Daily Papers

The growing availability of longitudinal Magnetic Resonance Imaging (MRI) datasets has facilitated Artificial Intelligence (AI)-driven modeling of disease progression, making it possible to predict future medical scans for individual patients. However, despite significant advancements in AI, current methods continue to face challenges including achieving patient-specific individualization, ensuring spatiotemporal consistency, efficiently utilizing longitudinal data, and managing the substantial memory demands of 3D scans. To address these challenges, we propose Brain Latent Progression (BrLP), a novel spatiotemporal model designed to predict individual-level disease progression in 3D brain MRIs. The key contributions in BrLP are fourfold: (i) it operates in a small latent space, mitigating the computational challenges posed by high-dimensional imaging data; (ii) it explicitly integrates subject metadata to enhance the individualization of predictions; (iii) it incorporates prior knowledge of disease dynamics through an auxiliary model, facilitating the integration of longitudinal data; and (iv) it introduces the Latent Average Stabilization (LAS) algorithm, which (a) enforces spatiotemporal consistency in the predicted progression at inference time and (b) allows us to derive a measure of the uncertainty for the prediction at the global and voxel level. We train and evaluate BrLP on 11,730 T1-weighted (T1w) brain MRIs from 2,805 subjects and validate its generalizability on an external test set comprising 2,257 MRIs from 962 subjects. Our experiments compare BrLP-generated MRI scans with real follow-up MRIs, demonstrating state-of-the-art accuracy compared to existing methods. The code is publicly available at: https://github.com/LemuelPuglisi/BrLP.

In this work, we introduce Brain Latent Progression (BrLP), a novel spatiotemporal disease progression model based on latent diffusion. BrLP is designed to predict the evolution of diseases at the individual level on 3D brain MRIs. Existing deep generative models developed for this task are primarily data-driven and face challenges in learning disease progressions. BrLP addresses these challenges by incorporating prior knowledge from disease models to enhance the accuracy of predictions. To implement this, we propose to integrate an auxiliary model that infers volumetric changes in various brain regions. Additionally, we introduce Latent Average Stabilization (LAS), a novel technique to improve spatiotemporal consistency of the predicted progression. BrLP is trained and evaluated on a large dataset comprising 11,730 T1-weighted brain MRIs from 2,805 subjects, collected from three publicly available, longitudinal Alzheimer's Disease (AD) studies. In our experiments, we compare the MRI scans generated by BrLP with the actual follow-up MRIs available from the subjects, in both cross-sectional and longitudinal settings. BrLP demonstrates significant improvements over existing methods, with an increase of 22% in volumetric accuracy across AD-related brain regions and 43% in image similarity to the ground-truth scans. The ability of BrLP to generate conditioned 3D scans at the subject level, along with the novelty of integrating prior knowledge to enhance accuracy, represents a significant advancement in disease progression modeling, opening new avenues for precision medicine. The code of BrLP is available at the following link: https://github.com/LemuelPuglisi/BrLP.

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

Accurate estimation of brain infarction (i.e., irreversibly damaged tissue) is critical for guiding treatment decisions in acute ischemic stroke. Reliable infarct prediction informs key clinical interventions, including the need for patient transfer to comprehensive stroke centers, the potential benefit of additional reperfusion attempts during mechanical thrombectomy, decisions regarding secondary neuroprotective treatments, and ultimately, prognosis of clinical outcomes. This work introduces the Ischemic Stroke Lesion Segmentation (ISLES) 2024 challenge, which focuses on the prediction of final infarct volumes from pre-interventional acute stroke imaging and clinical data. ISLES24 provides a comprehensive, multimodal setting where participants can leverage all clinically and practically available data, including full acute CT imaging, sub-acute follow-up MRI, and structured clinical information, across a train set of 150 cases. On the hidden test set of 98 cases, the top-performing model, a multimodal nnU-Net-based architecture, achieved a Dice score of 0.285 (+/- 0.213) and an absolute volume difference of 21.2 (+/- 37.2) mL, underlining the significant challenges posed by this task and the need for further advances in multimodal learning. This work makes two primary contributions: first, we establish a standardized, clinically realistic benchmark for post-treatment infarct prediction, enabling systematic evaluation of multimodal algorithmic strategies on a longitudinal stroke dataset; second, we analyze current methodological limitations and outline key research directions to guide the development of next-generation infarct prediction models.

Computed tomography perfusion (CTP) at admission is routinely used to estimate the ischemic core and penumbra, while follow-up diffusion-weighted MRI (DWI) provides the definitive infarct outcome. However, single time-point segmentations fail to capture the biological heterogeneity and temporal evolution of stroke. We propose a bi-temporal analysis framework that characterizes ischemic tissue using statistical descriptors, radiomic texture features, and deep feature embeddings from two architectures (mJ-Net and nnU-Net). Bi-temporal refers to admission (T1) and post-treatment follow-up (T2). All features are extracted at T1 from CTP, with follow-up DWI aligned to ensure spatial correspondence. Manually delineated masks at T1 and T2 are intersected to construct six regions of interest (ROIs) encoding both initial tissue state and final outcome. Features were aggregated per region and analyzed in feature space. Evaluation on 18 patients with successful reperfusion demonstrated meaningful clustering of region-level representations. Regions classified as penumbra or healthy at T1 that ultimately recovered exhibited feature similarity to preserved brain tissue, whereas infarct-bound regions formed distinct groupings. Both baseline GLCM and deep embeddings showed a similar trend: penumbra regions exhibit features that are significantly different depending on final state, whereas this difference is not significant for core regions. Deep feature spaces, particularly mJ-Net, showed strong separation between salvageable and non-salvageable tissue, with a penumbra separation index that differed significantly from zero (Wilcoxon signed-rank test). These findings suggest that encoder-derived feature manifolds reflect underlying tissue phenotypes and state transitions, providing insight into imaging-based quantification of stroke evolution.

Citation count of a paper is a commonly used proxy for evaluating the significance of a paper in the scientific community. Yet citation measures are widely criticized for failing to accurately reflect the true impact of a paper. Thus, we propose CausalCite, a new way to measure the significance of a paper by assessing the causal impact of the paper on its follow-up papers. CausalCite is based on a novel causal inference method, TextMatch, which adapts the traditional matching framework to high-dimensional text embeddings. TextMatch encodes each paper using text embeddings from large language models (LLMs), extracts similar samples by cosine similarity, and synthesizes a counterfactual sample as the weighted average of similar papers according to their similarity values. We demonstrate the effectiveness of CausalCite on various criteria, such as high correlation with paper impact as reported by scientific experts on a previous dataset of 1K papers, (test-of-time) awards for past papers, and its stability across various subfields of AI. We also provide a set of findings that can serve as suggested ways for future researchers to use our metric for a better understanding of the quality of a paper. Our code is available at https://github.com/causalNLP/causal-cite.

Accurate segmentation of Multiple Sclerosis (MS) lesions in longitudinal MRI scans is crucial for monitoring disease progression and treatment efficacy. Although changes across time are taken into account when assessing images in clinical practice, most existing deep learning methods treat scans from different timepoints separately. Among studies utilizing longitudinal images, a simple channel-wise concatenation is the primary albeit suboptimal method employed to integrate timepoints. We introduce a novel approach that explicitly incorporates temporal differences between baseline and follow-up scans through a unique architectural inductive bias called Difference Weighting Block. It merges features from two timepoints, emphasizing changes between scans. We achieve superior scores in lesion segmentation (Dice Score, Hausdorff distance) as well as lesion detection (lesion-level F_1 score) as compared to state-of-the-art longitudinal and single timepoint models across two datasets. Our code is made publicly available at www.github.com/MIC-DKFZ/Longitudinal-Difference-Weighting.

MRI is an indispensable clinical tool, offering a rich variety of tissue contrasts to support broad diagnostic and research applications. Clinical exams routinely acquire multiple structural sequences that provide complementary information for differential diagnosis, while research protocols often incorporate advanced functional, diffusion, spectroscopic, and relaxometry sequences to capture multidimensional insights into tissue structure and composition. However, these capabilities come at the cost of prolonged scan times, which reduce patient throughput, increase susceptibility to motion artifacts, and may require trade-offs in image quality or diagnostic scope. Over the last two decades, advances in image reconstruction algorithms--alongside improvements in hardware and pulse sequence design--have made it possible to accelerate acquisitions while preserving diagnostic quality. Central to this progress is the ability to incorporate prior information to regularize the solutions to the reconstruction problem. In this tutorial, we overview the basics of MRI reconstruction and highlight state-of-the-art approaches, beginning with classical methods that rely on explicit hand-crafted priors, and then turning to deep learning methods that leverage a combination of learned and crafted priors to further push the performance envelope. We also explore the translational aspects and eventual clinical implications of these methods. We conclude by discussing future directions to address remaining challenges in MRI reconstruction. The tutorial is accompanied by a Python toolbox (https://github.com/tutorial-MRI-recon/tutorial) to demonstrate select methods discussed in the article.

Clinical MRI encompasses diverse imaging protocols--spanning anatomical targets (cardiac, brain, knee), contrasts (T1, T2, mapping), sampling patterns (Cartesian, radial, spiral, kt-space), and acceleration factors--yet current deep learning reconstructions are typically protocol-specific, hindering generalization and deployment. We introduce Scalable Deep Unrolled Model (SDUM), a universal framework combining a Restormer-based reconstructor, a learned coil sensitivity map estimator (CSME), sampling-aware weighted data consistency (SWDC), universal conditioning (UC) on cascade index and protocol metadata, and progressive cascade expansion training. SDUM exhibits foundation-model-like scaling behavior: reconstruction quality follows PSNR {sim} log(parameters) with correlation r{=}0.986 (R^2{=}0.973) up to 18 cascades, demonstrating predictable performance gains with model depth. A single SDUM trained on heterogeneous data achieves state-of-the-art results across all four CMRxRecon2025 challenge tracks--multi-center, multi-disease, 5T, and pediatric--without task-specific fine-tuning, surpassing specialized baselines by up to {+}1.0~dB. On CMRxRecon2024, SDUM outperforms the winning method PromptMR+ by {+}0.55~dB; on fastMRI brain, it exceeds PC-RNN by {+}1.8~dB. Ablations validate each component: SWDC {+}0.43~dB over standard DC, per-cascade CSME {+}0.51~dB, UC {+}0.38~dB. These results establish SDUM as a practical path toward universal, scalable MRI reconstruction.

Accelerating MRI scans is one of the principal outstanding problems in the MRI research community. Towards this goal, we hosted the second fastMRI competition targeted towards reconstructing MR images with subsampled k-space data. We provided participants with data from 7,299 clinical brain scans (de-identified via a HIPAA-compliant procedure by NYU Langone Health), holding back the fully-sampled data from 894 of these scans for challenge evaluation purposes. In contrast to the 2019 challenge, we focused our radiologist evaluations on pathological assessment in brain images. We also debuted a new Transfer track that required participants to submit models evaluated on MRI scanners from outside the training set. We received 19 submissions from eight different groups. Results showed one team scoring best in both SSIM scores and qualitative radiologist evaluations. We also performed analysis on alternative metrics to mitigate the effects of background noise and collected feedback from the participants to inform future challenges. Lastly, we identify common failure modes across the submissions, highlighting areas of need for future research in the MRI reconstruction community.

Automated radiology report generation offers an effective solution to alleviate radiologists' workload. However, most existing methods focus primarily on single or fixed-view images to model current disease conditions, which limits diagnostic accuracy and overlooks disease progression. Although some approaches utilize longitudinal data to track disease progression, they still rely on single images to analyze current visits. To address these issues, we propose enhanced contrastive learning with Multi-view Longitudinal data to facilitate chest X-ray Report Generation, named MLRG. Specifically, we introduce a multi-view longitudinal contrastive learning method that integrates spatial information from current multi-view images and temporal information from longitudinal data. This method also utilizes the inherent spatiotemporal information of radiology reports to supervise the pre-training of visual and textual representations. Subsequently, we present a tokenized absence encoding technique to flexibly handle missing patient-specific prior knowledge, allowing the model to produce more accurate radiology reports based on available prior knowledge. Extensive experiments on MIMIC-CXR, MIMIC-ABN, and Two-view CXR datasets demonstrate that our MLRG outperforms recent state-of-the-art methods, achieving a 2.3% BLEU-4 improvement on MIMIC-CXR, a 5.5% F1 score improvement on MIMIC-ABN, and a 2.7% F1 RadGraph improvement on Two-view CXR.

Machine Learning methods can learn how to reconstruct Magnetic Resonance Images and thereby accelerate acquisition, which is of paramount importance to the clinical workflow. Physics-informed networks incorporate the forward model of accelerated MRI reconstruction in the learning process. With increasing network complexity, robustness is not ensured when reconstructing data unseen during training. We aim to embed data consistency (DC) in deep networks while balancing the degree of network complexity. While doing so, we will assess whether either explicit or implicit enforcement of DC in varying network architectures is preferred to optimize performance. We propose a scheme called Cascades of Independently Recurrent Inference Machines (CIRIM) to assess DC through unrolled optimization. Herein we assess DC both implicitly by gradient descent and explicitly by a designed term. Extensive comparison of the CIRIM to CS as well as to other methods is performed: the E2EVN, CascadeNet, KIKINet, LPDNet, RIM, IRIM, and UNet. Models were trained and evaluated on T1-weighted and FLAIR contrast brain data, and T2-weighted knee data. Both 1D and 2D undersampling patterns were evaluated. Robustness was tested by reconstructing 7.5x prospectively undersampled 3D FLAIR MRI data of Multiple Sclerosis (MS) patients with white matter lesions. The CIRIM performed best when implicitly enforcing DC, while the E2EVN required an explicit DC formulation. In reconstructing MS patient data, prospectively acquired with a sampling pattern unseen during model training, the CIRIM maintained lesion contrast while efficiently denoising the images. The CIRIM showed highly promising generalization capabilities maintaining a very fair trade-off between reconstructed image quality and fast reconstruction times, which is crucial in the clinical workflow.

Magnetic resonance imaging (MRI) provides high spatial resolution and excellent soft-tissue contrast without using harmful ionising radiation. Dynamic MRI is an essential tool for interventions to visualise movements or changes of the target organ. However, such MRI acquisition with high temporal resolution suffers from limited spatial resolution - also known as the spatio-temporal trade-off of dynamic MRI. Several approaches, including deep learning based super-resolution approaches, have been proposed to mitigate this trade-off. Nevertheless, such an approach typically aims to super-resolve each time-point separately, treating them as individual volumes. This research addresses the problem by creating a deep learning model which attempts to learn both spatial and temporal relationships. A modified 3D UNet model, DDoS-UNet, is proposed - which takes the low-resolution volume of the current time-point along with a prior image volume. Initially, the network is supplied with a static high-resolution planning scan as the prior image along with the low-resolution input to super-resolve the first time-point. Then it continues step-wise by using the super-resolved time-points as the prior image while super-resolving the subsequent time-points. The model performance was tested with 3D dynamic data that was undersampled to different in-plane levels. The proposed network achieved an average SSIM value of 0.951pm0.017 while reconstructing the lowest resolution data (i.e. only 4\% of the k-space acquired) - which could result in a theoretical acceleration factor of 25. The proposed approach can be used to reduce the required scan-time while achieving high spatial resolution.

