A systematic comparison between FEBio and PolyFEM for biomechanical systems.

BACKGROUND AND OBJECTIVES: Finite element simulations are widely employed as a non-invasive and cost-effective approach for predicting outcomes in biomechanical simulations. However, traditional finite element software, primarily designed for engineering materials, often encountered limitations in contact detection and enforcement, leading to simulation failure when dealing with complex biomechanical configurations. Currently, a lot of model tuning is required to get physically accurate finite element simulations without failures. This adds significant human interaction to each iteration of a biomechanical model. This study addressed these issues by introducing PolyFEM, a novel finite element solver that guarantees inversion- and intersection-free solutions with completely automatic collision detection. The objective of this research is to validate PolyFEM's capabilities by comparing its results with those obtained from a well-established finite element solver, FEBio. METHODS: To achieve this goal, five comparison scenarios were formulated to assess and validate PolyFEM's performance. The simulations were reproduced using both PolyFEM and FEBio, and the final results were compared. The five comparison scenarios included: (1) reproducing simulations from the FEBio test suite, consisting of static, dynamic, and contact-driven simulations; (2) replicating simulations from the verification paper published alongside the original release of FEBio; (3) a biomechanically based contact problem; (4) creating a custom simulation involving high-energy collisions between soft materials to highlight the difference in collision methods between the two solvers; and (5) performing biomechanical simulations of biting and quasi-stance. RESULTS: We found that PolyFEM was capable of replicating all simulations previously conducted in FEBio. Particularly noteworthy is PolyFEM's superiority in high-energy contact simulations, where FEBio fell short, unable to complete over half of the simulations in Scenario 4. Although some of the simulations required significantly more simulation time in PolyFEM compared to FEBio, it is important to highlight that PolyFEM achieved these results without the need for any additional model tuning or contact declaration. DISCUSSION: Despite being in the early stages of development, PolyFEM currently provides verified solutions for hyperelastic materials that are consistent with FEBio, both in previously published workflows and novel finite element scenarios. PolyFEM exhibited the ability to tackle challenging biomechanical problems where other solvers fell short, thus offering the potential to enhance the accuracy and realism of future finite element analyses.

Collision-constrained deformable image registration framework for discontinuity management.

Topological changes like sliding motion, sources and sinks are a significant challenge in image registration. This work proposes the use of the alternating direction method of multipliers as a general framework for constraining the registration of separate objects with individual deformation fields from overlapping in image registration. This constraint is enforced by introducing a collision detection algorithm from the field of computer graphics which results in a robust divide and conquer optimization strategy using Free-Form Deformations. A series of experiments demonstrate that the proposed framework performs superior with regards to the combination of intersection prevention and image registration including synthetic examples containing complex displacement patterns. The results show compliance with the non-intersection constraints while simultaneously preventing a decrease in registration accuracy. Furthermore, the application of the proposed algorithm to the DIR-Lab data set demonstrates that the framework generalizes to real data by validating it on a lung registration problem.

Pseudo-Label Guided Image Synthesis for Semi-Supervised COVID-19 Pneumonia Infection Segmentation.

Coronavirus disease 2019 (COVID-19) has become a severe global pandemic. Accurate pneumonia infection segmentation is important for assisting doctors in diagnosing COVID-19. Deep learning-based methods can be developed for automatic segmentation, but the lack of large-scale well-annotated COVID-19 training datasets may hinder their performance. Semi-supervised segmentation is a promising solution which explores large amounts of unlabelled data, while most existing methods focus on pseudo-label refinement. In this paper, we propose a new perspective on semi-supervised learning for COVID-19 pneumonia infection segmentation, namely pseudo-label guided image synthesis. The main idea is to keep the pseudo-labels and synthesize new images to match them. The synthetic image has the same COVID-19 infected regions as indicated in the pseudo-label, and the reference style extracted from the style code pool is added to make it more realistic. We introduce two representative methods by incorporating the synthetic images into model training, including single-stage Synthesis-Assisted Cross Pseudo Supervision (SA-CPS) and multi-stage Synthesis-Assisted Self-Training (SA-ST), which can work individually as well as cooperatively. Synthesis-assisted methods expand the training data with high-quality synthetic data, thus improving the segmentation performance. Extensive experiments on two COVID-19 CT datasets for segmenting the infections demonstrate our method is superior to existing schemes for semi-supervised segmentation, and achieves the state-of-the-art performance on both datasets. Code is available at: https://github.com/FeiLyu/SASSL.

