3) a meta-learning framework that alleviates paired-data scarcity by pretraining on simulated data and adapting to real-world conditions. Extensive experiments on dynamic-resolution datasets and standard benchmarks demonstrate that our method achieves state-of-the-art performance, highlighting its strong potential for clinical deployment.

Generating CT volumes from MRI and CBCT can improve treatment planning in adaptive radiotherapy while avoiding additional radiation exposure. However, direct regression of CT intensities is challenged by the inherently high dynamic range and long-tailed distributions, thereby averaging out sparse yet clinically important structures. To alleviate this issue, we reformulate the regression target into multiple windowed representations, leveraging the inductive prior that CT intensities are structure-deterministic and window-separable. These windowed views exhibit smoother distributions and admit structured fusion back to the full-range CT. Building on this reformulation, we introduce WING, a WINdow-prior-based Generative network comprising: 1) a new Gated Inception Generator to produce multi-window predictions, enabling multi-shape kernel interactions to capture cross-modality correspondence; 2) a Fuse-and-Refine Transformer to aggregate the windowed outputs and learn residuals for detail refinement; and 3) a joint adversarial training objective to enhance window-conditioned realism. Extensive experiments demonstrate that our compact WING achieves state-of-the-art performance on the MRI-to-CT and CBCT-to-CT benchmarks, while supporting multi-anatomy synthesis with a single model.

Non-invasive prediction of Gleason Grade Group (GGG) in prostate cancer using multiparametric MRI (mpMRI) is clinically vital for reducing unnecessary biopsies. Existing GGG prediction methods face two major limitations. First, they often overlook non-image information critical for GGG prediction, including age, prostate-specific antigen (PSA), and expert priors embedded in radiology reports. Second, they tend to oversimplify GGG as flat categorical labels, failing to account for its intrinsic hierarchy of primary and secondary Gleason patterns. To this end, we propose a novel Knowledge-Driven Ordinal-Aware Learning (KOAL) framework with three synergistic modules. Specifically, the Clinical-Context Modulation (CCM) module uses clinical variables (e.g., age and PSA) to dynamically modulate discriminative image representations. The Knowledge-Guided Prototype Alignment (KGPA) module leverages an LLM to extract group-specific expert knowledge from training radiology reports and clinical guidelines, producing offline semantic anchors describing grade-specific radiological findings without requiring patient-specific reports at inference. Through prototype contrastive alignment, patient-specific mpMRI representations are matched with these anchors to promote pathology-aligned representation learning. The Hierarchical Ordinal-aware Constraints (HOC) module decouples primary and secondary Gleason pattern prediction and maps their probabilistic outputs to GGG via a Differentiable Bio-logic Mapping Layer (DBML), ensuring pathological grading consistency. Experiments on public PI-CAI and in-house datasets demonstrate that KOAL outperforms state-of-the-art methods. Code is available at: https://github.com/Gother-GZ/KOAL.

Cerebral microbleeds (CMBs) are MRI markers of small vessel disease and the microbleed component of amyloid related imaging abnormalities (ARIA-H), but their small size, sparsity, and similarity to vessels, calcification-like foci, and artefacts make automated detection difficult. We propose CenSynCMB, a centre-guided and mimic-aware framework combining a 3D Attention U-Net, auxiliary centre-map supervision, false-negative-driven reweighting, and fold-wise physics-guided synthesis of positive CMBs and labelled hard negatives. Synthetic data expose the detector to compact lesions and common mimics without validation or test leakage. On VALDO Task 2, CenSynCMB achieved the best local-comparison lesion-level F1 (74.3%, p = 0.020); on external AIBL SWI, it achieved the highest local-comparison recall (88.5%, p = 0.0058) and F1 (65.0%, p = 0.0016). Together, these results support scalable CMB candidate extraction in large, unlabelled MRI cohorts, while highlighting cohort-specific calibration as the next step toward reliable burden estimation.

Lumbar spine degeneration is a major contributor to chronic low back pain and is routinely assessed on MRI using ordinal grading systems, e.g. normal, mild, moderate, severe. Consequently, most approaches to train models to grade these MRIs formulate grading as a multi-class classification problem, treating ordinal grades as categorical, ignoring differences in misclassification severity, and imposing hard decision boundaries on a continuous disease process. This work explores modeling spinal degeneration as a continuous severity ranking problem. We introduce SpineRankNet, a framework that learns scalar severity scores from lumbar spinal MRI, and compare it against multi-class classification and ordinal regression. Using multiple degeneration measures from the Genodisc dataset, we show that a model trained using a ranking loss to produce a continuous score enables fine-grained ordering of MRI scans. Furthermore, the ordinal grading classes can be recovered from the score with comparable accuracy to those from a model trained directly for classification. The score learned by ranking even improves discrimination between more distant classes. Source code is available at https://github.com/spinetools/spineranknet.

Cardiac cine Magnetic Resonance Imaging (MRI) is a critical diagnostic tool that provides dynamic insights for radiologists. To accelerate acquisition, under-sampled k-space data is often used, requiring reconstruction methods that combine coil sensitivity encoding with prior information to recover missing data. Deep learning approaches have gained more attention for leveraging data-adaptive priors. While supervised learning approaches are a common choice, they depend on fully sampled reference data, which is not always available. Unsupervised methods eliminate the need for fully sampled reference data, which can be advantageous in cardiac cine MRI reconstruction. Among them, implicit neural representations (INRs) have shown great potential due to their simple architecture and good quality reconstructions. In this work, we propose an image-domain dual-branch INR framework, termed I-FP-INR, which extends the original INR design by introducing an additional feature-processing branch. This design aims to extract complementary feature embeddings to enhance the overall representation, thereby benefiting reconstruction. Extensive evaluations on both public datasets and in-house data show consistent improvements over baseline methods in reconstruction quality, with strong robustness across varied scenarios.

Accelerated magnetic resonance imaging reduces acquisition time, but reconstruction from undersampled k-space can blur diagnostically relevant structures or introduce failures that are not captured by global image metrics. We propose SA-RDM-DC, a Self-Auditing Residual generative Drifting Model with Data Consistency for accelerated knee MRI. The method adapts the newly proposed generative drifting paradigm to accelerated MRI by training a physics-conditioned drift field from the zero-filled reconstruction toward the fully sampled residual correction. It predicts image- and missing-k-space residual corrections, enforces data consistency with acquired k-space, uses frequency-aware and residual drifting supervision to recover fine detail, and produces dense error maps and slice-level risk scores in the same inference pass. We evaluate SA-RDM-DC on multi-coil fastMRI knee data at acceleration factors of 4, 8, and 12, with fastMRI+ pathology annotations for region-level and classifier-based task preservation, and on SKM-TEA for zero-shot and fine-tuned protocol-shift evaluation. Compared with zero-filled reconstruction, UNet-image-SENSE, DC-UNet, Score-Diffusion, ELF-Diff, SENSE-VarNet, and MoDL baselines, SA-RDM-DC achieves the highest SSIM across fastMRI acceleration factors while retaining subsecond per-slice inference and avoiding the long sampling time of iterative diffusion baselines. In pathology-aware analysis, SA-RDM-DC preserves lesion-region structural fidelity and reduces meniscus prediction instability. Its self-auditing scores strongly identify high-error reconstructions on fastMRI and partially transfer as a selective-review signal under SKM-TEA protocol shift. These results support reconstruction evaluation that jointly considers image fidelity, pathology preservation, runtime, and case-specific reliability.

