Magnetic Resonance Imaging

We developed an anatomy-aware deep learning framework to synthesize post-contrast breast MRI from pre-contrast images, emphasizing tumor and background parenchymal enhancement (BPE) regions. This retrospective study included 649 patients with 6,251 paired pre-contrast and post-contrast images. The framework integrates breast mask consistency, lesion-region supervision, and BPE-region supervision into an image-to-image translation model. Evaluation included quantitative image quality metrics, a reader study with two breast radiologists, and downstream Ki-67 classification. The proposed method outperformed Pix2Pix, Pix2PixHD, diffusion-based synthesis, and mask-supervised baselines in whole-image and regional evaluations. Ki-67 classification showed no statistically significant performance differences across real- and synthetic-image training and testing settings, although this does not establish equivalence. These findings suggest that anatomy-aware supervision improves synthesis fidelity and support further investigation of synthetic post-contrast MRI for contrast-free imaging workflows.

Reliable quality control (QC) of magnetic resonance imaging (MRI) is essential for reliable diagnostic neuroimaging, yet standard manual assessment is subjective and time-consuming. MRIQC has established standardized automated extraction of image-quality metrics (IQMs), but its reliance on local computational imaging skills and capacity including high-performance computing, limits its adoption in resource-constrained settings (RCS). We present WebMRIQC (webmriqc.mailab.io), an open-source browser-based platform that wraps the validated MRIQC engine behind a zero-installation web interface. WebMRIQC automates the DICOM-to-BIDS conversion of de-identified MRI scans, executes the unmodified containerized MRIQC pipeline on a shared compute node governed by a fair-share job queue, and returns an interactive in-browser dashboard. The dashboard grounds every IQM in published quality thresholds, benchmarks each scan against the normative distribution of high-resource open datasets, and supports cross-site multicentre implementation of optimized scan protocols in RCS.We describe the system architecture and a validation framework establishing measurement equivalence between WebMRIQC and native MRIQC across thirteen IQMs on the BraTS-Africa and BraTS 2021 datasets. Preliminary results indicate strong agreement for contrast-, signal and noise-based metrics, demonstrating that web-based implementation lowers the barrier to standardized MRI QC and provides a foundation for harmonized, regionally adapted quality benchmarks across RCS imaging sites. The code is publicly available here https://github.com/CAMERA-MRI/WebMRIqc.

Automated quality assessment, enhancement, and segmentation of multiple structures in $0.064\,\mathrm{T}$ ultra-low-field pediatric MRI are limited by a low signal-to-noise ratio, weak anatomical boundaries, and frequent artifacts. We present a unified framework for the LISA 2026 Challenge that performs all three tasks together within one inference pipeline. A network with two coupled streams, built on a 3D U-Net, first reconstructs an enhanced uLF volume and then combines the original and enhanced images for subcortical segmentation. To improve boundary stability, we add an auxiliary class covering brain tissue outside the target structures, derived from whole brain masks. A head conditioned on an artifact graph predicts the seven artifact ratings from reconstruction residuals and frozen segmentation features. We address the scarcity of dense annotations using diffeomorphic registration from atlas to target for label propagation and to regularize anatomical reconstruction. We report validation results across all three tasks.

Magnetic Resonance Imaging (MRI) acquired at different field strengths exhibits pronounced variation in noise, resolution, homogeneity, and contrast, which limits comparability across acquisition settings and complicates downstream analysis. We address this with a unified conditional model for controllable field-to-field synthesis, built on the framework of conditional latent bridge matching. Our single model achieves highly competitive results across the validation phase for all three tasks of the MRIxFields2026 challenge without task-specific architectures or training. We achieve fast generation with only a single inference step, producing all modality and field-strength combinations for $30$ axial slices in under $90$ seconds, as well as cross-modality-strength translation for a full volume in under $70$ seconds, on a single NVIDIA A5000 GPU. We further provide extensive ablations regarding different components of our solution. Code: https://gitlab.com/siddharthsrivastava/mrixfields-2026

Cortical hypometabolism measured by Fluorodeoxyglucose Positron Emission Tomography (FDG-PET) is a highly sensitive biomarker for dementia diagnosis. However, high costs, radiation exposure, and limited accessibility constrain its clinical utility. While cross-modal synthesis from Magnetic Resonance Imaging (MRI) offers a promising alternative, existing volumetric generation methods do not explicitly account for the highly folded cortical geometry, where disease-related patterns predominantly reside. To address this, we introduce a novel surface-based diffusion bridge framework DB-SUiT for MRI-to-PET translation that operates natively on the cortical manifold. A conditional Spherical U-shaped vision Transformer (SUiT) is specifically designed to model the intricate cross-modal relationships while preserving surface topology. It combines spherical convolutional encoders for multi-scale surface feature extraction with bottleneck Transformers to capture long-range spatial dependencies, while incorporating demographic and subcortical conditions to refine the synthesis. Evaluated on two datasets, including subjects with different dementia types, DB-SUiT demonstrates high-fidelity synthesis that substantially outperforms other baselines. In automated dementia classification, synthesized PET surfaces improve performance over MRI by 14.2% and PET volumes by 11.3%, approaching the performance of real PET surfaces. In a blinded reader study, synthetic PET achieved 85.5% diagnostic accuracy, compared with 75.8% for MRI and 95.2% for real PET. This further demonstrates cross-cohort and cross-pathology generalization, as the model was evaluated without retraining on an external cohort that included a dementia subtype not represented during training. Our code is available at https://github.com/ai-med/DB-SUiT.

Pediatric brain tumors are a leading cause of cancer-related mortality in children, and their small, rare, and often low-contrast subregions make accurate manual delineation challenging. Reliable automated segmentation is therefore needed to support diagnosis, treatment planning, and response assessment. Accordingly, we introduce NeuroTS-Net, a three-dimensional encoder-decoder convolutional neural network architecture for multi-class semantic segmentation that incorporates a dual-scale raw-detail stream, adaptive low-resolution context selection, and detail-preserving multipath downsampling. These components preserve fine intensity and boundary information while efficiently modeling broader tumor context. NeuroTS-Net was trained on the BraTS 2026 pediatric dataset without external data or pretrained weights and evaluated against nnU-Net and MedNeXt under the same experimental protocol. NeuroTS-Net outperformed the baseline methods, achieving whole-tumor and tumor-core Dice scores of 0.938 and 0.937 on the internal validation set and 0.927 and 0.926 on the official challenge validation set. The code is open-sourced at: https://github.com/maenstru56/NeuroTS.

Deep networks trained on structural MRI for Alzheimer's disease (AD) staging often reach reasonable accuracy while attending to anatomically irrelevant regions, and multimodal models that add clinical tables frequently rely on variables that were used to assign the diagnostic label in the first place. We study both issues with a deliberately lightweight slice-based encoder (ResNet18 with a one-layer Transformer over slices) on 1,075 baseline T1-weighted scans from ADNI-1. First, we use FastSurfer segmentations as an anatomical reference: YOLOv8 models trained on segmentation-derived labels localize Alzheimer-relevant structures with mAP_50 above 0.96, and a Grad-CAM comparison shows that the image-only classifier frequently attends to the skull, orbits and background. Second, we adapt a CLIP-style image - tabular contrastive framework and organize ADNIMERGE variables along a label-leakage spectrum. Fusion with cognitive scores yields 87.3% three-way accuracy, which we treat as a leakage-driven upper bound rather than an imaging result; fusion with regional volumes yields 73.0%. We observe that the choice of contrastive target changes what the image encoder learns: on MCI vs. CN, the image-only head reaches 52.4% when the encoder is aligned to cognitive scores and 73.8% when aligned to volumes, although no tabular input is used at inference. Third, restricting the input to a per-subject crop of the medial temporal lobe raises image-only three-way accuracy from 58.7% to 65.1%. All results come from single runs on a small balanced test set, and we report confidence intervals and the protocol differences that prevent direct comparison with published numbers.

Dementia is a major and growing global health burden, with Alzheimer's disease (AD) accounting for most cases. Timely and accurate diagnosis is central to managing this burden and increasingly depends on integrating complementary clinical and imaging information. Multimodal deep learning can combine these modalities for AD diagnosis, but how its explanations behave across modalities, fusion strategies, and cohorts remains unclear. We developed an explainable multimodal framework pairing a 3D CNN encoder for T1-weighted MRI with a feedforward network for harmonized clinical and demographic data, comparing varied model setups on three-way and pairwise diagnostic tasks using 6,479 internal records from the ADNI and 1,703 independent records from the OASIS-3. On ADNI, the tabular-only model achieved the highest three-class AUC-ROC of 0.879 and best discriminated cognitively normal (CN) versus mild cognitive impairment (MCI; 0.903), while cross-attention performed best for MCI versus AD (0.861); CN versus AD was highly discriminative overall. On OASIS-3, the vision-only model performed best (three-class AUC-ROC 0.910); CN versus MCI remained difficult, and no fusion strategy consistently outperformed single modalities across tasks and cohorts. SHAP and Integrated Gradients identified the MMSE as the dominant tabular feature in both cohorts, with global feature rankings agreeing strongly in ADNI ($\rho=0.94$) and OASIS-3 ($\rho=0.96$); CAM-based explanations, however, changed with model configuration and cohort. These findings show that multimodal performance and explanations are task, modality, fusion, and cohort-dependent: a dominant cognitive signal persisted across cohorts, but feature contributions and CAM explanations did not, underscoring the need to evaluate explainability under cohort shift rather than as a stable, intrinsic property.

