Individual intervertebral disc (IVD) characteristics contribute to spinal mechanics and pain, but individualized biomechanical modeling is insufficiently examined, especially regarding the validity of using a single material model across different degeneration grades and disc geometries. Based on MRI images, we generated and simulated 241 patient-specific lumbar finite element method (FEM) IVD models using a single material model calibrated to a healthy L4-L5 disc. This study is twofold: In one respect, it establishes and evaluates the automated morphing algorithm femReg, which is used to generate the models. In another respect, it evaluates the capacity of the geometry-only individualized IVD models to represent the range of motion (ROM) of variously degenerated discs by simulating them in four load cases under 1, 2.5, 5 and 7.5 Nm load. To do so, we grouped numerical models by height loss and compared absolute and normalized ROM results with in vitro data across different degeneration grades. 241 high-quality hexahedral IVD models (mean aspect ratio: 1.65, mean Hausdorff distance: 0.037 mm) were created and simulated within an average runtime of 6 minutes per IVD. Healthy models (n = 149) reproduced experimental ROM with root mean square errors (RMSEs) of 0.96∘-2.05∘ across bending load cases. The closest agreement was observed in lateral bending (RMSE = 0.68∘), where facet joint contributions are minimal. In contrast, degenerated models exhibited reduced height-normalized ROM compared with in vitro data (RMSE = 0.05-0.24∘/mm), indicating an effectively stiffer response and suggesting that degeneration-specific material parameters, such as fiber loosening or reduced hydration, should be incorporated to better capture pathological behavior.

Abstract Rib-cage morphology is a determinant of thoracic biomechanics, ventilation, and injury response, yet statistical shape models (SSMs) of the rib cage have relied on small cohorts (∼100s of individuals) imaged by clinical computed tomography, which over-represents injury and disease. We constructed a surface-based SSM of the complete 24-rib cage from 26,275 standardised whole-body magnetic resonance imaging (MRI) scans of adults aged 19–74 years from the population-based German National Cohort (NAKO). Ribs were segmented with a deep- learning pipeline (a rib-extended SPINEPS model), reconstructed as per-rib surface meshes, and brought into dense vertex-wise correspondence by Gaussian-process morphable registration in Scalismo; the aligned ensemble was summarised by generalised Procrustes analysis and principal component analysis (PCA). Fourteen per-rib geometric descriptors provided a quantitative cross- walk between the abstract PCA modes and named shape features, and associations with sex, age, body size and composition (including body-fat percentage), and smoking exposure were estimated by multivariable regression with Benjamini–Hochberg false-discovery-rate control. Shape variation was strongly concentrated: 28 modes captured 95% of the total variance, and the first three alone accounted for 69.4% (PC1, 42.6%; PC2, 16.3%; PC3, 10.5%) and admitted consistent anatomical readings – a sexually dimorphic axis (PC1), a slender-versus-stout body- habitus contrast (PC2), and a free-rib-size axis at ribs 11–12 (PC3). The sexes were nearly fully separated along PC1 (Cohen’s d = 2.52). Body mass and body-fat percentage were the dominant modifiable correlates of rib-cage shape, whereas the association with cumulative smoking exposure was comparatively small. The model is released as a population-representative geometric reference for benchmarking and morphing donor-derived finite-element human-body models and for further large-cohort shape analysis.

Thoracolumbar stump ribs are one of the essential indicators of thoracolumbar transitional vertebrae or enumeration anomalies. While some studies manually assess these anomalies and describe the ribs qualitatively, this study aims to automate thoracolumbar stump rib detection and analyze their morphology quantitatively. To this end, we train a high-resolution deep learning model for rib segmentation using nnUNet and achieve significant improvements over existing models (Dice score 0.997 vs. 0.779, p-value < 0.01). In addition, we employ a novel iterative algorithm and piecewise linear interpolation to estimate rib length, achieving a success rate of 98.2%. When analyzing morphological features, we show that stump ribs articulate more posteriorly at the vertebrae (-19.2 +/- 3.8 vs. -13.8 +/- 2.5 mm, p-value < 0.01), are thinner (260.6 +/- 103.4 vs. 563.6 +/- 127.1 mm2, p-value < 0.01), and are oriented more downwards and sideways within the first centimeters in contrast to full-length ribs. We show that with partially visible ribs, these features can achieve an F1-score of 0.84 and an AUC of 0.98 in differentiating stump ribs from regular ones. We publish the model weights and masks for public use.