A hybrid approach to full-scale reconstruction of renal arterial network.

The renal vasculature, acting as a resource distribution network, plays an important role in both the physiology and pathophysiology of the kidney. However, no imaging techniques allow an assessment of the structure and function of the renal vasculature due to limited spatial and temporal resolution. To develop realistic computer simulations of renal function, and to develop new image-based diagnostic methods based on artificial intelligence, it is necessary to have a realistic full-scale model of the renal vasculature. We propose a hybrid framework to build subject-specific models of the renal vascular network by using semi-automated segmentation of large arteries and estimation of cortex area from a micro-CT scan as a starting point, and by adopting the Global Constructive Optimization algorithm for generating smaller vessels. Our results show a close agreement between the reconstructed vasculature and existing anatomical data obtained from a rat kidney with respect to morphometric and hemodynamic parameters.

Bundle geodesic convolutional neural network for diffusion-weighted imaging segmentation.

Purpose: Applying machine learning techniques to magnetic resonance diffusion-weighted imaging (DWI) data is challenging due to the size of individual data samples and the lack of labeled data. It is possible, though, to learn general patterns from a very limited amount of training data if we take advantage of the geometry of the DWI data. Therefore, we present a tissue classifier based on a Riemannian deep learning framework for single-shell DWI data. Approach: The framework consists of three layers: a lifting layer that locally represents and convolves data on tangent spaces to produce a family of functions defined on the rotation groups of the tangent spaces, i.e., a (not necessarily continuous) function on a bundle of rotational functions on the manifold; a group convolution layer that convolves this function with rotation kernels to produce a family of local functions over each of the rotation groups; a projection layer using maximization to collapse this local data to form manifold based functions. Results: Experiments show that our method achieves the performance of the same level as state-of-the-art while using way fewer parameters in the model ( < 10 % ). Meanwhile, we conducted a model sensitivity analysis for our method. We ran experiments using a proportion (69.2%, 53.3%, and 29.4%) of the original training set and analyzed how much data the model needs for the task. Results show that this does reduce the overall classification accuracy mildly, but it also boosts the accuracy for minority classes. Conclusions: This work extended convolutional neural networks to Riemannian manifolds, and it shows the potential in understanding structural patterns in the brain, as well as in aiding manual data annotation.

Open-Full-Jaw: An open-access dataset and pipeline for finite element models of human jaw.

BACKGROUND: State-of-the-art finite element studies on human jaws are mostly limited to the geometry of a single patient. In general, developing accurate patient-specific computational models of the human jaw acquired from cone-beam computed tomography (CBCT) scans is labor-intensive and non-trivial, which involves time-consuming human-in-the-loop procedures, such as segmentation, geometry reconstruction, and re-meshing tasks. Therefore, with the current practice, researchers need to spend considerable time and effort to produce finite element models (FEMs) to get to the point where they can use the models to answer clinically-interesting questions. Besides, any manual task involved in the process makes it difficult for the researchers to reproduce identical models generated in the literature. Hence, a quantitative comparison is not attainable due to the lack of surface/volumetric meshes and FEMs. METHODS: We share an open-access repository composed of 17 patient-specific computational models of human jaws and the utilized pipeline for generating them for reproducibility of our work. The used pipeline minimizes the required time for processing and any potential biases in the model generation process caused by human intervention. It gets the segmented geometries with irregular and dense surface meshes and provides reduced, adaptive, watertight, and conformal surface/volumetric meshes, which can directly be used in finite element (FE) analysis. RESULTS: We have quantified the variability of our 17 models and assessed the accuracy of the developed models from three different aspects; (1) the maximum deviations from the input meshes using the Hausdorff distance as an error measurement, (2) the quality of the developed volumetric meshes, and (3) the stability of the FE models under two different scenarios of tipping and biting. CONCLUSIONS: The obtained results indicate that the developed computational models are precise, and they consist of quality meshes suitable for various FE scenarios. We believe the provided dataset of models including a high geometrical variation obtained from 17 different models will pave the way for population studies focusing on the biomechanical behavior of human jaws.