Robust medical image segmentation across imaging modalities is challenging because of large differences in appearance and intensity distributions. Models trained on a single modality often show substantial performance drops when applied to unseen domains. In this work, we develop a unified 3D pancreas segmentation framework that applies domain-adversarial learning to 4,604 heterogeneous CT and MRI scans to learn anatomical representations. A shared nnU-Net encoder-decoder is trained for whole-pancreas segmentation, with a latent domain discriminator encouraging CT-MRI feature alignment. The learned encoder is subsequently transferred to pancreatic head-body-tail segmentation using limited MRI-only subregion annotations. An average Dice score of 87.31% on the in-distribution test set and Dice scores ranging from 84.20% to 88.09% across external OOD datasets were achieved in whole pancreas segmentation. Dice scores of 80.53% on MRI and 83.05% on CT were achieved for downstream subregion segmentation, without using CT subregion annotations. These results demonstrate that a unified anatomical representation can support both cross-modality pancreas segmentation and label-efficient downstream transfer.

Post-treatment MRI in patients with glioma provides serial observations for updating patient-specific tumor-state proxy estimates, but variable appearances and trajectories complicate forecasting. We formulate forecasting as an observation-aware digital-twin update in which an intermediate observation anchors the patient-specific state. Among 203 patients and 594 follow-up time points, a predefined no-new-treatment criterion retained 120 of 236 candidate triplets, split into 81/24/15 training/validation/test triplets at the patient level. Each time point was represented by a continuous voxel-wise tumor-state proxy map in [0,1] derived from MRI lesion labels. A SegMamba-based single-step forecaster predicted update proposals from multimodal source-state tensors. Observation-Anchored Selective Assimilation (OASA) retained the observed intermediate proxy as the state anchor and selectively applied updates through a validation-selected tiered case-level rule and voxel-wise soft gate. We compared initial-scan forecasting, rollout without assimilation, latest-observation persistence, direct prediction, OASA, OASA + calibration, and morphological dilation. Checkpoints, OASA rules, and calibration thresholds were selected using validation data only. Across three seeds on 15 held-out test triplets, OASA maintained Dice at $\tau$ = 0.2 comparable to persistence (0.6071 $\pm$ 0.0025 vs. 0.6070) while yielding numerically higher Dice at $\tau$ = 0.5 (0.4269 $\pm$ 0.0079 vs. 0.3981), with a small RMSE increase. Calibration increased Dice at $\tau$ = 0.2 to 0.6178 $\pm$ 0.0025, increased false-positive (FP) support (11,836$\rightarrow$18,663), and reduced false-negative (FN) support (22,107$\rightarrow$17,536). This reflects near-threshold support calibration rather than improved biological predictive capability. Code is publicly available at https://github.com/jsudg436/longitudinal-proxy-forecasting.

Brain age estimation has become a popular research proxy for assessing brain health and disease, yet longitudinal trajectories of brain ageing are still poorly defined, and clinical use is limited. Building on existing Siamese longitudinal frameworks, we develop Brain-Predicted Age Acceleration (Brain-PACE) to directly estimate the pace of structural brain ageing from paired T1-weighted MRI. Brain-PACE identified accelerated ageing in $42.6$% of participants with mild cognitive impairment. Faster Brain-PACE was associated with greater functional and cognitive impairment (FAQ; $r=0.35$, ADAS13; $r=0.30$, CDR-SB; $r=0.32$) and greater regional tau burden in the posterior cingulate ($r=0.59$), precuneus ($r=0.47$), and entorhinal cortex ($r=0.37$). These associations were stronger than those observed when pace was calculated indirectly from repeated cross-sectional brain age estimates, suggesting that direct longitudinal modelling captures complementary information relevant to ongoing pathological change. Methodologically, Brain-PACE extends the LILAC framework by combining spatial attention with soft label distribution learning and a Cram'er distance objective, improving probabilistic performance and reducing prediction bias while providing measures of predictive uncertainty. Together, these findings support Brain-PACE as a complementary longitudinal imaging phenotype with sensitivity to relevant clinical and biological changes in early neurodegeneration.

Detecting brain metastases in magnetic resonance imaging (MRI) remains challenging because lesions vary widely in size and appearance, with very small metastases occupying only a minute fraction of a three-dimensional input. We investigate whether combining different spatial fields of view (FOVs) improves lesion detection in multimodal MRI and present a scale-aware 3D deep-learning framework. The method uses independently trained $96^3$ and $64^3$ 3D U-Nets whose whole-volume probability maps are combined by weighted late fusion. This design allows us to study the effect of spatial context separately from image resolution and modality choice. On a 97-patient development cohort, cross-FOV fusion improved lesion-level precision and F1 while substantially reducing false positives relative to the individual models. A same-FOV ensemble control showed that these gains were not explained solely by averaging independently trained networks, supporting a contribution from complementary spatial context. An exploratory cross-FOV agreement filter reduced false positives but did not improve overall F1. These results support cross-FOV probability fusion as a simple and computationally practical strategy for improving the precision-false-positive trade-off in 3D brain-metastasis detection.

Longitudinal characterization of multiple sclerosis (MS) lesions remains constrained by the lack of frameworks capable of establishing consistent instance-level correspondences across time. Conventional segmentation approaches produce semantic lesion masks at each visit and therefore fail to capture the complex instance temporal patterns associated with lesion appearance, disappearance, splitting, or merging. This study presents a comparative evaluation of five strategies for automated tracking of spinal cord MS lesions in longitudinal MRI data from a multi-site cohort. The investigated strategies rely either on deformable registration or on a spinal anatomical reference system, and encompass overlap-based matching, coordinate-based Hungarian algorithm, gradient-boosted classification, and Siamese model classification. Tracking accuracy is quantified using instance-level true positives, false positives, and false negatives, allowing to assess the presence of one-to-many and many-to-one associations. Results show best performance for the registration-based overlap method. This study provides the first systematic analysis of lesion-instance correspondence in the spinal cord and outlines the strengths and limitations of registration-based and registration-free paradigms for longitudinal MS assessment. The code is available at http://github.com/ivadomed/longitudinal-sc-ms-lesion-tracking .

We present a unified computational approach to tensor-based morphometry in detecting the brain surface shape differences between two clinical groups based on magnetic resonance images. Our approach is novel in a sense that we combined surface modeling, surface data smoothing and statistical analysis in a coherent unified mathematical framework. The cerebral cortex has the topology of a 2D highly convoluted sheet. Between two different clinical groups, the local surface area and curvature of the cortex may differ. It is highly likely that such surface shape differences are not uniform over the whole cortex. By computing how such surface metrics differ, the regions of the most rapid structural differences can be localized. To increase the signal to noise ratio, diffusion smoothing based on the explicit estimation of Laplace-Beltrami operator has been developed and applied to the surface metrics. As an illustration, we demonstrate how this new tensor-based surface morphometry can be applied in localizing the cortical regions of the gray matter tissue growth and loss in the brain images longitudinally collected in the group of children.

Structural magnetic resonance imaging (MRI) images are sometimes corrupted over a contiguous set of slices, where acquisition, motion, hardware, or reconstruction effects leave a single slice or short interval inconsistent with its neighbors while the rest of the image remains usable. Such localized corruption can bias downstream morphometric analysis, yet discarding or reacquiring an otherwise usable image is costly. We formulate this as an image restoration problem: given the location of the affected interval, reconstruct those slices from the surrounding anatomical and imaging context. We propose SliceBridge, a framework for restoring corrupted slice intervals in T1-weighted MRI using rectified flow matching conditioned on the surrounding intact slices and their relative slice positions. Through-plane consistency is encouraged by coupling the slices within the interval through interval-correlated initial noise, a shared flow time, and synchronized sampling. The restored interval is then inserted back, leaving all other slices unchanged. We trained and validated the model on 9,877 T1-weighted brain MRI volumes from four datasets and evaluated it on 581 external subjects using clean interval withholding and controlled corruptions. Compared with a matched model that reconstructed target slices independently, SliceBridge reduced error in slice-to-slice changes within repaired intervals by 32.9%-41.3% across interval lengths and achieved higher SSIM at every interval length. In controlled-corruption cases, SliceBridge reduced the median error in regional brain volume estimates produced by a downstream segmentation model from 1.95% in corrupted volumes to 1.05%.