Aligning intraoperative biplanar digital subtraction angiography (DSA) to pre-procedural computed tomography angiography (CTA) requires rapid and accurate 3D-to-2D registration. Optimization-based methods are sensitive to initialization and may require hundreds of iterations, whereas learning-based approaches commonly rely on patient-specific training. We propose GeoPose, a population-trained framework that estimates the C-arm pose in a learned canonical frame and transfers it to the native frame of an unseen CTA through projection-space calibration and transform composition. A population-trained residual network refines the pose, followed optionally by low-budget image-driven optimization. GeoPose requires neither patient-specific adaptation nor explicit inter-volume preregistration. On 80 DSA observations from 20 held-out patients, optimization-free GeoPose achieved a carotid mean projected centerline distance (mPCD) of 5.8 mm and a clDice of 0.45, compared with 14.5 mm and 0.28 for the best-performing baseline, while requiring only 0.15 s. After 25 optimization iterations, GeoPose reached an mPCD of 4.6 mm and a clDice of 0.58 in approximately two seconds. Under the same budget, native-initialized optimization achieved 14.6 mm and 0.15, respectively. GeoPose thus provides rapid native-frame registration with fixed population-level weights and the geometric correspondence required for downstream biplanar 3D vascular reconstruction.

The human spine commonly consists of seven cervical, twelve thoracic, and five lumbar vertebrae. However, enumeration anomalies may result in individuals having eleven or thirteen thoracic vertebrae and four or six lumbar vertebrae. Although the identification of enumer- ation anomalies has potential clinical implications for chronic back pain and operation planning, the thoracolumbar junction is often poorly as- sessed and rarely described in clinical reports. Additionally, even though multiple deep-learning-based vertebra labeling algorithms exist, there is a lack of methods to automatically label enumeration anomalies. Our work closes that gap by introducing "Vertebra Identification with Anomaly Handling" (VERIDAH), a novel vertebra labeling algorithm based on multiple classification heads combined with a weighted vertebra sequence prediction algorithm. We show that our approach surpasses existing mod- els on T2w TSE sagittal (98.30

This study evaluated 31 elite winter wheat genotypes across 13 Canadian environments from 2019 to 2022. Because environments and genotype sets differed across years, the dataset was analyzed as two trial-year sets (2019/2020 and 2021/2022). Grain yield and stability were assessed using genotype main effect plus genotype by environment interaction. Results revealed different performance for genotypes across western and eastern locations. University of Guelph genotypes performed well in eastern Canada, whereas western genotypes showed lower yield and stability in eastern environments. Regional adaptation strongly influenced performance, with genotypes performing most consistently in their target environments, supporting region-specific breeding strategies.

Deep learning-based medical image segmentation is increasingly used to support clinical diagnosis and develop new treatment strategies. However, model performance remains limited by the scarcity of high-quality annotated data and insufficient generalization across imaging protocols. This limitation is particularly evident in MRI and CT, where models are typically trained on a single acquisition sequence and exhibit reduced robustness when applied to unseen sequences or contrasts. Although data augmentation is widely used to improve general robustness on medical images, its impact on cross-modality generalization has not been quantitatively explored. In this work, we study a targeted set of data augmentation techniques designed to improve cross-modality transfer. We train three spine segmentation models, each on a single-modality/sequence dataset, and evaluate them across seven out-of-distribution datasets (spanning CT and MRI), reflecting a realistic single-sequence training and multi-sequence/contrast/modality deployment scenario. Our results demonstrate substantial performance gains on unseen domains (average Dice gain of 155