Magnetic Resonance Imaging can produce detailed images of the anatomy and physiology of the human body that can assist doctors in diagnosing and treating pathologies such as tumours. However, MRI suffers from very long acquisition times that make it susceptible to patient motion artifacts and limit its potential to deliver dynamic treatments. Conventional approaches such as Parallel Imaging and Compressed Sensing allow for an increase in MRI acquisition speed by reconstructing MR images from sub-sampled MRI data acquired using multiple receiver coils. Recent advancements in Deep Learning combined with Parallel Imaging and Compressed Sensing techniques have the potential to produce high-fidelity reconstructions from highly accelerated MRI data. In this work we present a novel Deep Learning-based Inverse Problem solver applied to the task of Accelerated MRI Reconstruction, called the Recurrent Variational Network (RecurrentVarNet), by exploiting the properties of Convolutional Recurrent Neural Networks and unrolled algorithms for solving Inverse Problems. The RecurrentVarNet consists of multiple recurrent blocks, each responsible for one iteration of the unrolled variational optimization scheme for solving the inverse problem of multi-coil Accelerated MRI Reconstruction. Contrary to traditional approaches, the optimization steps are performed in the observation domain (k-space) instead of the image domain. Each block of the RecurrentVarNet refines the observed k-space and comprises a data consistency term and a recurrent unit which takes as input a learned hidden state and the prediction of the previous block. Our proposed method achieves new state of the art qualitative and quantitative reconstruction results on 5-fold and 10-fold accelerated data from a public multi-coil brain dataset, outperforming previous conventional and deep learning-based approaches.

Deep-learning-based brain magnetic resonance imaging (MRI) reconstruction methods have the potential to accelerate the MRI acquisition process. Nevertheless, the scientific community lacks appropriate benchmarks to assess MRI reconstruction quality of high-resolution brain images, and evaluate how these proposed algorithms will behave in the presence of small, but expected data distribution shifts. The Multi-Coil Magnetic Resonance Image (MC-MRI) Reconstruction Challenge provides a benchmark that aims at addressing these issues, using a large dataset of high-resolution, three-dimensional, T1-weighted MRI scans. The challenge has two primary goals: 1) to compare different MRI reconstruction models on this dataset and 2) to assess the generalizability of these models to data acquired with a different number of receiver coils. In this paper, we describe the challenge experimental design, and summarize the results of a set of baseline and state of the art brain MRI reconstruction models. We provide relevant comparative information on the current MRI reconstruction state-of-the-art and highlight the challenges of obtaining generalizable models that are required prior to broader clinical adoption. The MC-MRI benchmark data, evaluation code and current challenge leaderboard are publicly available. They provide an objective performance assessment for future developments in the field of brain MRI reconstruction.

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework. This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr/

Magnetic resonance imaging (MRI) is a crucial tool to identify brain abnormalities in a wide range of neurological disorders. In focal epilepsy MRI is used to identify structural cerebral abnormalities. For covert lesions, machine learning and artificial intelligence algorithms may improve lesion detection if abnormalities are not evident on visual inspection. The success of this approach depends on the volume and quality of training data. Herein, we release an open-source dataset of preprocessed MRI scans from 442 individuals with drug-refractory focal epilepsy who had neurosurgical resections, and detailed demographic information. The MRI scan data includes the preoperative 3D T1 and where available 3D FLAIR, as well as a manually inspected complete surface reconstruction and volumetric parcellations. Demographic information includes age, sex, age of onset of epilepsy, location of surgery, histopathology of resected specimen, occurrence and frequency of focal seizures with and without impairment of awareness, focal to bilateral tonic-clonic seizures, number of anti-seizure medications (ASMs) at time of surgery, and a total of 1764 patient years of post-surgical follow up. Crucially, we also include resection masks delineated from post-surgical imaging. To demonstrate the veracity of our data, we successfully replicated previous studies showing long-term outcomes of seizure freedom in the range of around 50%. Our imaging data replicates findings of group level atrophy in patients compared to controls. Resection locations in the cohort were predominantly in the temporal and frontal lobes. We envisage our dataset, shared openly with the community, will catalyse the development and application of computational methods in clinical neurology.

Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clinical deployment and clinician trust. To mitigate this challenge, we present the Stanford Knee MRI with Multi-Task Evaluation (SKM-TEA) dataset, a collection of quantitative knee MRI (qMRI) scans that enables end-to-end, clinically-relevant evaluation of MRI reconstruction and analysis tools. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies. We provide a framework for using qMRI parameter maps, along with image reconstructions and dense image labels, for measuring the quality of qMRI biomarker estimates extracted from MRI reconstruction, segmentation, and detection techniques. Finally, we use this framework to benchmark state-of-the-art baselines on this dataset. We hope our SKM-TEA dataset and code can enable a broad spectrum of research for modular image reconstruction and image analysis in a clinically informed manner. Dataset access, code, and benchmarks are available at https://github.com/StanfordMIMI/skm-tea.

In this work, we address the TrackRAD2025 challenge of real-time tumor tracking in cine-MRI sequences of the thoracic and abdominal regions under strong data scarcity constraints. Two complementary strategies were explored: (i) unsupervised registration with the IMPACT similarity metric and (ii) foundation model-based segmentation leveraging SAM 2.1 and its recent variants through prompt-based interaction. Due to the one-second runtime constraint, the SAM-based method was ultimately selected. The final configuration used SAM2.1 b+ with mask-based prompts from the first annotated slice, fine-tuned solely on the small labeled subset from TrackRAD2025. Training was configured to minimize overfitting, using 1024x1024 patches (batch size 1), standard augmentations, and a balanced Dice + IoU loss. A low uniform learning rate (0.0001) was applied to all modules (prompt encoder, decoder, Hiera backbone) to preserve generalization while adapting to annotator-specific styles. Training lasted 300 epochs (~12h on RTX A6000, 48GB). The same inference strategy was consistently applied across all anatomical sites and MRI field strengths. Test-time augmentation was considered but ultimately discarded due to negligible performance gains. The final model was selected based on the highest Dice Similarity Coefficient achieved on the validation set after fine-tuning. On the hidden test set, the model reached a Dice score of 0.8794, ranking 6th overall in the TrackRAD2025 challenge. These results highlight the strong potential of foundation models for accurate and real-time tumor tracking in MRI-guided radiotherapy.

Knee Osteoarthritis (KOA) is a highly prevalent chronic musculoskeletal condition with no currently available treatment. The manifestation of KOA is heterogeneous and prediction of its progression is challenging. Current literature suggests that the use of multi-modal data and advanced modeling methods, such as the ones based on Deep Learning, has promise in tackling this challenge. To date, however, the evidence on the efficacy of this approach is limited. In this study, we leveraged recent advances in Deep Learning and, using a Transformer approach, developed a unified framework for the multi-modal fusion of knee imaging data. Subsequently, we analyzed its performance across a range of scenarios by investigating multiple progression horizons -- from short-term to long-term. We report our findings using a large cohort (n=2421-3967) derived from the Osteoarthritis Initiative dataset. We show that structural knee MRI allows identifying radiographic KOA progressors on par with multi-modal fusion approaches, achieving an area under the ROC curve (ROC AUC) of 0.70-0.76 and Average Precision (AP) of 0.15-0.54 in 2-8 year horizons. Progression within 1 year was better predicted with a multi-modal method using X-ray, structural, and compositional MR images -- ROC AUC of 0.76(0.04), AP of 0.13(0.04) -- or via clinical data. Our follow-up analysis generally shows that prediction from the imaging data is more accurate for post-traumatic subjects, and we further investigate which subject subgroups may benefit the most. The present study provides novel insights into multi-modal imaging of KOA and brings a unified data-driven framework for studying its progression in an end-to-end manner, providing new tools for the design of more efficient clinical trials. The source code of our framework and the pre-trained models are made publicly available.

Automating radiology report generation can significantly alleviate radiologists' workloads. Previous research has primarily focused on realizing highly concise observations while neglecting the precise attributes that determine the severity of diseases (e.g., small pleural effusion). Since incorrect attributes will lead to imprecise radiology reports, strengthening the generation process with precise attribute modeling becomes necessary. Additionally, the temporal information contained in the historical records, which is crucial in evaluating a patient's current condition (e.g., heart size is unchanged), has also been largely disregarded. To address these issues, we propose RECAP, which generates precise and accurate radiology reports via dynamic disease progression reasoning. Specifically, RECAP first predicts the observations and progressions (i.e., spatiotemporal information) given two consecutive radiographs. It then combines the historical records, spatiotemporal information, and radiographs for report generation, where a disease progression graph and dynamic progression reasoning mechanism are devised to accurately select the attributes of each observation and progression. Extensive experiments on two publicly available datasets demonstrate the effectiveness of our model.

Accurate prediction of knee osteoarthritis (KOA) progression from structural MRI has a potential to enhance disease understanding and support clinical trials. Prior art focused on manually designed imaging biomarkers, which may not fully exploit all disease-related information present in MRI scan. In contrast, our method learns relevant representations from raw data end-to-end using Deep Learning, and uses them for progression prediction. The method employs a 2D CNN to process the data slice-wise and aggregate the extracted features using a Transformer. Evaluated on a large cohort (n=4,866), the proposed method outperforms conventional 2D and 3D CNN-based models and achieves average precision of 0.58pm0.03 and ROC AUC of 0.78pm0.01. This paper sets a baseline on end-to-end KOA progression prediction from structural MRI. Our code is publicly available at https://github.com/MIPT-Oulu/OAProgressionMR.

Purpose: Magnetic resonance imaging (MRI) to visualize anatomical motion is becoming increasingly important when treating cancer patients with radiotherapy. Hybrid MRI-linear accelerator (MRI-linac) systems allow real-time motion management during irradiation. This paper presents a multi-institutional real-time MRI time series dataset from different MRI-linac vendors. The dataset is designed to support developing and evaluating real-time tumor localization (tracking) algorithms for MRI-guided radiotherapy within the TrackRAD2025 challenge (https://trackrad2025.grand-challenge.org/). Acquisition and validation methods: The dataset consists of sagittal 2D cine MRIs in 585 patients from six centers (3 Dutch, 1 German, 1 Australian, and 1 Chinese). Tumors in the thorax, abdomen, and pelvis acquired on two commercially available MRI-linacs (0.35 T and 1.5 T) were included. For 108 cases, irradiation targets or tracking surrogates were manually segmented on each temporal frame. The dataset was randomly split into a public training set of 527 cases (477 unlabeled and 50 labeled) and a private testing set of 58 cases (all labeled). Data Format and Usage Notes: The data is publicly available under the TrackRAD2025 collection: https://doi.org/10.57967/hf/4539. Both the images and segmentations for each patient are available in metadata format. Potential Applications: This novel clinical dataset will enable the development and evaluation of real-time tumor localization algorithms for MRI-guided radiotherapy. By enabling more accurate motion management and adaptive treatment strategies, this dataset has the potential to advance the field of radiotherapy significantly.

Objective: To allow efficient learning using the Recurrent Inference Machine (RIM) for image reconstruction whereas not being strictly dependent on the training data distribution so that unseen modalities and pathologies are still accurately recovered. Methods: Theoretically, the RIM learns to solve the inverse problem of accelerated-MRI reconstruction whereas being robust to variable imaging conditions. The efficiency and generalization capabilities with different training datasets were studied, as well as recurrent network units with decreasing complexity: the Gated Recurrent Unit (GRU), the Minimal Gated Unit (MGU), and the Independently Recurrent Neural Network (IndRNN), to reduce inference times. Validation was performed against Compressed Sensing (CS) and further assessed based on data unseen during training. A pathology study was conducted by reconstructing simulated white matter lesions and prospectively undersampled data of a Multiple Sclerosis patient. Results: Training on a single modality of 3T T_1-weighted brain data appeared sufficient to also reconstruct 7T T_{2}^*-weighted brain and 3T T_2-weighted knee data. The IndRNN is an efficient recurrent unit, reducing inference time by 68\% compared to CS, whereas maintaining performance. The RIM was able to reconstruct lesions unseen during training more accurately than CS when trained on T_2-weighted knee data. Training on T_1-weighted brain data and on combined data slightly enhanced the signal compared to CS. Conclusion: The RIM is efficient when decreasing its complexity, which reduces the inference time, whereas still being able to reconstruct data and pathology that was unseen during training.

Deep learning has shown strong performance in musculoskeletal imaging, but prior work has largely targeted conditions where diagnosis is relatively straightforward. More challenging problems remain underexplored, such as detecting Bankart lesions (anterior-inferior glenoid labral tears) on standard MRIs. These lesions are difficult to diagnose due to subtle imaging features, often necessitating invasive MRI arthrograms (MRAs). We introduce ScopeMRI, the first publicly available, expert-annotated dataset for shoulder pathologies, and present a deep learning framework for Bankart lesion detection on both standard MRIs and MRAs. ScopeMRI contains shoulder MRIs from patients who underwent arthroscopy, providing ground-truth labels from intraoperative findings, the diagnostic gold standard. Separate models were trained for MRIs and MRAs using CNN- and transformer-based architectures, with predictions ensembled across multiple imaging planes. Our models achieved radiologist-level performance, with accuracy on standard MRIs surpassing radiologists interpreting MRAs. External validation on independent hospital data demonstrated initial generalizability across imaging protocols. By releasing ScopeMRI and a modular codebase for training and evaluation, we aim to accelerate research in musculoskeletal imaging and foster development of datasets and models that address clinically challenging diagnostic tasks.

Motion artefacts in magnetic resonance brain images can have a strong impact on diagnostic confidence. The assessment of MR image quality is fundamental before proceeding with the clinical diagnosis. Motion artefacts can alter the delineation of structures such as the brain, lesions or tumours and may require a repeat scan. Otherwise, an inaccurate (e.g. correct pathology but wrong severity) or incorrect diagnosis (e.g. wrong pathology) may occur. "Image quality assessment" as a fast, automated step right after scanning can assist in deciding if the acquired images are diagnostically sufficient. An automated image quality assessment based on the structural similarity index (SSIM) regression through a residual neural network is proposed in this work. Additionally, a classification into different groups - by subdividing with SSIM ranges - is evaluated. Importantly, this method predicts SSIM values of an input image in the absence of a reference ground truth image. The networks were able to detect motion artefacts, and the best performance for the regression and classification task has always been achieved with ResNet-18 with contrast augmentation. The mean and standard deviation of residuals' distribution were mu=-0.0009 and sigma=0.0139, respectively. Whilst for the classification task in 3, 5 and 10 classes, the best accuracies were 97, 95 and 89\%, respectively. The results show that the proposed method could be a tool for supporting neuro-radiologists and radiographers in evaluating image quality quickly.