Magnetic resonance images of the same subject look markedly different across field strengths, which complicates the comparison and pooling of data across sites. We address cross-field brain-MRI translation for the MRIxFields2026 challenge, and in particular its Task~3: a single model that translates between any directed pair of the five field strengths and across three contrasts. We phrase the problem as a conditional flow matching path: because the source and target volumes are spatially registered, we learn a velocity field that carries the source slice directly to the target slice, rather than starting from noise. To learn this mapping from only three paired subjects, the unified model is trained in three stages: a degradation-bridge pretraining that distills a restoration prior from the abundant unpaired retrospective cohort, a cross-field finetuning over all directed pairs on the paired cohort, and an adversarial refinement that sharpens the output. At inference, we integrate the learned velocity with a second-order Heun solver in a handful of steps. A restoration prior learned without any paired data already reaches a mean SSIM of 0.837, and each subsequent training stage improves on it. A single 6.3M-parameter model thereby covers all 60 field-pair and contrast combinations, with inference in five solver steps per slice. On the challenge evaluation set the model reaches a mean SSIM of 0.909, averaged over the three contrasts, outperforming regression and diffusion baselines built on the identical network on all three challenge metrics.

Combining whole-body magnetic resonance imaging (WB-MRI) with clinical variables has the potential to improve systemic disease diagnosis by leveraging complementary sources of patient information. However, structured clinical variables are often incomplete or missing, limiting the applicability of conventional multimodal fusion methods that assume fixed inputs. In this work, we propose TACTIC (Tabular-Attribute Conditioned Transformer for Image Classification), a prompt-based multimodal framework that integrates WB-MRI and structured clinical data through conditional visual feature learning. By encoding clinical attributes as prompts, TACTIC supports an arbitrary number of tabular inputs and naturally handles missing data without requiring imputation or fixed input structures. We evaluate TACTIC on five WB-MRI classification tasks spanning systemic and oncologic applications, including diabetes, chronic obstructive pulmonary disease (COPD), breast cancer, prostate cancer, and metastasis diagnosis. Across all tasks, TACTIC consistently improves performance over image-only baselines when clinical information is available while maintaining strong predictive capability under incomplete tabular inputs. Our results demonstrate the effectiveness of prompt-based models as a flexible approach for improving WB-MRI analysis using clinical context. The model weights and code are available at https://github.com/lauradaza/TACTIC

Brain tumor segmentation in magnetic resonance imaging (MRI) is a critical task for diagnosis and treatment planning. Despite the success of deep learning architectures such as U-Net and its variants, performance degradation across datasets remains a major challenge, particularly under domain shift and limited annotated data. To address this issue, this study systematically evaluates how individual MRI sequences influence model robustness across two well-known datasets. A ResUNet-based framework is employed, where each modality is trained independently to isolate its effect under a controlled cross-dataset evaluation protocol with tumor size stratification, without target-domain training, or with limited domain adaptation. Results show that the T2f/FLAIR sequence achieves the best cross-dataset performance, with Dice scores exceeding 75%. It consistently outperforms other modalities across most tumor size ranges, while multi-sequence training further improves performance. Additionally, even limited target-domain adaptation yields rapid initial gains, reducing the need for extensive annotations and costly retraining. Our source code is publicly available at https://github.com/henrique-zan/brain_tumor_segmentation/.

3D brain MRI generation has made significant advances in medical imaging, simulation, and controllable anatomical analysis. However, existing generative models typically synthesize 3D volumes monolithically, often overlooking regional anatomical structures and limiting local controllability. To address these limitations, we introduce AnaDiffusion, an anatomically compositional latent diffusion framework that factorizes the generation process into distinct, anatomically meaningful regions, followed by part-to-whole assembly and global refinement. Our approach first trains part diffusion models to capture local structural priors. We then inject an assembled anatomical composite of the parts into the whole-brain latent representation and continue denoising. This mechanism enables the model to resolve global context while preserving the injected anatomy. As a result, AnaDiffusion produces both explicit part assets and a globally coherent volume, thereby enabling controllable part editing without requiring subject-specific dense segmentation maps at inference time while maintaining consistent part-to-whole brain structure. On the subject-disjoint ADNI test split, AnaDiffusion achieves the lowest FID across the whole brain, left and right hemispheres, cerebellar-brainstem complex, and seam regions. It also achieves the best cerebellar and second-best ventricular and brainstem absolute Cohen's d values among the evaluated methods. In localized editing experiments, paired MS-SSIM demonstrates high target transfer and off-target preservation, supporting controllable part replacement with minimal unintended anatomical alterations.

Magnetic Resonance Imaging (MRI) interpretation is fundamental to clinical decision-making, requiring radiologists to integrate multi-view anatomical planes across sequential timepoints while precisely localizing interval changes. However, existing vision-language benchmarks remain confined to single-timepoint, single-view interpretation, failing to capture the temporal-spatial reasoning essential to radiologic practice. We introduce the Time-Aware Multi-View MRI Benchmark, an evaluation framework unifying multi-view anatomical input, temporal reasoning across longitudinal scans, and structured localization guidance. The benchmark comprises 3,920 expert-verified question-answer pairs derived from 890 patients across over 3,200 longitudinal MRI timepoints, drawn from seven clinical cohorts covering glioblastoma, neurodegeneration, vestibular schwannoma, and brain metastases, in open-ended, multiple-choice, and binary formats, requiring models to identify anatomical regions of maximal change, characterize progression across sequences and views, and provide structured guidance specifying boundaries, imaging features, and confounders. Experiments across 16 vision-language models reveal moderate temporal alignment but systematic failure on change direction recognition and volumetric quantification, while multi-view inputs improve spatial localization yet degrade temporal reasoning in compact architectures. Our benchmark provides a systematic framework for evaluating progression tracking, interval change localization, and temporal ordering, which are essential for clinical deployment. Code, evaluation splits, and the dataset are available at: https://github.com/wafaAlghallabi/Time-Aware-MRI.

Multi-parametric magnetic resonance imaging (mpMRI) is a cornerstone for brain tumor diagnosis and treatment, yet current AI models face critical limitations: their lack of natural language interaction and interpretability impedes spatial information integration and cross-modal reasoning required clinically. Key challenges arise from significant physical meaning differences across modalities, spatial misalignment due to scan intervals, and the need for complex multi-feature interpretation in tasks like glioma grading. While visual-language models (VLMs) show promise in cross-modal understanding, existing methods focus mainly on 2D image modeling, neglecting direct perception of 3D volumetric space. Although 3D VLMs have been proposed for report generation and feature alignment in 3D CT imaging, mpMRI applications demand collaborative inference across multiple imaging modalities-a requirement unmet by current solutions. To address this, we introduce Mr3D-VL, a dedicated visual-language foundation model for multi-parametric 3D MRI. With 4 billion parameters, it employs an unsupervised pre-trained shared 3D encoder and 4D rotational positional embedding for dual modality-spatial integration. Its cross-modal projection layer uses a multi-resolution feature implantation strategy to enhance feature perception across resolutions. Experimental results show significant improvements over existing 4B/7B/30B domain-specific and general-purpose models in text generation tasks, achieving a BERTScore of 0.856 for report generation, with question-answering accuracy at 0.713 and multiple-choice accuracy at 0.912.

Quantitative MRI (qMRI) provides standardised tissue parameter maps, but the reliability of deep learning-based qMRI mapping methods is often not explicitly characterised. In this work we systematically evaluate uncertainty maps for quantitative MRI derived from multiple inferences of a data-consistent diffusion model-based qMRI framework. Evaluation on synthetic test data assessed error-awareness, high-error detection, selective prediction, and Gaussian interval calibration. Diffusion model-derived uncertainty was positively associated with the mapping error, while risk-coverage analysis showed that excluding high-uncertainty voxels reduced the retained error. However, the raw uncertainty was poorly calibrated for quantitative interval interpretation. Calibration was substantially improved using a post-hoc procedure combining prediction-value-dependent bias correction with scalar uncertainty scaling. Qualitative evaluation on a healthy volunteer showed spatially meaningful uncertainty patterns. These results indicate that diffusion model-derived uncertainty is informative for reliability assessment and selective prediction, but requires calibration for quantitative interval interpretation.

Pancreatic cancer is among the most lethal malignancies; risk stratification of intraductal papillary mucinous neoplasms (IPMNs) offers a crucial opportunity for early intervention but typically requires invasive tissue biopsy. Dominant vision-based approaches, including radiomics and deep learning, provide promising but initially separate discrimination opportunities. Similarly, multisequence MRI (T1W/T2W) and anatomically decomposed (head, body and tail) analysis of the pancreas provide additional and potentially complementary signals. Effective fusion of this information is crucial in ordinal IPMN dysplasia risk prediction and can be accomplished via a meticulously regularized and calibrated ensemble stacking combiner. We present cUPMI, a class-conditional Gaussian augmentation of a combiner's log-probability meta-features, and test it on various prediction paradigms. In our multi-center analysis, we find cUPMI adds limited value to properly regularized L2-logistic binary classification stacks, but consistently regularizes higher-capacity tree combiners in the binary and radiomics-only setting (RF +0.015 and XGBoost +0.024 binary AUC, positive in all seeds). Its cleanest ordinal benefit appears for XGBoost on an 8-stream radiomics task (3-class no < low < high, +0.022 QWK in all seeds). Separately, fold-locked fusion of radiomics and 2.5D CNN streams yields the strongest overall model, an RF stack reaching QWK 0.595 (95% CI [0.54, 0.64]) and binary AUC 0.839, surpassing radiomics, 2.5D ResNet, and 3D DenseNet-121 baselines.

