SPINEPS-automatic whole spine segmentation of T2-weighted MR images using a two-phase approach to multi-class semantic and instance segmentation.

OBJECTIVES: Introducing SPINEPS, a deep learning method for semantic and instance segmentation of 14 spinal structures (ten vertebra substructures, intervertebral discs, spinal cord, spinal canal, and sacrum) in whole-body sagittal T2-weighted turbo spin echo images. MATERIAL AND METHODS: This local ethics committee-approved study utilized a public dataset (train/test 179/39 subjects, 137 female), a German National Cohort (NAKO) subset (train/test 1412/65 subjects, mean age 53, 694 female), and an in-house dataset (test 10 subjects, mean age 70, 5 female). SPINEPS is a semantic segmentation model, followed by a sliding window approach utilizing a second model to create instance masks from the semantic ones. Segmentation evaluation metrics included the Dice score and average symmetrical surface distance (ASSD). Statistical significance was assessed using the Wilcoxon signed-rank test. RESULTS: On the public dataset, SPINEPS outperformed a nnUNet baseline on every structure and metric (e.g., an average over vertebra instances: dice 0.933 vs 0.911, p < 0.001, ASSD 0.21 vs 0.435, p < 0.001). SPINEPS trained on automated annotations of the NAKO achieves an average global Dice score of 0.918 on the combined NAKO and in-house test split. Adding the training data from the public dataset outperforms this (average instance-wise Dice score over the vertebra substructures 0.803 vs 0.778, average global Dice score 0.931 vs 0.918). CONCLUSION: SPINEPS offers segmentation of 14 spinal structures in T2w sagittal images. It provides a semantic mask and an instance mask separating the vertebrae and intervertebral discs. This is the first publicly available algorithm to enable this segmentation. KEY POINTS: Question No publicly available automatic approach can yield semantic and instance segmentation masks for the whole spine (including posterior elements) in T2-weighted sagittal TSE images. Findings Segmenting semantically first and then instance-wise outperforms a baseline trained directly on instance segmentation. The developed model produces high-resolution MRI segmentations for the whole spine. Clinical relevance This study introduces an automatic approach to whole spine segmentation, including posterior elements, in arbitrary fields of view T2w sagittal MR images, enabling easy biomarker extraction, automatic localization of pathologies and degenerative diseases, and quantifying analyses as downstream research.

Automated detection of the contrast phase in MDCT by an artificial neural network improves the accuracy of opportunistic bone mineral density measurements.

OBJECTIVES: To determine the accuracy of an artificial neural network (ANN) for fully automated detection of the presence and phase of iodinated contrast agent in routine abdominal multidetector computed tomography (MDCT) scans and evaluate the effect of contrast correction for osteoporosis screening. METHODS: This HIPPA-compliant study retrospectively included 579 MDCT scans in 193 patients (62.4 ± 14.6 years, 48 women). Three different ANN models (2D DenseNet with random slice selection, 2D DenseNet with anatomy-guided slice selection, 3D DenseNet) were trained in 462 MDCT scans of 154 patients (threefold cross-validation), who underwent triphasic CT. All ANN models were tested in 117 unseen triphasic scans of 39 patients, as well as in a public MDCT dataset containing 311 patients. In the triphasic test scans, trabecular volumetric bone mineral density (BMD) was calculated using a fully automated pipeline. Root-mean-square errors (RMSE) of BMD measurements with and without correction for contrast application were calculated in comparison to nonenhanced (NE) scans. RESULTS: The 2D DenseNet with anatomy-guided slice selection outperformed the competing models and achieved an F1 score of 0.98 and an accuracy of 98.3% in the test set (public dataset: F1 score 0.93; accuracy 94.2%). Application of contrast agent resulted in significant BMD biases (all p < .001; portal-venous (PV): RMSE 18.7 mg/ml, mean difference 17.5 mg/ml; arterial (AR): RMSE 6.92 mg/ml, mean difference 5.68 mg/ml). After the fully automated correction, this bias was no longer significant (p > .05; PV: RMSE 9.45 mg/ml, mean difference 1.28 mg/ml; AR: RMSE 3.98 mg/ml, mean difference 0.94 mg/ml). CONCLUSION: Automatic detection of the contrast phase in multicenter CT data was achieved with high accuracy, minimizing the contrast-induced error in BMD measurements. KEY POINTS: • A 2D DenseNet with anatomy-guided slice selection achieved an F1 score of 0.98 and an accuracy of 98.3% in the test set. In a public dataset, an F1 score of 0.93 and an accuracy of 94.2% were obtained. • Automated adjustment for contrast injection improved the accuracy of lumbar bone mineral density measurements (RMSE 18.7 mg/ml vs. 9.45 mg/ml respectively, in the portal-venous phase). • An artificial neural network can reliably reveal the presence and phase of iodinated contrast agent in multidetector CT scans ( https://github.com/ferchonavarro/anatomy_guided_contrast_c ). This allows minimizing the contrast-induced error in opportunistic bone mineral density measurements.