BACKGROUND:Chronic rhinosinusitis (CRS) is a common and persistent sinus inflammation that affects 5%-12% of the general population. It substantially reduces quality of life, yet its severity is often challenging to assess objectively. The Lund-Mackay score (LMS) rates sinus opacification but is typically assessed manually and subjectively. METHODS:We introduce Paranasal Segmentation for Imaging-based Disease Evaluation (PARASIDE), an automatic tool for segmenting air and soft tissue volumes of the structures of the sinus maxillaris, frontalis, sphenoidalis, and ethmoidalis in T1-weighted magnetic resonance imaging. Utilizing that segmentation, we quantify feature relations such as volume, thickness, and intensity relations which were previously observed only manually and subjectively. Using these features, we regress the Total Lund-Mackay Score (TLMS) of each subject. We compare our approach against established baselines: the Quantitative Opacification Score (QOS) and the Quantitative Lund-Mackay Score (QLMS). RESULTS:PARASIDE achieves a mean-squared error (MSE) of 2.444 and mean absolute error (MAE) of 1.181 for TLMS prediction, outperforming the QOS/QLMS baseline (MSE = 3.784, MAE = 1.445). The segmentation achieves a mean Dice similarity coefficient of 0.882 ± 0.138 and an average symmetric surface distance (ASSD) of 0.311 ± 0.354 mm across all structures. CONCLUSION:PARASIDE enables the first automated whole-paranasal sinus segmentation for T1-weighted MRI, extracting quantitative features that predict CRS severity more accurately than existing volumetric scoring methods. By integrating high-quality segmentation with fully automated TLMS estimation, our system offers a reproducible and objective assessment tool in clinical workflows, with the potential to reduce inter-rater variability, accelerate reporting, and support large-scale retrospective studies.

Volume Interpolated Breath-Hold Examination (VIBE) MRI generates images suitable for water and fat signal composition estimation. While the two-point VIBE provides rapid water-fat-separated images, the six-point VIBE allows estimation of the effective transversal relaxation rate R2* and the proton density fat fraction (PDFF), which are imaging markers for health and disease. Ambiguity during signal reconstruction can lead to water-fat swaps. This shortcoming challenges the application of VIBE-MRI for automated PDFF analyses of large-scale clinical data and population studies. This study develops an automated pipeline to detect and correct water-fat swaps in non-contrast-enhanced VIBE images. Our three-step pipeline begins with training a segmentation network to classify volumes as “fat-like” or “water-like”, using synthetic water-fat swaps generated by merging fat and water volumes with Perlin noise. Next, a denoising diffusion image-to-image network predicts water volumes as signal priors for correction. Finally, we integrate this prior into a physics-constrained model to recover accurate water and fat signals. Our approach achieves a <1

The correct identification of the thoracolumbar junction is mandatory for labeling of the lumbar spine, particularly if visualized incompletely. The current state-of-the-art relies on a continuous counting-based (CCBC), a rib-length-based (RLBC), or rib-based classification (RBC) of the spine enumeration. However, the CCBC and RBC often lead to inconsistent labels depending on the visualized spine segments. In this retrospective study, three classifications for assessing the thoracolumbar junction were evaluated in CT scans from 2005 to 2018, covering the complete thoracolumbar spine: (1) CCBC, (2) RLBC/RBC, and (3) a vertebra-shape-based classification (VSBC). The classifications were compared regarding consistent labels depending on the visualized spine segments, agreement with nerve morphology, and inter-rater reliability. CT-imaging data from 1,242 subjects (mean age, 63 years ± 12; 771 women) were included. The VSBC led to more consistent labels than all other classifications. Only the VSBC perfectly complied with the nerve morphology (VSBC, 100