Magnetic field strength is a major source of domain shift in magnetic resonance imaging (MRI), affecting signal-to-noise ratio, tissue contrast, spatial detail, and the visibility of anatomical boundaries. The MRIxFields 2026 challenge investigates this problem through cross-field MRI translation across acquisitions at 0.1T, 1.5T, 3T, 5T, and 7T. Its three tasks, Any-to-7T, 0.1T-to-High, and Any-to-Any synthesis, require the generation of target-field image characteristics while preserving subject-specific anatomy. This problem is particularly challenging because paired acquisitions of the same subject across multiple field strengths are rarely available for training. We propose a 3D unpaired cross-field MRI translation framework based on field-conditioned content-style pretraining. The proposed framework first learns controllable field-to-field translation across all available field strengths by disentangling anatomical content from field-dependent contrast characteristics. The pretrained backbone is then adapted to task-specific target domains. Our model comprises a 3D content encoder, a 3D style encoder, a field-conditioned style generator, an AdaIN-modulated decoder, and a multi-field discriminator. Adversarial learning encourages realistic target-field appearance, while cycle-consistency, identity, content, style, and diversity constraints promote anatomical fidelity and controllable translation. We evaluate the proposed method on MRIxFields data spanning five field strengths and three MRI modalities. Experiments on paired test data demonstrate that the framework can adapt to the three challenge settings while preserving three-dimensional anatomical structure in the synthesized volumes. The implementation code is publicly available at https://github.com/Idea89560041/3D-MRI-Field-Translation.

Objective. MRI provides excellent soft-tissue contrast, but long acquisition times can cause patient discomfort and lead to motion artifacts, forcing a trade-off between spatial resolution and scan time. Diffusion-based super-resolution (SR) reconstructs high-resolution (HR) images from low-resolution (LR) inputs, but typically needs many sampling steps and initializes from a Gaussian prior ill-suited to image restoration. We developed an efficient diffusion framework that reconstructs HR MRI directly from LR data. Approach. We propose super-resolution diffusion bridge model (SR-DBM), a super-resolution diffusion bridge model that casts SR as a stochastic transport between the LR and HR image distributions. Through a Doob's h-transform of a mean-reverting stochastic differential equation, SR-DBM pins the process to the paired HR and LR images at its endpoints, initializing reconstruction from the measured anatomy rather than from Gaussian noise. The HR image is recovered by a deterministic reverse trajectory in which a network predicts the clean image at each of only ten sampling steps. We evaluated SR-DBM on ultra-high-field 7T brain T1 MP2RAGE maps and pelvic T2-weighted prostate images against nine comparison methods using PSNR, SSIM, GMSD, and LPIPS. Main results. SR-DBM attained the highest PSNR and SSIM and the lowest GMSD on both datasets (brain: 27.66+-1.52 dB, 0.96+-0.02, 7.96+-1.86$; prostate: 27.87+-2.29 dB, 0.80+-0.05, 8.38+- 1.44), with statistically significant gains over every comparison method (two-sided Wilcoxon signed-rank test with Holm correction, p<0.05). The strongest baseline, SR-EMamba, ranked second. Qualitatively, SR-DBM produced the smallest residual errors and best preserved fine structures and lesions.

Quantitative T2* maps have strong potential for biomarker discovery but are limited by long scan times, rendering them impractical in clinical settings. Significant acceleration can be achieved through undersampling in k-space combined with learning-based reconstruction. However, reconstruction artifacts and noise can propagate into downstream T2* fitting, degrading its accuracy. We introduce CUPA-T2*, a framework that explicitly propagates voxel-wise inter-echo uncertainty from stochastic Monte Carlo dropout reconstructions to downstream T2* fitting via covariance-aware sampling. T2* fitting is performed with a heteroscedastic MLP and a correlation-based regularizer that encourages alignment between predicted variance and reconstruction uncertainty. Experiments on accelerated brain MRI data show tissue-dependent behavior: CUPA-T2* achieves competitive overall T2* fitting performance and improves white-matter performance at higher accelerations. Compared with a heteroscedastic baseline, the proposed framework substantially increases alignment between reconstruction uncertainty and predicted T2* variance, while also revealing a trade-off with calibration (ECE) and selective prediction performance (AURC). CUPA-T2* enables reconstruction uncertainty-aware T2* fitting and delivers voxel-wise uncertainty maps to support the interpretation of quantitative T2* estimates.

T2-weighted (T2w) brain MRI provides fluid-sensitive soft-tissue contrast that is important for neuro-oncology and radiotherapy planning. However, T2w scans are acquired with anisotropic voxels and appear blurred or stair-stepped on coronal and sagittal views, which obscures small structures and weakens any downstream 3D analysis. We propose VIPP-SR (View-Independent Patched Projection Super-Resolution), a cross-contrast guided super-resolution framework that restores the inter-plane resolution of an existing anisotropic T2w volume without an isotropic ground-truth T2w. VIPP-SR first trains a view-independent patched generator (VIP-GAN) to learn local T1c-to-T2w anatomical correspondence from high-resolution axial slices. The trained generator is then applied to axial, coronal, and sagittal views of the T1c volume to generate three orthogonal T2w estimates. Shape-preserving patching and deepest-skip removal reduce view-specific shortcuts, thereby constraining the generator to learn patch-local representations and enabling the zero-shot inter-plane transfer. Central to VIPP-SR, a projection-based optimization then enforces anatomical consistency across the three view-specific volumes, fusing them by balancing inter-plane self-consistency against per-view data fidelity. The generator is trained on BraTS-MET and evaluated on both the held-out BraTS-MET testing set and the BraTS-GLI cohort without retraining, assessing the cross-cohort generalizability. The results validate that VIPP-SR improves downstream segmentation over the real anisotropic T2w baseline, raising mean-label Dice from 0.330 to 0.465 on BraTS-MET and, zero-shot, from 0.473 to 0.563 on BraTS-GLI and ablation studies identify inter-plane self-consistency as the main source of the gain.

Longitudinal MRI enables sensitive measurement of structural brain change for studying aging and neurodegenerative disease. Deformable image registration is a key tool for estimating such change by computing a dense deformation that captures geometric differences between longitudinal scans. However, MRI scanners introduce geometric distortions that vary across acquisition systems and protocols, such as gradient non-linearity (GNL) distortion. Existing registration methods estimate a single field that conflates biological and technical effects, potentially biasing downstream morphometric measurements if distortions remain (partially) uncorrected. We propose $\texttt{DisMorph}$, a registration framework trained entirely on synthetic data that explicitly decomposes longitudinal deformation into technical and anatomical transforms. It predicts two dense deformations, each encoding one effect. During training, a novel generative model synthesizes both effects separately to provide disentanglement supervision, while domain randomization promotes generalization across imaging protocols. We evaluate our method in three complementary settings. On simulated data with known ground truth, our method detects anatomical change more accurately and consistently than conventional registration. On real image pairs that differ only by GNL distortion, our method assigns most geometric change to the distortion field, demonstrating specificity in the absence of anatomical change. On longitudinal Alzheimer's disease (AD) pairs, our method detects anatomical change in AD-related brain structures while identifying residual distortion left after standard correction. By disentangling MRI-induced distortion from biological change in the longitudinal deformation, our method paves the way for more accurate longitudinal morphometry in clinical settings where maintaining acquisition consistency is challenging.

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.

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is central to breast cancer imaging, but gadolinium administration increases scan burden and motivates contrast-reduced alternatives, including synthetic contrast generation. We propose a latent bridge matching (LBM) framework for synthesizing peak-enhanced breast DCE-MRI from pre-contrast images in the MAMA-SYNTH challenge setting. Instead of starting from Gaussian noise as in conventional latent diffusion models (LDMs), the proposed model learns a conditional bridge between paired pre-contrast and peak-enhanced VAE latents. A latent UNet predicts the remaining correction from intermediate bridge states to the peak-enhanced latent, enabling iterative refinement while keeping the trajectory anchored to patient-specific anatomy. We evaluated two LBM conditioning variants on 91 DUKE validation cases. For the tumor-conditioned variant, tumor masks were used as conditioning inputs. Tumor-conditioning improved performance compared with pre-contrast conditioning, reducing MSE from 1.023 to 0.940 and FRD from 7.523 to 4.716, while increasing tumor SSIM from 0.355 to 0.429. The tumor-conditioned LBM also outperformed the evaluated LDM baseline on this validation cohort. These results suggest that latent bridge matching is a promising pre-contrast-anchored formulation for virtual contrast enhancement, while further work is needed to validate generalization and remove dependence on ground-truth tumor masks at inference.