Proposed diagnostic volumetric bone mineral density thresholds for osteoporosis and osteopenia at the cervicothoracic spine in correlation to the lumbar spine.

OBJECTIVES: To determine the correlation between cervicothoracic and lumbar volumetric bone mineral density (vBMD) in an average cohort of adults and to identify specific diagnostic thresholds for the cervicothoracic spine on the individual subject level. METHODS: In this HIPPA-compliant study, we retrospectively included 260 patients (59.7 ± 18.3 years, 105 women), who received a contrast-enhanced or non-contrast-enhanced CT scan. vBMD was extracted using an automated pipeline ( https://anduin.bonescreen.de ). The association of vBMD between each vertebra spanning C2-T12 and the averaged values at the lumbar spine (L1-L3) was analyzed before and after semiquantitative assessment of fracture status and degeneration, and respective vertebra-specific cut-off values for osteoporosis were calculated using linear regression. RESULTS: In both women and men, trabecular vBMD decreased with age in the cervical, thoracic, and lumbar regions. vBMD values of cervicothoracic vertebrae showed strong correlations with lumbar vertebrae (L1-L3), with a median Pearson value of r = 0.87 (range: rC2 = 0.76 to rT12 = 0.96). The correlation coefficients were significantly lower (p < 0.0001) without excluding fractured and degenerated vertebrae, median r = 0.82 (range: rC2 = 0.69 to rT12 = 0.93). Respective cut-off values for osteoporosis peaked at C4 (209.2 mg/ml) and decreased to 83.8 mg/ml at T12. CONCLUSION: Our data show a high correlation between clinically used mean L1-L3 values and vBMD values elsewhere in the spine, independent of age. The proposed cut-off values for the cervicothoracic spine therefore may allow the determination of low bone mass even in clinical cases where only parts of the spine are imaged. KEY POINTS: vBMD of all cervicothoracic vertebrae showed strong correlation with lumbar vertebrae (L1-L3), with a median Pearson's correlation coefficient of r = 0.87 (range: rC2 = 0.76 to rT12 = 0.96). The correlation coefficients were significantly lower (p < 0.0001) without excluding fractured and moderate to severely degenerated vertebrae, median r = 0.82 (range: rC2 = 0.69 to rT12 = 0.93). We postulate that trabecular vBMD < 200 mg/ml for the cervical spine and < 100 mg/ml for the thoracic spine are strong indicators of osteoporosis, similar to < 80 mg/ml at the lumbar spine.

Automatic opportunistic osteoporosis screening in routine CT: improved prediction of patients with prevalent vertebral fractures compared to DXA.

OBJECTIVES: To compare spinal bone measures derived from automatic and manual assessment in routine CT with dual energy X-ray absorptiometry (DXA) in their association with prevalent osteoporotic vertebral fractures using our fully automated framework ( https://anduin.bonescreen.de ) to assess various bone measures in clinical CT. METHODS: We included 192 patients (141 women, 51 men; age 70.2 ± 9.7 years) who had lumbar DXA and CT available (within 1 year). Automatic assessment of spinal bone measures in CT included segmentation of vertebrae using a convolutional neural network (CNN), reduction to the vertebral body, and extraction of bone mineral content (BMC), trabecular and integral volumetric bone mineral density (vBMD), and CT-based areal BMD (aBMD) using asynchronous calibration. Moreover, trabecular bone was manually sampled (manual vBMD). RESULTS: A total of 148 patients (77%) had vertebral fractures and significantly lower values in all bone measures compared to patients without fractures (p ≤ 0.001). Except for BMC, all CT-based measures performed significantly better as predictors for vertebral fractures compared to DXA (e.g., AUC = 0.885 for trabecular vBMD and AUC = 0.86 for integral vBMD vs. AUC = 0.668 for DXA aBMD, respectively; both p < 0.001). Age- and sex-adjusted associations with fracture status were strongest for manual vBMD (OR = 7.3, [95%] CI 3.8-14.3) followed by automatically assessed trabecular vBMD (OR = 6.9, CI 3.5-13.4) and integral vBMD (OR = 4.3, CI 2.5-7.6). Diagnostic cutoffs of integral vBMD for osteoporosis (< 160 mg/cm3) or low bone mass (160 ≤ BMD < 190 mg/cm3) had sensitivity (84%/41%) and specificity (78%/95%) similar to trabecular vBMD. CONCLUSIONS: Fully automatic osteoporosis screening in routine CT of the spine is feasible. CT-based measures can better identify individuals with reduced bone mass who suffered from vertebral fractures than DXA. KEY POINTS: • Opportunistic osteoporosis screening of spinal bone measures derived from clinical routine CT is feasible in a fully automatic fashion using a deep learning-driven framework ( https://anduin.bonescreen.de ). • Manually sampled volumetric BMD (vBMD) and automatically assessed trabecular and integral vBMD were the best predictors for prevalent vertebral fractures. • Except for bone mineral content, all CT-based bone measures performed significantly better than DXA-based measures. • We introduce diagnostic thresholds of integral vBMD for osteoporosis (< 160 mg/cm3) and low bone mass (160 ≤ BMD < 190 mg/cm3) with almost equal sensitivity and specificity compared to conventional thresholds of quantitative CT as proposed by the American College of Radiology (osteoporosis < 80 mg/cm3).

