Brain network analysis plays a crucial role in identifying distinctive patterns associated with neurological disorders. Functional magnetic resonance imaging (fMRI) enables the construction of brain networks by analyzing correlations in blood-oxygen-level-dependent (BOLD) signals across different brain regions, known as regions of interest (ROIs). These networks are typically constructed using atlases that parcellate the brain based on various hypotheses of functional and anatomical divisions. However, there is no standard atlas for brain network classification, leading to limitations in detecting abnormalities in disorders. Recent methods leveraging multiple atlases fail to ensure consistency across atlases and lack effective ROI-level information exchange, limiting their efficacy. To address these challenges, we propose the Atlas-Integrated Distillation and Fusion network (AIDFusion), a novel framework designed to enhance brain network classification using fMRI data. AIDFusion introduces a disentangle Transformer to filter out inconsistent atlas-specific information and distill meaningful cross-atlas connections. Additionally, it enforces subject- and population-level consistency constraints to improve cross-atlas coherence. To further enhance feature integration, AIDFusion incorporates an inter-atlas message-passing mechanism that facilitates the fusion of complementary information across brain regions. We evaluate AIDFusion on four resting-state fMRI datasets encompassing different neurological disorders. Experimental results demonstrate its superior classification performance and computational efficiency compared to state-of-the-art methods. Furthermore, a case study highlights AIDFusion's ability to extract interpretable patterns that align with established neuroscience findings, reinforcing its potential as a robust tool for multi-atlas brain network analysis. The code is publicly available at https://github.com/AngusMonroe/AIDFusion.

The emergence of Large Language Models (LLMs) presents unprecedented opportunities to revolutionize medical contrastive vision-language pre-training. In this paper, we show how LLMs can facilitate large-scale supervised pre-training, thereby advancing vision-language alignment. We begin by demonstrate that modern LLMs can automatically extract diagnostic labels from radiology reports with remarkable precision (>96\% AUC in our experiments) without complex prompt engineering, enabling the creation of large-scale "silver-standard" datasets at a minimal cost (~\$3 for 50k CT image-report pairs). Further, we find that vision encoder trained on this "silver-standard" dataset achieves performance comparable to those trained on labels extracted by specialized BERT-based models, thereby democratizing the access to large-scale supervised pre-training. Building on this foundation, we proceed to reveal that supervised pre-training fundamentally improves contrastive vision-language alignment. Our approach achieves state-of-the-art performance using only a 3D ResNet-18 with vanilla CLIP training, including 83.8\% AUC for zero-shot diagnosis on CT-RATE, 77.3\% AUC on RAD-ChestCT, and substantial improvements in cross-modal retrieval (MAP@50=53.7\% for image-image, Recall@100=52.2\% for report-image). These results demonstrate the potential of utilizing LLMs to facilitate {\bf more performant and scalable} medical AI systems. Our code is avaiable at https://github.com/SadVoxel/More-performant-and-scalable.

Accurate 3D medical image segmentation is crucial for diagnosis and treatment. Diffusion models demonstrate promising performance in medical image segmentation tasks due to the progressive nature of the generation process and the explicit modeling of data distributions. However, the weak guidance of conditional information and insufficient feature extraction in diffusion models lead to the loss of fine-grained features and structural consistency in the segmentation results, thereby affecting the accuracy of medical image segmentation. To address this challenge, we propose a Mamba-Enhanced Diffusion Model for 3D Medical Image Segmentation. We extract multilevel semantic features from the original images using an encoder and tightly integrate them with the denoising process of the diffusion model through a Semantic Hierarchical Embedding (SHE) mechanism, to capture the intricate relationship between the noisy label and image data. Meanwhile, we design a Global-Slice Perception Mamba (GSPM) layer, which integrates multi-dimensional perception mechanisms to endow the model with comprehensive spatial reasoning and feature extraction capabilities. Experimental results show that our proposed MambaDiff achieves more competitive performance compared to prior arts with substantially fewer parameters on four public medical image segmentation datasets including BraTS 2021, BraTS 2024, LiTS and MSD Hippocampus. The source code of our method is available at https://github.com/yuliu316316/MambaDiff.

Understanding 3D medical image volumes is critical in the medical field, yet existing 3D medical convolution and transformer-based self-supervised learning (SSL) methods often lack deep semantic comprehension. Recent advancements in multimodal large language models (MLLMs) provide a promising approach to enhance image understanding through text descriptions. To leverage these 2D MLLMs for improved 3D medical image understanding, we propose Med3DInsight, a novel pretraining framework that integrates 3D image encoders with 2D MLLMs via a specially designed plane-slice-aware transformer module. Additionally, our model employs a partial optimal transport based alignment, demonstrating greater tolerance to noise introduced by potential noises in LLM-generated content. Med3DInsight introduces a new paradigm for scalable multimodal 3D medical representation learning without requiring human annotations. Extensive experiments demonstrate our state-of-the-art performance on two downstream tasks, i.e., segmentation and classification, across various public datasets with CT and MRI modalities, outperforming current SSL methods. Med3DInsight can be seamlessly integrated into existing 3D medical image understanding networks, potentially enhancing their performance. Our source code, generated datasets, and pre-trained models will be available upon acceptance.