Penile measurement is clinically relevant across male reproductive and urogenital health, including conditions such as micropenis, congenital and endocrine disorders, and sexual or urinary dysfunction. However, quantitative assessment of penile size has relied mainly on external length or circumference measurements, which are difficult to standardize, sensitive to measurement conditions, and unable to capture the internal portion of the penis. MRI enables volumetric assessment of the whole penis in vivo, but automated segmentation has not previously been established at population scale. Automated whole-organ volumetry would enable high-throughput phenotyping for multi-omics and clinical studies of male reproductive disease. Here, we present a deep learning framework for whole-penis segmentation in multi-channel DIXON MRI. Using a newly curated expert-annotated training dataset ($n = 145$ subjects; $13,050$ annotated slices) and a double-annotated independent test benchmark ($n = 24$ subjects; $2,160$ double-annotated slices), we optimized a 3D nnU-Net architecture. The model achieved a 5-fold cross-validation Dice score of $0.90$ and performed at observer-level accuracy on the independent test set (Dice: $0.92$; Hausdorff distance: $3.58$). We deployed the model in $34,412$ UK Biobank participants, enabling automated quantification of total penile tissue, including both external and internal components. Longitudinal evaluation in 2,282 men demonstrated high inter-session reproducibility ($r = 0.87$). This framework establishes a reproducible and population-scalable method for MRI-based assessment of penile anatomy and provides an open technical resource for future studies in urological imaging and male reproductive health. The trained model weights will be publicly released.

Accurate 4D whole-heart mesh reconstruction from sparse cine MRI is critical for creating cardiac digital twins, but remains challenging due to limited 2D slice coverage and the complex coupling between cardiac shape and motion. Existing methods often rely on intermediate contour fitting and typically reconstruct static, single-phase, or partial cardiac geometries, limiting their ability to capture full-chamber dynamics. We propose a novel end-to-end framework for reconstructing temporally resolved whole-heart meshes from multi-view 2D cine MRI sequences by learning an image-to-mesh mapping. The framework incorporates a differentiable contour renderer inspired by the Beer-Lambert attenuation principle, enabling anatomy-aware supervision of 3D+t mesh deformation through contour-based projection losses. To improve temporal consistency across the cardiac cycle, we further introduce a multi-scale temporal modeling module that integrates global cycle-level dynamics with local inter-frame coherence to generate smooth and physiologically plausible mesh trajectories. The proposed method achieved a whole-heart mean absolute error of 1.68 $\pm$ 0.31 mm and a motion jitter of 0.77 $\pm$ 0.17 $\mathrm{mm}/\mathrm{frame}^{3}$, outperforming existing methods with lower reconstruction error and substantially improved motion smoothness. It also improved 2D contour alignment across multiple cine MRI views and supported downstream proof-of-concept electrophysiological simulation. The code will be released publicly upon acceptance of the manuscript for publication.

Image-guided therapies, including radiotherapy, biopsy and deep brain stimulation, rely on real-time targeting of anatomical structures. However, in the presence of motion, imaging latencies create a temporal misalignment between observed and true anatomy, compromising treatment accuracy. Artificial intelligence-based frameworks have increasingly been presented to close this latency gap, but leading personalised models can fail due to a lack of stable anatomical grounding. Foundation models can provide grounded behaviour, but they do not adapt to real-time, individual patient dynamics. Here we introduce a closed-loop coupling framework that synergises patient-specific temporal prediction with continuous segmentation-based anatomical interpretation from a foundation model. A personalised model predicts future anatomy to compensate for system latency, while a streaming foundation model provides anatomical supervision used to continuously update the temporal predictor in real time during treatment. We validate the framework using a digital phantom and intrafraction magnetic resonance imaging (MRI) from patients undergoing MRI-guided radiotherapy. For a prediction horizon of 400 ms, the proposed method improves anatomical prediction and reduces dosimetric error compared with existing approaches, within clinically relevant latency constraints. These results establish closed-loop coupling as a general strategy for real-time image-guided intervention.

Multimodal CT-MRI registration is central to image-guided radiotherapy, surgical navigation, and diagnostic workflows, but most pipelines report only aggregate quality metrics without per-case reliability signals. We propose a reliability-aware framework that converts registration quality into Green/Yellow/Red risk categories using data-learned thresholds. CT images were registered to T1-weighted MRI using rigid and affine transformations on 90 paired slices from 18 patients across brain, abdominal, and neck anatomies. Reliability was assessed using Delta NMI, Delta SSIM, Dice overlap, registration stability, and inverse consistency error, combined into a single score R. Thresholds learned from training patients were applied unchanged to held-out test patients. Affine registration outperformed rigid registration on NMI and SSIM, yielding 44% Green classifications versus 33% for rigid. Reliability-filtered registrations improved the average alignment profile compared with unfiltered methods. Per-anatomy analysis showed substantial variation, with stronger reliability for abdominal registrations than brain registrations. Weight sensitivity analysis identified Dice overlap as the dominant reliability component. The proposed framework provides an interpretable quality-control layer for multimodal registration, while risk thresholds reflect statistical rather than clinical validation.

Echo Planar Imaging (EPI) is the standard acquisition technique for diffusion and functional neuroimaging, enabling rapid imaging but suffering from geometric distortions caused by B0 field inhomogeneities. Existing correction methods first reconstruct distorted images using parallel imaging, then estimate the B0 field and correct the distortion in the image domain. In this sequential process, reconstruction artifacts at high acceleration factors and low SNR at high diffusion b-values degrade B0 estimation and limit the overall correction quality. We propose a physics-informed framework that jointly estimates the B0 field and distortion-free image directly from k-space data, without depending on an intermediate parallel-imaging reconstruction for the correction. The image and the B0 field are each represented as a superposition of Gaussian primitives embedded within an MRI physics forward model. The explicit, continuous parameterization captures both smooth regions and tissue boundaries and supports rotated-view EPI acquisitions without interpolation. The diffusion-weighted image is modeled as real and non-negative, with the image phase absorbed into a per-shot phase factor. Rotated views distribute distortions across multiple phase-encoding orientations, improving point spread function isotropy and providing stronger constraints for B0 estimation. On in vivo brain diffusion EPI, the proposed method attains the closest brain-boundary agreement with a distortion-free structural reference, with the largest improvement over sequential methods at high b-value and high acceleration. Extensive visual comparisons further show improved detail fidelity and noise suppression.

Image quality is critical for accurate medical diagnosis. However, MRI, CT, and ultrasound images are often of low resolution and quality due to cost constraints, complicating the visualization of key anatomical structures and lesions. While such limitations are common in practice, traditional methods treat image enhancement as a separate preprocessing step, failing to fully leverage its potential synergy with image segmentation. To address this, we propose DiSIINet (Diffusion-based Symbiotic Information Interaction Network), which is built on the principle that enhancement and segmentation should mutually reinforce each other in a unified model. Based on Denoising Diffusion Implicit Models (DDIM), DiSIINet integrates an enhancement branch and a segmentation branch. These branches interact through a novel Symbiotic Information Interaction (SII) module, which facilitates dynamic, feature-level information exchange via cross-attention during the reverse diffusion process. This design enables both tasks to iteratively improve each other. The DDIM backbone ensures high-quality output and efficient inference through deterministic sampling. Experiments on multi-modal medical datasets (MRI, CT, ultrasound) show that DiSIINet achieves significant performance improvements compared to sequential or independent enhancement and segmentation approaches. The code is available at: https://github.com/Reconsider80/DiSIINet.