Reproducibility of CT-based opportunistic vertebral volumetric bone mineral density measurements from an automated segmentation framework.

BACKGROUND: To investigate the reproducibility of automated volumetric bone mineral density (vBMD) measurements from routine thoracoabdominal computed tomography (CT) assessed with segmentations by a convolutional neural network and automated correction of contrast phases, on diverse scanners, with scanner-specific asynchronous or scanner-agnostic calibrations. METHODS: We obtained 679 observations from 278 CT scans in 121 patients (77 males, 63.6%) studied from 04/2019 to 06/2020. Observations consisted of two vBMD measurements from Δdifferent reconstruction kernels (n = 169), Δcontrast phases (n = 133), scan Δsessions (n = 123), Δscanners (n = 63), or Δall of the aforementioned (n = 20), and observations lacking scanner-specific calibration (n = 171). Precision was assessed using root-mean-square error (RMSE) and root-mean-square coefficient of variation (RMSCV). Cross-measurement agreement was assessed using Bland-Altman plots; outliers within 95% confidence interval of the limits of agreement were reviewed. RESULTS: Repeated measurements from Δdifferent reconstruction kernels were highly precise (RMSE 3.0 mg/cm3; RMSCV 1.3%), even for consecutive scans with different Δcontrast phases (RMSCV 2.9%). Measurements from different Δscan sessions or Δscanners showed decreased precision (RMSCV 4.7% and 4.9%, respectively). Plot-review identified 12 outliers from different scan Δsessions, with signs of hydropic decompensation. Observations with Δall differences showed decreased precision compared to those lacking scanner-specific calibration (RMSCV 5.9 and 3.7, respectively). CONCLUSION: Automatic vBMD assessment from routine CT is precise across varying setups, when calibrated appropriately. Low precision was found in patients with signs of new or worsening hydropic decompensation, what should be considered an exclusion criterion for both opportunistic and dedicated quantitative CT. RELEVANCE STATEMENT: Automated CT-based vBMD measurements are precise in various scenarios, including cross-session and cross-scanner settings, and may therefore facilitate opportunistic screening for osteoporosis and surveillance of BMD in patients undergoing routine clinical CT scans. KEY POINTS: Artificial intelligence-based tools facilitate BMD measurements in routine clinical CT datasets. Automated BMD measurements are highly reproducible in various settings. Reliable, automated opportunistic osteoporosis diagnostics allow for large-scale application.

Musculoskeletal spine modeling in large patient cohorts: how morphological individualization affects lumbar load estimation.

Introduction: Achieving an adequate level of detail is a crucial part of any modeling process. Thus, oversimplification of complex systems can lead to overestimation, underestimation, and general bias of effects, while elaborate models run the risk of losing validity due to the uncontrolled interaction of multiple influencing factors and error propagation. Methods: We used a validated pipeline for the automated generation of multi-body models of the trunk to create 279 models based on CT data from 93 patients to investigate how different degrees of individualization affect the observed effects of different morphological characteristics on lumbar loads. Specifically, individual parameters related to spinal morphology (thoracic kyphosis (TK), lumbar lordosis (LL), and torso height (TH)), as well as torso weight (TW) and distribution, were fully or partly considered in the respective models according to their degree of individualization, and the effect strengths of these parameters on spinal loading were compared between semi- and highly individualized models. T-distributed stochastic neighbor embedding (T-SNE) analysis was performed for overarching pattern recognition and multiple regression analyses to evaluate changes in occurring effects and significance. Results: We were able to identify significant effects (p < 0.05) of various morphological parameters on lumbar loads in models with different degrees of individualization. Torso weight and lumbar lordosis showed the strongest effects on compression (ß ≈ 0.9) and anterior-posterior shear forces (ß ≈ 0.7), respectively. We could further show that the effect strength of individual parameters tended to decrease if more individual characteristics were included in the models. Discussion: The induced variability due to model individualization could only partly be explained by simple morphological parameters. Our study shows that model simplification can lead to an emphasis on individual effects, which needs to be critically assessed with regard to in vivo complexity. At the same time, we demonstrated that individualized models representing a population-based cohort are still able to identify relevant influences on spinal loading while considering a variety of influencing factors and their interactions.

Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA.

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neuro-vascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited public datasets with annotations on CoW anatomy, especially for CTA. Therefore we organized the TopCoW Challenge in 2023 with the release of an annotated CoW dataset. The TopCoW dataset was the first public dataset with voxel-level annotations for thirteen possible CoW vessel components, enabled by virtual-reality (VR) technology. It was also the first large dataset with paired MRA and CTA from the same patients. TopCoW challenge formalized the CoW characterization problem as a multiclass anatomical segmentation task with an emphasis on topological metrics. We invited submissions worldwide for the CoW segmentation task, which attracted over 140 registered participants from four continents. The top performing teams managed to segment many CoW components to Dice scores around 90%, but with lower scores for communicating arteries and rare variants. There were also topological mistakes for predictions with high Dice scores. Additional topological analysis revealed further areas for improvement in detecting certain CoW components and matching CoW variant topology accurately. TopCoW represented a first attempt at benchmarking the CoW anatomical segmentation task for MRA and CTA, both morphologically and topologically.

Incidental vertebral fracture prediction using neuronal network-based automatic spine segmentation and volumetric bone mineral density extraction from routine clinical CT scans.

Objectives: To investigate vertebral osteoporotic fracture (VF) prediction by automatically extracted trabecular volumetric bone mineral density (vBMD) from routine CT, and to compare the model with fracture prevalence-based prediction models. Methods: This single-center retrospective study included patients who underwent two thoraco-abdominal CT scans during clinical routine with an average inter-scan interval of 21.7 ± 13.1 months (range 5-52 months). Automatic spine segmentation and vBMD extraction was performed by a convolutional neural network framework (anduin.bonescreen.de). Mean vBMD was calculated for levels T5-8, T9-12, and L1-5. VFs were identified by an expert in spine imaging. Odds ratios (ORs) for prevalent and incident VFs were calculated for vBMD (per standard deviation decrease) at each level, for baseline VF prevalence (yes/no), and for baseline VF count (n) using logistic regression models, adjusted for age and sex. Models were compared using Akaike's and Bayesian information criteria (AIC & BIC). Results: 420 patients (mean age, 63 years ± 9, 276 males) were included in this study. 40 (25 female) had prevalent and 24 (13 female) had incident VFs. Individuals with lower vBMD at any spine level had higher odds for VFs (L1-5, prevalent VF: OR,95%-CI,p: 2.2, 1.4-3.5,p=0.001; incident VF: 3.5, 1.8-6.9,p<0.001). In contrast, VF status (2.15, 0.72-6.43,p=0.170) and count (1.38, 0.89-2.12,p=0.147) performed worse in incident VF prediction. Information criteria revealed best fit for vBMD-based models (AIC vBMD=165.2; VF status=181.0; count=180.7). Conclusions: VF prediction based on automatically extracted vBMD from routine clinical MDCT outperforms prediction models based on VF status and count. These findings underline the importance of opportunistic quantitative osteoporosis screening in clinical routine MDCT data.

Denoising diffusion-based MRI to CT image translation enables automated spinal segmentation.

BACKGROUND: Automated segmentation of spinal magnetic resonance imaging (MRI) plays a vital role both scientifically and clinically. However, accurately delineating posterior spine structures is challenging. METHODS: This retrospective study, approved by the ethical committee, involved translating T1-weighted and T2-weighted images into computed tomography (CT) images in a total of 263 pairs of CT/MR series. Landmark-based registration was performed to align image pairs. We compared two-dimensional (2D) paired - Pix2Pix, denoising diffusion implicit models (DDIM) image mode, DDIM noise mode - and unpaired (SynDiff, contrastive unpaired translation) image-to-image translation using "peak signal-to-noise ratio" as quality measure. A publicly available segmentation network segmented the synthesized CT datasets, and Dice similarity coefficients (DSC) were evaluated on in-house test sets and the "MRSpineSeg Challenge" volumes. The 2D findings were extended to three-dimensional (3D) Pix2Pix and DDIM. RESULTS: 2D paired methods and SynDiff exhibited similar translation performance and DCS on paired data. DDIM image mode achieved the highest image quality. SynDiff, Pix2Pix, and DDIM image mode demonstrated similar DSC (0.77). For craniocaudal axis rotations, at least two landmarks per vertebra were required for registration. The 3D translation outperformed the 2D approach, resulting in improved DSC (0.80) and anatomically accurate segmentations with higher spatial resolution than that of the original MRI series. CONCLUSIONS: Two landmarks per vertebra registration enabled paired image-to-image translation from MRI to CT and outperformed all unpaired approaches. The 3D techniques provided anatomically correct segmentations, avoiding underprediction of small structures like the spinous process. RELEVANCE STATEMENT: This study addresses the unresolved issue of translating spinal MRI to CT, making CT-based tools usable for MRI data. It generates whole spine segmentation, previously unavailable in MRI, a prerequisite for biomechanical modeling and feature extraction for clinical applications. KEY POINTS: • Unpaired image translation lacks in converting spine MRI to CT effectively. • Paired translation needs registration with two landmarks per vertebra at least. • Paired image-to-image enables segmentation transfer to other domains. • 3D translation enables super resolution from MRI to CT. • 3D translation prevents underprediction of small structures.