Deep learning models have achieved remarkable success in segmenting brain white matter lesions in multiple sclerosis (MS), becoming integral to both research and clinical workflows. While brain lesions have gained significant attention in MS research, the involvement of spinal cord lesions in MS is relatively understudied. This is largely owing to the variability in spinal cord magnetic resonance imaging (MRI) acquisition protocols, high individual anatomical differences, the complex morphology and size of spinal cord lesions, and lastly, the scarcity of labeled datasets required to develop robust segmentation tools. As a result, automatic segmentation of spinal cord MS lesions remains a significant challenge. Although some segmentation tools exist for spinal cord lesions, most have been developed using sagittal T2-weighted (T2w) sequences primarily focusing on cervical spines. With the growing importance of spinal cord imaging in MS, axial T2w scans are becoming increasingly relevant due to their superior sensitivity in detecting lesions compared to sagittal acquisition protocols. However, most existing segmentation methods struggle to effectively generalize to axial sequences due to differences in image characteristics caused by the highly anisotropic spinal cord scans. To address these challenges, we developed a robust, open-source lesion segmentation tool tailored specifically for axial T2w scans covering the whole spinal cord. We investigated key factors influencing lesion segmentation, including the impact of stitching together individually acquired spinal regions, straightening the spinal cord, and comparing the effectiveness of 2D and 3D convolutional neural networks (CNNs). Drawing on these insights, we trained a multi-center model using an extensive dataset of 582 MS patients, resulting in a dataset comprising an entirety of 2,167 scans. We empirically evaluated the model's segmentation performance across various spinal segments for lesions with varying sizes. Our model significantly outperforms the current state-of-the-art methods, providing consistent segmentation across cervical, thoracic, and lumbar regions. To support the broader research community, we integrate our model into the widely-used Spinal Cord Toolbox (v7.0 and above), making it accessible via the command sct_deepseg lesion_ms_axial_t2 -i .

Digital twins offer a powerful framework for subject-specific simulation and clinical decision support, yet their development often hinges on accurate, individualized anatomical modeling. In this work, we present a rule-based approach for subpixel-accurate key-point extraction from MRI, adapted from prior CT-based methods. Our approach incorporates robust image alignment and vertebra-specific orientation estimation to generate anatomically meaningful landmarks that serve as boundary conditions and force application points, like muscle and ligament insertions in biomechanical models. These models enable the simulation of spinal mechanics considering the subject's individual anatomy, and thus support the development of tailored approaches in clinical diagnostics and treatment planning. By leveraging MR imaging, our method is radiation-free and well-suited for large-scale studies and use in underrepresented populations. This work contributes to the digital twin ecosystem by bridging the gap between precise medical image analysis with biomechanical simulation, and aligns with key themes in personalized modeling for healthcare.

Accurate calibration of finite element (FE) models is essential across various biomechanical applications, including human intervertebral discs (IVDs), to ensure their reliability and use in diagnosing and planning treatments. However, traditional calibration methods are computationally intensive, requiring iterative, derivative-free optimization algorithms that often take days to converge. This study addresses these challenges by introducing a novel, efficient, and effective calibration method demonstrated on a human L4-L5 IVD FE model as a case study using a neural network (NN) surrogate. The NN surrogate predicts simulation outcomes with high accuracy, outperforming other machine learning models, and significantly reduces the computational cost associated with traditional FE simulations. Next, a Projected Gradient Descent (PGD) approach guided by gradients of the NN surrogate is proposed to efficiently calibrate FE models. Our method explicitly enforces feasibility with a projection step, thus maintaining material bounds throughout the optimization process. The proposed method is evaluated against state-of-the-art Genetic Algorithm (GA) and inverse model baselines on synthetic and in vitro experimental datasets. Our approach demonstrates superior performance on synthetic data, achieving a Mean Absolute Error (MAE) of 0.06 compared to the baselines' MAE of 0.18 and 0.54, respectively. On experimental specimens, our method outperforms the baseline in 5 out of 6 cases. While our approach requires initial dataset generation and surrogate training, these steps are performed only once, and the actual calibration takes under three seconds. In contrast, traditional calibration time scales linearly with the number of specimens, taking up to 8 days in the worst-case. Such efficiency paves the way for applying more complex FE models, potentially extending beyond IVDs, and enabling accurate patient-specific simulations.