Multimodal MRI is essential for accurate brain tumor segmentation. However, acquiring all modalities at inference is often challenging in practice, which causes intrinsic uncertainty due to unavoidable information loss. Without modeling this uncertainty, existing methods encode incomplete evidence into deterministic representations that appear plausible but lack reliability. In this regime, we propose a probabilistic representation framework that models representations as Gaussian distributions, where their mean captures task information and their variance measures uncertainty from missing evidence. To make variance reflect information deficiency, we regularize the mean from each partial configuration toward its full-modality counterpart, while scaling the variance with the discrepancy between their aligned means. We further introduce a set-inclusive strategy that exploits the hierarchical structure of modality subsets and enforces an ordering constraint to maintain their consistent uncertainty relationships. Extensive experiments on BraTS 2018 and 2020 demonstrate that our approach offers superior performance over baselines across diverse missing-modality scenarios. Code and model checkpoint are available at https://github.com/atlas-sky/SIUM.

Diffusion posterior samplers for accelerated MRI can reconstruct accurately yet still disagree on the acquired k-space across samples, placing posterior variability on coefficients the scanner has already measured. We identify this measured-subspace leakage as a physical-admissibility failure. Under a hard-constraint model it violates the measurement constraint and inflates the reported uncertainty with disagreement about coefficients the scanner has already determined. To quantify this leakage, we introduce complementary measured- and unmeasured-subspace k-space dispersion metrics (MSD/USD). We then present Measured-Subspace Consistency (MSC), a training-free terminal correction that wraps any compatible image-space posterior sampler with a standard multi-coil consistency lock. The ideal lock follows classical range/null-space data consistency. Our contribution is to repurpose it as a black-box posterior audit and correction rather than a new reconstructor or learned sampler. Theoretically, we prove that the ideal transform confines pairwise sample differences to the MRI null space and bound the residual cross-subspace coupling left by practical sensitivity-weighted implementations. Across six base samplers and two MRI anatomies, including out-of-distribution transfer where a knee prior reconstructs brain, MSC substantially reduces measured-subspace dispersion for Soft samplers (a median 16.5x reduction for DPS across five brain contrasts, up to ~29x), while preserving unmeasured-subspace diversity and acting as a near-identity map for Consistent ones. Furthermore, MSC maintains or modestly improves PSNR/SSIM, with no retraining, retuning, or significant computational overhead.

Brain MRI poses a fundamental challenge for machine learning: models must learn from high-dimensional 3D data spanning multiple co-registered modalities, despite the limited sample sizes typical of neuroimaging studies relative to the diversity in anatomy, pathology, and acquisition conditions. While multimodal imaging provides complementary information critical for clinical interpretation, effectively integrating these signals remains difficult. We propose Multimodal Intra- and Cross-Context Vision Transformer (MICViT), a 3D vision transformer that explicitly models both modality-specific representations and cross-modal interactions across local and global contexts. Concretely, MICViT combines four attention mechanisms: modality-specific local and global attention for intra-modal feature learning, and cross-modal local and global attention to capture interactions between modalities. We evaluate MICViT on brain age prediction across three heterogeneous datasets (UK Biobank, n=41,404; SOOP, n=1,062; Cam-CAN, n=613) using multiple MRI modalities (e.g. T1, FLAIR, DWI, SWI). MICViT consistently outperforms state-of-the-art CNN and transformer baselines in 3D settings. Notably, it benefits more strongly from multimodal inputs, yielding larger performance gains as additional modalities are incorporated. These results demonstrate that explicitly modeling intra- and cross-modal interactions is key to unlocking the full potential of multimodal brain MRI, highlighting a promising direction for representation learning in neuroimaging.

Deep learning has shown significant potential in medical image analysis, particularly for disease detection using MRI scans. Accurate and early diagnosis of brain tumors remains challenging due to the complexity of brain structures and reliance on manual interpretation. This work presents an automated deep learning-based approach for brain tumor detection from MRI images using Convolutional Neural Networks and Residual Networks. Transfer learning is applied with two pretrained architectures, ResNet18 and ResNet50, to classify MRI scans into tumor and non-tumor categories. Experiments are conducted on a dataset of 3,929 brain MRI images, evaluating the impact of model depth and fine-tuning strategies. The results show that ResNet18 achieves a higher accuracy of 97% compared to 96% for ResNet50, demonstrating better generalization on limited medical data. The proposed framework enables fast, accurate, and cost-effective brain tumor detection, supporting early diagnosis and clinical decision-making.

The objective of this paper is to improve radiological gradings measured on MRIs of spines, by resampling scans so that the new view planes are better aligned with the target anatomy than the original sparse images. To this end, we adapt 3D Gaussian Splatting to form a volumetric reconstruction starting from sparse anisotropic MRIs, and imaging planes aligned with the anatomy relevant for clinical evaluation are then sampled and rendered. The novel view plane is optimal for diagnostic radiological grading of the target anatomy, whereas the original MRI is not. The resampled scans are then used to predict ordinal severity grades of localised stenosis conditions in spinal MRIs. We compare our method against Voxel Interpolation resampling, which takes the average of inverse-distance weighted nearest neighbour intensities for each target coordinate. Experiments show that across all stenosis conditions, resampled scans using Gaussian Splatting produce more accurate stenosis gradings compared to the raw scans which do not include the complete anatomy in-plane, as well as images resampled using Voxel Interpolation.

Quantitative maps from dynamic contrast-enhanced MRI (DCE-MRI) are essential for tumor assessment but are often unavailable due to contrast-agent risks and protocol variability. Prior methods predict these maps from other MRI modalities, yet most assume fixed, fully observed inputs and fail under realistic missingness. We present Spatio-Temporal Mixture-of-Modality-Experts (ST-MoME), a conditional diffusion framework that synthesizes 3D DCE parameter maps from diverse subsets of multimodal MRI. ST-MoME fuses modality-specific expert features through a spatio-temporal gating network that produces voxel-wise, timestep-dependent weights, forming a conditioning tensor that guides denoising. To preserve quantitative fidelity, ST-MoME performs diffusion directly in image space with 3D patch-based training and a Swin-based backbone. On a clinical brain-tumor cohort of 386 patients, we evaluate ST-MoME across 16 controlled modality-availability scenarios. It achieves the lowest mean Normalized Mean Square Error (NMSE) aggregated across all three DCE parameters, with leading performance on $v_p$ and $v_e$, competitive results on $K^{\mathrm{trans}}$, and the lowest reconstruction error within the clinically critical tumor region. A post-hoc analysis of the learned gating dynamics shows a structural-early, physiological-late fusion schedule consistent with clinical intuition.

Standardized assessment of uterine MRI remains challenging due to anatomical variability, observer dependence, and the lack of workflow-integrated automated analysis tools. This work presents Female-RHINO: (R)eproductive (H)ealth (I)maging A(N)alysis T(O)ol, a real-time AI-assisted framework for automated quantitative uterine MRI analysis and structured reporting during image acquisition. We present an end-to-end system that integrates inline communication with the MRI scanner and deep learning-based analysis to derive quantitative uterine biomarkers from sagittal T2-weighted pelvic MRI. The framework combines segmentation and anatomical landmark detection models trained and evaluated on more than 500 multi-center datasets spanning diverse protocols, vendors, and patient populations. It performs volumetry, detects and quantifies common incidental findings such as fibroids and Nabothian cysts, and extracts six anatomical landmarks for biometric assessment. Results are compiled into a structured clinician-oriented report with integrated visualizations, without manual interaction. Evaluation on independent retrospective and prospective cohorts demonstrated robust performance across varying acquisition settings. Mean Dice similarity coefficients were 0.82 for the uterus and 0.80 for fibroids, with lower but consistent agreement for Nabothian cysts. Landmark detection achieved a mean radial error of 3.7 mm. End-to-end processing was completed in under 70 seconds, enabling availability of results during the ongoing scan. Prospective deployment yielded immediate, standardized, and reproducible analyses supported by inter-observer agreement. The proposed system enables real-time scanner-integrated AI for automated uterine MRI analysis and reporting, with potential to improve standardization, efficiency, and clinical workflow in pelvic imaging.

