Medical segmentation plays an important role in clinical applications like radiation therapy and surgical guidance, but acquiring clinically acceptable results is difficult. In recent years, progress has been witnessed with the success of utilizing transformer-like models, such as combining the attention mechanism with CNN. In particular, transformer-based segmentation models can extract global information more effectively, compensating for the drawbacks of CNN modules that focus on local features. However, utilizing transformer architecture is not easy, because training transformer-based models can be resource-demanding. Moreover, due to the distinct characteristics in the medical field, especially when encountering mid-sized and small organs with compact regions, their results often seem unsatisfactory. For example, using ViT to segment medical images directly only gives a DSC of less than 50\%, which is far lower than the clinically acceptable score of 80\%. In this paper, we used Mask2Former with deformable attention to reduce computation and proposed offset adjustment strategies to encourage sampling points within the same organs during attention weights computation, thereby integrating compact foreground information better. Additionally, we utilized the 4th feature map in Mask2Former to provide a coarse location of organs, and employed an FCN-based auxiliary head to help train Mask2Former more quickly using Dice loss. We show that our model achieves SOTA (State-of-the-Art) performance on the HaNSeg and SegRap2023 datasets, especially on mid-sized and small organs.Our code is available at link https://github.com/earis/Offsetadjustment\_Background-location\_Decoder\_Mask2former.

Correcting motion artifacts in MRI is important, as they can hinder accurate diagnosis. However, evaluating deep learning-based and classical motion correction methods remains fundamentally difficult due to the lack of accessible ground-truth target data. To address this challenge, we study three evaluation approaches: real-world evaluation based on reference scans, simulated motion, and reference-free evaluation, each with its merits and shortcomings. To enable evaluation with real-world motion artifacts, we release PMoC3D, a dataset consisting of unprocessed Paired Motion-Corrupted 3D brain MRI data. To advance evaluation quality, we introduce MoMRISim, a feature-space metric trained for evaluating motion reconstructions. We assess each evaluation approach and find real-world evaluation together with MoMRISim, while not perfect, to be most reliable. Evaluation based on simulated motion systematically exaggerates algorithm performance, and reference-free evaluation overrates oversmoothed deep learning outputs.

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.

Sparse-view computed tomography (CT) is a practical solution to reduce radiation dose, but the resulting ill-posed inverse problem poses significant challenges for accurate image reconstruction. Although deep learning and diffusion-based methods have shown promising results, they often lack physical interpretability or suffer from high computational costs due to iterative sampling starting from random noise. Recent advances in generative modeling, particularly Poisson Flow Generative Models (PFGM), enable high-fidelity image synthesis by modeling the full data distribution. In this work, we propose Residual Poisson Flow (ResPF) Generative Models for efficient and accurate sparse-view CT reconstruction. Based on PFGM++, ResPF integrates conditional guidance from sparse measurements and employs a hijacking strategy to significantly reduce sampling cost by skipping redundant initial steps. However, skipping early stages can degrade reconstruction quality and introduce unrealistic structures. To address this, we embed a data-consistency into each iteration, ensuring fidelity to sparse-view measurements. Yet, PFGM sampling relies on a fixed ordinary differential equation (ODE) trajectory induced by electrostatic fields, which can be disrupted by step-wise data consistency, resulting in unstable or degraded reconstructions. Inspired by ResNet, we introduce a residual fusion module to linearly combine generative outputs with data-consistent reconstructions, effectively preserving trajectory continuity. To the best of our knowledge, this is the first application of Poisson flow models to sparse-view CT. Extensive experiments on synthetic and clinical datasets demonstrate that ResPF achieves superior reconstruction quality, faster inference, and stronger robustness compared to state-of-the-art iterative, learning-based, and diffusion models.

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.

IntroductionThe assessment of vestibular schwannoma (VS) requires a standardized measurement approach as growth is a key element in defining treatment strategy for VS. Volumetric measurements offer higher sensitivity and precision, but existing methods of segmentation, are labour-intensive, lack standardisation and are prone to variability and subjectivity. A new core set of measurement indicators reported consistently, will support clinical decision-making and facilitate evidence synthesis. This systematic review aimed to identify indicators used in 1) magnetic resonance imaging (MRI) acquisition and 2) measurement or 3) growth of VS. This work is expected to inform a Delphi consensus. MethodsSystematic searches of Medline, Embase and Cochrane Central were undertaken on 4th October 2024. Studies that assessed the evaluation of VS with MRI, between 2014 and 2024 were included. ResultsThe final dataset consisted of 102 studies and 19001 patients. Eighty-six (84.3%) studies employed post contrast T1 as the MRI acquisition of choice for evaluating VS. Nine (8.8%) studies additionally employed heavily weighted T2 sequences such as constructive interference in steady state (CISS) and FIESTA-C. Only 45 (44.1%) studies reported the slice thickness with the majority 38 (84.4%) choosing <3mm in thickness. Fifty-eight (56.8%) studies measured volume whilst 49 (48.0%) measured the largest linear dimension; 14 (13.7%) studies used both measurements. Four studies employed semi-automated or automated segmentation processes to measure the volumes of VS. Of 68 studies investigating growth, 54 (79.4%) provided a threshold. Significant variation in volumetric growth was observed but the threshold for significant percentage change reported by most studies was 20% (n = 18). ConclusionSubstantial variation in MRI acquisition, and methods for evaluating measurement and growth of VS, exists across the literature. This lack of standardization is likely attributed to resource constraints and the fact that currently available volumetric segmentation methods are very labour-intensive. Following the identification of the indicators employed in the literature, this study aims to develop a Delphi consensus for the standardized measurement of VS and uptake in employing a data-driven artificial intelligence-based measuring tools.