Dynamic imaging is a beneficial tool for interventions to assess physiological changes. Nonetheless during dynamic MRI, while achieving a high temporal resolution, the spatial resolution is compromised. To overcome this spatio-temporal trade-off, this research presents a super-resolution (SR) MRI reconstruction with prior knowledge based fine-tuning to maximise spatial information while reducing the required scan-time for dynamic MRIs. An U-Net based network with perceptual loss is trained on a benchmark dataset and fine-tuned using one subject-specific static high resolution MRI as prior knowledge to obtain high resolution dynamic images during the inference stage. 3D dynamic data for three subjects were acquired with different parameters to test the generalisation capabilities of the network. The method was tested for different levels of in-plane undersampling for dynamic MRI. The reconstructed dynamic SR results after fine-tuning showed higher similarity with the high resolution ground-truth, while quantitatively achieving statistically significant improvement. The average SSIM of the lowest resolution experimented during this research (6.25~\% of the k-space) before and after fine-tuning were 0.939 pm 0.008 and 0.957 pm 0.006 respectively. This could theoretically result in an acceleration factor of 16, which can potentially be acquired in less than half a second. The proposed approach shows that the super-resolution MRI reconstruction with prior-information can alleviate the spatio-temporal trade-off in dynamic MRI, even for high acceleration factors.

Multimodal magnetic resonance imaging (MRI) constitutes the first line of investigation for clinicians in the care of brain tumors, providing crucial insights for surgery planning, treatment monitoring, and biomarker identification. Pre-training on large datasets have been shown to help models learn transferable representations and adapt with minimal labeled data. This behavior is especially valuable in medical imaging, where annotations are often scarce. However, applying this paradigm to multimodal medical data introduces a challenge: most existing approaches assume that all imaging modalities are available during both pre-training and fine-tuning. In practice, missing modalities often occur due to acquisition issues, specialist unavailability, or specific experimental designs on small in-house datasets. Consequently, a common approach involves training a separate model for each desired modality combination, making the process both resource-intensive and impractical for clinical use. Therefore, we introduce BM-MAE, a masked image modeling pre-training strategy tailored for multimodal MRI data. The same pre-trained model seamlessly adapts to any combination of available modalities, extracting rich representations that capture both intra- and inter-modal information. This allows fine-tuning on any subset of modalities without requiring architectural changes, while still benefiting from a model pre-trained on the full set of modalities. Extensive experiments show that the proposed pre-training strategy outperforms or remains competitive with baselines that require separate pre-training for each modality subset, while substantially surpassing training from scratch on several downstream tasks. Additionally, it can quickly and efficiently reconstruct missing modalities, highlighting its practical value. Code and trained models are available at: https://github.com/Lucas-rbnt/BM-MAE

Off-resonance artifacts in magnetic resonance imaging (MRI) are visual distortions that occur when the actual resonant frequencies of spins within the imaging volume differ from the expected frequencies used to encode spatial information. These discrepancies can be caused by a variety of factors, including magnetic field inhomogeneities, chemical shifts, or susceptibility differences within the tissues. Such artifacts can manifest as blurring, ghosting, or misregistration of the reconstructed image, and they often compromise its diagnostic quality. We propose to resolve these artifacts by lifting the 2D MRI reconstruction problem to 3D, introducing an additional "spectral" dimension to model this off-resonance. Our approach is inspired by recent progress in modeling radiance fields, and is capable of reconstructing both static and dynamic MR images as well as separating fat and water, which is of independent clinical interest. We demonstrate our approach in the context of PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) MRI acquisitions, which are popular for their robustness to motion artifacts. Our method operates in a few minutes on a single GPU, and to our knowledge is the first to correct for chemical shift in gradient echo PROPELLER MRI reconstruction without additional measurements or pretraining data.

Contrast agents in dynamic contrast enhanced magnetic resonance imaging allow to localize tumors and observe their contrast kinetics, which is essential for cancer characterization and respective treatment decision-making. However, contrast agent administration is not only associated with adverse health risks, but also restricted for patients during pregnancy, and for those with kidney malfunction, or other adverse reactions. With contrast uptake as key biomarker for lesion malignancy, cancer recurrence risk, and treatment response, it becomes pivotal to reduce the dependency on intravenous contrast agent administration. To this end, we propose a multi-conditional latent diffusion model capable of acquisition time-conditioned image synthesis of DCE-MRI temporal sequences. To evaluate medical image synthesis, we additionally propose and validate the Fréchet radiomics distance as an image quality measure based on biomarker variability between synthetic and real imaging data. Our results demonstrate our method's ability to generate realistic multi-sequence fat-saturated breast DCE-MRI and uncover the emerging potential of deep learning based contrast kinetics simulation. We publicly share our accessible codebase at https://github.com/RichardObi/ccnet and provide a user-friendly library for Fréchet radiomics distance calculation at https://pypi.org/project/frd-score.

MRI is an inherently slow process, which leads to long scan time for high-resolution imaging. The speed of acquisition can be increased by ignoring parts of the data (undersampling). Consequently, this leads to the degradation of image quality, such as loss of resolution or introduction of image artefacts. This work aims to reconstruct highly undersampled Cartesian or radial MR acquisitions, with better resolution and with less to no artefact compared to conventional techniques like compressed sensing. In recent times, deep learning has emerged as a very important area of research and has shown immense potential in solving inverse problems, e.g. MR image reconstruction. In this paper, a deep learning based MR image reconstruction framework is proposed, which includes a modified regularised version of ResNet as the network backbone to remove artefacts from the undersampled image, followed by data consistency steps that fusions the network output with the data already available from undersampled k-space in order to further improve reconstruction quality. The performance of this framework for various undersampling patterns has also been tested, and it has been observed that the framework is robust to deal with various sampling patterns, even when mixed together while training, and results in very high quality reconstruction, in terms of high SSIM (highest being 0.990pm0.006 for acceleration factor of 3.5), while being compared with the fully sampled reconstruction. It has been shown that the proposed framework can successfully reconstruct even for an acceleration factor of 20 for Cartesian (0.968pm0.005) and 17 for radially (0.962pm0.012) sampled data. Furthermore, it has been shown that the framework preserves brain pathology during reconstruction while being trained on healthy subjects.

Industry standards require medical device manufacturers to perform implant-induced artefact testing in phantoms at a pre-clinical stage to define the extent of artefacts that can be expected during MRI. Once a device is commercially available, studies on volunteers, cadavers or patients are performed to investigate implant-induced artefacts and artefact reduction methods more in-depth. This study describes the design and evaluation of a realistic head phantom for pre-clinical implant-induced artefact testing in a relevant environment. A case study is performed where a state-of-the-art piezoelectric bone conduction implant is used in the 1.5 T and 3 T MRI environments. Images were acquired using clinical and novel metal artefact reducing (MARS) sequences at both field strengths. Artefact width and length were measured in a healthy volunteer and compared with artefact sizes obtained in the phantom. Artefact sizes are reported that are similar in shape between the phantom and a volunteer, yet with dimensions differing up to 20% between both. When the implant magnet is removed, the artefact size can be reduced below a diameter of 5 cm, whilst the presence of an implant magnet and splint creates higher artefacts up to 20 cm in diameter. Pulse sequences have been altered to reduce the scan time up to 7 minutes, while preserving the image quality. These results show that the anthropomorphic phantom can be used at a preclinical stage to provide clinically relevant images, illustrating the impact of the artefact on important brain structures.

In MRI, motion artefacts are among the most common types of artefacts. They can degrade images and render them unusable for accurate diagnosis. Traditional methods, such as prospective or retrospective motion correction, have been proposed to avoid or alleviate motion artefacts. Recently, several other methods based on deep learning approaches have been proposed to solve this problem. This work proposes to enhance the performance of existing deep learning models by the inclusion of additional information present as image priors. The proposed approach has shown promising results and will be further investigated for clinical validity.

Accurate differentiation of pseudoprogression (PsP) from True Progression (TP) following radiotherapy (RT) in glioblastoma (GBM) patients is crucial for optimal treatment planning. However, this task remains challenging due to the overlapping imaging characteristics of PsP and TP. This study therefore proposes a multimodal deep-learning approach utilizing complementary information from routine anatomical MR images, clinical parameters, and RT treatment planning information for improved predictive accuracy. The approach utilizes a self-supervised Vision Transformer (ViT) to encode multi-sequence MR brain volumes to effectively capture both global and local context from the high dimensional input. The encoder is trained in a self-supervised upstream task on unlabeled glioma MRI datasets from the open BraTS2021, UPenn-GBM, and UCSF-PDGM datasets to generate compact, clinically relevant representations from FLAIR and T1 post-contrast sequences. These encoded MR inputs are then integrated with clinical data and RT treatment planning information through guided cross-modal attention, improving progression classification accuracy. This work was developed using two datasets from different centers: the Burdenko Glioblastoma Progression Dataset (n = 59) for training and validation, and the GlioCMV progression dataset from the University Hospital Erlangen (UKER) (n = 20) for testing. The proposed method achieved an AUC of 75.3%, outperforming the current state-of-the-art data-driven approaches. Importantly, the proposed approach relies on readily available anatomical MRI sequences, clinical data, and RT treatment planning information, enhancing its clinical feasibility. The proposed approach addresses the challenge of limited data availability for PsP and TP differentiation and could allow for improved clinical decision-making and optimized treatment plans for GBM patients.

Brain MRI scans are often found in four modalities, consisting of T1-weighted with and without contrast enhancement (T1ce and T1w), T2-weighted imaging (T2w), and Flair. Leveraging complementary information from these different modalities enables models to learn richer, more discriminative features for understanding brain anatomy, which could be used in downstream tasks such as anomaly detection. However, in clinical practice, not all MRI modalities are always available due to various reasons. This makes missing modality generation a critical challenge in medical image analysis. In this paper, we propose SLaM-DiMM, a novel missing modality generation framework that harnesses the power of diffusion models to synthesize any of the four target MRI modalities from other available modalities. Our approach not only generates high-fidelity images but also ensures structural coherence across the depth of the volume through a dedicated coherence enhancement mechanism. Qualitative and quantitative evaluations on the BraTS-Lighthouse-2025 Challenge dataset demonstrate the effectiveness of the proposed approach in synthesizing anatomically plausible and structurally consistent results. Code is available at https://github.com/BheeshmSharma/SLaM-DiMM-MICCAI-BraTS-Challenge-2025.

Typical quantitative MRI (qMRI) methods estimate parameter maps after image reconstructing, which is prone to biases and error propagation. We propose a Nonlinear Conjugate Gradient (NLCG) optimizer for model-based T2/T1 estimation, which incorporates U-Net regularization trained in a scan-specific manner. This end-to-end method directly estimates qMRI maps from undersampled k-space data using mono-exponential signal modeling with zero-shot scan-specific neural network regularization to enable high fidelity T1 and T2 mapping. T2 and T1 mapping results demonstrate the ability of the proposed NLCG-Net to improve estimation quality compared to subspace reconstruction at high accelerations.

Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed. Eighty-One T2-weighted MRI scans from 28 patients with non-small cell lung cancers were analyzed. Cross-modality prior encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning model. This model augmented training data arising from 6 expert-segmented T2w MR patient scans with 377 pseudo MRI from non-small cell lung cancer CT patient scans with obtained from the Cancer Imaging Archive. A two-dimensional Unet implemented with batch normalization was trained to segment the tumors from T2w MRI. This method was benchmarked against (a) standard data augmentation and two state-of-the art cross-modality pseudo MR-based augmentation and (b) two segmentation networks. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdroff distance metrics, and volume ratio. The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of 0.75 and the lowest Hausdroff distance on the test dataset. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37). A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality priors to augment training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods.

Medical imaging is critical for diagnostics, but clinical adoption of advanced AI-driven imaging faces challenges due to patient variability, image artifacts, and limited model generalization. While deep learning has transformed image analysis, 3D medical imaging still suffers from data scarcity and inconsistencies due to acquisition protocols, scanner differences, and patient motion. Traditional augmentation uses a single pipeline for all transformations, disregarding the unique traits of each augmentation and struggling with large data volumes. To address these challenges, we propose a Multi-encoder Augmentation-Aware Learning (MEAL) framework that leverages four distinct augmentation variants processed through dedicated encoders. Three fusion strategies such as concatenation (CC), fusion layer (FL), and adaptive controller block (BD) are integrated to build multi-encoder models that combine augmentation-specific features before decoding. MEAL-BD uniquely preserves augmentation-aware representations, enabling robust, protocol-invariant feature learning. As demonstrated in a Computed Tomography (CT)-to-T1-weighted Magnetic Resonance Imaging (MRI) translation study, MEAL-BD consistently achieved the best performance on both unseen- and predefined-test data. On both geometric transformations (like rotations and flips) and non-augmented inputs, MEAL-BD outperformed other competing methods, achieving higher mean peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) scores. These results establish MEAL as a reliable framework for preserving structural fidelity and generalizing across clinically relevant variability. By reframing augmentation as a source of diverse, generalizable features, MEAL supports robust, protocol-invariant learning, advancing clinically reliable medical imaging solutions.

Deep learning (DL) has shown promise for faster, high quality accelerated MRI reconstruction. However, supervised DL methods depend on extensive amounts of fully-sampled (labeled) data and are sensitive to out-of-distribution (OOD) shifts, particularly low signal-to-noise ratio (SNR) acquisitions. To alleviate this challenge, we propose Noise2Recon, a model-agnostic, consistency training method for joint MRI reconstruction and denoising that can use both fully-sampled (labeled) and undersampled (unlabeled) scans in semi-supervised and self-supervised settings. With limited or no labeled training data, Noise2Recon outperforms compressed sensing and deep learning baselines, including supervised networks, augmentation-based training, fine-tuned denoisers, and self-supervised methods, and matches performance of supervised models, which were trained with 14x more fully-sampled scans. Noise2Recon also outperforms all baselines, including state-of-the-art fine-tuning and augmentation techniques, among low-SNR scans and when generalizing to other OOD factors, such as changes in acceleration factors and different datasets. Augmentation extent and loss weighting hyperparameters had negligible impact on Noise2Recon compared to supervised methods, which may indicate increased training stability. Our code is available at https://github.com/ad12/meddlr.

Lung cancer is the deadliest type of cancer worldwide and late detection is the major factor for the low survival rate of patients. Low dose computed tomography has been suggested as a potential screening tool but manual screening is costly, time-consuming and prone to variability. This has fueled the development of automatic methods for the detection, segmentation and characterisation of pulmonary nodules but its application to clinical routine is challenging. In this study, a new database for the development and testing of pulmonary nodule computer-aided strategies is presented which intends to complement current databases by giving additional focus to radiologist variability and local clinical reality. State-of-the-art nodule detection, segmentation and characterization methods are tested and compared to manual annotations as well as collaborative strategies combining multiple radiologists and radiologists and computer-aided systems. It is shown that state-of-the-art methodologies can determine a patient's follow-up recommendation as accurately as a radiologist, though the nodule detection method used shows decreased performance in this database.

Magnetic Resonance Imaging (MRI) is a widely-accepted imaging technique for knee injury analysis. Its advantage of capturing knee structure in three dimensions makes it the ideal tool for radiologists to locate potential tears in the knee. In order to better confront the ever growing workload of musculoskeletal (MSK) radiologists, automated tools for patients' triage are becoming a real need, reducing delays in the reading of pathological cases. In this work, we present the Efficiently-Layered Network (ELNet), a convolutional neural network (CNN) architecture optimized for the task of initial knee MRI diagnosis for triage. Unlike past approaches, we train ELNet from scratch instead of using a transfer-learning approach. The proposed method is validated quantitatively and qualitatively, and compares favorably against state-of-the-art MRNet while using a single imaging stack (axial or coronal) as input. Additionally, we demonstrate our model's capability to locate tears in the knee despite the absence of localization information during training. Lastly, the proposed model is extremely lightweight (< 1MB) and therefore easy to train and deploy in real clinical settings. The code for our model is provided at: https://github.com/mxtsai/ELNet.