AI-driven image-to-image synthesis is rapidly advancing, with growing applications in medical imaging. Multi-modal image analysis plays a crucial role in optimizing examination quality, yet acquiring multiple imaging modalities in clinical settings remains resource-intensive and time-consuming, especially for 3D imaging. To address this challenge, we propose a novel image-to-image translation model based on Brownian Bridge Diffusion Models (BBDM), which synthesizes magnetic resonance imaging (MRI) sequences from 2D axial slices. Our approach integrates a variational encoder-guided diffusion mechanism, leveraging probabilistic image distributions to enhance synthesis quality. Evaluated on the BraTS 2021 dataset, our Probabilistic-BBDM (Prob-BBDM) achieves superior performance across multiple translation tasks, reaching up to 88.46% SSIM and 26.09 dB PSNR, with consistent improvements over baselines. Notably, our diffusion process requires only 4 steps, making it computationally efficient while maintaining high-quality synthesis. To further validate generalizability, we test Prob-BBDM on an external third-party dataset, demonstrating consistent performance across domains. Additionally, we assess the clinical utility of the synthesized slices by using them as input to a pre-trained segmentation model. Tumor segmentation yields a Dice score of 88.71% and an HD95 of 3.49 mm, confirming that the synthesized slices preserve critical diagnostic information. These results highlight the potential of Prob-BBDM for high-quality, efficient, and generalizable MRI synthesis, offering a promising step toward improved medical image translation.

While longitudinal brain PET imaging is the gold standard for quantifying the spatiotemporal accumulation of Beta-amyloid, its widespread clinical utility is constrained by high operational costs and cumulative radiation risks. Recent deep generative models show promise in longitudinal image synthesis; however, they often fail to capture subtle pathological progression due to identity drift and a persistent bias toward trivially replicating baseline signal intensities rather than modeling temporal transition. To this end, we propose Delta-Diffusion, a novel progression-aware framework that redefines longitudinal PET synthesis as a conditional Poisson Diffusion Bridge (PDB) process. Unlike standard diffusion models that start from Gaussian noise, our PDB formulation is mathematically anchored to the subject's baseline PET, effectively transforming the generative task into a conditional distribution transition of the amyloid trajectory. To handle heteroscedastic nature of PET imaging, we introduce a physically-grounded Poisson perturbation within a Diffusion Transformer (DiT). This architecture uses adaptive scale-shift modulation to precisely calibrate the synthesis with the elapsed clinical interval and structural MRI context. A volume-of-interest balanced objective is designed to emphasize sparse, high-risk regions of amyloid accumulation. Validated on two cohorts with 542 subjects, Delta-Diffusion demonstrates superior performance in capturing longitudinal variations in amyloid deposition compared to state-of-the-art methods, offering a robust computational framework for tracking disease progression.

Deep unrolled networks (DUNs) integrate physical forward models with learned regularization in cascaded network architectures, achieving exceptional performance in inverse problems while maintaining interpretability. While most DUNs operate in the object domain (e.g., image space), recent variants explored representation spaces for improved information flow. However, these methods rely on heuristic methods for data consistency (DC), sacrificing fidelity with measurements. In this work, we introduce DUNE (Deep Unrolled Networks in rEpresentation space), a framework that maintains exact adherence to physical measurements while operating in learned representation spaces. By deriving the DC gradient via the chain rule and implementing it through the Vector-Jacobian Product (VJP), we enable exact backpropagation of measurement residuals into the representation space. This formulation supports diverse architectural backbones, including pre-trained encoders to guide the iterative process. We assess DUNE against state-of-the-art baselines on accelerated MRI reconstruction tasks, demonstrating that exact VJP-based gradients yield superior reconstruction quality and structural fidelity across both single-channel portable low-field and multi-channel clinical high-field MRI acquisitions. The code will be available upon publication at https://github.com/EfeIlicak/DUNE.

Segmenting the temporomandibular joint (TMJ) disc from MRI is essential for accurate diagnosis of internal derangement, yet it remains unreliable in practice due to its small size, low contrast, and morphological variability. Existing methods, primarily adapted from general segmentation architectures, often produce fragmented or anatomically inconsistent masks, leading to unstable measurements of disc position and shape for downstream diagnosis. To address these challenges, we propose TISC, a TMJ disc segmentation framework that integrates semantic anchoring with clinical metadata-guided boundary refinement. The framework first establishes robust disc localization in the foundation model feature space via a Prototypical Semantic Anchoring (PSA) module that aggregates adjacent-slice MedDINOv3 features and derives a prototype-driven similarity map. It then performs targeted boundary refinement through a Clinical-Metadata Point Refinement (C-MPR) module, with point-wise predictions modulated by Mouth Open Limitation (MOL), a clinical indicator associated with disc displacement without reduction. On a large-scale cohort of 2,488 PD MRI volumes from 1,300 patients, our method achieves up to a 4.96 Dice improvement over strong baselines across diverse architectures, delivering more anatomically coherent and clinically reliable TMJ disc segmentation.

Alzheimer's disease (AD) is an irreversible neurodegenerative disorder and a leading cause of death worldwide. Early diagnosis plays an important part especially at the Mild Cognitive Impairment stage, where timely intervention can help slow its progression before it advances to AD. Neuroimaging data, like Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) scans, can help detect brain changes early by providing structural and functional brain changes related to the disease. Yet, many multimodal models still fuse MRI and PET with static concatenation and apply identical computation to all subjects, which limits robustness to patient/site heterogeneity and can waste computation. To address these limitations, we present the first study of combining 3D convolutional feature extractors with three fusion strategies - concatenation, Gated Multimodal Unit (GMU), and gated self-attention - and a sparsely gated Mixture-of-Experts (MoE) classifier that performs input-adaptive routing, activating only the most informative experts per case. Finally, we utilize Grad-CAM to visualize disease-related regions, ensuring model interpretability. Experiments are performed across three binary classification tasks (NC vs. MCI, MCI vs. AD, and NC vs. AD). Results show that GMU achieves accuracies of 80.46 % (NC vs. MCI) and 95.47 % (NC vs. AD), while gated self-attention attains 82.08 % on MCI vs. AD. Ablations show that removing the MoE consistently degrades accuracy across all tasks. These findings underscore the value of input-adaptive, multimodal modeling for AD diagnosis by leveraging the complementary nature of MRI and PET.

Clinical prostate multi-parametric MRI relies heavily on high-quality diffusion-weighted imaging (DWI), yet reading DWI is frequently compromised by geometric distortion, often caused by rectal air. Assessing quality via the PI-QUAL scoring system is an emerging clinical standard, but it is subjective, time-consuming and suffers from a class imbalance where low-quality cases are diverse and relatively scarce. Using the PRIME clinical trial as an example, there are $6\%$ images with PI-QUAL scores lower than 4, $87\%$ of DWI issues are due to distortion. Many of the other clinical quality issues are under-represented. To address this common dual-scarcity of annotated clinical data, we propose a few-shot biparametric prototypical network for automated image quality assessment (IQA). Our framework utilizes a dual-branch 3D ResNet to fuse T2-weighted and DWI features, providing anatomical context to distinguish true morphology from distortion. To handle real-world heterogeneity, we introduce feature-wise linear modulation (FiLM) and a gradient reversal layer (GRL) to align feature distributions conditioned on varying b-values while suppressing acquisition-related biases. We demonstrate that a model meta-trained solely on comparatively objective, readily obtainable distortion labels can effectively adapt to predicting complex, multi-factorial clinical quality scores such as PI-QUAL using only five representative samples. Experimental results on two datasets show that our method significantly outperforms few-shot learning baselines for this challenging IQA task, offering a practically feasible and data-efficient solution for standardizing prostate MRI quality control in clinical workflows.