The fine-grained surface reconstruction of different organs from 3D medical imaging can provide advanced diagnostic support and improved surgical planning. However, the representation of the organs is often limited by the resolution, with a detailed higher resolution requiring more memory and computing footprint. Implicit representations of objects have been proposed to alleviate this problem in general computer vision by providing compact and differentiable functions to represent the 3D object shapes. However, architectural and data-related differences prevent the direct application of these methods to medical images. This work introduces ImplMORe, an end-to-end deep learning method using implicit surface representations for multi-organ reconstruction from 3D medical images. ImplMORe incorporates local features using a 3D CNN encoder and performs multi-scale interpolation to learn the features in the continuous domain using occupancy functions. We apply our method for single and multiple organ reconstructions using the totalsegmentator dataset. By leveraging the continuous nature of occupancy functions, our approach outperforms the discrete explicit representation based surface reconstruction approaches, providing fine-grained surface details of the organ at a resolution higher than the given input image. The source code will be made publicly available at: https://github.com/CAMMA-public/ImplMORe

Artificial intelligence (AI) that can effectively learn ultrasound representations by integrating multi-source data holds significant promise for advancing clinical care. However, the scarcity of large labeled datasets in real-world clinical environments and the limited generalizability of task-specific models have hindered the development of generalizable clinical AI models for ultrasound applications. In this study, we present EchoCare, a novel ultrasound foundation model for generalist clinical use, developed via self-supervised learning on our curated, publicly available, large-scale dataset EchoCareData. EchoCareData comprises 4.5 million ultrasound images, sourced from over 23 countries across 5 continents and acquired via a diverse range of distinct imaging devices, thus encompassing global cohorts that are multi-center, multi-device, and multi-ethnic. Unlike prior studies that adopt off-the-shelf vision foundation model architectures, we introduce a hierarchical classifier into EchoCare to enable joint learning of pixel-level and representation-level features, capturing both global anatomical contexts and local ultrasound characteristics. With minimal training, EchoCare outperforms state-of-the-art comparison models across 10 representative ultrasound benchmarks of varying diagnostic difficulties, spanning disease diagnosis, lesion segmentation, organ detection, landmark prediction, quantitative regression, imaging enhancement and report generation. The code and pretrained model are publicly released, rendering EchoCare accessible for fine-tuning and local adaptation, supporting extensibility to additional applications. EchoCare provides a fully open and generalizable foundation model to boost the development of AI technologies for diverse clinical ultrasound applications.

Cone-Beam Computed Tomography (CBCT) is a widely used 3D imaging technique in dentistry, providing volumetric information about the anatomical structures of jaws and teeth. Accurate segmentation of these anatomies is critical for clinical applications such as diagnosis and surgical planning, but remains time-consuming and challenging. In this paper, we present U-Mamba2, a new neural network architecture designed for multi-anatomy CBCT segmentation in the context of the ToothFairy3 challenge. U-Mamba2 integrates the Mamba2 state space models into the U-Net architecture, enforcing stronger structural constraints for higher efficiency without compromising performance. In addition, we integrate interactive click prompts with cross-attention blocks, pre-train U-Mamba2 using self-supervised learning, and incorporate dental domain knowledge into the model design to address key challenges of dental anatomy segmentation in CBCT. Extensive experiments, including independent tests, demonstrate that U-Mamba2 is both effective and efficient, securing top 3 places in both tasks of the Toothfairy3 challenge. In Task 1, U-Mamba2 achieved a mean Dice of 0.792, HD95 of 93.19 with the held-out test data, with an average inference time of XX (TBC during the ODIN workshop). In Task 2, U-Mamba2 achieved the mean Dice of 0.852 and HD95 of 7.39 with the held-out test data. The code is publicly available at https://github.com/zhiqin1998/UMamba2.

Anomaly detection and classification in medical imaging are critical for early diagnosis but remain challenging due to limited annotated data, class imbalance, and the high cost of expert labeling. Emerging vision foundation models such as DINOv2, pretrained on extensive, unlabeled datasets, offer generalized representations that can potentially alleviate these limitations. In this study, we propose an attention-based global aggregation framework tailored specifically for 3D medical image anomaly classification. Leveraging the self-supervised DINOv2 model as a pretrained feature extractor, our method processes individual 2D axial slices of brain MRIs, assigning adaptive slice-level importance weights through a soft attention mechanism. To further address data scarcity, we employ a composite loss function combining supervised contrastive learning with class-variance regularization, enhancing inter-class separability and intra-class consistency. We validate our framework on the ADNI dataset and an institutional multi-class headache cohort, demonstrating strong anomaly classification performance despite limited data availability and significant class imbalance. Our results highlight the efficacy of utilizing pretrained 2D foundation models combined with attention-based slice aggregation for robust volumetric anomaly detection in medical imaging. Our implementation is publicly available at https://github.com/Rafsani/DinoAtten3D.git.