Self-supervised 3D medical foundation models are increasingly used as general-purpose feature extractors, yet their sensitivity to MRI artifacts remains poorly understood. We present a controlled evaluation of representation robustness across five pretrained 3D encoders spanning different architectures, objectives, pretraining domains, and dataset scales. Using BraTS-Africa cases with four MRI sequences, we generate seven frequency- and image-domain artifacts at five predefined corruption settings. Robustness is assessed using linear centered kernel alignment (CKA), RankMe, and UMAP, complemented by an independent segmentation-consistency analysis. We find that robustness is strongly model- and artifact-dependent. 3DINO exhibits the most consistently stable representations, while BrainIAC is highly sensitive to several corruptions; NeuroVFM, BrainFM, and Neuro-SimCLR show intermediate but distinct artifact-specific profiles. Across many conditions, CKA decreases substantially while RankMe remains comparatively stable, indicating that artifacts often distort representation geometry without causing dimensional collapse. Segmentation consistency also degrades under corruption, particularly for ghosting and Rician noise, but aligns only partially with representation-level robustness. These findings show that larger-scale or domain-specific pretraining alone does not guarantee artifact invariance and motivate explicit robustness evaluation before deploying 3D foundation models in heterogeneous MRI settings.

We present a MR safe, master-slave robot manipulator for abdominal interventions in the MRI chamber. A human operated 2+1-DoF master controller manipulator transmits motion and force to a 2+1-DoF slave manipulator via fluid transmission. Jointly, a digital master controller provides multimodal control capability beyond common split axis or mode switchable hybrid human-digital controller configurations found in previous studies. High input impedance, low-leakage, elastomeric fluid actuators are delegated to remote angulation control. Low-friction graphite piston cylinders are delegated to needle insertion axis remote actuation given the sub-newton force transparency and sub-millimeter motion transmission over bedside fluid piping lengths. The device enables real-time MRI guided interventions allowing manual, digital, hybrid, and collaborative control modes. Collaborative tasks such as assisted tissue penetration, fault-driven virtual fixture, and motion compensation through feedback control are presented in this paper. Preliminary MR scanner results demonstrate manipulator functional viability for an in-vivo pig experiment in bedside, manual control mode configuration.

Radiology foundation models learn transferable representations that can be adapted to new tasks by training only small layers on top of a frozen encoder. Dense prediction tasks such as 3D segmentation are, however, underrepresented in their evaluation, and, with the encoder kept frozen, pre-trained models still fall short of nnU-Net, the state-of-the-art reference trained from scratch. To close this gap we extend convolutional MAE pre-training with a robust reconstruction objective, a feature regularizer, and a local-global similarity objective. Using this method, we propose Curia-MAE, a multi-modal, multi-anatomy MAE model pre-trained on 300,000 CT and MRI images covering a large number of anatomical sites. On eight anatomy- and lesion-focused segmentation benchmarks, Curia-MAE improves frozen-encoder performance over a strong MAE baseline, while remaining competitive under full finetuning and superior on lesion tasks, where labeled data is scarce. These results indicate that a single frozen encoder can be reused across diverse segmentation tasks, reducing the cost of adapting and deploying such models in clinical workflows. Curia-MAE pre-trained model weights are made publicly available at https://huggingface.co/raidium/Curia-MAE.

Slice-wise 2D object detectors are increasingly applied to volumetric data due to their computational efficiency and scalability, yet they often yield fragmented and unstable predictions along the depth axis. We propose YOLO-PVC, a lightweight and model-agnostic framework for 2D-to-3D consolidation of slice-wise detections. The method enforces depth continuity, aggregates bounding box coordinates using robust percentile statistics, and further refines axial extent through a lightweight MLP-based calibration module. Unlike naïve stacking or averaging strategies, YOLO-PVC explicitly addresses missing detections and outlier slices along the depth dimension. Experiments on 3D liver MRI volumes across three tumor categories demonstrate consistent improvements over multiple aggregation baselines. The heuristic PVC achieves an overall $\mathrm{IoU}_{3D}$ of $0.665$, while the calibrated variant further improves performance to $0.710$, with high planar overlap ($\mathrm{BEV\ IoU} \approx 0.78$). These results demonstrate that structured geometric consolidation provides an effective and practical solution for volumetric liver tumor localization in clinical MRI.

Uterine peristalsis is a key physiological phenomenon responsible for various functions across the menstrual cycle, intimately linked to uterine wall microstructure. Alterations in uterine motion and tissue properties are implicated in the etiology of gynecological diseases, yet these processes have been studied in isolation. We introduce a dynamic multi-echo gradient echo EPI framework for simultaneous characterization and correlation of uterine peristaltic activity and time-resolved T2* changes at 0.55T. Inherent susceptibility artifacts, reduced resolution, and burden of manual uterine layer annotation are addressed by an unsupervised adversarial domain adaptation framework, transferring segmentation knowledge from labeled cine MRI to unlabeled dynamic EPI. We implemented Unet-LSTM with multi-scale domain discriminators that exploits temporal layer dynamics. A Dice score of 0.88 and Jaccard index of 0.80 was achieved. Mean T2* values were 108ms, 76ms, and 124ms for the myometrium, junctional zone, and endometrium. A negative correlation between junctional zone area and T2* was observed in 14/39 cases, providing first insights into oxygenation patterns associated with junctional zone contraction and motion, demonstrating feasibility of assessing the interplay between contractility and dynamic T2* changes.

Fetal brain biometry is essential for quantitative assessment of brain development, supporting gestational age estimation, developmental monitoring, and detection of abnormalities. In clinical practice, measurements are manually performed, making them time-consuming and prone to variability. While automated approaches have been proposed, reproducible methods remain limited, particularly those providing anatomically interpretable landmark localization. We present a fully automated deep learning-based framework for reliable and reproducible brain biometry from 3D super-resolution-reconstructed fetal brain MRI. The proposed four-step pipeline derives biometric parameters by jointly estimating linear measurements and their corresponding anatomical landmarks. A 3D convolutional neural network is trained to regress landmark coordinates from brain segmentation label maps, followed by measurement-specific geometric optimization to refine landmark positions and compute measurements. The pipeline is evaluated on two publicly available fetal MRI datasets comprising 150 volumes (gestational age range: 20-37 weeks) acquired across different scanners and protocols, assessing five key biometric measurements across varying acquisition settings and providing a comprehensive evaluation of both measurement accuracy and landmark localization using quantitative metrics and visual assessment. Compared with the only available automated pipeline, the proposed method achieves comparable or improved accuracy for most measurements. In conclusion, we introduce a straightforward pipeline for reliable biometry estimations, with efficiency, interpretability and scalability that support integration into clinical workflows.

Virtual contrast enhancement (VCE) synthesizes enhanced breast MR images from pre-contrast acquisitions. Modern latent generators offer strong image priors, but their bounded natural-image autoencoders conflict with the non-canonical intensity scale of MRI. We show that the upper bound can alter radiomic fidelity before generation, while scaling source and target independently creates a coordinate inconsistency. We propose Predictive Enhancement Calibration (PEC), which represents each pair in a shared, case-adaptive coordinate during training and predicts its unavailable upper endpoint from the pre-contrast image at inference. We integrate PEC with a pretrained FLUX latent flow transformer via parameter-efficient reference conditioning. Target round trips first isolate representation loss before generation; near-matched conditional models then compare PEC with fixed-wide and separate coordinates under comparable training budgets and backbone settings. On the fixed internal MAMA100 development cohort, PEC improves all eight point estimates in this source-only VCE setting, with paired evidence strongest for MSE and LPIPS.\noindent\textbf{Code:} https://github.com/tanlei0/pec-breast-mri-vce

Multimodal medical large language models remain structurally weak for neuro-oncology because volumetric evidence is compressed into generic visual tokens and diagnostic conclusions often lack an auditable link to MRI regions. We present NeuroMosaic, a 3D multimodal language model that converts multi-sequence brain MRI into anatomy-indexed regional tokens, aligns them with clinical narrative and molecular concepts, and generates evidence-linked outputs. The architecture combines a multi-resolution volumetric tokenizer, a neuroanatomical graph router, a molecular concept memory, and selective risk control. Across four glioma cohorts, NeuroMosaic achieved an internal subtype macro-F1 of 0.827 and external macro-F1 values of 0.784, 0.761, and 0.742. On UPenn-GBM, it improved over the strongest matched-input baseline by 3.6 percentage points (95% CI: 1.8 to 5.4, adjusted p = 0.0018), with IDH, 1p/19q, and MGMT AUROCs of 0.918, 0.861, and 0.781. Evidence pointing accuracy reached 0.703, and targeted evidence deletion reduced correct-answer probability by 0.187, compared with 0.046 for random deletion. These results establish anatomy-indexed routing as a measurable mechanism for accurate, grounded, and calibrated volumetric medical-language reasoning.