Body mass index (BMI) does not account for substantial inter-individual differences in regional fat and muscle compartments, which are relevant for the prevalence of cardiometabolic and cancer conditions. We applied a validated deep learning pipeline for automated segmentation of whole-body MRI scans in 45,851 adults from the UK Biobank and German National Cohort, enabling harmonized quantification of visceral (VAT), gluteofemoral (GFAT), and abdominal subcutaneous adipose tissue (ASAT), liver fat fraction (LFF), and trunk muscle volume. Associations with clinical conditions were evaluated using compartment measures adjusted for age, sex, height, and BMI. Our analysis demonstrates that regional adiposity and muscle volume show distinct associations with cardiometabolic and cancer prevalence, and that substantial disease heterogeneity exists within BMI strata. The analytic framework and reference data presented here will support future risk stratification efforts and facilitate the integration of automated MRI phenotyping into large-scale population and clinical research.

Glaucoma is increasingly recognized as a neurodegenerative condition involving both retinal and central nervous system structures. Here, we present an integrated framework that combines MK-Curve-corrected diffusion kurtosis imaging (DKI), tractometry, and deep autoencoder-based normative modeling to detect localized white matter abnormalities associated with glaucoma. Using UK Biobank diffusion MRI data, we show that MK-Curve approach corrects anatomically implausible values and improves the reliability of DKI metrics - particularly mean (MK), radial (RK), and axial kurtosis (AK) - in regions of complex fiber architecture. Tractometry revealed reduced MK in glaucoma patients along the optic radiation, inferior longitudinal fasciculus, and inferior fronto-occipital fasciculus, but not in a non-visual control tract, supporting disease specificity. These abnormalities were spatially localized, with significant changes observed at multiple points along the tracts. MK demonstrated greater sensitivity than MD and exhibited altered distributional features, reflecting microstructural heterogeneity not captured by standard metrics. Node-wise MK values in the right optic radiation showed weak but significant correlations with retinal OCT measures (ganglion cell layer and retinal nerve fiber layer thickness), reinforcing the biological relevance of these findings. Deep autoencoder-based modeling further enabled subject-level anomaly detection that aligned spatially with group-level changes and outperformed traditional approaches. Together, our results highlight the potential of advanced diffusion modeling and deep learning for sensitive, individualized detection of glaucomatous neurodegeneration and support their integration into future multimodal imaging pipelines in neuro-ophthalmology.

Epiretinal membrane (ERM) is a vitreoretinal interface disease that, if not properly addressed, can lead to vision impairment and negatively affect quality of life. For ERM detection and treatment planning, Optical Coherence Tomography (OCT) has become the primary imaging modality, offering non-invasive, high-resolution cross-sectional imaging of the retina. Deep learning models have also led to good ERM detection performance on OCT images. Nevertheless, most deep learning models cannot be easily understood by clinicians, which limits their acceptance in clinical practice. Post-hoc explanation methods have been utilised to support the uptake of models, albeit, with partial success. In this study, we trained a sparse BagNet model, an inherently interpretable deep learning model, to detect ERM in OCT images. It performed on par with a comparable black-box model and generalised well to external data. In a multitask setting, it also accurately predicted other changes related to the ERM pathophysiology. Through a user study with ophthalmologists, we showed that the visual explanations readily provided by the sparse BagNet model for its decisions are well-aligned with clinical expertise. We propose potential directions for clinical implementation of the sparse BagNet model to guide clinical decisions in practice.

Transparency is a paramount concern in the medical field, prompting researchers to delve into the realm of explainable AI (XAI). Among these XAI methods, Concept Bottleneck Models (CBMs) aim to restrict the model's latent space to human-understandable high-level concepts by generating a conceptual layer for extracting conceptual features, which has drawn much attention recently. However, existing methods rely solely on concept features to determine the model's predictions, which overlook the intrinsic feature embeddings within medical images. To address this utility gap between the original models and concept-based models, we propose Vision Concept Transformer (VCT). Furthermore, despite their benefits, CBMs have been found to negatively impact model performance and fail to provide stable explanations when faced with input perturbations, which limits their application in the medical field. To address this faithfulness issue, this paper further proposes the Stable Vision Concept Transformer (SVCT) based on VCT, which leverages the vision transformer (ViT) as its backbone and incorporates a conceptual layer. SVCT employs conceptual features to enhance decision-making capabilities by fusing them with image features and ensures model faithfulness through the integration of Denoised Diffusion Smoothing. Comprehensive experiments on four medical datasets demonstrate that our VCT and SVCT maintain accuracy while remaining interpretable compared to baselines. Furthermore, even when subjected to perturbations, our SVCT model consistently provides faithful explanations, thus meeting the needs of the medical field.