Despite recent advancements in deep learning, accurately classifying brain tumors from MRI images continues to pose challenges. In this research, we present a comprehensive evaluation of five different convolutional neural networks (CNN) architectures, including a customized baseline model and four pre-trained models - for use in classifying multi-class brain tumors using a clinically-sourced dataset of approximately 10,000 MRI images. We have utilized five different architectures; VGG16, VGG19, DenseNet121, and EfficientNetB0, which were all tested and trained within an identical experimental framework. Performance was measured by both overall accuracy and tumor-wise recall as a means to measure the clinically-relevant performance of each architecture. We found that EfficientNetB0 had the best overall classification accuracy at 95%, when compared to the other architectures tested; specifically VGG16 (94.37%), VGG19 (92.29%), DenseNet121 (90.91%) and the customized CNN (78.00%). An especially important finding of our research was the considerable improvement in detecting meningiomas; specifically, while simple CNNs could detect meningiomas with a recall rate of approximately 20%, EfficientNetB0 was able to detect meningiomas with a recall rate of 89%. Meningiomas are often difficult to detect because they can appear very subtly on MRI images. Additionally, an interesting finding was that the deeper VGG19 performed worse than the shallower VGG16. This indicates that in many cases the architectural efficiency of a CNN model may be more important than its depth when working with medical images. Overall, EfficientNetB0 appears to provide the optimal trade-off between classification accuracy, number of parameters used in the model and clinically meaningful performance.

The noise of Magnetic Resonance Imaging MRI poses challenges for Deep Learning DL when tumor boundaries are obscured tumor location and appearance are complex Therefore we develop BrainFusionNet that combines Convolutional Neural Networks CNNs Vision Transformers ViT and Gated Recurrent Units GRUs to extract spatial contextual and sequential features from MRI images for improved brain tumor classification Furthermore explainable AI such as SHAP LIME and GradCAM are integrated to visualise and highlight image regions that contribute to BrainFusionNets decisionmaking process The proposed BrainFusionNet model is evaluated on two publicly available MRI datasets Kfold validation suggests 98 accuracy on both datasets The model was compared with the six stateoftheart SOTA CNNs and transfer learning Among the SOTA CNNs DenseNet121 and VGG16 achieved the highest accuracy of 96 The novelty of BrainFusionNet is that the hybrid model effectively extracts local and global features from MRI images even in smallscale tumor regions and small tumor sizes The model has a balanced sequential CNN architecture to capture lowlevel and deeperlayer features a customized ViT that captures local features stabilizes gradient flow and reduces the risk of vanishing gradients during MRI image training The CNN and ViT outputs are fed into a GRU for final classification Furthermore we analyze pixel intensities to determine whether MRI image quality affects image classification Our findings are very novel in image interpretation as we found that the distribution of pixel intensities in MRI images affects DL performance

Recent advances in generative machine learning models have significantly improved medical imaging, offering promising solutions for data augmentation, privacy preservation, and improved model generalization. However, synthesizing high-quality structural MRI data for Alzheimer's Disease (AD) remains challenging due to the subtle, region-specific, and progressive anatomical changes associated with neurodegeneration. In this paper, we extend the Med-DDPM conditional diffusion model -- originally designed for brain tumor synthesis -- to generate 3D structural MRIs specifically tailored to AD. We adopted Med-DDPM due to its established stability and structural fidelity compared to other generative models, which makes it particularly suitable for capturing the subtle anatomical changes characteristic of AD. Our approach conditions the diffusion process on anatomical segmentation masks derived from the ADNI dataset, incorporating key AD-relevant brain structures into the generation process. We systematically evaluate the quality and utility of the synthetic images by training segmentation models on real, synthetic, and hybrid (mixed) datasets. Experimental results demonstrate that segmentation models trained exclusively on synthetic data achieve comparable Dice scores (0.6532) to those trained on real data (0.6513), while exhibiting significantly enhanced recall. Notably, models trained on hybrid datasets (mixing real and synthetic images) outperform both real and synthetic-only baselines, achieving a Dice score of 0.7244. These findings underscore the successful use of conditional diffusion models for generating anatomically accurate, AD-specific synthetic MRIs, and highlight their potential for enhancing training data availability, improving diagnostic accuracy, and promoting research reproducibility in neuroimaging studies.

Multi-contrast magnetic resonance imaging (MRI) provides complementary information for clinical diagnosis. However, acquiring all MRI sequences is often time-consuming and costly. Recent generative models perform cross-contrast synthesis to address this issue by inferring absent contrasts from the available ones. Nevertheless, synthesizing 3D MRI presents significant challenges. Due to the massive volume sizes, operating directly in the pixel space is computationally prohibitive; therefore, a common approach is to first compress the 3D volumes into a latent space and subsequently train generative models in that space. We observe that existing compression architectures face several critical issues: they under-preserve long-range anatomical coherence, discard clinically meaningful semantics, and rely on optimization objectives that lead to over-smoothed reconstructions. Ultimately, these shortcomings compromise the performance of subsequent generative models. In this work, we propose a semantics-first latent modeling framework for 3D MRI reconstruction and cross-contrast synthesis. Specifically, we introduce a Latent Harmonization Encoder (LHE) to capture global anatomical dependencies, ensuring coherent volumetric representations. To mitigate semantic degradation during latent compression, we further design a Semantic Recovery Block (SRB) that injects high-level priors from a self-supervised semantic teacher, enhancing contrast-aware separability in the latent space. Additionally, we propose an Anatomy-aware Frequency Loss (AFL) to adaptively preserve diagnostically relevant high-frequency structures. Extensive experiments on two public multi-contrast MRI datasets demonstrate consistent improvements in reconstruction fidelity and cross-contrast synthesis quality. Our code is available at https://github.com/script-Yang/RSF.

Patient-specific 3D reconstruction of pelvic organ geometry from MRI is important for pelvic floor modeling and downstream patient-specific analysis. However, while previous studies have focused primarily on either image segmentation or downstream use of 3D models, the reconstruction of high-fidelity, high-quality geometries remains labor-intensive and poorly standardized. The study introduced a hybrid deformable shape modeling framework that integrates deep learning prediction with iterative optimization for the reconstruction of the bladder, uterus, and rectum. The framework consists of three core components: a geometry-aware multi-level deep learning architecture that preserves topological consistency of pelvic organs; a two-stage amortized optimization training strategy that balances global shape capture and local surface refinement; and a holistic synergy mechanism--where iterative optimization provides supervision for deep learning during the training phase, and during inference, deep learning rapidly predicts the global organ morphology, followed by iterative optimization to refine local surfaces and mesh quality. This framework demonstrated marked superiority in geometric fidelity than current mainstream deep learning-based organ reconstruction models. For individual anatomical structures, the reconstructed 3D geometries for the bladder, rectum, and uterus achieved significantly lower Chamfer Distance values and higher Dice Similarity Coefficient scores. In addition, while maintaining high computational efficiency, the proposed architecture yielded superior overall volumetric mesh quality. At the patient level, the framework achieved higher mean values for the 10 worst elements for both minSICN and minSIGE compared to traditional geometric post-processing algorithms.