Bankart lesions, or anterior-inferior glenoid labral tears, are diagnostically challenging on standard MRIs due to their subtle imaging features-often necessitating invasive MRI arthrograms (MRAs). This study develops deep learning (DL) models to detect Bankart lesions on both standard MRIs and MRAs, aiming to improve diagnostic accuracy and reduce reliance on MRAs. We curated a dataset of 586 shoulder MRIs (335 standard, 251 MRAs) from 558 patients who underwent arthroscopy. Ground truth labels were derived from intraoperative findings, the gold standard for Bankart lesion diagnosis. Separate DL models for MRAs and standard MRIs were trained using the Swin Transformer architecture, pre-trained on a public knee MRI dataset. Predictions from sagittal, axial, and coronal views were ensembled to optimize performance. The models were evaluated on a 20% hold-out test set (117 MRIs: 46 MRAs, 71 standard MRIs). Bankart lesions were identified in 31.9% of MRAs and 8.6% of standard MRIs. The models achieved AUCs of 0.87 (86% accuracy, 83% sensitivity, 86% specificity) and 0.90 (85% accuracy, 82% sensitivity, 86% specificity) on standard MRIs and MRAs, respectively. These results match or surpass radiologist performance on our dataset and reported literature metrics. Notably, our model's performance on non-invasive standard MRIs matched or surpassed the radiologists interpreting MRAs. This study demonstrates the feasibility of using DL to address the diagnostic challenges posed by subtle pathologies like Bankart lesions. Our models demonstrate potential to improve diagnostic confidence, reduce reliance on invasive imaging, and enhance accessibility to care.

Magnetic Resonance Imaging (MRI) is a critical medical imaging modality in clinical diagnosis and research, yet its complexity and heterogeneity pose challenges for automated analysis, particularly in scalable and generalizable machine learning applications. While foundation models have revolutionized natural language and vision tasks, their application to MRI remains limited due to data scarcity and narrow anatomical focus. In this work, we present Decipher-MR, a 3D MRI-specific vision-language foundation model trained on a large-scale dataset comprising 200,000 MRI series from over 22,000 studies spanning diverse anatomical regions, sequences, and pathologies. Decipher-MR integrates self-supervised vision learning with report-guided text supervision to build robust, generalizable representations, enabling effective adaptation across broad applications. To enable robust and diverse clinical tasks with minimal computational overhead, Decipher-MR supports a modular design that enables tuning of lightweight, task-specific decoders attached to a frozen pretrained encoder. Following this setting, we evaluate Decipher-MR across diverse benchmarks including disease classification, demographic prediction, anatomical localization, and cross-modal retrieval, demonstrating consistent performance gains over existing foundation models and task-specific approaches. Our results establish Decipher-MR as a scalable and versatile foundation for MRI-based AI, facilitating efficient development across clinical and research domains.

High-resolution (HR) magnetic resonance imaging (MRI) is crucial for many clinical and research applications. However, achieving it remains costly and constrained by technical trade-offs and experimental limitations. Super-resolution (SR) presents a promising computational approach to overcome these challenges by generating HR images from more affordable low-resolution (LR) scans, potentially improving diagnostic accuracy and efficiency without requiring additional hardware. This survey reviews recent advances in MRI SR techniques, with a focus on deep learning (DL) approaches. It examines DL-based MRI SR methods from the perspectives of computer vision, computational imaging, inverse problems, and MR physics, covering theoretical foundations, architectural designs, learning strategies, benchmark datasets, and performance metrics. We propose a systematic taxonomy to categorize these methods and present an in-depth study of both established and emerging SR techniques applicable to MRI, considering unique challenges in clinical and research contexts. We also highlight open challenges and directions that the community needs to address. Additionally, we provide a collection of essential open-access resources, tools, and tutorials, available on our GitHub: https://github.com/mkhateri/Awesome-MRI-Super-Resolution. IEEE keywords: MRI, Super-Resolution, Deep Learning, Computational Imaging, Inverse Problem, Survey.

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (>0.87/0.90) and gamma pass rates for photon (>98.1%/99.0%) and proton (>99.0%/97.3%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy.

Multi-modality magnetic resonance imaging data with various sequences facilitate the early diagnosis, tumor segmentation, and disease staging in the management of nasopharyngeal carcinoma (NPC). The lack of publicly available, comprehensive datasets limits advancements in diagnosis, treatment planning, and the development of machine learning algorithms for NPC. Addressing this critical need, we introduce the first comprehensive NPC MRI dataset, encompassing MR axial imaging of 277 primary NPC patients. This dataset includes T1-weighted, T2-weighted, and contrast-enhanced T1-weighted sequences, totaling 831 scans. In addition to the corresponding clinical data, manually annotated and labeled segmentations by experienced radiologists offer high-quality data resources from untreated primary NPC.

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

We participated in the SynthRAD2025 challenge (Tasks 1 and 2) with a unified pipeline for synthetic CT (sCT) generation from MRI and CBCT, implemented using the KonfAI framework. Our model is a 2.5D U-Net++ with a ResNet-34 encoder, trained jointly across anatomical regions and fine-tuned per region. The loss function combined pixel-wise L1 loss with IMPACT-Synth, a perceptual loss derived from SAM and TotalSegmentator to enhance structural fidelity. Training was performed using AdamW (initial learning rate = 0.001, halved every 25k steps) on patch-based, normalized, body-masked inputs (320x320 for MRI, 256x256 for CBCT), with random flipping as the only augmentation. No post-processing was applied. Final predictions leveraged test-time augmentation and five-fold ensembling. The best model was selected based on validation MAE. Two registration strategies were evaluated: (i) Elastix with mutual information, consistent with the challenge pipeline, and (ii) IMPACT, a feature-based similarity metric leveraging pretrained segmentation networks. On the local test sets, IMPACT-based registration achieved more accurate and anatomically consistent alignments than mutual-information-based registration, resulting in improved sCT synthesis with lower MAE and more realistic anatomical structures. On the public validation set, however, models trained with Elastix-aligned data achieved higher scores, reflecting a registration bias favoring alignment strategies consistent with the evaluation pipeline. This highlights how registration errors can propagate into supervised learning, influencing both training and evaluation, and potentially inflating performance metrics at the expense of anatomical fidelity. By promoting anatomically consistent alignment, IMPACT helps mitigate this bias and supports the development of more robust and generalizable sCT synthesis models.

Magnetic Resonance Imaging (MRI) is a critical tool in modern medical diagnostics, yet its prolonged acquisition time remains a critical limitation, especially in time-sensitive clinical scenarios. While undersampling strategies can accelerate image acquisition, they often result in image artifacts and degraded quality. Recent diffusion models have shown promise for reconstructing high-fidelity images from undersampled data by learning powerful image priors; however, most existing approaches either (i) rely on unsupervised score functions without paired supervision or (ii) apply data consistency only as a post-processing step. In this work, we introduce a conditional denoising diffusion framework with iterative data-consistency correction, which differs from prior methods by embedding the measurement model directly into every reverse diffusion step and training the model on paired undersampled-ground truth data. This hybrid design bridges generative flexibility with explicit enforcement of MRI physics. Experiments on the fastMRI dataset demonstrate that our framework consistently outperforms recent state-of-the-art deep learning and diffusion-based methods in SSIM, PSNR, and LPIPS, with LPIPS capturing perceptual improvements more faithfully. These results demonstrate that integrating conditional supervision with iterative consistency updates yields substantial improvements in both pixel-level fidelity and perceptual realism, establishing a principled and practical advance toward robust, accelerated MRI reconstruction.

Magnetic Resonance Imaging with tagging (tMRI) has long been utilized for quantifying tissue motion and strain during deformation. However, a phenomenon known as tag fading, a gradual decrease in tag visibility over time, often complicates post-processing. The first contribution of this study is to model tag fading by considering the interplay between T_1 relaxation and the repeated application of radio frequency (RF) pulses during serial imaging sequences. This is a factor that has been overlooked in prior research on tMRI post-processing. Further, we have observed an emerging trend of utilizing raw tagged MRI within a deep learning-based (DL) registration framework for motion estimation. In this work, we evaluate and analyze the impact of commonly used image similarity objectives in training DL registrations on raw tMRI. This is then compared with the Harmonic Phase-based approach, a traditional approach which is claimed to be robust to tag fading. Our findings, derived from both simulated images and an actual phantom scan, reveal the limitations of various similarity losses in raw tMRI and emphasize caution in registration tasks where image intensity changes over time.

This paper presents a large publicly available multi-center lumbar spine magnetic resonance imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 MRI series from 218 patients with a history of low back pain. It was collected from four different hospitals and was divided into a training (179 patients) and validation (39 patients) set. An iterative data annotation approach was used by training a segmentation algorithm on a small part of the dataset, enabling semi-automatic segmentation of the remaining images. The algorithm provided an initial segmentation, which was subsequently reviewed, manually corrected, and added to the training data. We provide reference performance values for this baseline algorithm and nnU-Net, which performed comparably. We set up a continuous segmentation challenge to allow for a fair comparison of different segmentation algorithms. This study may encourage wider collaboration in the field of spine segmentation, and improve the diagnostic value of lumbar spine MRI.

Chest X-ray (CXR) radiology report generation (RRG) models have shown rapid progress, yet their clinical utility remains uncertain due to limited evaluation by radiologists. We present CXRMate-2, a state-of-the-art CXR RRG model that integrates structured multimodal conditioning and reinforcement learning with a composite reward for semantic alignment with radiologist reports. Across the MIMIC-CXR, CheXpert Plus, and ReXgradient datasets, CXRMate-2 achieves statistically significant improvements over strong benchmarks, including gains of 11.2% and 24.4% in GREEN and RadGraph-XL, respectively, on MIMIC-CXR relative to MedGemma 1.5 (4B). To directly compare CXRMate-2 against radiologist reporting, we conduct a blinded, randomised qualitative retrospective evaluation. Three consultant radiologists compare generated and radiologist reports across 120 studies from the MIMIC-CXR test set. Generated reports were deemed acceptable (defined as preferred or rated equally to radiologist reports) in 45% of ratings, with no statistically significant difference in preference rates between radiologist reports and acceptable generated reports for seven of the eight analysed findings. Preference for radiologist reports was driven primarily by higher recall, while generated reports were often preferred for readability. Together, these results suggest a credible pathway to clinically acceptable CXR RRG. Improvements in recall, alongside better detection of subtle findings (e.g., pulmonary congestion), are likely sufficient to achieve non-inferiority to radiologist reporting. With these targeted advances, CXR RRG systems may be ready for prospective evaluation in assistive roles within radiologist-led workflows.

Self-supervised deep learning has accelerated 2D natural image analysis but remains difficult to translate into 3D MRI, where data are scarce and pre-trained 2D backbones cannot capture volumetric context. We present a sequence-invariant self-supervised framework leveraging quantitative MRI (qMRI). By simulating multiple MRI contrasts from a single 3D qMRI scan and enforcing consistent representations across these contrasts, we learn anatomy-centric rather than sequence-specific features. The result is a single 3D encoder that excels across tasks and protocols. Experiments on healthy brain segmentation (IXI), stroke lesion segmentation (ARC), and MRI denoising show significant gains over baseline SSL approaches, especially in low-data settings (up to +8.3\% Dice, +4.2 dB PSNR). It also generalises to unseen sites, supporting scalable clinical use. Code and trained models are publicly available at https://github.com/liamchalcroft/contrast-squared

A radiology report comprises several sections, including the Findings and Impression of the diagnosis. Automatically generating the Impression from the Findings is crucial for reducing radiologists' workload and improving diagnostic accuracy. Pretrained models that excel in common abstractive summarization problems encounter challenges when applied to specialized medical domains largely due to the complex terminology and the necessity for accurate clinical context. Such tasks in medical domains demand extracting core information, avoiding context shifts, and maintaining proper flow. Misuse of medical terms can lead to drastic clinical errors. To address these issues, we introduce a sequential transfer learning that ensures key content extraction and coherent summarization. Sequential transfer learning often faces challenges like initial parameter decay and knowledge loss, which we resolve with the Fisher matrix regularization. Using MIMIC-CXR and Open-I datasets, our model, CSTRL - Context-driven Sequential TRansfer Learning - achieved state-of-the-art performance, showing 56.2% improvement in BLEU-1, 40.5% in BLEU-2, 84.3% in BLEU-3, 28.9% in ROUGE-1, 41.0% in ROUGE-2 and 26.5% in ROGUE-3 score over benchmark studies. We also analyze factual consistency scores while preserving the medical context. Our code is publicly available at https://github.com/fahmidahossain/Report_Summarization.

Deep learning (DL) has recently emerged as a pivotal technology for enhancing magnetic resonance imaging (MRI), a critical tool in diagnostic radiology. This review paper provides a comprehensive overview of recent advances in DL for MRI reconstruction. It focuses on DL approaches and architectures designed to improve image quality, accelerate scans, and address data-related challenges. These include end-to-end neural networks, pre-trained networks, generative models, and self-supervised methods. The paper also discusses the role of DL in optimizing acquisition protocols, enhancing robustness against distribution shifts, and tackling subtle bias. Drawing on the extensive literature and practical insights, it outlines current successes, limitations, and future directions for leveraging DL in MRI reconstruction, while emphasizing the potential of DL to significantly impact clinical imaging practices.

Resection and whole brain radiotherapy (WBRT) are the standards of care for the treatment of patients with brain metastases (BM) but are often associated with cognitive side effects. Stereotactic radiosurgery (SRS) involves a more targeted treatment approach and has been shown to avoid the side effects associated with WBRT. However, SRS requires precise identification and delineation of BM. While many AI algorithms have been developed for this purpose, their clinical adoption has been limited due to poor model performance in the clinical setting. Major reasons for non-generalizable algorithms are the limitations in the datasets used for training the AI network. The purpose of this study was to create a large, heterogenous, annotated BM dataset for training and validation of AI models to improve generalizability. We present a BM dataset of 200 patients with pretreatment T1, T1 post-contrast, T2, and FLAIR MR images. The dataset includes contrast-enhancing and necrotic 3D segmentations on T1 post-contrast and whole tumor (including peritumoral edema) 3D segmentations on FLAIR. Our dataset contains 975 contrast-enhancing lesions, many of which are sub centimeter, along with clinical and imaging feature information. We used a streamlined approach to database-building leveraging a PACS-integrated segmentation workflow.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. Here we introduce BrainFM, a modality-agnostic, multi-task vision foundation model for human brain imaging. With the proposed "mild-to-severe" intra-subject generation and "real-synth" mix-up training strategy, BrainFM is resilient to the appearance of acquired images (e.g., modality, contrast, deformation, resolution, artifacts), and can be directly applied to five fundamental brain imaging tasks, including image synthesis for CT and T1w/T2w/FLAIR MRI, anatomy segmentation, scalp-to-cortical distance, bias field estimation, and registration. We evaluate the efficacy of BrainFM on eleven public datasets, and demonstrate its robustness and effectiveness across all tasks and input modalities. Code is available at https://github.com/jhuldr/BrainFM.