The utility of Magnetic Resonance Imaging (MRI) in anomaly detection and disease diagnosis is well recognized. However, the current imaging protocol is often hindered by long scanning durations and a misalignment between the scanning process and the specific requirements of subsequent clinical assessments. While recent studies have actively explored accelerated MRI techniques, the majority have concentrated on improving overall image quality across all voxel locations, overlooking the attention to specific abnormalities that hold clinical significance. To address this discrepancy, we propose a model-unrolled deep-learning method, guided by weakly supervised lesion attention, for accelerated MRI oriented by downstream clinical needs. In particular, we construct a lesion-focused MRI reconstruction model, which incorporates customized learnable regularizations that can be learned efficiently by using only image-level labels to improve potential lesion reconstruction but preserve overall image quality. We then design a dedicated iterative algorithm to solve this task-driven reconstruction model, which is further unfolded as a cascaded deep network for lesion-focused fast imaging. Comprehensive experiments on two public datasets, i.e., fastMRI and Stanford Knee MRI Multi-Task Evaluation (SKM-TEA), demonstrate that our approach, referred to as Lesion-Focused MRI (LF-MRI), surpassed existing accelerated MRI methods by relatively large margins. Remarkably, LF-MRI led to substantial improvements in areas showing pathology. The source code and pretrained models will be publicly available at https://github.com/ladderlab-xjtu/LF-MRI.

BackgroundBrain atrophy is a hallmark of multiple sclerosis (MS). For clinical translatability and individual-level predictions, brain atrophy needs to be put into context of the broader population, using reference or normative models. MethodsReference models of MRI-derived brain volumes were established from a large healthy control (HC) multi-cohort dataset (N=63 115, 51% females). The reference models were applied to two independent MS cohorts (N=362, T1w-scans=953, follow-up time up to 12 years) to assess deviations from the reference, defined as Z-values. We assessed the overlap of deviation profiles and their stability over time using individual-level transitions towards or out of significant reference deviation states (|Z|>1{middle dot}96). A negative binomial model was used for case-control comparisons of the number of extreme deviations. Linear models were used to assess differences in Z-score deviations between MS and propensity-matched HCs, and associations with clinical scores at baseline and over time. The utilized normative BrainReference models, scripts and usage instructions are freely available. FindingsWe identified a temporally stable, brain morphometric phenotype of MS. The right and left thalami most consistently showed significantly lower-than-reference volumes in MS (25% and 26% overlap across the sample). The number of such extreme smaller-than-reference values was 2{middle dot}70 in MS compared to HC (4{middle dot}51 versus 1{middle dot}67). Additional deviations indicated stronger disability (Expanded Disability Status Scale: {beta}=0{middle dot}22, 95% CI 0{middle dot}12 to 0{middle dot}32), Paced Auditory Serial Addition Test score ({beta}=-0{middle dot}27, 95% CI -0{middle dot}52 to -0{middle dot}02), and Fatigue Severity Score ({beta}=0{middle dot}29, 95% CI 0{middle dot}05 to 0{middle dot}53) at baseline, and over time with EDSS ({beta}=0{middle dot}07, 95% CI 0{middle dot}02 to 0{middle dot}13). We additionally provide detailed maps of reference-deviations and their associations with clinical assessments. InterpretationWe present a heterogenous brain phenotype of MS which is associated with clinical manifestations, and particularly implicating the thalamus. The findings offer potential to aid diagnosis and prognosis of MS. FundingNorwegian MS-union, Research Council of Norway (#223273; #324252); the South-Eastern Norway Regional Health Authority (#2022080); and the European Unions Horizon2020 Research and Innovation Programme (#847776, #802998). Research in contextO_ST_ABSEvidence before this studyC_ST_ABSReference values and normative models have yet to be widely applied to neuroimaging assessments of neurological disorders such as multiple sclerosis (MS). We conducted a literature search in PubMed and Embase (Jan 1, 2000-September 12, 2025) using the terms "MRI" AND "multiple sclerosis", with and without the keywords "normative model*" and "atrophy", without language restrictions. While normative models have been applied in psychiatric and developmental disorders, few studies have addressed their use in neurological conditions. Existing MS research has largely focused on global atrophy and has not provided regional reference charts or established links to clinical and cognitive outcomes. Added value of this studyWe provide regionally detailed brain morphometry maps derived from a heterogeneous MS cohort spanning wide ranges of age, sex, clinical phenotype, disease duration, disability, and scanner characteristics. By leveraging normative modelling, our approach enables individualised brain phenotyping of MS in relation to a population based normative sample. The analyses reveal clinically meaningful and spatially consistent patterns of smaller brain volumes, particularly in the thalamus and frontal cortical regions, which are linked to disability, cognitive impairment, and fatigue. Robustness across scanners, centres, and longitudinal follow-up supports the stability and generalisability of these findings to real-world MS populations. Implications of all the available evidenceNormative modelling offers an individualised, sensitive, and interpretable approach to quantifying brain structure in MS by providing individual-specific reference values, supporting earlier detection of neurodegeneration and improved patient stratification. A consistent pattern of thalamic and fronto-parietal deviations defines a distinct morphometric profile of MS, with potential utility for early and personalised diagnosis and disease monitoring in clinical practice and clinical trials.