The Liver Tumor Segmentation Benchmark (LiTS).

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in http://medicaldecathlon.com/. In addition, both data and online evaluation are accessible via https://competitions.codalab.org/competitions/17094.

Level-Specific Volumetric BMD Threshold Values for the Prediction of Incident Vertebral Fractures Using Opportunistic QCT: A Case-Control Study.

Purpose: To establish and evaluate the diagnostic accuracy of volumetric bone mineral density (vBMD) threshold values at different spinal levels, derived from opportunistic quantitative computed tomography (QCT), for the prediction of incident vertebral fractures (VF). Materials and Methods: In this case-control study, 35 incident VF cases (23 women, 12 men; mean age: 67 years) and 70 sex- and age-matched controls were included, based on routine multi detector CT (MDCT) scans of the thoracolumbar spine. Trabecular vBMD was measured from routine baseline CT scans of the thoracolumbar spine using an automated pipeline including vertebral segmentation, asynchronous calibration for HU-to-vBMD conversion, and correction of intravenous contrast medium (https://anduin.bonescreen.de). Threshold values at T1-L5 were calculated for the optimal operating point according to the Youden index and for fixed sensitivities (60 - 85%) in receiver operating characteristic (ROC) curves. Results: vBMD at each single level of the thoracolumbar spine was significantly associated with incident VFs (odds ratio per SD decrease [OR], 95% confidence interval [CI] at T1-T4: 3.28, 1.66-6.49; at T5-T8: 3.28, 1.72-6.26; at T9-T12: 3.37, 1.78-6.36; and at L1-L4: 3.98, 1.97-8.06), independent of adjustment for age, sex, and prevalent VF. AUC showed no significant difference between vertebral levels and was highest at the thoracolumbar junction (AUC = 0.75, 95%-CI = 0.63 - 0.85 for T11-L2). Optimal threshold values increased from lumbar (L1-L4: 52.0 mg/cm³) to upper thoracic spine (T1-T4: 69.3 mg/cm³). At T11-L2, T12-L3 and L1-L4, a threshold of 80.0 mg/cm³ showed sensitivities of 85 - 88%, and specificities of 41 - 49%. To achieve comparable sensitivity (85%) at more superior spinal levels, resulting thresholds were higher: 114.1 mg/cm³ (T1-T4), 92.0 mg/cm³ (T5-T8), 88.2 mg/cm³ (T9-T12). Conclusions: At all levels of the thoracolumbar spine, lower vBMD was associated with incident VFs in an elderly, predominantly oncologic patient population. Automated opportunistic osteoporosis screening of vBMD along the entire thoracolumbar spine allows for risk assessment of imminent VFs. We propose level-specific vBMD threshold at the thoracolumbar spine to identify individuals at high fracture risk.

Validation of a Patient-Specific Musculoskeletal Model for Lumbar Load Estimation Generated by an Automated Pipeline From Whole Body CT.

Background: Chronic back pain is a major health problem worldwide. Although its causes can be diverse, biomechanical factors leading to spinal degeneration are considered a central issue. Numerical biomechanical models can identify critical factors and, thus, help predict impending spinal degeneration. However, spinal biomechanics are subject to significant interindividual variations. Therefore, in order to achieve meaningful findings on potential pathologies, predictive models have to take into account individual characteristics. To make these highly individualized models suitable for systematic studies on spinal biomechanics and clinical practice, the automation of data processing and modeling itself is inevitable. The purpose of this study was to validate an automatically generated patient-specific musculoskeletal model of the spine simulating static loading tasks. Methods: CT imaging data from two patients with non-degenerative spines were processed using an automated deep learning-based segmentation pipeline. In a semi-automated process with minimal user interaction, we generated patient-specific musculoskeletal models and simulated various static loading tasks. To validate the model, calculated vertebral loadings of the lumbar spine and muscle forces were compared with in vivo data from the literature. Finally, results from both models were compared to assess the potential of our process for interindividual analysis. Results: Calculated vertebral loads and muscle activation overall stood in close correlation with data from the literature. Compression forces normalized to upright standing deviated by a maximum of 16% for flexion and 33% for lifting tasks. Interindividual comparison of compression, as well as lateral and anterior-posterior shear forces, could be linked plausibly to individual spinal alignment and bodyweight. Conclusion: We developed a method to generate patient-specific musculoskeletal models of the lumbar spine. The models were able to calculate loads of the lumbar spine for static activities with respect to individual biomechanical properties, such as spinal alignment, bodyweight distribution, and ligament and muscle insertion points. The process is automated to a large extent, which makes it suitable for systematic investigation of spinal biomechanics in large datasets.