Deep neural networks have enabled improved image quality and fast inference times for various inverse problems, including accelerated magnetic resonance imaging (MRI) reconstruction. However, such models require a large number of fully-sampled ground truth datasets, which are difficult to curate, and are sensitive to distribution drifts. In this work, we propose applying physics-driven data augmentations for consistency training that leverage our domain knowledge of the forward MRI data acquisition process and MRI physics to achieve improved label efficiency and robustness to clinically-relevant distribution drifts. Our approach, termed VORTEX, (1) demonstrates strong improvements over supervised baselines with and without data augmentation in robustness to signal-to-noise ratio change and motion corruption in data-limited regimes; (2) considerably outperforms state-of-the-art purely image-based data augmentation techniques and self-supervised reconstruction methods on both in-distribution and out-of-distribution data; and (3) enables composing heterogeneous image-based and physics-driven data augmentations. Our code is available at https://github.com/ad12/meddlr.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

Reconstruction of magnetic resonance imaging (MRI) data has been positively affected by deep learning. A key challenge remains: to improve generalisation to distribution shifts between the training and testing data. Most approaches aim to address this via inductive design or data augmentation. However, they can be affected by misleading data, e.g. random noise, and cases where the inference stage data do not match assumptions in the modelled shifts. In this work, by employing a conditional hyperparameter network, we eliminate the need of augmentation, yet maintain robust performance under various levels of Gaussian noise. We demonstrate that our model withstands various input noise levels while producing high-definition reconstructions during the test stage. Moreover, we present a hyperparameter sampling strategy that accelerates the convergence of training. Our proposed method achieves the highest accuracy and image quality in all settings compared to baseline methods.

Accurate prostate cancer diagnosis remains challenging. Even when using MRI, radiologists exhibit low specificity and significant inter-observer variability, leading to potential delays or inaccuracies in identifying clinically significant cancers. This leads to numerous unnecessary biopsies and risks of missing clinically significant cancers. Here we present prostate vision contrastive network (ProViCNet), prostate organ-specific vision foundation models for Magnetic Resonance Imaging (MRI) and Trans-Rectal Ultrasound imaging (TRUS) for comprehensive cancer detection. ProViCNet was trained and validated using 4,401 patients across six institutions, as a prostate cancer detection model on radiology images relying on patch-level contrastive learning guided by biopsy confirmed radiologist annotations. ProViCNet demonstrated consistent performance across multiple internal and external validation cohorts with area under the receiver operating curve values ranging from 0.875 to 0.966, significantly outperforming radiologists in the reader study (0.907 versus 0.805, p<0.001) for mpMRI, while achieving 0.670 to 0.740 for TRUS. We also integrated ProViCNet with standard PSA to develop a virtual screening test, and we showed that we can maintain the high sensitivity for detecting clinically significant cancers while more than doubling specificity from 15% to 38% (p<0.001), thereby substantially reducing unnecessary biopsies. These findings highlight that ProViCNet's potential for enhancing prostate cancer diagnosis accuracy and reduce unnecessary biopsies, thereby optimizing diagnostic pathways.

Disease progression simulation is a crucial area of research that has significant implications for clinical diagnosis, prognosis, and treatment. One major challenge in this field is the lack of continuous medical imaging monitoring of individual patients over time. To address this issue, we develop a novel framework termed Progressive Image Editing (PIE) that enables controlled manipulation of disease-related image features, facilitating precise and realistic disease progression simulation. Specifically, we leverage recent advancements in text-to-image generative models to simulate disease progression accurately and personalize it for each patient. We theoretically analyze the iterative refining process in our framework as a gradient descent with an exponentially decayed learning rate. To validate our framework, we conduct experiments in three medical imaging domains. Our results demonstrate the superiority of PIE over existing methods such as Stable Diffusion Walk and Style-Based Manifold Extrapolation based on CLIP score (Realism) and Disease Classification Confidence (Alignment). Our user study collected feedback from 35 veteran physicians to assess the generated progressions. Remarkably, 76.2% of the feedback agrees with the fidelity of the generated progressions. To our best knowledge, PIE is the first of its kind to generate disease progression images meeting real-world standards. It is a promising tool for medical research and clinical practice, potentially allowing healthcare providers to model disease trajectories over time, predict future treatment responses, and improve patient outcomes.

Tagged magnetic resonance imaging (tMRI) has been employed for decades to measure the motion of tissue undergoing deformation. However, registration-based motion estimation from tMRI is difficult due to the periodic patterns in these images, particularly when the motion is large. With a larger motion the registration approach gets trapped in a local optima, leading to motion estimation errors. We introduce a novel "momenta, shooting, and correction" framework for Lagrangian motion estimation in the presence of repetitive patterns and large motion. This framework, grounded in Lie algebra and Lie group principles, accumulates momenta in the tangent vector space and employs exponential mapping in the diffeomorphic space for rapid approximation towards true optima, circumventing local optima. A subsequent correction step ensures convergence to true optima. The results on a 2D synthetic dataset and a real 3D tMRI dataset demonstrate our method's efficiency in estimating accurate, dense, and diffeomorphic 2D/3D motion fields amidst large motion and repetitive patterns.

BACKGROUND: Radiology reports are typically written in a free-text format, making clinical information difficult to extract and use. Recently the adoption of structured reporting (SR) has been recommended by various medical societies thanks to the advantages it offers, e.g. standardization, completeness and information retrieval. We propose a pipeline to extract information from free-text radiology reports, that fits with the items of the reference SR registry proposed by a national society of interventional and medical radiology, focusing on CT staging of patients with lymphoma. METHODS: Our work aims to leverage the potential of Natural Language Processing (NLP) and Transformer-based models to deal with automatic SR registry filling. With the availability of 174 radiology reports, we investigate a rule-free generative Question Answering approach based on a domain-specific version of T5 (IT5). Two strategies (batch-truncation and ex-post combination) are implemented to comply with the model's context length limitations. Performance is evaluated in terms of strict accuracy, F1, and format accuracy, and compared with the widely used GPT-3.5 Large Language Model. A 5-point Likert scale questionnaire is used to collect human-expert feedback on the similarity between medical annotations and generated answers. RESULTS: The combination of fine-tuning and batch splitting allows IT5 to achieve notable results; it performs on par with GPT-3.5 albeit its size being a thousand times smaller in terms of parameters. Human-based assessment scores show a high correlation (Spearman's correlation coefficients>0.88, p-values<0.001) with AI performance metrics (F1) and confirm the superior ability of LLMs (i.e., GPT-3.5, 175B of parameters) in generating plausible human-like statements.

Glioblastomas are the most aggressive type of glioma, having a 5-year survival rate of 6.9%. Treatment typically involves surgery, followed by radiotherapy and chemotherapy, and frequent magnetic resonance imaging (MRI) scans to monitor disease progression. To assess treatment response, radiologists use the Response Assessment in Neuro-Oncology (RANO) criteria to categorize the tumor into one of four labels based on imaging and clinical features: complete response, partial response, stable disease, and progressive disease. This assessment is very complex and time-consuming. Since deep learning (DL) has been widely used to tackle classification problems, this work aimed to implement the first DL pipeline for the classification of RANO criteria based on two consecutive MRI acquisitions. The models were trained and tested on the open dataset LUMIERE. Five approaches were tested: 1) subtraction of input images, 2) different combinations of modalities, 3) different model architectures, 4) different pretraining tasks, and 5) adding clinical data. The pipeline that achieved the best performance used a Densenet264 considering only T1-weighted, T2-weighted, and Fluid Attenuated Inversion Recovery (FLAIR) images as input without any pretraining. A median Balanced Accuracy of 50.96% was achieved. Additionally, explainability methods were applied. Using Saliency Maps, the tumor region was often successfully highlighted. In contrast, Grad-CAM typically failed to highlight the tumor region, with some exceptions observed in the Complete Response and Progressive Disease classes, where it effectively identified the tumor region. These results set a benchmark for future studies on glioblastoma treatment response assessment based on the RANO criteria while emphasizing the heterogeneity of factors that might play a role when assessing the tumor's response to treatment.

Diffusion-weighted magnetic resonance imaging (DW-MRI) can be used to characterise the microstructure of the nervous tissue, e.g. to delineate brain white matter connections in a non-invasive manner via fibre tracking. Magnetic Resonance Imaging (MRI) in high spatial resolution would play an important role in visualising such fibre tracts in a superior manner. However, obtaining an image of such resolution comes at the expense of longer scan time. Longer scan time can be associated with the increase of motion artefacts, due to the patient's psychological and physical conditions. Single Image Super-Resolution (SISR), a technique aimed to obtain high-resolution (HR) details from one single low-resolution (LR) input image, achieved with Deep Learning, is the focus of this study. Compared to interpolation techniques or sparse-coding algorithms, deep learning extracts prior knowledge from big datasets and produces superior MRI images from the low-resolution counterparts. In this research, a deep learning based super-resolution technique is proposed and has been applied for DW-MRI. Images from the IXI dataset have been used as the ground-truth and were artificially downsampled to simulate the low-resolution images. The proposed method has shown statistically significant improvement over the baselines and achieved an SSIM of 0.913pm0.045.

Detecting breast cancer early is of the utmost importance to effectively treat the millions of women afflicted by breast cancer worldwide every year. Although mammography is the primary imaging modality for screening breast cancer, there is an increasing interest in adding magnetic resonance imaging (MRI) to screening programmes, particularly for women at high risk. Recent guidelines by the European Society of Breast Imaging (EUSOBI) recommended breast MRI as a supplemental screening tool for women with dense breast tissue. However, acquiring and reading MRI scans requires significantly more time from expert radiologists. This highlights the need to develop new automated methods to detect cancer accurately using MRI and Artificial Intelligence (AI), which have the potential to support radiologists in breast MRI interpretation and classification and help detect cancer earlier. For this reason, the ODELIA consortium has made this multi-centre dataset publicly available to assist in developing AI tools for the detection of breast cancer on MRI.

We present a new neural network, the XPDNet, for MRI reconstruction from periodically under-sampled multi-coil data. We inform the design of this network by taking best practices from MRI reconstruction and computer vision. We show that this network can achieve state-of-the-art reconstruction results, as shown by its ranking of second in the fastMRI 2020 challenge.

Intraoperative registration of real-time ultrasound (iUS) to preoperative Magnetic Resonance Imaging (MRI) remains an unsolved problem due to severe modality-specific differences in appearance, resolution, and field-of-view. To address this, we propose a novel 3D cross-modal keypoint descriptor for MRI-iUS matching and registration. Our approach employs a patient-specific matching-by-synthesis approach, generating synthetic iUS volumes from preoperative MRI. This enables supervised contrastive training to learn a shared descriptor space. A probabilistic keypoint detection strategy is then employed to identify anatomically salient and modality-consistent locations. During training, a curriculum-based triplet loss with dynamic hard negative mining is used to learn descriptors that are i) robust to iUS artifacts such as speckle noise and limited coverage, and ii) rotation-invariant. At inference, the method detects keypoints in MR and real iUS images and identifies sparse matches, which are then used to perform rigid registration. Our approach is evaluated using 3D MRI-iUS pairs from the ReMIND dataset. Experiments show that our approach outperforms state-of-the-art keypoint matching methods across 11 patients, with an average precision of 69.8%. For image registration, our method achieves a competitive mean Target Registration Error of 2.39 mm on the ReMIND2Reg benchmark. Compared to existing iUS-MR registration approaches, our framework is interpretable, requires no manual initialization, and shows robustness to iUS field-of-view variation. Code, data and model weights are available at https://github.com/morozovdd/CrossKEY.

Chest Xray imaging is a widely used diagnostic tool in modern medicine, and its high utilization creates substantial workloads for radiologists. To alleviate this burden, vision language models are increasingly applied to automate Chest Xray radiology report generation (CXRRRG), aiming for clinically accurate descriptions while reducing manual effort. Conventional approaches, however, typically rely on single images, failing to capture the longitudinal context necessary for producing clinically faithful comparison statements. Recently, growing attention has been directed toward incorporating longitudinal data into CXR RRG, enabling models to leverage historical studies in ways that mirror radiologists diagnostic workflows. Nevertheless, existing surveys primarily address single image CXRRRG and offer limited guidance for longitudinal settings, leaving researchers without a systematic framework for model design. To address this gap, this survey provides the first comprehensive review of longitudinal radiology report generation (LRRG). Specifically, we examine dataset construction strategies, report generation architectures alongside longitudinally tailored designs, and evaluation protocols encompassing both longitudinal specific measures and widely used benchmarks. We further summarize LRRG methods performance, alongside analyses of different ablation studies, which collectively highlight the critical role of longitudinal information and architectural design choices in improving model performance. Finally, we summarize five major limitations of current research and outline promising directions for future development, aiming to lay a foundation for advancing this emerging field.

In the field of medical sciences, reliable detection and classification of brain tumors from images remains a formidable challenge due to the rarity of tumors within the population of patients. Therefore, the ability to detect tumors in anomaly scenarios is paramount for ensuring timely interventions and improved patient outcomes. This study addresses the issue by leveraging deep learning (DL) techniques to detect and classify brain tumors in challenging situations. The curated data set from the National Brain Mapping Lab (NBML) comprises 81 patients, including 30 Tumor cases and 51 Normal cases. The detection and classification pipelines are separated into two consecutive tasks. The detection phase involved comprehensive data analysis and pre-processing to modify the number of image samples and the number of patients of each class to anomaly distribution (9 Normal per 1 Tumor) to comply with real world scenarios. Next, in addition to common evaluation metrics for the testing, we employed a novel performance evaluation method called Patient to Patient (PTP), focusing on the realistic evaluation of the model. In the detection phase, we fine-tuned a YOLOv8n detection model to detect the tumor region. Subsequent testing and evaluation yielded competitive performance both in Common Evaluation Metrics and PTP metrics. Furthermore, using the Data Efficient Image Transformer (DeiT) module, we distilled a Vision Transformer (ViT) model from a fine-tuned ResNet152 as a teacher in the classification phase. This approach demonstrates promising strides in reliable tumor detection and classification, offering potential advancements in tumor diagnosis for real-world medical imaging scenarios.

Extent of resection after surgery is one of the main prognostic factors for patients diagnosed with glioblastoma. To achieve this, accurate segmentation and classification of residual tumor from post-operative MR images is essential. The current standard method for estimating it is subject to high inter- and intra-rater variability, and an automated method for segmentation of residual tumor in early post-operative MRI could lead to a more accurate estimation of extent of resection. In this study, two state-of-the-art neural network architectures for pre-operative segmentation were trained for the task. The models were extensively validated on a multicenter dataset with nearly 1000 patients, from 12 hospitals in Europe and the United States. The best performance achieved was a 61\% Dice score, and the best classification performance was about 80\% balanced accuracy, with a demonstrated ability to generalize across hospitals. In addition, the segmentation performance of the best models was on par with human expert raters. The predicted segmentations can be used to accurately classify the patients into those with residual tumor, and those with gross total resection.