Magnetic resonance imaging-signal fat fraction (MRI-SFF) quantifies tissue fat and serves as an established biomarker for metabolic and musculoskeletal disorders. The acquisition requires, however, specialized MRI sequences, which are not available routinely. We investigate whether SFF can be estimated from widely available T2-weighted (T2w) MRI via image-to-image translation (I2I). We further compare a lightweight 4-level U-Net to a state-of-the-art Denoising Diffusion Probabilistic Model (DDPM) using a dataset of 230 048 paired 2D images (183 517 train, 23 621 val, 22 910 test) from the German National Cohort (NAKO). Both models clearly outperform the identity baseline (Pearson correlation r = 0.769, mean absolute error MAE = 0.070 +/- 0.054), which confirms that the models learn a non-trivial cross-modal mapping. Interestingly, the lightweight U-Net outperforms the DDPM in both correlation (r = 0.975 vs. 0.962) and error (MAE = 0.014 +/- 0.015 vs. 0.019 +/- 0.019), while reducing inference time by a factor of 208 (25.2 ms vs. 5 227.2 ms per image using 50 Denoising Diffusion Implicit Model (DDIM) steps). The strong clinical performance at substantially reduced computational cost enables real-time clinical use.

We propose a novel Bayesian framework for joint image reconstruction and uncertainty quantification from compressed sensing magnetic resonance imaging data. The problem is formulated as a linear inverse problem, where prior distributions are assigned to the unknown image parameters. Specifically, the image is assumed to be sparse in a given transform domain. We develop a general framework applicable to any sparsifying transform and demonstrate its performance using (1) a total variation transform based on image spatial gradients and (2) a wavelet-domain transform. Bayesian inference is performed using a split-and-augmented Gibbs sampler, while the resulting non-differentiable conditional distributions are efficiently sampled using a proximal Markov chain Monte Carlo method. The proposed algorithms are validated on both single-coil and multi-coil datasets using various k-space sampling patterns and acceleration factors. The results demonstrate that the proposed Bayesian methods consistently outperform their optimisation-based counterparts in image reconstruction while providing uncertainty estimates for the reconstructed images. Furthermore, the estimated uncertainty maps show a strong correlation with the true reconstruction errors and substantially outperformed deep learning-based uncertainty estimation methods.

Paramagnetic rim lesions (Rim$^+$) identified on susceptibility-sensitive MRI have recently emerged as a specific biomarker of chronic active inflammation in Multiple Sclerosis (MS) and are associated with long-term disability progression. However, susceptibility imaging and expert interpretation remain limited to specialized centers, visual assessment is time-consuming and variable, and the low prevalence of Rim$^+$ lesions poses severe class imbalance challenges for automated analysis. We propose a 3D multimodal deep learning framework for lesion-level Rim$^+$/Rim$^-$ classification from Quantitative Susceptibility Mapping (QSM) and FLAIR MRI. The architecture explicitly models modality asymmetry by treating QSM as the primary susceptibility-driven signal and conditioning it with FLAIR-derived structural context. To improve robustness under limited data, we employ self-supervised multimodal pretraining followed by supervised fine-tuning with contrastive regularization. The method was evaluated on a clinically acquired cohort of 88 people with MS with expert lesion annotations as reference standard. Results highlight improved performance compared to prior architectures, supporting the effectiveness of asymmetric multimodal modeling for automated chronic active lesion identification.

Multimodal large language models (MLLMs) hold great potential for medicine, as they inherit knowledge from LLM and allow multiple data modalities to be integrated, analysed and interpreted in natural language. However, the field of medical MLLMs is constrained by non-trivial challenges, notably the scarcity of high-quality training data and the frequent occurrence of missing data in the real-world clinical setting. Here, we propose a novel unified multimodal model, UniBrain, for brain magnetic resonance image (MRI) analysis. To address potential missing brain MRI modalities, we employ a unified training strategy to perform joint imaging modality imputation and brain image understanding. During training, an interleaved and description-enriched data flow is constructed to train the model in an autoregressive manner, enabling medical reasoning with generated multimodal data. A self-alignment strategy is introduced to leverage dense image embeddings to learn fine-grained anatomical features without requiring detailed image captions. Furthermore, we propose a dynamic hidden state mechanism to alleviate the exposure bias during long-context multimodal inference. Extensive experiments on multi-disease brain MRI dataset demonstrate that UniBrain achieves high performance for brain image imputation, understanding, and disease diagnosis under various extents of modality incompleteness.

3D FLAIR MRI is widely recommended as one of the standard MRI sequences for brain imaging in multiple sclerosis (MS), but publicly available MS datasets remain relatively small and vary across scanners, acquisition protocols, and lesion patterns. This scarcity and variability hinder the development of robust neuroimaging machine learning models and are particularly challenging for generative models that aim to synthesize images while preserving small, sparse lesions. We propose Lesion-DDPM, a 3D conditional diffusion framework for lesion-aware FLAIR synthesis that incorporates multi-level anatomical mask injection together with a lesion-weighted reconstruction loss to emphasize lesion voxels while maintaining global brain structure. Using a curated subset of the MSLesSeg dataset, we compare Lesion-DDPM with representative state-of-the-art GAN- and diffusion-based models, assessing both image-generation metrics and downstream 3D U-Net segmentation. In our experiments, Lesion-DDPM achieved the lowest lesion-region reconstruction error among all methods. In a downstream 3D U-Net lesion segmentation task, a model trained only on Lesion-DDPM-generated scans and evaluated on real MRIs reached a Dice score of 0.616 compared with 0.569 for the best competing synthetic dataset. When Lesion-DDPM images were added to the real training set, the Dice score further increased to 0.685.

Fully sampled MRI requires dense k-space acquisition, leading to long scan times, reduced clinical throughput, and increased sensitivity to patient motion. Accelerated MRI addresses this by acquiring undersampled k-space data and reconstructing the missing information computationally. However, reconstruction from undersampled measurements is highly ill-posed and can introduce aliasing artifacts, noise amplification, and loss of anatomical detail. Although conventional parallel imaging and compressed sensing methods mitigate these issues, and deep learning methods have further improved reconstruction quality, preserving high-frequency structures under aggressive undersampling remains challenging. In this work, we propose a Variational Network with a Wavelet-based U-Net (W-UNet) for accelerated MRI reconstruction. The framework combines physics-guided iterative reconstruction with learnable multi-scale frequency representations. Standard pooling operations are replaced with Discrete Wavelet Transform and Inverse Wavelet Transform modules, enabling lossless downsampling while preserving low-frequency structure and high-frequency edge details. Integrated into the refinement and sensitivity map estimation stages, the proposed design improves artifact suppression, feature preservation, and reconstruction fidelity in both single-coil and multi-coil settings. Experiments on fastMRI knee and M4Raw brain datasets show state-of-the-art performance. Ablation studies further confirm the effectiveness of wavelet-based feature decomposition for accelerated MRI reconstruction.

Zero-Shot Self-Supervised Learning (ZS-SSL) has emerged as a promising paradigm for accelerated Magnetic Resonance Imaging (MRI) reconstruction, eliminating the reliance on fully-sampled external datasets. However, learning solely from a single under-sampled scan suffers from supervision scarcity and optimization instability, often leading to overfitting or artifacts. To address these challenges, we propose a robust physics-driven ZS-SSL framework that synergizes physical consistency with image-domain non-local priors. Our method introduces three core innovations: (1) a Coil Sensitivity Map (CSM)-Guided Dynamic Repository, which stabilizes the training trajectory by filtering physically inconsistent artifacts based on coil sensitivity constraints; (2) a SPIRiT-based regularization, which enforces k-space self-consistency via a learned correlation kernel and stochastic masking; (3) a Non-Local Self-Similarity (NSS) Pixel Bank, which leverages the high-fidelity reference established by the former modules to explicitly mine non-local anatomical similarities, thereby augmenting supervision in the image domain. Extensive experiments on the FastMRI dataset demonstrate that our approach achieves state-of-the-art performance, particularly under high acceleration factors, effectively bridging the gap between zero-shot learning and supervised methods. The code is available at https://github.com/Zolento/NS-SSL.