Self-Supervised Pretext Tasks in Model Robustness & Generalizability: A Revisit from Medical Imaging Perspective.

Self-supervised pretext tasks have been introduced as an effective strategy when learning target tasks on small annotated data sets. However, while current research focuses on exploring novel pretext tasks for meaningful and reusable representation learning for the target task, the study of its robustness and generalizability has remained relatively under-explored. Specifically, it is crucial in medical imaging to proactively investigate performance under different perturbations for reliable deployment of clinical applications. In this work, we revisit medical imaging networks pre-trained with self-supervised learnings and categorically evaluate robustness and generalizability compared to vanilla supervised learning. Our experiments on pneumonia detection in X-rays and multi-organ segmentation in CT yield conclusive results exposing the hidden benefits of self-supervision pre-training for learning robust feature representations.

A Unified 3D Framework for Organs-at-Risk Localization and Segmentation for Radiation Therapy Planning.

Automatic localization and segmentation of organs-at-risk (OAR) in CT are essential pre-processing steps in medical image analysis tasks, such as radiation therapy planning. For instance, the segmentation of OAR surrounding tumors enables the maximization of radiation to the tumor area without compromising the healthy tissues. However, the current medical workflow requires manual delineation of OAR, which is prone to errors and is annotator-dependent. In this work, we aim to introduce a unified 3D pipeline for OAR localization-segmentation rather than novel localization or segmentation architectures. To the best of our knowledge, our proposed framework fully enables the exploitation of 3D context information inherent in medical imaging. In the first step, a 3D multi-variate regression network predicts organs' centroids and bounding boxes. Secondly, 3D organ-specific segmentation networks are leveraged to generate a multi-organ segmentation map. Our method achieved an overall Dice score of 0.9260 ± 0.18% on the VISCERAL dataset containing CT scans with varying fields of view and multiple organs.

Anatomy-Aware Inference of the 3D Standing Spine Posture from 2D Radiographs.

An important factor for the development of spinal degeneration, pain and the outcome of spinal surgery is known to be the balance of the spine. It must be analyzed in an upright, standing position to ensure physiological loading conditions and visualize load-dependent deformations. Despite the complex 3D shape of the spine, this analysis is currently performed using 2D radiographs, as all frequently used 3D imaging techniques require the patient to be scanned in a prone position. To overcome this limitation, we propose a deep neural network to reconstruct the 3D spinal pose in an upright standing position, loaded naturally. Specifically, we propose a novel neural network architecture, which takes orthogonal 2D radiographs and infers the spine's 3D posture using vertebral shape priors. In this work, we define vertebral shape priors using an atlas and a spine shape prior, incorporating both into our proposed network architecture. We validate our architecture on digitally reconstructed radiographs, achieving a 3D reconstruction Dice of 0.95, indicating an almost perfect 2D-to-3D domain translation. Validating the reconstruction accuracy of a 3D standing spine on real data is infeasible due to the lack of a valid ground truth. Hence, we design a novel experiment for this purpose, using an orientation invariant distance metric, to evaluate our model's ability to synthesize full-3D, upright, and patient-specific spine models. We compare the synthesized spine shapes from clinical upright standing radiographs to the same patient's 3D spinal posture in the prone position from CT.

Automated Opportunistic Osteoporosis Screening in Routine Computed Tomography of the Spine: Comparison With Dedicated Quantitative CT.