Focal cortical dysplasia (FCD) type II is an important structural cause of drug-resistant focal epilepsy, but its small size, heterogeneous appearance, and subtle MRI characteristics make automated segmentation challenging. Conventional multimodal networks commonly concatenate T1-weighted (T1w) and fluid-attenuated inversion recovery (FLAIR) images, requiring subsequent layers to learn useful cross-modal relationships implicitly. We propose CRIL-U-Net, a 3D U-Net incorporating a Compact Ratio-Interaction Learning module that combines local spatial features, voxel-wise cross-modal mixing, and bidirectional ratio-inspired interactions. CRIL-U-Net was compared with a conventional 3D U-Net and an input self-attention U-Net using five-fold cross-validation on 85 FCD subjects and 25 healthy controls. Each architecture was trained independently using Dice-binary cross-entropy (Dice-BCE) and Focal Tversky-Focal (FTF) losses. With FTF, CRIL-U-Net achieved the highest mean Dice score (0.196 +/- 0.262), compared with 0.136 +/- 0.224 for the U-Net and 0.135 +/- 0.214 for the attention comparator. It produced nonzero lesion overlap in 44 of 85 cases, compared with 36 for the U-Net. Under FTF, CRIL-U-Net significantly outperformed both comparison architectures after false-discovery-rate correction. These findings suggest that compact cross-modal representation learning can improve FCD segmentation within a controlled U-Net setting when combined with an imbalance-aware objective, although the remaining zero-overlap rate of 48.2% highlights the need for further validation and methodological development.

Longitudinal multiparametric MRI is central to follow-up imaging in oncology, yet real-world clinical data are characterised by missing sequences, heterogeneous acquisition protocols, and varying spatial resolutions across time points. We propose a patient-specific conditional implicit neural representation (INR) that models multimodal longitudinal MRI as a continuous function of world coordinates, time, and modality conditioning. The model is trained with stochastic modality dropout to handle incomplete data, and its continuous coordinate-space formulation enables both spatial and temporal interpolation without resampling to a fixed voxel grid. A self-consistency-based confidence estimator is derived from cross-modal reconstruction performance at inference time. We evaluate the framework on longitudinal MRI from paediatric brain tumour patients, demonstrating statistically significant improvements over linear interpolation for T1CE and FLAIR (p < 0.05), with mean MS-SSIM of 0.95 $\pm$ 0.02 for T1CE. Predicted confidence correlates strongly with true reconstruction quality (Pearson r up to 0.996), suggesting reliable deployment potential in heterogeneous clinical settings.

Brain tissue microstructure estimation with machine learning provides higher computational efficiency than conventional fitting. However, machine learning still presents important limitations that hamper its clinical utility. Specifically, current models typically lack generalisation across diffusion MRI acquisition protocols and require retraining whenever b-vectors or b-values change. Moreover, the recent machine learning methods that were developed to address protocol generalisation lack rotational equivariance. Particularly suitable for dMRI parameter estimation is a geometric deep learning model known as spherical convolutional neural network (SCNN), which guarantees rotational equivariance and b-vector generalisation. However, this architecture currently does not account for b-values. Therefore, obtaining a model that combines protocol generalisation and rotational equivariance remains an open challenge. In this paper, we directly address this issue by incorporating explicit b-value dependence into an SCNN architecture via a hypernetwork. This new approach is illustrated using NODDI as an example forward model for estimating brain tissue microstructure. To evaluate b-value generalisation, the original and newly proposed SCNN architectures are trained on synthetic data and tested on both synthetic and real data across different b-value pairs. Results demonstrate that the proposed method achieves reduced RMSE and bias on synthetic data, as well as higher agreement with conventional NODDI fitting on real data, indicating improved robustness to unseen b-values and a reduced need for retraining. By combining generalisation across b-values with generalisation across b-vectors and rotational equivariance, the proposed framework enhances the applicability of deep learning to clinical diffusion MRI parameter estimation. Code available at https://github.com/aerdnairo/arXiv\_generalisedSCNN.

High-resolution 3D segmentation of hip and shoulder anatomy from CT and MRI is essential for surgical planning, yet frozen segmentation models often fail under domain shift. CNN-based expert models are fully automatic but lack adaptability, whereas promptable foundation models generalize better but require manual prompting. We present MedSAM2-Anatomy, a training-free inference-time optimization framework that improves frozen segmentation models without retraining or human interaction. A frozen expert model generates anatomical priors that are automatically converted into multiple prompt hypotheses for a frozen 3D foundation model. Candidate masks are fused while anatomically implausible priors are rejected. No model weights are updated and no manual prompts are required. TotalSegmentator and MedSAM2 are used as representative expert and foundation models, allowing the contribution of the inference policy to be isolated. Evaluation on the independent Balgrist-V0 CT and MRI cohorts shows that inference-time optimization increases median Dice from 0.71 to 0.92 on hip MRI and from 0.89 to 0.92 on shoulder CT, while reducing median HD95 on hip MRI from 22.0 mm to 5.0 mm. On public TotalSegmentator benchmarks, the expert model remains strongest, indicating that the optimal fusion strategy depends on the reliability of the expert prior. These results demonstrate that training-free inference-time optimization provides a practical strategy for improving frozen segmentation models without manual prompting.

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is essential for breast cancer management, but reliance on gadolinium-based contrast agents (GBCAs) restricts use in contraindicated populations, prolongs scan protocols, and presents environmental toxicity concerns. Contrast synthesis offers a non-invasive alternative; however, existing approaches struggle to balance spatial realism with temporal continuity, suffer from slow iterative sampling, underutilize structural priors, and lack clinical validation. We propose a novel conditioned latent transport framework that predicts contrast enhancement in a single forward pass. By anchoring the latent trajectory to the pre-contrast anatomy and applying continuous time conditioning, the model synthesizes patient-specific contrast evolution at any acquisition time. The proposed approach outperforms baseline and the state-of-the-art models across spatial, perceptual, temporal, and distributional metrics. Evaluated on an independent external cohort, the method demonstrates robustness to domain shifts induced by scanner noise as well as differing acquisition protocol. Furthermore, our synthetic contrast enhancement significantly improved downstream tumor segmentation performance, yielding a 22.4% relative increase in Dice coefficient (0.60 vs. 0.49 baseline pre-contrast, p < 0.01), reducing boundary segmentation error by over 39%, while outperforming all other generative model baselines. Finally, a reader study involving four breast radiologists evaluated the image quality, kinetic fidelity, and diagnostic viability of our synthesized sequences across 40 randomly selected cases. The results demonstrated that in 70% of cases, synthesized images provided sufficient clinical information to support the same management decisions as real DCE-MRI, suggesting a path toward safer and faster contrast-free or contrast-reduced imaging workflows.

Automatic brain tumor segmentation from magnetic resonance imaging (MRI) has become a fundamental task in computer-assisted diagnosis, treatment planning, and disease monitoring. Although numerous deep learning architectures have recently been proposed, objective comparisons remain challenging because published studies often employ different datasets, preprocessing strategies, training protocols, and evaluation procedures. This work presents a unified experimental benchmark for comparing representative convolutional neural networks (CNNs), Transformer-based models, and recent State Space Model (SSM) architectures under homogeneous experimental conditions. Five state-of-the-art three-dimensional segmentation models, including 3D U-Net, SegResNet, Swin UNETR, SegMamba, and SegMambaV2, are evaluated on two brain tumor segmentation datasets representing distinct clinical scenarios: intracranial meningioma segmentation (BraTS 2023) and post-treatment glioma segmentation (BraTS 2024). All architectures are trained using identical preprocessing, data augmentation, optimization strategies, and evaluation protocols to ensure a fair comparison. Performance is assessed using segmentation accuracy metrics together with computational cost indicators, including inference time and the size of each model. The results provide practical insights into the trade-offs between segmentation accuracy and computational efficiency, highlighting the suitability of different architectural paradigms for challenging three-dimensional brain tumor segmentation tasks.

Brain tumor diagnosis is a time-sensitive process in which patients may wait weeks for a finalized pathology report. This problem motivates automated systems that classify tumor subtype from multimodal inputs. This paper details the DS@GT ARC team's work for ImageCLEFmed MEDIQA-CORE 2026 Task~1, Brain Tumor Subtype Classification. The task evaluates three glioma classification problems: Level-1 Molecular Type, LGG vs HGG, and WHO Grade. We combine pre-extracted MRI (NeuroVFM) and histopathology (Prov-GigaPath) embeddings with free-text radiology reports. Our team explored two trimodal fusion architectures, two report encoders (RadBERT and Llama-3.1-8B-Instruct), and a biologically motivated post-processing stage. We achieve a mean macro-F1 of 0.801 under the Fully Multimodal condition, exceeding the organizers' baseline of 0.796 and ranking second among the teams whose code passed verification. Additional evaluation across modality-dropping conditions shows that this advantage depends heavily on the availability of the histopathology modality, and that our system falls behind the baseline when modalities are missing. Our code is available on GitHub at https://github.com/dsgt-arc/imageclef-mediqacore-2026.