Brain MRIs are routinely acquired as multiple complementary sequences with unique contrast weighting, including T1-weighed imaging (T1w) anatomic and fluid-sensitive T2-weighted (T2w) contrasts. However, methods for learning unified representations across the multitude of MRI contrast mechanisms at health-system scale are lacking. In this study, we introduce Neuro-JEPA, a sparse multimodal neuroimaging foundation model that combines a latent predictive objective with a Mixture-of-Experts architecture to encode brain MRI across core T1w, T2w, and fluid-suppressed FLAIR imaging (FLAIR). We further provide a systematic methodological study of architectural, masking, objective, and sparsity design choices beneficial for robust neuroimaging multimodal representation learning. Neuro-JEPA was pretrained on 1,551,862 scans from 428,647 studies after modality-specific preprocessing with data curation across three core structural brain MRI sequences. We evaluated the learned representations across clinical and research settings, including 25 tasks from three health systems: NYU Langone, NYU Long Island, and Massachusetts General Hospital, and 22 tasks from 12 public datasets, covering unimodal, multimodal and cross-domain evaluation configurations. Across these benchmarks, existing neuroimaging foundation models showed inconsistent gains over a simple convolutional neural network (CNN) baseline, whereas Neuro-JEPA achieved stronger and more consistent performance across all evaluated settings. These results establish a scalable methodological framework for multimodal neuroimaging representation learning and highlight the need for foundation model evaluation protocols that include simple baselines, clinically heterogeneous cohorts and controlled multimodal comparisons.

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that affects millions of older adults, with prevalence expected to rise significantly in the coming years. Early diagnosis, particularly during the mild cognitive impairment (MCI) stage, is critical for timely intervention. Structural Magnetic Resonance Imaging (sMRI) has emerged as a key modality for detecting AD-related brain changes, but traditional graph-based approaches often struggle with modality and inter-site heterogeneity, limiting diagnostic performance. In this paper, we propose Graph Matching Network for Alzheimer's Disease Diagnosis (GMN4AD), designed to model interactions between heterogeneous brain graphs derived from neuroimaging data. Unlike conventional methods that treat each brain graph independently, GMN4AD leverages graph matching to capture cross-graph relationships, enhancing diagnostic precision. Furthermore, we introduce a test-time domain adaptation strategy that combines contrastive learning to mitigate domain shifts during inference. Extensive experiments on three public AD datasets demonstrate that GMN4AD achieves superior performance compared to state-of-the-art methods, offering a robust and generalizable solution for AD diagnosis.

Self-supervised foundation models have shown strong promise in medical imaging. However, existing MRI foundation-model studies have primarily emphasized segmentation and dense prediction tasks, while systematic investigation of self-supervised foundation models for MRI-based disease detection remains limited. In this work, we investigate two major self-supervised pretraining paradigms for MRI-based disease detection: reconstruction-based learning via Masked Autoencoders (MAE) and predictive representation learning via Joint Embedding Predictive Architectures (JEPA). We study the role of auxiliary objectives by introducing a novel spectral-domain reconstruction loss for MAE to enhance sensitivity to fine-grained anatomical structure, and by integrating variance--covariance regularization (VCR) within our JEPA framework to encourage decorrelated latent representations. Our models are pretrained on heterogeneous single-contrast MRI volumes in a contrast-agnostic setting, without modality concatenation. Across five downstream disease detection tasks, our results highlight the importance of self-supervised objective design for medical foundation model pretraining, demonstrating that the downstream benefit of each objective is determined by its relevance to the task's structure. Specifically, spectral regularization yields the largest improvements when the downstream discriminative signal is characterized by strong high-frequency anatomical structures, while covariance regularization is most beneficial when discriminative information spans multiple decorrelated feature dimensions. MAE with spectral-domain supervision consistently achieves superior downstream performance for MRI-based disease detection. These findings suggest that self-supervised objectives in medical imaging encode specific biases, and their downstream benefit is fundamentally conditioned on the task's structure.

Neurodegenerative diseases such as Alzheimer's disease (AD) require accurate and scalable tools for assessing disease severity, yet current clinical staging remains time-intensive and prone to variability. We propose an attention-enhanced multimodal machine learning framework with ordinal regression for automated and interpretable AD severity staging. The framework integrates T1-weighted MRI with demographic and genetic variables and compares unimodal and multimodal architectures using ordinal and non-ordinal prediction heads. Models were trained and validated using cohort-stratified splits derived from the ADNI, AIBL, and NIFD datasets. A strictly held-out test set was constructed using subjects excluded from all training, validation, preprocessing, and hyperparameter tuning procedures, with subject-level splitting employed throughout to prevent data leakage. Among unimodal approaches, the T1-weighted MRI model achieved slightly higher adjacent-stage accuracy (0.963) and agreement with clinical staging (QWK 0.444) than the tabular model (QWK 0.433). Integrating imaging, demographic, and genetic information improved overall performance. The multimodal non-ordinal baseline achieved the lowest prediction error (MAE 0.340), whereas the ordinal multimodal model achieved the highest adjacent-stage accuracy (0.970) and strongest agreement with clinical staging (QWK 0.549). These findings indicate that ordinal formulations better capture the ordered structure of the CDR scale and yield predictions more consistent with clinical staging. Explainability analyses using Grad CAM++ and SHAP demonstrated anatomically and clinically plausible model behavior, supporting transparent decision-making. Overall, attention-based multimodal learning with ordinal regression represents a robust, interpretable, and scalable approach for automated AD severity staging and AI-assisted clinical decision support.

Lumbar spine conditions are a leading cause of disability worldwide, yet reliable quantification of degeneration from MRI remains challenging. In clinical practice, analysis is predominantly performed in two dimensions (2D), as manual three-dimensional (3D) assessment is time-consuming. However, 2D measurements suffer from limited reproducibility, particularly when anatomical structures are not aligned with the imaging plane. Existing automated approaches are often restricted to 2D, rely on discrete grading, or lack robustness and interpretability. We introduce SpineReport, an open-source, fully automated framework for comprehensive 3D morphometric analysis of lumbar spine MRI. Leveraging robust anatomical segmentations, the method extracts quantitative metrics from key structures, including the spinal canal, spinal cord, vertebrae, intervertebral discs, and foramina. These include both morphological and signal-based features, enabling cross-subject and longitudinal assessment. SpineReport further generates subject-specific reports that allow comparison with cohort distributions, improving interpretability and objective characterization of spinal morphology. Clinical relevance was evaluated against radiologist-reported severity grades for central canal, lateral recess, and foraminal stenosis. Metrics showed strong associations with central canal stenosis severity, with T2-weighted CSF signal providing the highest performance (AUC = 0.95). Canal AP diameter and area ratios also demonstrated strong correlations and high discriminative ability (AUC > 0.80). For lateral recess stenosis, associations were moderate, with lateral CSF signal being the most informative (AUC = 0.73). No significant associations were observed for foraminal stenosis despite robust region-of-interest extraction. SpineReport is released as an open-access tool: https://ivadomed.github.io/SpineReport/

Spinal pathology is a leading cause of pain and disability worldwide. Spine MRI is central to clinical evaluation, yet its interpretation remains complex and time-consuming, requiring integration of information across multiple imaging sequences and anatomical regions. Despite recent advances in automated MRI analysis, effectively combining multi-sequence data while preserving sequence-specific diagnostic information remains an open challenge. Here we present SpineAgent, a multi-agent framework for spine MRI report generation built upon a multi-sequence foundation model trained on routine clinical data from 32,047 patients and 453,683 MRI series, comprising a total of 13,441,191 MRI slices. To accommodate diverse modalities of sequences, we first pre-train two DINOv3-based encoders separately on T1- and T2-weighted sequences. We then introduce a continual training strategy that learns a synthesizer to embed images of other sequences using the T1 and T2 encoders, producing patient-level embedding that integrates various signals across MRI sequences. Using these embeddings, SpineAgent achieves state-of-the-art performance, and demonstrates strong generalizability under cross-manufacturer and cross-cohort evaluation. Beyond classification, SpineAgent enables pathology localization by identifying findings-relevant slices and segmenting pathological regions. It also supports multimodal image-report retrieval, providing a solid foundation for scalable and explainable MRI report generation. We further integrate these validated capabilities of SpineAgent into 37 specialized agents. Finally, we incorporate their outputs as structured tokens within a Medical Report Agent trained end-to-end for report generation. Through both automated metrics and expert evaluation by five radiologists, SpineAgent achieves leading performance in spine MRI report generation.

