MRI-based Deep Radiomic Phenotyping of Neuromuscular Disorders: A Topology-driven Characterization

Quantitative assessment of muscle MRI is crucial for monitoring neuromuscular disorders (NMD). This study introduces an automated radiomic phenotyping framework based on original features engineered across five main architectural domains: quantitative morphometry, spatial distribution, geometric shape, interactions between progressive fat replacement stages, and graph-based topology. Utilizing 1184 MRI scans from the CoMPaSS-NMD project, we map the complex 3D architecture of heterogeneous intramuscular lipodegeneration into objective, morphologically interpretable biomarkers. We introduce a graph-based skeletonization of fat infiltrates to quantify muscle architectural changes, establishing a multi-dimensional extension of traditional, spatially-agnostic volume metrics by mapping topological networks across the entire 3D muscle volume. Statistical screening via non-parametric Kruskal-Wallis analysis confirmed the discriminative power of these novel descriptors across the genetic hierarchy. Notably, topological network metrics (e.g., SF1_Skel_Nodes, $ε^2$ = 0.2656) and interface dynamics metrics (e.g., SF2_To_SF1_Dist_Min, $ε^2$ = 0.2092) demonstrated substantial effect sizes, providing deeper structural insights than classical volumetric assessments. Post-hoc pairwise evaluations and UMAP projections further indicated the capability of these topological and 3D geometric invariants to capture disease-specific macroscopic infiltration patterns. These results demonstrate that global architectural features represent a highly promising class of biomarkers for differential diagnosis, offering new avenues for tracking longitudinal disease dynamics in neuromuscular diagnostics. The developed automated feature extraction pipeline is integrated and available within the MUSCAT (MUSCle fAt Topology) library.

Measurements Automatically Extracted from Zero Echo Time MRI Using Deep Learning Image Segmentation and Geometric Modeling Agree with Expert Manual Readings

Computed tomography (CT) remains the reference for 3D osseous morphometry in femoroacetabular impingement (FAI) but requires ionizing radiation and manual measurement. Zero echo time (ZTE) MRI visualizes cortical bone and yields FAI angles that agree with CT, but automated angle extraction remains limited. We developed and validated automated FAI angle computation from ZTE MRI and assessed agreement with expert manual measurements in a cross-sectional study (level of evidence, 3). Pelvic ZTE MRI was acquired in 73 participants (mean age 36.8 +/- 18.5 years; 51 women, 22 men), yielding 135 hips. nnU-Net was trained on 100 manually curated hips to segment the femur, pelvis, and three osseous landmarks. Custom geometric algorithms computed alpha, femoral neck-shaft, Tonnis, coronal and sagittal center-edge, and acetabular version angles from inferred segmentations. Measurements on 35 test hips were compared with the mean of two radiologists' manual measures using intraclass correlation (ICC) and Bland-Altman analysis. Dice exceeded 0.96 for bone and ranged from 0.65 to 0.83 for landmarks. Median landmark error was 0.38 mm (femoral head), 0.82 mm (lateral acetabulum), and <2.5 mm (medial acetabulum, greater trochanter). Interrater ICC was excellent for acetabular version, coronal center-edge, and Tonnis (>=0.82) but poor for alpha and femoral neck-shaft. Model versus rater-mean agreement was excellent for acetabular version, coronal center-edge, and Tonnis (0.92-0.96), good for mid-acetabular sagittal center-edge (0.74), and fair for alpha (0.45) and femoral neck-shaft (0.55). Model Bland-Altman limits of agreement were narrower than interrater limits for most angles. Fully automated morphometric assessment from ZTE MRI is feasible and performs comparably to expert readers for most coverage and version angles.

Female-RHINO: A Real-Time Scanner-Integrated Framework for Automated Quantitative Uterine MRI Analysis and Structured Reporting

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

SpineReport: Automated 3D Quantification and Reporting of Lumbar Spine Degeneration on MRI

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

A multi-agent system for spine MRI report generation from multi-sequence imaging

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

An interpretable and trustworthy AI framework for large-scale longitudinal structure-pain association studies using data from the Osteoarthritis Initiative (OAI)

Purpose: To develop an interpretable and trustworthy AI framework that combines deep learning based MRI Osteoarthritis Knee Score (MOAKS) prediction with interpretable statistical modeling to study structure-pain relationships at scale using data from the Osteoarthritis Initiative (OAI). Materials and Methods: We first developed a deep learning framework to predict MOAKS features directly from knee MRIs and incorporated conformal prediction to provide prediction uncertainty quantification. This uncertainty-aware strategy enables explicit filtering of model outputs, retaining only high-confidence MOAKS predictions at the knee level. Second, we applied a longitudinal latent class mixed model (LCMM) to examine associations between key structural abnormalities and four complementary knee pain measurements. Results: Among the three MRI-defined abnormalities (i.e., bone marrow lesions (BML), cartilage loss (CART), and meniscal extrusion (ME)), our framework substantially improved the Matthews correlation coefficient (MCC) and some other metrics. For example, MCC increased from 0.69 to 0.91 for BML, from 0.45 to 0.80 for CART, and from 0.59 to 0.89 for ME. Using these high-confidence predictions, we expanded the sample size to 2,175 knees for the LCMM analysis. Two distinct pain trajectories were identified (rapid and stable pain progression). The estimated odds ratios (95% CI) for the rapid progression group were 1.62 (1.12-2.35) for BML, 1.83 (1.24-2.70) for CART loss, and 2.50 (1.75-3.57) for ME. Conclusion: These results highlight the importance of these structural abnormalities as risk factors for pain and functional progression in osteoarthritis.