Predicting future structural MRI of a brain is challenging because longitudinal changes are often subtle and confined to specific anatomical regions, while most subject-specific brain structure remains stable over time. An effective model should therefore preserve global brain structural consistency while remaining sensitive to fine-grained disease progression. Existing latent-space-based methods improve computational efficiency, but suffer from information loss during their compression-reconstruction procedure. In contrast, direct voxel-space methods avoid latent reconstruction but commonly use a unified prediction pathway to model brain structure and progression-related changes. Subtle local changes may therefore be overshadowed by the dominant stable brain structure. To address these challenges, we propose ProgFormer, a hierarchical voxel-space Diffusion Transformer for longitudinal brain MRI prediction. ProgFormer uses a coarse pathway to perform the primary volumetric prediction from 3D patch tokens. This pathway models overall brain structure and longitudinal context. The fine pathway then uses the coarse representations as spatio-temporal grounding for voxel-level refinement within individual patches. The two pathways jointly estimate a velocity field directly in voxel space through conditional flow matching, enabling end-to-end prediction without a separately learned image autoencoder. The predicted future scan is then generated from Gaussian noise by integrating the estimated velocity field over a sequence of Euler steps. Extensive experimental results on three widely used benchmarks, ADNI, AIBL, and OASIS, under both pairwise and trajectory settings demonstrate favourable performance compared against several state-of-the-art methods.

Accelerated magnetic resonance imaging (MRI) aims to recover the k-space signal from acquired measurements, where accurate estimation of missing samples is essential for high-fidelity reconstruction. Existing k-space reconstruction methods estimate missing samples through interpolation operators or structure priors defined on discrete sampling grids. Although these formulations effectively exploit local interpolation relationships and global k-space redundancy, they reconstruct only discrete frequency coefficients and therefore do not explicitly model the underlying continuous signal. To overcome this limitation, we propose K-space Gaussian Representation (KGR), the first explicit continuous representation formulated directly in the native k-space domain. Rather than estimating unknown samples on discrete grids, KGR parameterizes the continuous signal using Gabor-Gaussian primitives with shared spatial geometry, yielding a compact representation that naturally preserves inter-coil correlations. Because unconstrained continuous fitting does not necessarily satisfy the intrinsic structural properties of multi-coil signal, the estimated representation is projected onto a low-rank manifold to enforce the algebraic constraints arising from smoothly varying phase and coil redundancy. A frequency-adaptive fitting strategy accommodates the heterogeneous characteristics of different k-space regions. Comprehensive validation across multiple datasets and sampling schemes shows consistent improvements over representative reconstruction baselines in both quantitative metrics and visual quality. These results suggest that explicit continuous parameterization of native k-space provides a principled framework for integrating continuous signal modeling with structured low-rank reconstruction.

Breast DCE-MRI AI is increasingly being explored for breast-level classification of no-lesion, benign, and malignant findings, beyond conventional lesion-centered diagnosis. Within this broader diagnostic scope, however, patient-specific background variability remains a major source of imaging confounding across classification tasks. Existing approaches predominantly focus on unilateral or lesion-centric analysis, whereas bilateral methods offer limited explicit modeling of spatially adaptive cross-breast correspondence. We propose PRISM-Net, a registration-free bilateral framework that leverages contralateral breast features as patient-specific references for background-aware representation learning. PRISM-Net integrates bilateral feature matching and asymmetry-aware attention to establish adaptive inter-breast correspondence and enhance representations of discriminative asymmetric patterns. On ODELIA, Macro AUC, Micro AUC, and quadratic weighted kappa were $84.11 \pm 2.33$, $90.64 \pm 1.61$, and $60.94 \pm 5.64$ on the in-distribution test set, and $68.51 \pm 4.54$, $80.74 \pm 2.68$, and $43.45 \pm 7.10$ on the held-out institution, respectively, outperforming the evaluated baseline methods across the primary evaluation metrics. PRISM-Net further demonstrated performance on independent institutional and background-complexity evaluations. Ablation experiments revealed that both bilateral relation modeling and asymmetry-aware reweighting contributed to improved classification performance. These findings highlight patient-specific bilateral reference modeling as a clinically grounded strategy for DCE-MRI interpretation, improving asymmetric pattern discrimination through explicit modeling of background complexity.

Attention Mechanism (AM) selectively focuses on essential information for imaging tasks and captures relationships between distant pixel neighborhoods to compute feature representations. Accelerated MRI reconstruction benefits from AM, as the imaging process involves Fourier domain measurements that influence image representation non-locally. However, AM-based models are more adept at capturing low-frequency information with limited capacity for high-frequency representations, restricting models to smooth reconstruction. Additionally, AM-based models need mode-specific retraining for multimodal MRI data, as their knowledge is restricted to local contextual variations that may be inadequate to capture transferable features across heterogeneous domains. To address these challenges, we propose a neuromodulation-based discriminative multi-spectral AM for scalable MRI reconstruction that can (i) propagate context-aware high-frequency details for high-quality reconstruction, and (ii) capture features reusable across deviated unseen domains in multimodal MRI. The proposed network consists of a spectral filtering CNN to capture mode-specific transferable features and a dynamic high-pass kernel generation transformer focusing on high-frequency details. We evaluate our model on comparative studies in supervised and self-supervised learning, diffusion model-based training, closed-set and open-set generalization under heterogeneous MRI data, and interpretation-based analysis. Our method offers scalable, high-quality reconstruction with best improvement margins of ~1 dB in PSNR and ~0.01 in SSIM under unseen scenarios. Code: https://github.com/sriprabhar/SHFormer

Active sampling for accelerated MRI must distribute a tight sampling budget across spatial frequencies that carry very different kinds of information. Low frequencies hold most of the anatomical context; high frequencies carry the fine details that drive pathology assessment. Existing active samplers either treat both regions identically or restrict the action space to entire Cartesian rows, which forces a poor compromise at high acceleration. We propose HieraSample, a task-driven framework built around this hierarchy. A cosine-annealed curriculum lowers the acceleration factor from 20x to 4x across 80 acquisition steps while keeping a fully-sampled low-frequency disk at every step; a Mamba-based policy then picks individual high-frequency coordinates from features extracted by dual disease and severity classifiers. The reward is the per-sample reduction in class-weighted cross-entropy after each action, so a positive reward corresponds directly to a more confident correct prediction. On the fastMRI+ knee benchmark, HieraSample matches the fully-sampled oracle on ACL diagnosis from 4x to 10x acceleration, and improves on a recent Cartesian baseline by as much as 20.4 AUC points on ACL severity.

The accurate diagnosis of spinal pathologies depends heavily on radiological interpretation, yet automated systems are hindered by the lack of diverse, high-quality benchmarks. In this study, we present PhenSPINE, a Magnetic Resonance Imaging dataset comprising 16,813 images from 250 patients, curated to facilitate advanced deep learning research. We propose a robust diagnostic benchmark that integrates state-of-theart convolutional backbones with a Positional Encoding mechanism to explicitly model the anatomical context of intervertebral discs. Evaluating across four standard MRI sequences, our experiments demonstrate that the Sagittal T2-weighted sequence offers the most robust diagnostic value, achieving a superior Macro F1-score of 50.31%. We find that multisequence fusion strategies yield inferior performance compared to this single-sequence baseline, as the images across sequences in our dataset are significantly compromised by noise interference from surrounding anatomical regions. This work establishes a robust baseline and offers critical insights into sequence selection for spine analysis.

Inferring contrast enhancement from one pre-contrast breast MRI slice is underdetermined: post-contrast appearance contains physiological information that is not uniquely encoded in baseline anatomy. Optimizing only paired pixel fidelity can suppress uncertain lesion enhancement, whereas adversarial or stochastic generative objectives can favor realistic post-contrast appearance without guaranteeing patient-specific lesion fidelity. We introduce MIRAGE, a residual 2D U-Net that combines global reconstruction and perceptual losses with three forms of lesion-aware supervision available only during training: an asymmetric penalty for missed tumor enhancement, multi-scale auxiliary tumor segmentation, and guidance through a frozen post-contrast tumor segmentation nnU-Net. We evaluate the method on 301 cases from the multi-centre MAMA-SYNTH data using eight complementary image-, region-, radiomics-, and segmentation-based metrics. MIRAGE ranks first on six metrics and markedly improves downstream lesion localization over tuned pix2pix, conditional diffusion, and latent bridge-matching baselines. The generative alternatives retain advantages in LPIPS or contrast classification, revealing a clear fidelity-utility trade-off. Leave-one-in and leave-one-out ablations show that the losses are partly redundant for lesion localization but exert distinct effects on appearance, radiomics, and boundary accuracy. These results support task-aware synthesis while also showing that its apparent optimality is conditional on the downstream models and metrics used to define utility.

Magnetic resonance imaging comes in various modality contrasts that provide complementary anatomical and pathological information. Complete multimodal acquisitions are often unavailable due to time and protocol constraints. This leads to real-world datasets with missing modalities, where conventional medical image translation methods are typically limited to fixed source-target settings or require retraining for each observed source-target pair. We propose a unified framework that formulates missing-modality generation as a linear inverse problem under a joint distribution and solves it via posterior sampling with a flow matching model. By learning a joint prior over the complete modality set, our method can reconstruct arbitrary missing modalities at inference time by guiding the sampling trajectory to enforce measurement consistency with observed modalities. We further mitigate inter-modality error propagation in multi-target generation by adopting a many-to-one sampling strategy. Experiments on BraTS and IXI datasets show that our method achieves the best performance over baselines across most missing-modality scenarios. In downstream tumor segmentation, synthesized images from our method result in higher segmentation performance, indicating better preservation of clinically relevant structures.