Multi-contrast brain MRI provide complementary soft-tissue characteristics that aid in the screening and diagnosis of diseases. However, limited scanning time, image corruption and various imaging protocols often result in incomplete multi-contrast images. While current approaches excel in image synthesis, they often struggle to synthesize critical tumor regions and exploit contextual information in multi-contrast brain MRI effectively. To address this issue, we propose a synthesis-centric, segmentation-assisted closed-loop framework with retrieval augmentation synthesis. Our method overall takes a generative adversarial architecture, which aims to synthesize missing contrasts from any combination of available ones with a single model. To explicitly capture tumor semantics and focus synthesis on tumor regions, we add an auxiliary segmentation branch that predicts tumor masks and feeds them back as semantic conditioning in synthesis branch, thereby learning tumor-aware representations in the model and improving synthesis fidelity. Furthermore, we propose a dual-bank retrieval augmentation strategy. It dynamically queries two external knowledge bases, namely a tumor masks memory bank for crucial tumor context and cross-image contrast feature memory bank for global style information, to augment synthesis. Verified on two public multi-contrast magnetic resonance brain datasets: BraTs2020 and UCSF-BMSR, the proposed method is effective in handling medical brain images synthesis tasks and shows superior performance compared to previous methods. Code is available at:https://github.com/iBizzard/SSCF.git

Background and Purpose: Automated detection of focal cortical dysplasia (FCD) requires large volumes of voxelwise lesion-delineated MRI data, which are difficult to acquire. This study aims to generate synthetic MRI data exhibiting FCD, assess their realism, and evaluate their impact on automated FCD detection, particularly in reducing the need for manual annotations. Methods: T1-weighted (T1w) and T2-weighted Fluid-Attenuated Inversion Recovery (FLAIR) MRI scans from 131 FCD patients and 90 healthy controls from multiple (3) sites were retrospectively studied. Synthetic MRIs were generated by conditioning a generative network on binary FCD masks. Two neuroradiologists identified real images from a random set of 14 real and 14 synthetic scans. Three nnU-Net models were trained to detect FCD using: (i) real-only (35 FCD / 35 controls), (ii) real (35 FCD / 35 controls) plus synthetic augmentation, and (iii) expanded real data (70 FCD / 70 controls). Results: Experts showed limited ability to distinguish real from synthetic images, with classification accuracy of 60% for T1w and 70% for FLAIR (inter-rater agreement kappa = 0.86). Augmenting automated FCD detection with synthetic data increased sensitivity by 8.14% (p = 0.12) and improved model confidence at true lesion sites (0.83 +/- 0.11 to 0.89 +/- 0.12; p = 0.02). The expanded real-data model further improved sensitivity to 73.8% (p < 0.001) and confidence to 0.90 +/- 0.14 (p = 0.01). Conclusion: Conditional generative networks can generate realistic synthetic FCD-MRIs, reducing labeled data needs by approximately 20% while maintaining equivalent sensitivity. Equivalent amounts of real data, when available, remain more effective than synthetic augmentation.

Maximal safe resection is the primary objective in glioma surgery. Neuronavigation guidance is progressively degraded by brain shift after dural opening. Intraoperative MRI can compensate but needs dedicated infrastructure and is rarely available, whereas intraoperative ultrasound (ioUS) is inexpensive, repeatable, and compatible with routine workflows. Navigation systems combining ioUS with preoperative MRI usually rely on rigid registration; even deformable multimodal registration is limited by ultrasound speckle contrast, a narrow field of view, and the inability to represent structures absent from the preoperative scan, most critically the resection cavity and residual tumor. We propose an end-to-end pipeline that generates a new whole-brain MRI volume in the preoperative imaging space by merging the preoperative MRI, a synthetic MRI generated from the ioUS, and a deformable registration anchored on that synthetic image. It integrates a 2.5D residual-transformer synthesis backbone (ResViT-2.5D) and a two-stage registration coupling NiftyReg with a synthesis-anchored SynthMorph stage, operating directly on raw scanner inputs. On a post-resection ReMIND cohort, ResViT-2.5D produced synthetic images closely matching the intraoperative T2 across structural, intensity, and perceptual metrics. In 14 subjects with 215 expert landmarks, the synthesis-anchored registration reduced the mean target registration error from 6.27 to 5.86 mm, matching a strong classical NiftyReg baseline (5.85 mm) while yielding a diffeomorphic deformation field in every subject. The contribution is not a gain in registration accuracy but the integrated volume itself, which inside the ultrasound field of view it reflects the intraoperative post-resection state. This provides the surgeon with an MRI-like update of the operative field with potential for integration into surgical-navigation workflows.

This study introduces an automated deep learning framework for predicting brain injury (BI) in preterm infants from T2-weighted MRI (dHCP dataset). We propose GloResNet, a lightweight 3D CNN based on ResNet-10, pretrained on MedicalNet to address data scarcity. A global manifold mapping strategy first resamples each 3D volume to 128x128x128 and then applies subject-wise z-score intensity normalization, thereby preserving global topology while standardizing appearance. Training integrates mixup, class weighting, and test-time augmentation for robustness. In 5-fold cross-validation, GloResNet achieved 75.18% average accuracy (peak 81.82%), with specificity 0.81 and sensitivity 0.76. Results demonstrate that a topology-aware lightweight CNN has the capability to effectively predict neonatal BI, offering a non-invasive screening tool. The source code of this paper can be obtained from the GitHub repository: https://github.com/ICL-SUST/GloResNet-Preterm-Brain

Accurate 3D geometric characterization of myocardial infarction (MI) is essential for building cardiac digital twins (CDTs) to precisely simulate infarct-related electrophysiology. Late gadolinium enhancement magnetic resonance imaging (LGE MRI) is the clinical reference for locating MI, yet its reliance on contrast agents restricts use in renally impaired patients and limits longitudinal follow-ups. As an alternative, contrast-free cine MRI visualizes abnormal ventricular wall motion, which is highly indicative of the infarcted area. In this study, we propose a novel explicit geometry-motion embedded model to fully automatically reconstruct personalized, simulation-ready 3D MI geometries directly from multi-view cine MRIs. Specifically, we construct a 4D (3D + t) biventricular mesh to explicitly extract and decouple geometry-aware and motion-aware features. We further design a dual-branch module for adaptive geometry-motion fusion to capture spatiotemporal dependencies for mapping infarcted region. Furthermore, we introduce multi-scale supervision utilizing an AHA-17 segment-guided cross-attention mechanism to steer the prediction, ensuring biophysically consistent reconstruction. Experimental results on 225 cine MRIs demonstrated that the proposed 3D MI reconstruction achieved high performance with an average Dice score of 0.678 $\pm$ 0.011. In the downstream in-silico electrophysiological simulation evaluations, the results were highly consistent with the LGE-derived ground truth, highlighting the great potential of the proposed model for contrast-free scar characterization and seamless integration into CDT modeling. The code will be released publicly upon acceptance of the manuscript for publication.