Opportunistic osteoporosis screening in nondedicated routine computed tomography (CT) is of increasing importance. The purpose of this study was to compare lumbar volumetric bone mineral density (vBMD) assessed by a convolutional neural network (CNN)-based framework in routine CT to vBMD from dedicated quantitative CT (QCT), and to evaluate the ability of vBMD and surrogate measurements of Hounsfield units (HU) to distinguish between patients with and without osteoporotic vertebral fractures (VFs). A total of 144 patients (median age: 70.7 years, 93 females) with clinical routine CT (eight different CT scanners, 120 kVp or 140 kVp, with and without intravenous contrast medium) and dedicated QCT acquired within ≤30 days were included. Vertebral measurements included (i) vBMD from the CNN-based approach including automated vertebral body labeling, segmentation, and correction of the contrast media phase for routine CT data (vBMD_OPP), (ii) vBMD from dedicated QCT (vBMD_QCT), and (iii) noncalibrated HU from vertebral bodies of routine CT data as previously proposed for immanent opportunistic osteoporosis screening based on CT attenuation. The intraclass correlation coefficient (ICC) for vBMD_QCT versus vBMD_OPP indicated better agreement (ICC = 0.913) than the ICC for vBMD_QCT versus noncalibrated HU (ICC = 0.704). Bland-Altman analysis showed data points from 137 patients (95.1%) within the limits of agreement (LOA) of -23.2 to 25.0 mg/cm3 for vBMD_QCT versus vBMD_OPP. Osteoporosis (vBMD <80 mg/cm3 ) was detected in 89 patients (vBMD_QCT) and 88 patients (vBMD_OPP), whereas no patient crossed the diagnostic thresholds from normal vBMD to osteoporosis or vice versa. In a subcohort of 88 patients (thoracolumbar spine covered by imaging for VF reading), 69 patients showed one or more prevalent VFs, and the performance for discrimination between patients with and without VFs was best for vBMD_OPP (area under the curve [AUC] = 0.862; 95% confidence interval [CI], 0.771-0.953). In conclusion, automated opportunistic osteoporosis screening in routine CT of various scanner setups is feasible and may demonstrate high diagnostic accuracy for prevalent VFs. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

Learning residual motion correction for fast and robust 3D multiparametric MRI.

Voluntary and involuntary patient motion is a major problem for data quality in clinical routine of Magnetic Resonance Imaging (MRI). It has been thoroughly investigated and, yet it still remains unresolved. In quantitative MRI, motion artifacts impair the entire temporal evolution of the magnetization and cause errors in parameter estimation. Here, we present a novel strategy based on residual learning for retrospective motion correction in fast 3D whole-brain multiparametric MRI. We propose a 3D multiscale convolutional neural network (CNN) that learns the non-linear relationship between the motion-affected quantitative parameter maps and the residual error to their motion-free reference. For supervised model training, despite limited data availability, we propose a physics-informed simulation to generate self-contained paired datasets from a priori motion-free data. We evaluate motion-correction performance of the proposed method for the example of 3D Quantitative Transient-state Imaging at 1.5T and 3T. We show the robustness of the motion correction for various motion regimes and demonstrate the generalization capabilities of the residual CNN in terms of real-motion in vivo data of healthy volunteers and clinical patient cases, including pediatric and adult patients with large brain lesions. Our study demonstrates that the proposed motion correction outperforms current state of the art, reliably providing a high, clinically relevant image quality for mild to pronounced patient movements. This has important implications in clinical setups where large amounts of motion affected data must be discarded as they are rendered diagnostically unusable.

Gender-, Age- and Region-Specific Characterization of Vertebral Bone Microstructure Through Automated Segmentation and 3D Texture Analysis of Routine Abdominal CT.

Purpose: To identify long-term reproducible texture features (TFs) of spinal computed tomography (CT), and characterize variations with regard to gender, age and vertebral level using our automated quantification framework. Methods: We performed texture analysis (TA) on baseline and follow-up CT (follow-up duration: 30-90 days) of 21 subjects (8 females, 13 males, age at baseline 61.2 ± 9.2 years) to determine long-term reproducibility. TFs with a long-term reproducibility error Δrel<5% were further analyzed for an association with age and vertebral level in a cohort of 376 patients (129 females, 247 males, age 62.5 ± 9.2 years). Automated analysis comprised labeling and segmentation of vertebrae into subregions using a convolutional neural network, calculation of volumetric bone mineral density (vBMD) with asynchronous calibration and TF extraction. Varianceglobal measures the spread of the gray-level distribution in an image while Entropy reflects the uniformity of gray-levels. Short-run emphasis (SRE), Long-run emphasis (LRE), Run-length non-uniformity (RLN) and Run percentage (RP) contain information on consecutive voxels of a particular grey-level, or grey-level range, in a particular direction. Long runs (LRE) represent coarse texture while short runs (SRE) represent fine texture. RLN reflects similarities in the length of runs while RP reflects distribution and homogeneity of runs with a specific direction. Results: Six of the 24 extracted TFs had Δrel<5% (Varianceglobal, Entropy, SRE, LRE, RLN, RP), and were analyzed further in 4716 thoracolumbar vertebrae. Five TFs (Varianceglobal,SRE,LRE, RLN,RP) showed a significant difference between genders (p<0.001), potentially being caused by a finer and more directional vertebral trabecular microstructure in females compared to males. Varianceglobal and Entropy showed a significant increase from the thoracic to the lumbar spine (p<0.001), indicating a higher degree and earlier initiation of trabecular microstructure deterioration at lower spinal levels. The four higher-order TFs showed significant variations between spine regions without a clear directional gradient (p ≤ 0.001-0.012). No TF showed a clear age dependence. vBMD differed significantly between genders, age groups and spine regions (p ≤ 0.001-0.002). Conclusion: Long-term reproducible CT-based TFs of the thoracolumbar spine were established and characterized in a predominantly older adult study population. The gender-, age- and vertebral-level-specific values may serve as foundation for osteoporosis diagnostics and facilitate future studies investigating vertebral microstructure.