Deep learning underpins a wide range of applications in MRI, including reconstruction, artifact removal, and segmentation. However, progress has been driven largely by public datasets focused on brain and knee imaging, shaping how models are trained and evaluated. As a result, careful studies of the reliability of these models across diverse anatomical settings remain limited. In this work, we introduce MosaicMRI, a large and diverse collection of fully sampled raw musculoskeletal (MSK) MR measurements designed for training and evaluating machine-learning-based methods. MosaicMRI is the largest open-source raw MSK MRI dataset to date, comprising 2,671 volumes and 80,156 slices. The dataset offers substantial diversity in volume orientation (e.g., axial, sagittal), imaging contrasts (e.g., PD, T1, T2), anatomies (e.g., spine, knee, hip, ankle, and others), and numbers of acquisition coils. Using VarNet as a baseline for accelerated reconstruction task, we perform a comprehensive set of experiments to study scaling behavior with respect to both model capacity and dataset size. Interestingly, models trained on the combined anatomies significantly outperform anatomy-specific models in low-sample regimes, highlighting the benefits of anatomical diversity and the presence of exploitable cross-anatomical correlations. We further evaluate robustness and cross-anatomy generalization by training models on one anatomy (e.g., spine) and testing them on another (e.g., knee). Notably, we identify groups of body parts (e.g., foot and elbow) that generalize well with each other, and highlight that performance under domain shifts depends on both training set size, anatomy, and protocol-specific factors.

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

We introduce a new type of foundational model for parsing human anatomy in medical images that works for different modalities. It supports supervised or unsupervised training and can perform matching, registration, classification, or segmentation with or without user interaction. We achieve this by training a neural network estimator that maps query locations to atlas coordinates via regression. Efficiency is improved by sparsely sampling the input, enabling response times of less than 1 ms without additional accelerator hardware. We demonstrate the utility of the algorithm in both CT and MRI modalities.

The detailed images produced by Magnetic Resonance Imaging (MRI) provide life-critical information for the diagnosis and treatment of prostate cancer. To provide standardized acquisition, interpretation and usage of the complex MRI images, the PI-RADS v2 guideline was proposed. An automated segmentation following the guideline facilitates consistent and precise lesion detection, staging and treatment. The guideline recommends a division of the prostate into four zones, PZ (peripheral zone), TZ (transition zone), DPU (distal prostatic urethra) and AFS (anterior fibromuscular stroma). Not every zone shares a boundary with the others and is present in every slice. Further, the representations captured by a single model might not suffice for all zones. This motivated us to design a dual-branch convolutional neural network (CNN), where each branch captures the representations of the connected zones separately. Further, the representations from different branches act complementary to each other at the second stage of training, where they are fine-tuned through an unsupervised loss. The loss penalises the difference in predictions from the two branches for the same class. We also incorporate multi-task learning in our framework to further improve the segmentation accuracy. The proposed approach improves the segmentation accuracy of the baseline (mean absolute symmetric distance) by 7.56%, 11.00%, 58.43% and 19.67% for PZ, TZ, DPU and AFS zones respectively.

The ability to recover MRI signal from noise is key to achieve fast acquisition, accurate quantification, and high image quality. Past work has shown convolutional neural networks can be used with abundant and paired low and high-SNR images for training. However, for applications where high-SNR data is difficult to produce at scale (e.g. with aggressive acceleration, high resolution, or low field strength), training a new denoising network using a large quantity of high-SNR images can be infeasible. In this study, we overcome this limitation by improving the generalization of denoising models, enabling application to many settings beyond what appears in the training data. Specifically, we a) develop a training scheme that uses complex MRIs reconstructed in the SNR units (i.e., the images have a fixed noise level, SNR unit training) and augments images with realistic noise based on coil g-factor, and b) develop a novel imaging transformer (imformer) to handle 2D, 2D+T, and 3D MRIs in one model architecture. Through empirical evaluation, we show this combination improves performance compared to CNN models and improves generalization, enabling a denoising model to be used across field-strengths, image contrasts, and anatomy.

Purpose: In radiology, large language models (LLMs), including ChatGPT, have recently gained attention, and their utility is being rapidly evaluated. However, concerns have emerged regarding their reliability in clinical applications due to limitations such as hallucinations and insufficient referencing. To address these issues, we focus on the latest technology, retrieval-augmented generation (RAG), which enables LLMs to reference reliable external knowledge (REK). Specifically, this study examines the utility and reliability of a recently released RAG-equipped LLM (RAG-LLM), NotebookLM, for staging lung cancer. Materials and methods: We summarized the current lung cancer staging guideline in Japan and provided this as REK to NotebookLM. We then tasked NotebookLM with staging 100 fictional lung cancer cases based on CT findings and evaluated its accuracy. For comparison, we performed the same task using a gold-standard LLM, GPT-4 Omni (GPT-4o), both with and without the REK. Results: NotebookLM achieved 86% diagnostic accuracy in the lung cancer staging experiment, outperforming GPT-4o, which recorded 39% accuracy with the REK and 25% without it. Moreover, NotebookLM demonstrated 95% accuracy in searching reference locations within the REK. Conclusion: NotebookLM successfully performed lung cancer staging by utilizing the REK, demonstrating superior performance compared to GPT-4o. Additionally, it provided highly accurate reference locations within the REK, allowing radiologists to efficiently evaluate the reliability of NotebookLM's responses and detect possible hallucinations. Overall, this study highlights the potential of NotebookLM, a RAG-LLM, in image diagnosis.

Radiology report generation (RRG) has attracted significant attention due to its potential to reduce the workload of radiologists. Current RRG approaches are still unsatisfactory against clinical standards. This paper introduces a novel RRG method, LM-RRG, that integrates large models (LMs) with clinical quality reinforcement learning to generate accurate and comprehensive chest X-ray radiology reports. Our method first designs a large language model driven feature extractor to analyze and interpret different regions of the chest X-ray image, emphasizing specific regions with medical significance. Next, based on the large model's decoder, we develop a multimodal report generator that leverages multimodal prompts from visual features and textual instruction to produce the radiology report in an auto-regressive way. Finally, to better reflect the clinical significant and insignificant errors that radiologists would normally assign in the report, we introduce a novel clinical quality reinforcement learning strategy. It utilizes the radiology report clinical quality (RadCliQ) metric as a reward function in the learning process. Extensive experiments on the MIMIC-CXR and IU-Xray datasets demonstrate the superiority of our method over the state of the art.

Previous research on radiology report generation has made significant progress in terms of increasing the clinical accuracy of generated reports. In this paper, we emphasize another crucial quality that it should possess, i.e., inter-report consistency, which refers to the capability of generating consistent reports for semantically equivalent radiographs. This quality is even of greater significance than the overall report accuracy in terms of ensuring the system's credibility, as a system prone to providing conflicting results would severely erode users' trust. Regrettably, existing approaches struggle to maintain inter-report consistency, exhibiting biases towards common patterns and susceptibility to lesion variants. To address this issue, we propose ICON, which improves the inter-report consistency of radiology report generation. Aiming at enhancing the system's ability to capture the similarities in semantically equivalent lesions, our approach involves first extracting lesions from input images and examining their characteristics. Then, we introduce a lesion-aware mix-up augmentation technique to ensure that the representations of the semantically equivalent lesions align with the same attributes, by linearly interpolating them during the training phase. Extensive experiments on three publicly available chest X-ray datasets verify the effectiveness of our approach, both in terms of improving the consistency and accuracy of the generated reports.

Segmenting stroke lesions in Magnetic Resonance Imaging (MRI) is challenging due to diverse clinical imaging domains, with existing models struggling to generalise across different MRI acquisition parameters and sequences. In this work, we propose two novel physics-constrained approaches using synthetic quantitative MRI (qMRI) images to enhance the robustness and generalisability of segmentation models. We trained a qMRI estimation model to predict qMRI maps from MPRAGE images, which were used to simulate diverse MRI sequences for segmentation training. A second approach built upon prior work in synthetic data for stroke lesion segmentation, generating qMRI maps from a dataset of tissue labels. The proposed approaches improved over the baseline nnUNet on a variety of out-of-distribution datasets, with the second approach outperforming the prior synthetic data method.

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. To exploit this structured information, we propose the use of Space-aware Memory Queues for In-painting and Detecting anomalies from radiography images (abbreviated as SQUID). We show that SQUID can taxonomize the ingrained anatomical structures into recurrent patterns; and in the inference, it can identify anomalies (unseen/modified patterns) in the image. SQUID surpasses 13 state-of-the-art methods in unsupervised anomaly detection by at least 5 points on two chest X-ray benchmark datasets measured by the Area Under the Curve (AUC). Additionally, we have created a new dataset (DigitAnatomy), which synthesizes the spatial correlation and consistent shape in chest anatomy. We hope DigitAnatomy can prompt the development, evaluation, and interpretability of anomaly detection methods.

Advances in medical imaging technologies have enabled the collection of longitudinal images, which involve repeated scanning of the same patients over time, to monitor disease progression. However, predictive modeling of such data remains challenging due to high dimensionality, irregular sampling, and data sparsity. To address these issues, we propose ImageFlowNet, a novel model designed to forecast disease trajectories from initial images while preserving spatial details. ImageFlowNet first learns multiscale joint representation spaces across patients and time points, then optimizes deterministic or stochastic flow fields within these spaces using a position-parameterized neural ODE/SDE framework. The model leverages a UNet architecture to create robust multiscale representations and mitigates data scarcity by combining knowledge from all patients. We provide theoretical insights that support our formulation of ODEs, and motivate our regularizations involving high-level visual features, latent space organization, and trajectory smoothness. We validate ImageFlowNet on three longitudinal medical image datasets depicting progression in geographic atrophy, multiple sclerosis, and glioblastoma, demonstrating its ability to effectively forecast disease progression and outperform existing methods. Our contributions include the development of ImageFlowNet, its theoretical underpinnings, and empirical validation on real-world datasets. The official implementation is available at https://github.com/KrishnaswamyLab/ImageFlowNet.

For patients suffering from central nervous system tumors, prognosis estimation, treatment decisions, and postoperative assessments are made from the analysis of a set of magnetic resonance (MR) scans. Currently, the lack of open tools for standardized and automatic tumor segmentation and generation of clinical reports, incorporating relevant tumor characteristics, leads to potential risks from inherent decisions' subjectivity. To tackle this problem, the proposed Raidionics open-source software has been developed, offering both a user-friendly graphical user interface and stable processing backend. The software includes preoperative segmentation models for each of the most common tumor types (i.e., glioblastomas, lower grade gliomas, meningiomas, and metastases), together with one early postoperative glioblastoma segmentation model. Preoperative segmentation performances were quite homogeneous across the four different brain tumor types, with an average Dice around 85% and patient-wise recall and precision around 95%. Postoperatively, performances were lower with an average Dice of 41%. Overall, the generation of a standardized clinical report, including the tumor segmentation and features computation, requires about ten minutes on a regular laptop. The proposed Raidionics software is the first open solution enabling an easy use of state-of-the-art segmentation models for all major tumor types, including preoperative and postsurgical standardized reports.

Radiology reports are crucial for planning treatment strategies and enhancing doctor-patient communication, yet manually writing these reports is burdensome for radiologists. While automatic report generation offers a solution, existing methods often rely on single-view radiographs, limiting diagnostic accuracy. To address this problem, we propose MCL, a Multi-view enhanced Contrastive Learning method for chest X-ray report generation. Specifically, we first introduce multi-view enhanced contrastive learning for visual representation by maximizing agreements between multi-view radiographs and their corresponding report. Subsequently, to fully exploit patient-specific indications (e.g., patient's symptoms) for report generation, we add a transitional ``bridge" for missing indications to reduce embedding space discrepancies caused by their presence or absence. Additionally, we construct Multi-view CXR and Two-view CXR datasets from public sources to support research on multi-view report generation. Our proposed MCL surpasses recent state-of-the-art methods across multiple datasets, achieving a 5.0% F1 RadGraph improvement on MIMIC-CXR, a 7.3% BLEU-1 improvement on MIMIC-ABN, a 3.1% BLEU-4 improvement on Multi-view CXR, and an 8.2% F1 CheXbert improvement on Two-view CXR.

Although deep learning (DL) has received much attention in accelerated magnetic resonance imaging (MRI), recent studies show that tiny input perturbations may lead to instabilities of DL-based MRI reconstruction models. However, the approaches of robustifying these models are underdeveloped. Compared to image classification, it could be much more challenging to achieve a robust MRI image reconstruction network considering its regression-based learning objective, limited amount of training data, and lack of efficient robustness metrics. To circumvent the above limitations, our work revisits the problem of DL-based image reconstruction through the lens of robust machine learning. We find a new instability source of MRI image reconstruction, i.e., the lack of reconstruction robustness against spatial transformations of an input, e.g., rotation and cutout. Inspired by this new robustness metric, we develop a robustness-aware image reconstruction method that can defend against both pixel-wise adversarial perturbations as well as spatial transformations. Extensive experiments are also conducted to demonstrate the effectiveness of our proposed approaches.

While highly accelerated non-Cartesian acquisition protocols significantly reduce scan time, they often entail long reconstruction delays. Deep learning based reconstruction methods can alleviate this, but often lack stability and robustness to distribution shifts. As an alternative, we train a rotation invariant weakly convex ridge regularizer (WCRR). The resulting variational reconstruction approach is benchmarked against state of the art methods on retrospectively simulated data and (out of distribution) on prospective GoLF SPARKLING and CAIPIRINHA acquisitions. Our approach consistently outperforms widely used baselines and achieves performance comparable to Plug and Play reconstruction with a state of the art 3D DRUNet denoiser, while offering substantially improved computational efficiency and robustness to acquisition changes. In summary, WCRR unifies the strengths of principled variational methods and modern deep learning based approaches.

This paper presents a comprehensive evaluation of GPT-4V's capabilities across diverse medical imaging tasks, including Radiology Report Generation, Medical Visual Question Answering (VQA), and Visual Grounding. While prior efforts have explored GPT-4V's performance in medical image analysis, to the best of our knowledge, our study represents the first quantitative evaluation on publicly available benchmarks. Our findings highlight GPT-4V's potential in generating descriptive reports for chest X-ray images, particularly when guided by well-structured prompts. Meanwhile, its performance on the MIMIC-CXR dataset benchmark reveals areas for improvement in certain evaluation metrics, such as CIDEr. In the domain of Medical VQA, GPT-4V demonstrates proficiency in distinguishing between question types but falls short of the VQA-RAD benchmark in terms of accuracy. Furthermore, our analysis finds the limitations of conventional evaluation metrics like the BLEU scores, advocating for the development of more semantically robust assessment methods. In the field of Visual Grounding, GPT-4V exhibits preliminary promise in recognizing bounding boxes, but its precision is lacking, especially in identifying specific medical organs and signs. Our evaluation underscores the significant potential of GPT-4V in the medical imaging domain, while also emphasizing the need for targeted refinements to fully unlock its capabilities.