Accurate segmentation of vertebral metastasis in CT is clinically important yet difficult to scale, as voxel-level annotations are scarce and both lytic and blastic lesions often resemble benign degenerative changes. We introduce a weakly supervised method trained solely on vertebra-level healthy/malignant labels, without any lesion masks. The method combines a Diffusion Autoencoder (DAE) that produces a classifier-guided healthy edit of each vertebra with pixel-wise difference maps that propose candidate lesion regions. To determine which regions truly reflect malignancy, we introduce Hide-and-Seek Attribution: each candidate is revealed in turn while all others are hidden, the edited image is projected back to the data manifold by the DAE, and a latent-space classifier quantifies the isolated malignant contribution of that component. High-scoring regions form the final lytic or blastic segmentation. On held-out radiologist annotations, we achieve strong blastic/lytic performance despite no mask supervision (F1: 0.91/0.85; Dice: 0.87/0.78), exceeding baselines (F1: 0.79/0.67; Dice: 0.74/0.55). These results show that vertebra-level labels can be transformed into reliable lesion masks, demonstrating that generative editing combined with selective occlusion supports accurate weakly supervised segmentation in CT.

Deep learning has made significant strides in medical imaging, leveraging the use of large datasets to improve diagnostics and prognostics. However, large datasets often come with inherent errors through subject selection and acquisition. In this paper, we investigate the use of Diffusion Autoencoder (DAE) embeddings for uncovering and understanding data characteristics and biases, including biases for protected variables like sex and data abnormalities indicative of unwanted protocol variations. We use sagittal T2-weighted magnetic resonance (MR) images of the neck, chest, and lumbar region from 11186 German National Cohort (NAKO) participants. We compare DAE embeddings with existing generative models like StyleGAN and Variational Autoencoder. Evaluations on a large-scale dataset consisting of sagittal T2-weighted MR images of three spine regions show that DAE embeddings effectively separate protected variables such as sex and age. Furthermore, we used t-SNE visualization to identify unwanted variations in imaging protocols, revealing differences in head positioning. Our embedding can identify samples where a sex predictor will have issues learning the correct sex. Our findings highlight the potential of using advanced embedding techniques like DAEs to detect data quality issues and biases in medical imaging datasets. Identifying such hidden relations can enhance the reliability and fairness of deep learning models in healthcare applications, ultimately improving patient care and outcomes.

Accurate delineation of anatomical structures in volumetric CT scans is crucial for diagnosis and treatment planning. While AI has advanced automated segmentation, current approaches typically target individual structures, creating a fragmented landscape of incompatible models with varying performance and disparate evaluation protocols. Foundational segmentation models address these limitations by providing a holistic anatomical view through a single model. Yet, robust clinical deployment demands comprehensive training data, which is lacking in existing whole-body approaches, both in terms of data heterogeneity and, more importantly, anatomical coverage. In this work, rather than pursuing incremental optimizations in model architecture, we present CADS, an open-source framework that prioritizes the systematic integration, standardization, and labeling of heterogeneous data sources for whole-body CT segmentation. At its core is a large-scale dataset of 22,022 CT volumes with complete annotations for 167 anatomical structures, representing a significant advancement in both scale and coverage, with 18 times more scans than existing collections and 60