Prediction of incident vertebral fractures in routine MDCT: Comparison of global texture features, 3D finite element parameters and volumetric BMD.

PURPOSE: In this case-control study, we evaluated different quantitative parameters derived from routine multi-detector computed tomography (MDCT) scans with respect to their ability to predict incident osteoporotic vertebral fractures of the thoracolumbar spine. METHODS: 16 patients who received baseline and follow-up contrast-enhanced MDCT and were diagnosed with an incident osteoporotic vertebral fracture at follow-up, and 16 age-, sex-, and follow-up-time-matched controls were included in the study. Vertebrae were labelled and segmented using a fully automated pipeline. Volumetric bone mineral density (vBMD), finite element analysis (FEA)-based failure load (FL) and failure displacement (FD), as well as 24 texture features were extracted from L1 - L3 and averaged. Odds ratios (OR) with 95% confidence intervals (CI), expressed per standard deviation decrease, receiver operating characteristic (ROC) area under the curve (AUC), as well as logistic regression models, including all analyzed parameters as independent variables, were used to assess the prediction of incident vertebral fractures. RESULTS: The texture feature Correlation (AUC = 0.754, p = 0.014; OR = 2.76, CI = 1.16-6.58) and vBMD (AUC = 0.750, p = 0.016; OR = 2.67, CI = 1.12-6.37) classified incident vertebral fractures best, while the best FEA-based parameter FL showed an AUC = 0.719 (p = 0.035). Correlation was the only significant predictor of incident fractures in the logistic regression analysis of all parameters (p = 0.022). CONCLUSION: MDCT-derived FEA parameters and texture features, averaged from L1 - L3, showed only a moderate, but no statistically significant improvement of incident vertebral fracture prediction beyond BMD, supporting the hypothesis that vertebral-specific parameters may be superior for fracture risk assessment.

MDCT-Based Finite Element Analyses: Are Measurements at the Lumbar Spine Associated with the Biomechanical Strength of Functional Spinal Units of Incidental Osteoporotic Fractures along the Thoracolumbar Spine?

Assessment of osteoporosis-associated fracture risk during clinical routine is based on the evaluation of clinical risk factors and T-scores, as derived from measurements of areal bone mineral density (aBMD). However, these parameters are limited in their ability to identify patients at high fracture risk. Finite element models (FEMs) have shown to improve bone strength prediction beyond aBMD. This study aims to investigate whether FEM measurements at the lumbar spine can predict the biomechanical strength of functional spinal units (FSUs) with incidental osteoporotic vertebral fractures (VFs) along the thoracolumbar spine. Multi-detector computed tomography (MDCT) data of 11 patients (5 females and 6 males, median age: 67 years) who underwent MDCT twice (median interval between baseline and follow-up MDCT: 18 months) and sustained an incidental osteoporotic VF between baseline and follow-up scanning were used. Based on baseline MDCT data, two FSUs consisting of vertebral bodies and intervertebral discs (IVDs) were modeled: one standardly capturing L1-IVD-L2-IVD-L3 (FSU_L1-L3) and one modeling the incidentally fractured vertebral body at the center of the FSU (FSU_F). Furthermore, volumetric BMD (vBMD) derived from MDCT, FEM-based displacement, and FEM-based load of the single vertebrae L1 to L3 were determined. Statistically significant correlations (adjusted for a BMD ratio of fracture/L1-L3 segments) were revealed between the FSU_F and mean load of L1 to L3 (r = 0.814, p = 0.004) and the mean vBMD of L1 to L3 (r = 0.745, p = 0.013), whereas there was no statistically significant association between the FSU_F and FSU_L1-L3 or between FSU_F and the mean displacement of L1 to L3 (p > 0.05). In conclusion, FEM measurements of single vertebrae at the lumbar spine may be able to predict the biomechanical strength of incidentally fractured vertebral segments along the thoracolumbar spine, while FSUs seem to predict only segment-specific fracture risk.