X-ray images play a vital role in the intraoperative processes due to their high resolution and fast imaging speed and greatly promote the subsequent segmentation, registration and reconstruction. However, over-dosed X-rays superimpose potential risks to human health to some extent. Data-driven algorithms from volume scans to X-ray images are restricted by the scarcity of paired X-ray and volume data. Existing methods are mainly realized by modelling the whole X-ray imaging procedure. In this study, we propose a learning-based approach termed CT2X-GAN to synthesize the X-ray images in an end-to-end manner using the content and style disentanglement from three different image domains. Our method decouples the anatomical structure information from CT scans and style information from unpaired real X-ray images/ digital reconstructed radiography (DRR) images via a series of decoupling encoders. Additionally, we introduce a novel consistency regularization term to improve the stylistic resemblance between synthesized X-ray images and real X-ray images. Meanwhile, we also impose a supervised process by computing the similarity of computed real DRR and synthesized DRR images. We further develop a pose attention module to fully strengthen the comprehensive information in the decoupled content code from CT scans, facilitating high-quality multi-view image synthesis in the lower 2D space. Extensive experiments were conducted on the publicly available CTSpine1K dataset and achieved 97.8350, 0.0842 and 3.0938 in terms of FID, KID and defined user-scored X-ray similarity, respectively. In comparison with 3D-aware methods (pi-GAN, EG3D), CT2X-GAN is superior in improving the synthesis quality and realistic to the real X-ray images.

Respiratory motion complicates accurate irradiation of thoraco-abdominal tumors during radiotherapy, as treatment-system latency entails target-location uncertainties. This work addresses frame forecasting in chest and liver cine MRI to compensate for such delays. We investigate RNNs trained with online learning algorithms, enabling adaptation to changing respiratory patterns via on-the-fly parameter updates, and transformers, increasingly common in time-series forecasting for their ability to capture long-term dependencies. Experiments used 12 sagittal thoracic and upper-abdominal cine-MRI sequences from ETH Zürich and OvGU; the OvGU data exhibited higher motion variability, noise, and lower contrast. PCA decomposes the Lucas-Kanade optical-flow field into static deformation modes and low-dimensional, time-dependent weights. We compare various methods for forecasting these weights: linear filters, population and sequence-specific transformer encoders, and RNNs trained with real-time recurrent learning (RTRL), unbiased online recurrent optimization, decoupled neural interfaces, and sparse one-step approximation (SnAp-1). Predicted displacements were used to warp the reference frame and generate future images. Prediction accuracy decreased with the horizon h. Linear regression performed best at short horizons (1.3mm geometrical error at h=0.32s, ETH Zürich dataset), while RTRL and SnAp-1 outperformed the other algorithms at medium-to-long horizons, with geometrical errors below 1.4mm and 2.8mm on the sequences from ETH Zürich and OvGU, respectively. The sequence-specific transformer was competitive for low-to-medium horizons, but transformers remained overall limited by data scarcity and domain shift between datasets. Predicted frames visually resembled the ground truth, with notable errors occurring near the diaphragm at end-inspiration and regions affected by out-of-plane motion.

Magnetization transfer contrast magnetic resonance fingerprinting (MTC-MRF) is a novel quantitative imaging technique that simultaneously measures several tissue parameters of semisolid macromolecule and free bulk water. In this study, we propose an Only-Train-Once MR fingerprinting (OTOM) framework that estimates the free bulk water and MTC tissue parameters from MR fingerprints regardless of MRF schedule, thereby avoiding time-consuming process such as generation of training dataset and network training according to each MRF schedule. A recurrent neural network is designed to cope with two types of variants of MRF schedules: 1) various lengths and 2) various patterns. Experiments on digital phantoms and in vivo data demonstrate that our approach can achieve accurate quantification for the water and MTC parameters with multiple MRF schedules. Moreover, the proposed method is in excellent agreement with the conventional deep learning and fitting methods. The flexible OTOM framework could be an efficient tissue quantification tool for various MRF protocols.

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation regularization. The experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise.

Dynamic MRI is a technique of acquiring a series of images continuously to follow the physiological changes over time. However, such fast imaging results in low resolution images. In this work, abdominal deformation model computed from dynamic low resolution images have been applied to high resolution image, acquired previously, to generate dynamic high resolution MRI. Dynamic low resolution images were simulated into different breathing phases (inhale and exhale). Then, the image registration between breathing time points was performed using the B-spline SyN deformable model and using cross-correlation as a similarity metric. The deformation model between different breathing phases were estimated from highly undersampled data. This deformation model was then applied to the high resolution images to obtain high resolution images of different breathing phases. The results indicated that the deformation model could be computed from relatively very low resolution images.

Large language models (LLMs) often generate outdated or inaccurate information based on static training datasets. Retrieval-augmented generation (RAG) mitigates this by integrating outside data sources. While previous RAG systems used pre-assembled, fixed databases with limited flexibility, we have developed Radiology RAG (RadioRAG), an end-to-end framework that retrieves data from authoritative radiologic online sources in real-time. We evaluate the diagnostic accuracy of various LLMs when answering radiology-specific questions with and without access to additional online information via RAG. Using 80 questions from the RSNA Case Collection across radiologic subspecialties and 24 additional expert-curated questions with reference standard answers, LLMs (GPT-3.5-turbo, GPT-4, Mistral-7B, Mixtral-8x7B, and Llama3 [8B and 70B]) were prompted with and without RadioRAG in a zero-shot inference scenario RadioRAG retrieved context-specific information from Radiopaedia in real-time. Accuracy was investigated. Statistical analyses were performed using bootstrapping. The results were further compared with human performance. RadioRAG improved diagnostic accuracy across most LLMs, with relative accuracy increases ranging up to 54% for different LLMs. It matched or exceeded non-RAG models and the human radiologist in question answering across radiologic subspecialties, particularly in breast imaging and emergency radiology. However, the degree of improvement varied among models; GPT-3.5-turbo and Mixtral-8x7B-instruct-v0.1 saw notable gains, while Mistral-7B-instruct-v0.2 showed no improvement, highlighting variability in RadioRAG's effectiveness. LLMs benefit when provided access to domain-specific data beyond their training data. RadioRAG shows potential to improve LLM accuracy and factuality in radiology question answering by integrating real-time domain-specific data.

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficiency metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications.

Brain tumor growth is unique to each glioma patient and extends beyond what is visible in imaging scans, infiltrating surrounding brain tissue. Understanding these hidden patient-specific progressions is essential for effective therapies. Current treatment plans for brain tumors, such as radiotherapy, typically involve delineating a uniform margin around the visible tumor on pre-treatment scans to target this invisible tumor growth. This "one size fits all" approach is derived from population studies and often fails to account for the nuances of individual patient conditions. We present the GliODIL framework, which infers the full spatial distribution of tumor cell concentration from available multi-modal imaging, leveraging a Fisher-Kolmogorov type physics model to describe tumor growth. This is achieved through the newly introduced method of Optimizing the Discrete Loss (ODIL), where both data and physics-based constraints are softly assimilated into the solution. Our test dataset comprises 152 glioblastoma patients with pre-treatment imaging and post-treatment follow-ups for tumor recurrence monitoring. By blending data-driven techniques with physics-based constraints, GliODIL enhances recurrence prediction in radiotherapy planning, challenging traditional uniform margins and strict adherence to the Fisher-Kolmogorov partial differential equation (PDE) model, which is adapted for complex cases.

Longitudinal multimodal data, including electronic health records (EHR) and sequential chest X-rays (CXRs), is critical for modeling disease progression, yet remains underutilized due to two key challenges: (1) redundancy in consecutive CXR sequences, where static anatomical regions dominate over clinically-meaningful dynamics, and (2) temporal misalignment between sparse, irregular imaging and continuous EHR data. We introduce DiPro, a novel framework that addresses these challenges through region-aware disentanglement and multi-timescale alignment. First, we disentangle static (anatomy) and dynamic (pathology progression) features in sequential CXRs, prioritizing disease-relevant changes. Second, we hierarchically align these static and dynamic CXR features with asynchronous EHR data via local (pairwise interval-level) and global (full-sequence) synchronization to model coherent progression pathways. Extensive experiments on the MIMIC dataset demonstrate that DiPro could effectively extract temporal clinical dynamics and achieve state-of-the-art performance on both disease progression identification and general ICU prediction tasks.

Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation. Automating report generation has emerged as a critical need to alleviate the workload of radiologists. While machine learning has facilitated report generation for 2D medical imaging, extending this to 3D has been unexplored due to computational complexity and data scarcity. We introduce the first method to generate radiology reports for 3D medical imaging, specifically targeting chest CT volumes. Given the absence of comparable methods, we establish a baseline using an advanced 3D vision encoder in medical imaging to demonstrate our method's effectiveness, which leverages a novel auto-regressive causal transformer. Furthermore, recognizing the benefits of leveraging information from previous visits, we augment CT2Rep with a cross-attention-based multi-modal fusion module and hierarchical memory, enabling the incorporation of longitudinal multimodal data. Access our code at https://github.com/ibrahimethemhamamci/CT2Rep

The rapid increase of computed tomography (CT) scans and their time-consuming manual analysis have created an urgent need for robust automated analysis techniques in clinical settings. These aim to assist radiologists and help them managing their growing workload. Existing methods typically generate entire reports directly from 3D CT images, without explicitly focusing on observed abnormalities. This unguided approach often results in repetitive content or incomplete reports, failing to prioritize anomaly-specific descriptions. We propose a new anomaly-guided report generation model, which first predicts abnormalities and then generates targeted descriptions for each. Evaluation on a public dataset demonstrates significant improvements in report quality and clinical relevance. We extend our work by conducting an ablation study to demonstrate its effectiveness.

Cardiac MRI, crucial for evaluating heart structure and function, faces limitations like slow imaging and motion artifacts. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on MICCAI. CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techniques, physical modeling, and model complexity, thereby providing valuable insights for further developments in this field.

Purpose: To introduce a deep learning model capable of multi-organ segmentation in MRI scans, offering a solution to the current limitations in MRI analysis due to challenges in resolution, standardized intensity values, and variability in sequences. Materials and Methods: he model was trained on 1,200 manually annotated MRI scans from the UK Biobank, 221 in-house MRI scans and 1228 CT scans, leveraging cross-modality transfer learning from CT segmentation models. A human-in-the-loop annotation workflow was employed to efficiently create high-quality segmentations. The model's performance was evaluated on NAKO and the AMOS22 dataset containing 600 and 60 MRI examinations. Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD) was used to assess segmentation accuracy. The model will be open sourced. Results: The model showcased high accuracy in segmenting well-defined organs, achieving Dice Similarity Coefficient (DSC) scores of 0.97 for the right and left lungs, and 0.95 for the heart. It also demonstrated robustness in organs like the liver (DSC: 0.96) and kidneys (DSC: 0.95 left, 0.95 right), which present more variability. However, segmentation of smaller and complex structures such as the portal and splenic veins (DSC: 0.54) and adrenal glands (DSC: 0.65 left, 0.61 right) revealed the need for further model optimization. Conclusion: The proposed model is a robust, tool for accurate segmentation of 40 anatomical structures in MRI and CT images. By leveraging cross-modality learning and interactive annotation, the model achieves strong performance and generalizability across diverse datasets, making it a valuable resource for researchers and clinicians. It is open source and can be downloaded from https://github.com/hhaentze/MRSegmentator.

Dynamic contrast-enhanced (DCE) MRI is essential for breast cancer diagnosis and treatment. However, its reliance on contrast agents introduces safety concerns, contraindications, increased cost, and workflow complexity. To this end, we present pre-contrast conditioned denoising diffusion probabilistic models to synthesize DCE-MRI, introducing, evaluating, and comparing a total of 22 generative model variants in both single-breast and full breast settings. Towards enhancing lesion fidelity, we introduce both tumor-aware loss functions and explicit tumor segmentation mask conditioning. Using a public multicenter dataset and comparing to respective pre-contrast baselines, we observe that subtraction image-based models consistently outperform post-contrast-based models across five complementary evaluation metrics. Apart from assessing the entire image, we also separately evaluate the region of interest, where both tumor-aware losses and segmentation mask inputs improve evaluation metrics. The latter notably enhance qualitative results capturing contrast uptake, albeit assuming access to tumor localization inputs that are not guaranteed to be available in screening settings. A reader study involving 2 radiologists and 4 MRI technologists confirms the high realism of the synthetic images, indicating an emerging clinical potential of generative contrast-enhancement. We share our codebase at https://github.com/sebastibar/conditional-diffusion-breast-MRI.

Accelerated magnetic resonance (MR) imaging attempts to reduce acquisition time by collecting data below the Nyquist rate. As an ill-posed inverse problem, many plausible solutions exist, yet the majority of deep learning approaches generate only a single solution. We instead focus on sampling from the posterior distribution, which provides more comprehensive information for downstream inference tasks. To do this, we design a novel conditional normalizing flow (CNF) that infers the signal component in the measurement operator's nullspace, which is later combined with measured data to form complete images. Using fastMRI brain and knee data, we demonstrate fast inference and accuracy that surpasses recent posterior sampling techniques for MRI. Code is available at https://github.com/jwen307/mri_cnf/

Multimodal cardiovascular magnetic resonance (CMR) imaging provides comprehensive and non-invasive insights into cardiovascular disease (CVD) diagnosis and underlying mechanisms. Despite decades of advancements, its widespread clinical adoption remains constrained by prolonged scan times and heterogeneity across medical environments. This underscores the urgent need for a generalist reconstruction foundation model for ultra-fast CMR imaging, one capable of adapting across diverse imaging scenarios and serving as the essential substrate for all downstream analyses. To enable this goal, we curate MMCMR-427K, the largest and most comprehensive multimodal CMR k-space database to date, comprising 427,465 multi-coil k-space data paired with structured metadata across 13 international centers, 12 CMR modalities, 15 scanners, and 17 CVD categories in populations across three continents. Building on this unprecedented resource, we introduce CardioMM, a generalist reconstruction foundation model capable of dynamically adapting to heterogeneous fast CMR imaging scenarios. CardioMM unifies semantic contextual understanding with physics-informed data consistency to deliver robust reconstructions across varied scanners, protocols, and patient presentations. Comprehensive evaluations demonstrate that CardioMM achieves state-of-the-art performance in the internal centers and exhibits strong zero-shot generalization to unseen external settings. Even at imaging acceleration up to 24x, CardioMM reliably preserves key cardiac phenotypes, quantitative myocardial biomarkers, and diagnostic image quality, enabling a substantial increase in CMR examination throughput without compromising clinical integrity. Together, our open-access MMCMR-427K database and CardioMM framework establish a scalable pathway toward high-throughput, high-quality, and clinically accessible cardiovascular imaging.

Magnetic Resonance Imaging (MRI) is a crucial imaging modality for viewing internal body structures. This research work analyses the performance of popular GAN models for accurate and precise MRI reconstruction by enhancing image quality and improving diagnostic accuracy. Three GAN architectures considered in this study are Vanilla GAN, Deep Convolutional GAN (DCGAN), and Wasserstein GAN (WGAN). They were trained and evaluated using knee, brain, and cardiac MRI datasets to assess their generalizability across body regions. While the Vanilla GAN operates on the fundamentals of the adversarial network setup, DCGAN advances image synthesis by securing the convolutional layers, giving a superior appearance to the prevalent spatial features. Training instability is resolved in WGAN through the Wasserstein distance to minimize an unstable regime, therefore, ensuring stable convergence and high-quality images. The GAN models were trained and tested using 1000 MR images of an anonymized knee, 805 images of Heart, 90 images of Brain MRI dataset. The Structural Similarity Index (SSIM) for Vanilla GAN is 0.84, DCGAN is 0.97, and WGAN is 0.99. The Peak Signal to Noise Ratio (PSNR) for Vanilla GAN is 26, DCGAN is 49.3, and WGAN is 43.5. The results were further statistically validated. This study shows that DCGAN and WGAN-based frameworks are promising in MR image reconstruction because of good image quality and superior accuracy. With the first cross-organ benchmark of baseline GANs under a common preprocessing pipeline, this work provides a reproducible benchmark for future hybrid GANs and clinical MRI applications.