Chronic rhinosinusitis (CRS) is a common and persistent sinus imflammation that affects 5 - 12% of the general population. It significantly impacts quality of life and is often difficult to assess due to its subjective nature in clinical evaluation. We introduce PARASIDE, an automatic tool for segmenting air and soft tissue volumes of the structures of the sinus maxillaris, frontalis, sphenodalis and ethmoidalis in T1 MRI. By utilizing that segmentation, we can quantify feature relations that have been observed only manually and subjectively before. We performed an exemplary study and showed both volume and intensity relations between structures and radiology reports. While the soft tissue segmentation is good, the automated annotations of the air volumes are excellent. The average intensity over air structures are consistently below those of the soft tissues, close to perfect separability. Healthy subjects exhibit lower soft tissue volumes and lower intensities. Our developed system is the first automated whole nasal segmentation of 16 structures, and capable of calculating medical relevant features such as the Lund-Mackay score.

IntroductionBiomechanical simulations can enhance our understanding of spinal disorders. Applied to large cohorts, they can reveal complex mechanisms beyond conventional imaging. Therefore, automating the patient-specific modeling process is essential.MethodsWe developed an automated and robust pipeline that generates and simulates biofidelic vertebrae and intervertebral disc finite element method (FEM) models based on automated magnetic resonance imaging (MRI) segmentations. In a first step, anatomically-constrained smoothing approaches were implemented to ensure seamless contact surfaces between vertebrae and discs with shared nodes. Subsequently, surface meshes were filled isotropically with tetrahedral elements. Lastly, simulations were executed. The performance of our pipeline was evaluated using a set of 30 patients from an in-house dataset that comprised an overall of 637 vertebrae and 600 intervertebral discs. We rated mesh quality metrics and processing times.ResultsWith an average number of 21 vertebrae and 20 IVDs per subject, the average processing time was 4.4 min for a vertebra and 31 s for an IVD. The average percentage of poor quality elements stayed below 2% in all generated FEM models, measured by their aspect ratio. Ten vertebra and seven IVD FE simulations failed to converge.DiscussionThe main goal of our work was to automate the modeling and FEM simulation of both patient-specific vertebrae and intervertebral discs with shared-node surfaces directly from MRI segmentations. The biofidelity, robustness and time-efficacy of our pipeline marks an important step towards investigating large patient cohorts for statistically relevant, biomechanical insight.

To present a publicly available deep learning-based torso segmentation model that provides comprehensive voxel-wise coverage, including delineations that extend to the boundaries of anatomical compartments. We extracted preliminary segmentations from TotalSegmentator, spine, and body composition models for magnetic resonance tomography (MR) images, then improved them iteratively and retrained an nnUNet model. Using a random retrospective subset of German National Cohort (NAKO), UK Biobank, internal MR and computed tomography (CT) data (Training: 2897 series from 626 subjects, 290 female; mean age 53 ± 16; 3-fold-cross validation (20

Counterfactual explanations (CEs) aim to enhance the interpretability of machine learning models by illustrating how alterations in input features would affect the resulting predictions. Common CE approaches require an additional model and are typically constrained to binary counterfactuals. In contrast, we propose a novel method that operates directly on the latent space of a generative model, specifically a Diffusion Autoencoder (DAE). This approach offers inherent interpretability by enabling the generation of CEs and the continuous visualization of the model's internal representation across decision boundaries. Our method leverages the DAE's ability to encode images into a semantically rich latent space in an unsupervised manner, eliminating the need for labeled data or separate feature extraction models. We show that these latent representations are helpful for medical condition classification and the ordinal regression of severity pathologies, such as vertebral compression fractures (VCF) and diabetic retinopathy (DR). Beyond binary CEs, our method supports the visualization of ordinal CEs using a linear model, providing deeper insights into the model's decision-making process and enhancing interpretability. Experiments across various medical imaging datasets demonstrate the method's advantages in interpretability and versatility. The linear manifold of the DAE's latent space allows for meaningful interpolation and manipulation, making it a powerful tool for exploring medical image properties. Our code is available at https://doi.org/10.5281/zenodo.13859266.