Foundation models such as Segment Anything Model 2 (SAM2) have transformed natural-image and video segmentation, and recent work has begun adapting them to medical imaging. These adaptations, however, are largely general-purpose models that treat MRI as one modality among many; large-scale, MRI-specific modelling and benchmarking remain limited, even though MRI's low soft-tissue contrast leaves many boundaries effectively invisible on individual slices. We present SAMRI-3D, a benchmark and method for 3D MRI segmentation with SAM2. The SAMRI-3D benchmark is the largest MRI-only evaluation to date - 10,392 volumes from 34 datasets (27 public, 7 in-house) spanning 12 anatomical domains and 10+ sequences, with explicit seen/unseen splits. Freezing the image encoder and fine-tuning only the lightweight decoder and memory modules raises mean Dice from 0.58 (zero-shot SAM2) to 0.76, surpassing recent SAM-based medical models (SAMed-2 0.69, Medical-SAM2 0.49, SAM-Med3D 0.37) with strong statistical significance. To target invisible boundaries, we introduce Global Volume Tokens (GVT): persistent memory tokens trained with a Truncated Signed Distance Field (TSDF) reconstruction objective that is discarded at inference (zero added cost). This full model, SAMRI-3D, attains the best accuracy (0.78) and lowest variance across all 34 datasets and, uniquely, shows no drop on 8 held-out datasets (0.79 unseen vs. 0.78 seen); per-sequence analysis confirms the TSDF objective helps most where per-slice contrast is weakest. We will release the benchmark, code, and models in this paper.

Magnetic Resonance Imaging (MRI) is often acquired with anisotropic resolution to reduce scan time, producing stair-step artifacts along the through-plane direction. In through-plane MRI super-resolution, an efficiency-fidelity trade-off arises: feed-forward regressors are fast but oversmooth at large slice-thicknesses, while sampling-based methods improve fidelity at high inference cost. We propose DRIFT, a two-stage thickness-conditioned rectified flow framework for through-plane MRI super-resolution with continuous input slice-thickness. Stage 1 employs an Anatomical Projection Network (APN) to map low-resolution patches to a coarse high-resolution manifold, providing a deterministic anatomical initialization that shortens the residual transport of Stage 2 and stabilizes slice-wise refinement. Stage 2 refines details via rectified flow and introduces a Physics-Aware Difficulty (PAD) metric derived from slice-thickness induced through-plane bandwidth deficit to guide an Adaptive Integration Scheduler (AIS), allocating ODE steps by thickness. A Consistent Endpoint Trajectory Alignment (CETA) loss enforces thickness-consistent reconstructions. Experiments show that DRIFT outperforms super-resolution baselines while reducing inference cost. Code, models, and interactive demos are available at https://yoonseokchoi-ai.github.io/drift-eccv2026/.

Focal cortical dysplasia (FCD) is one of the leading structural causes of drug-resistant focal epilepsy, yet its subtle and heterogeneous imaging characteristics make accurate identification and delineation challenging on conventional magnetic resonance imaging (MRI). Although T1-weighted (T1w) and fluid-attenuated inversion recovery (FLAIR) images are routinely acquired for presurgical evaluation, the contribution of different MRI representations to deep learning-based FCD segmentation remains poorly understood. In this study, we present a systematic benchmark of MRI representations for automated FCD segmentation using the nnU-Net framework. A publicly available presurgical MRI dataset comprising 85 FCD subjects and 25 healthy controls was used to evaluate eight input configurations, including conventional MRI contrasts (T1w and FLAIR), ratio-derived representations, and their multimodal combinations. To isolate the effect of MRI representation, all experiments employed identical preprocessing, network architecture, optimization strategy, and five-fold cross-validation. Among the evaluated single-modality representations, FLAIR achieved the strongest overall performance, whereas ratio-derived representations alone were insufficient for reliable identification of subtle FCD. Incorporating ratio-derived representations with conventional T1w and FLAIR images consistently improved lesion delineation, with the four-channel multimodal configuration achieving the highest overall Dice score (0.376), representing a 5.0% relative improvement over the conventional T1w+FLAIR representation. These findings demonstrate that MRI representation design is an important yet underexplored component of deep learning-based FCD segmentation and should be optimized alongside network architecture.

Light-field disparity estimation requires global consistency in smooth or textureless regions and local precision near occlusion boundaries, thin structures, and abrupt depth transitions. Existing methods address these requirements through EPI matching, cost-volume or focal-stack construction, view aggregation, or direct convolutional regression, often relying on local windows, discrete disparity hypotheses, memory-intensive volumes, or attention-based aggregation. We instead formulate disparity estimation at the field level, predicting disparity from globally and locally updated EPI-derived latent features without explicitly constructing a disparity volume. We introduce FreqLF, an EPI-guided Fourier-local framework that encodes angular parallax cues from horizontal and vertical EPI stacks together with central-view appearance features. These cues are projected into a latent field and updated through stacked hybrid Fourier-local layers. Fourier low-mode updates enable global feature interaction, while local convolutions preserve spatial variations needed for fine disparity detail. A coordinate-conditioned Gaussian-mixture decoder then predicts disparity, using the mixture mean as the final estimate. Experiments on the HCI 4D Light Field Benchmark show that FreqLF approaches the accuracy of strong supervised baselines while avoiding explicit cost-volume construction in the base model. Ablations confirm the complementary roles of the Fourier and local branches, and scaling experiments demonstrate practical behavior across spatial resolutions. These results suggest that Fourier-local latent field learning is a competitive alternative for light-field disparity estimation. The code will be published soon.

Recent advances in large language models (LLMs) and their extension to vision-language models (VLMs) have made it easier to combine text and images for tasks such as report generation. Existing VLMs in medicine typically focus on 2D images (chest X-rays), and their extension to 3D imaging has been difficult because of the lack of paired 3D imaging-text data. Thus, we introduce a new method for creating a 3D image-text dataset for brain oncology using 3D MRI scans of glioma and meningioma cases. We use a cooperative system in which several LLMs work together to generate and check reports, ensuring that they are accurate and clear. By leveraging the new 3D MRI-text dataset, we further build a VLM that converts MRI scans into tokens and aligns them with text instructions. Our VLM performed better in report generation and visual question answering tasks than other 2D and 3D methods. Our method not only improves the quality of reports but also helps with better diagnosis and treatment in brain oncology.

Active surveillance (AS) is the preferred strategy for favorable-risk prostate cancer, yet current protocols rely on scheduled repeat biopsies, most of which reveal no progression and are unnecessary. Existing risk-stratification tools operate on single time-point imaging or depend on explicit lesion segmentation, limiting their ability to capture longitudinal change and excluding patients without an MRI-visible lesion. In this study, we propose an end-to-end temporal and multimodal model for predicting pathological progression during AS without lesion segmentation. We encode each serial scan with a pretrained 3D MRI foundation model and introduce a temporal attention gate that recalibrates the multi-visit features to amplify focal imaging changes associated with progression. The gated imaging representation is then fused with clinical variables in a multimodal framework to estimate the probability of progression. Validated on a longitudinal AS cohort, our approach consistently outperforms competing baselines and performs comparably to the radiologist assessment representing current clinical practice. It maintains high negative predictive value while achieving higher positive predictive value, demonstrating its potential to safely reduce unnecessary biopsies during surveillance.

Objective: Radiomic texture features are usually computed in voxel-index neighborhoods, implicitly assuming isotropic spatial relationships. In anisotropic images, this can confound voxel geometry with interpolation-induced signal changes. We developed a voxel-spacing-aware radiomic framework that incorporates physical geometry into texture computation without resampling. Approach: We modified PyRadiomics to account for voxel spacing while preserving the native image signal. Four configurations were compared: native non-resampled extraction (NR), isotropic resampling (RS), voxel-spacing-aware extraction (VS), and fake-isotropic preprocessing (FK), in which spacing metadata were overwritten without altering the image array. Experiments included 685 LIDC-IDRI pulmonary nodules and 209 I-SPY2 breast MRI cases, with 196 radiomic descriptors. Robustness was assessed using ICC, within-subject variability, Friedman testing, feature selection, machine learning, a multilayer perceptron, and external validation. Main results: VS showed near-native agreement with NR: median ICC(A,1) was 0.9976 in CT and 0.9984 in MRI. RS produced lower agreement and larger deviations, while FK showed intermediate behavior, confirming that spacing metadata alone can affect radiomic features. Gradient-derived and neighborhood-sensitive descriptors were most affected by preprocessing. VS preserved predictive performance comparable to NR in external CT validation, whereas MRI showed greater variability across preprocessing strategies and classifiers. Significance: Voxel-spacing-aware extraction separates geometric modeling from interpolation-induced signal modification while preserving the native image signal, offering a coherent alternative to isotropic resampling for radiomic analysis of anisotropic CT and MRI.