Multiparametric magnetic resonance imaging (mpMRI) has demonstrated promising results in prostate cancer (PCa) detection using deep convolutional neural networks (CNNs). Recently, transformers have achieved competitive performance compared to CNNs in computer vision. Large-scale transformers need abundant annotated data for training, which are difficult to obtain in medical imaging. Self-supervised learning can effectively leverage unlabeled data to extract useful semantic representations without annotation and its associated costs. This can improve model performance on downstream tasks with limited labelled data and increase generalizability. We introduce a novel end-to-end Cross-Shaped windows (CSwin) transformer UNet model, CSwin UNet, to detect clinically significant prostate cancer (csPCa) in prostate bi-parametric MR imaging (bpMRI) and demonstrate the effectiveness of our proposed self-supervised pre-training framework. Using a large prostate bpMRI dataset with 1500 patients, we first pre-train CSwin transformer using multi-task self-supervised learning to improve data-efficiency and network generalizability. We then finetuned using lesion annotations to perform csPCa detection. Five-fold cross validation shows that self-supervised CSwin UNet achieves 0.888 AUC and 0.545 Average Precision (AP), significantly outperforming four state-of-the-art models (Swin UNETR, DynUNet, Attention UNet, UNet). Using a separate bpMRI dataset with 158 patients, we evaluated our model robustness to external hold-out data. Self-supervised CSwin UNet achieves 0.79 AUC and 0.45 AP, still outperforming all other comparable methods and demonstrating generalization to a dataset shift.

A major challenge of the long measurement times in magnetic resonance imaging (MRI), an important medical imaging technology, is that patients may move during data acquisition. This leads to severe motion artifacts in the reconstructed images and volumes. In this paper, we propose a deep learning-based test-time-training method for accurate motion estimation. The key idea is that a neural network trained for motion-free reconstruction has a small loss if there is no motion, thus optimizing over motion parameters passed through the reconstruction network enables accurate estimation of motion. The estimated motion parameters enable to correct for the motion and to reconstruct accurate motion-corrected images. Our method uses 2D reconstruction networks to estimate rigid motion in 3D, and constitutes the first deep learning based method for 3D rigid motion estimation towards 3D-motion-corrected MRI. We show that our method can provably reconstruct motion parameters for a simple signal and neural network model. We demonstrate the effectiveness of our method for both retrospectively simulated motion and prospectively collected real motion-corrupted data.

Extracranial tissues visible on brain magnetic resonance imaging (MRI) may hold significant value for characterizing health conditions and clinical decision-making, yet they are rarely quantified. Current tools have not been widely validated, particularly in settings of developing brains or underlying pathology. We present TissUnet, a deep learning model that segments skull bone, subcutaneous fat, and muscle from routine three-dimensional T1-weighted MRI, with or without contrast enhancement. The model was trained on 155 paired MRI-computed tomography (CT) scans and validated across nine datasets covering a wide age range and including individuals with brain tumors. In comparison to AI-CT-derived labels from 37 MRI-CT pairs, TissUnet achieved a median Dice coefficient of 0.79 [IQR: 0.77-0.81] in a healthy adult cohort. In a second validation using expert manual annotations, median Dice was 0.83 [IQR: 0.83-0.84] in healthy individuals and 0.81 [IQR: 0.78-0.83] in tumor cases, outperforming previous state-of-the-art method. Acceptability testing resulted in an 89% acceptance rate after adjudication by a tie-breaker(N=108 MRIs), and TissUnet demonstrated excellent performance in the blinded comparative review (N=45 MRIs), including both healthy and tumor cases in pediatric populations. TissUnet enables fast, accurate, and reproducible segmentation of extracranial tissues, supporting large-scale studies on craniofacial morphology, treatment effects, and cardiometabolic risk using standard brain T1w MRI.

Quantitative susceptibility maps from magnetic resonance images can provide both prognostic and diagnostic information in multiple sclerosis, a neurodegenerative disease characterized by the formation of lesions in white matter brain tissue. In particular, susceptibility maps provide adequate contrast to distinguish between "rim" lesions, surrounded by deposited paramagnetic iron, and "non-rim" lesion types. These paramagnetic rim lesions (PRLs) are an emerging biomarker in multiple sclerosis. Much effort has been devoted to both detection and segmentation of such lesions to monitor longitudinal change. As paramagnetic rim lesions are rare, addressing this problem requires confronting the class imbalance between rim and non-rim lesions. We produce synthetic quantitative susceptibility maps of paramagnetic rim lesions and show that inclusion of such synthetic data improves classifier performance and provide a multi-channel extension to generate accompanying contrasts and probabilistic segmentation maps. We exploit the projection capability of our trained generative network to demonstrate a novel denoising approach that allows us to train on ambiguous rim cases and substantially increase the minority class. We show that both synthetic lesion synthesis and our proposed rim lesion label denoising method best approximate the unseen rim lesion distribution and improve detection in a clinically interpretable manner. We release our code and generated data at https://github.com/agr78/PRLx-GAN upon publication.

Accelerating Magnetic Resonance Imaging (MRI) by taking fewer measurements has the potential to reduce medical costs, minimize stress to patients and make MRI possible in applications where it is currently prohibitively slow or expensive. We introduce the fastMRI dataset, a large-scale collection of both raw MR measurements and clinical MR images, that can be used for training and evaluation of machine-learning approaches to MR image reconstruction. By introducing standardized evaluation criteria and a freely-accessible dataset, our goal is to help the community make rapid advances in the state of the art for MR image reconstruction. We also provide a self-contained introduction to MRI for machine learning researchers with no medical imaging background.

Since the introduction of TotalSegmentator CT, there is demand for a similar robust automated MRI segmentation tool that can be applied across all MRI sequences and anatomic structures. In this retrospective study, a nnU-Net model (TotalSegmentator) was trained on MRI and CT examinations to segment 80 anatomic structures relevant for use cases such as organ volumetry, disease characterization, surgical planning and opportunistic screening. Examinations were randomly sampled from routine clinical studies to represent real-world examples. Dice scores were calculated between the predicted segmentations and expert radiologist reference standard segmentations to evaluate model performance on an internal test set, two external test sets and against two publicly available models, and TotalSegmentator CT. The model was applied to an internal dataset containing abdominal MRIs to investigate age-dependent volume changes. A total of 1143 examinations (616 MRIs, 527 CTs) (median age 61 years, IQR 50-72) were split into training (n=1088, CT and MRI) and an internal test set (n=55; only MRI), two external test sets (AMOS, n=20; CHAOS, n=20; only MRI), and an internal aging-study dataset of 8672 abdominal MRIs (median age 59 years, IQR 45-70) were included. The model showed a Dice Score of 0.839 on the internal test set and outperformed two other models (Dice Score, 0.862 versus 0.759; and 0.838 versus 0.560; p<.001 for both). The proposed open-source, easy-to-use model allows for automatic, robust segmentation of 80 structures, extending the capabilities of TotalSegmentator to MRIs of any sequence. The ready-to-use online tool is available at https://totalsegmentator.com, the model at https://github.com/wasserth/TotalSegmentator, and the dataset at https://zenodo.org/records/14710732.

Rationale and Objectives: To develop and validate PARROT (Polyglottal Annotated Radiology Reports for Open Testing), a large, multicentric, open-access dataset of fictional radiology reports spanning multiple languages for testing natural language processing applications in radiology. Materials and Methods: From May to September 2024, radiologists were invited to contribute fictional radiology reports following their standard reporting practices. Contributors provided at least 20 reports with associated metadata including anatomical region, imaging modality, clinical context, and for non-English reports, English translations. All reports were assigned ICD-10 codes. A human vs. AI report differentiation study was conducted with 154 participants (radiologists, healthcare professionals, and non-healthcare professionals) assessing whether reports were human-authored or AI-generated. Results: The dataset comprises 2,658 radiology reports from 76 authors across 21 countries and 13 languages. Reports cover multiple imaging modalities (CT: 36.1%, MRI: 22.8%, radiography: 19.0%, ultrasound: 16.8%) and anatomical regions, with chest (19.9%), abdomen (18.6%), head (17.3%), and pelvis (14.1%) being most prevalent. In the differentiation study, participants achieved 53.9% accuracy (95% CI: 50.7%-57.1%) in distinguishing between human and AI-generated reports, with radiologists performing significantly better (56.9%, 95% CI: 53.3%-60.6%, p<0.05) than other groups. Conclusion: PARROT represents the largest open multilingual radiology report dataset, enabling development and validation of natural language processing applications across linguistic, geographic, and clinical boundaries without privacy constraints.

This paper describes a novel nonparametric model for modeling diffusion MRI signals in q-space. In q-space, diffusion MRI signal is measured for a sequence of magnetic strengths (b-values) and magnetic gradient directions (b-vectors). We propose a Poly-RBF model, which employs a bidirectional framework with polynomial bases to model the signal along the b-value direction and Gaussian radial bases across the b-vectors. The model can accommodate sparse data on b-values and moderately dense data on b-vectors. The utility of Poly-RBF is inspected for two applications: 1) prediction of the dMRI signal, and 2) harmonization of dMRI data collected under different acquisition protocols with different scanners. Our results indicate that the proposed Poly-RBF model can more accurately predict the unmeasured diffusion signal than its competitors such as the Gaussian process model in {\tt Eddy} of FSL. Applying it to harmonizing the diffusion signal can significantly improve the reproducibility of derived white matter microstructure measures.

Early and accurate detection of brain abnormalities, such as tumors and strokes, is essential for timely intervention and improved patient outcomes. In this study, we present a deep learning-based system capable of identifying both brain tumors and strokes from MRI images, along with their respective stages. We have executed two groundbreaking strategies involving convolutional neural networks, MobileNet V2 and ResNet-50-optimized through transfer learning to classify MRI scans into five diagnostic categories. Our dataset, aggregated and augmented from various publicly available MRI sources, was carefully curated to ensure class balance and image diversity. To enhance model generalization and prevent overfitting, we applied dropout layers and extensive data augmentation. The models achieved strong performance, with training accuracy reaching 93\% and validation accuracy up to 88\%. While ResNet-50 demonstrated slightly better results, Mobile Net V2 remains a promising option for real-time diagnosis in low resource settings due to its lightweight architecture. This research offers a practical AI-driven solution for early brain abnormality detection, with potential for clinical deployment and future enhancement through larger datasets and multi modal inputs.

Counterfactual medical image generation enables clinicians to explore clinical hypotheses, such as predicting disease progression, facilitating their decision-making. While existing methods can generate visually plausible images from disease progression prompts, they produce silent predictions that lack interpretation to verify how the generation reflects the hypothesized progression -- a critical gap for medical applications that require traceable reasoning. In this paper, we propose Interpretable Counterfactual Generation (ICG), a novel task requiring the joint generation of counterfactual images that reflect the clinical hypothesis and interpretation texts that outline the visual changes induced by the hypothesis. To enable ICG, we present ICG-CXR, the first dataset pairing longitudinal medical images with hypothetical progression prompts and textual interpretations. We further introduce ProgEmu, an autoregressive model that unifies the generation of counterfactual images and textual interpretations. We demonstrate the superiority of ProgEmu in generating progression-aligned counterfactuals and interpretations, showing significant potential in enhancing clinical decision support and medical education. Project page: https://progemu.github.io.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

Cardiac MRI allows for a comprehensive assessment of myocardial structure, function, and tissue characteristics. Here we describe a foundational vision system for cardiac MRI, capable of representing the breadth of human cardiovascular disease and health. Our deep learning model is trained via self-supervised contrastive learning, by which visual concepts in cine-sequence cardiac MRI scans are learned from the raw text of the accompanying radiology reports. We train and evaluate our model on data from four large academic clinical institutions in the United States. We additionally showcase the performance of our models on the UK BioBank, and two additional publicly available external datasets. We explore emergent zero-shot capabilities of our system, and demonstrate remarkable performance across a range of tasks; including the problem of left ventricular ejection fraction regression, and the diagnosis of 35 different conditions such as cardiac amyloidosis and hypertrophic cardiomyopathy. We show that our deep learning system is capable of not only understanding the staggering complexity of human cardiovascular disease, but can be directed towards clinical problems of interest yielding impressive, clinical grade diagnostic accuracy with a fraction of the training data typically required for such tasks.

A brain tumour is a mass or cluster of abnormal cells in the brain, which has the possibility of becoming life-threatening because of its ability to invade neighbouring tissues and also form metastases. An accurate diagnosis is essential for successful treatment planning and magnetic resonance imaging is the principal imaging modality for diagnostic of brain tumours and their extent. Deep Learning methods in computer vision applications have shown significant improvement in recent years, most of which can be credited to the fact that a sizeable amount of data is available to train models on, and the improvements in the model architectures yielding better approximations in a supervised setting. Classifying tumours using such deep learning methods has made significant progress with the availability of open datasets with reliable annotations. Typically those methods are either 3D models, which use 3D volumetric MRIs or even 2D models considering each slice separately. However, by treating the slice spatial dimension separately, spatiotemporal models can be employed as spatiospatial models for this task. These models have the capabilities of learning specific spatial and temporal relationship, while reducing computational costs. This paper uses two spatiotemporal models, ResNet (2+1)D and ResNet Mixed Convolution, to classify different types of brain tumours. It was observed that both these models performed superior to the pure 3D convolutional model, ResNet18. Furthermore, it was also observed that pre-training the models on a different, even unrelated dataset before training them for the task of tumour classification improves the performance. Finally, Pre-trained ResNet Mixed Convolution was observed to be the best model in these experiments, achieving a macro F1-score of 0.93 and a test accuracy of 96.98\%, while at the same time being the model with the least computational cost.

The ODELIA Breast MRI Challenge 2025 addresses a critical issue in breast cancer screening: improving early detection through more efficient and accurate interpretation of breast MRI scans. Even though methods for general-purpose whole-body lesion segmentation as well as multi-time-point analysis exist, breast cancer detection remains highly challenging, largely due to the limited availability of high-quality segmentation labels. Therefore, developing robust classification-based approaches is crucial for the future of early breast cancer detection, particularly in applications such as large-scale screening. In this write-up, we provide a comprehensive overview of our approach to the challenge. We begin by detailing the underlying concept and foundational assumptions that guided our work. We then describe the iterative development process, highlighting the key stages of experimentation, evaluation, and refinement that shaped the evolution of our solution. Finally, we present the reasoning and evidence that informed the design choices behind our final submission, with a focus on performance, robustness, and clinical relevance. We release our full implementation publicly at https://github.com/MIC-DKFZ/MeisenMeister