Accuracy and consistency of intensity-based deformable image registration in 4DCT for tumor motion estimation in liver radiotherapy planning.

We investigate the accuracy of intensity-based deformable image registration (DIR) for tumor localization in liver stereotactic body radiotherapy (SBRT). We included 4DCT scans to capture the breathing motion of eight patients receiving SBRT for liver metastases within a retrospective clinical study. Each patient had three fiducial markers implanted. The liver and the tumor were delineated in the mid-ventilation phase, and their positions in the other phases were estimated with deformable image registration. We tested referenced and sequential registrations strategies. The fiducial markers were the gold standard to evaluate registration accuracy. The registration errors related to measured versus estimated fiducial markers showed a mean value less than 1.6mm. The positions of some fiducial markers appeared not stable on the 4DCT throughout the respiratory phases. Markers' center of mass tends to be a more reliable measurement. Distance errors of tumor location based on registration versus markers center of mass were less than 2mm. There were no statistically significant differences between the reference and the sequential registration, i.e., consistency and errors were comparable to resolution errors. We demonstrated that intensity-based DIR is accurate up to resolution level for locating the tumor in the liver during breathing motion.

LibHip: An open-access hip joint model repository suitable for finite element method simulation.

BACKGROUND AND OBJECTIVE: population-based finite element analysis of hip joints allows us to understand the effect of inter-subject variability on simulation results. Developing large subject-specific population models is challenging and requires extensive manual effort. Thus, the anatomical representations are often subjected to simplification. The discretized geometries do not guarantee conformity in shared interfaces, leading to complications in setting up simulations. Additionally, these models are not openly accessible, challenging reproducibility. Our work provides multiple subject-specific hip joint finite element models and a novel semi-automated modeling workflow. METHODS: we reconstruct 11 healthy subject-specific models, including the sacrum, the paired pelvic bones, the paired proximal femurs, the paired hip joints, the paired sacroiliac joints, and the pubic symphysis. The bones are derived from CT scans, and the cartilages are generated from the bone geometries. We generate the whole complex's volume mesh with conforming interfaces. Our models are evaluated using both mesh quality metrics and simulation experiments. RESULTS: the geometry of all the models are inspected by our clinical expert and show high-quality discretization with accurate geometries. The simulations produce smooth stress patterns, and the variance among the subjects highlights the effect of inter-subject variability and asymmetry in the predicted results. CONCLUSIONS: our work is one of the largest model repositories with respect to the number of subjects and regions of interest in the hip joint area. Our detailed research data, including the clinical images, the segmentation label maps, the finite element models, and software tools, are openly accessible on GitHub and the link is provided in Moshfeghifar et al.(2022)[1]. Our aim is to empower clinical researchers to have free access to verified and reproducible models. In future work, we aim to add additional structures to our models.

A multi-patient analysis of the center of rotation trajectories using finite element models of the human mandible.

Studying different types of tooth movements can help us to better understand the force systems used for tooth position correction in orthodontic treatments. This study considers a more realistic force system in tooth movement modeling across different patients and investigates the effect of the couple force direction on the position of the center of rotation (CRot). The finite-element (FE) models of human mandibles from three patients are used to investigate the position of the CRots for different patients' teeth in 3D space. The CRot is considered a single point in a 3D coordinate system and is obtained by choosing the closest point on the axis of rotation to the center of resistance (CRes). A force system, consisting of a constant load and a couple (pair of forces), is applied to each tooth, and the corresponding CRot trajectories are examined across different patients. To perform a consistent inter-patient analysis, different patients' teeth are registered to the corresponding reference teeth using an affine transformation. The selected directions and applied points of force on the reference teeth are then transformed into the registered teeth domains. The effect of the direction of the couple on the location of the CRot is also studied by rotating the couples about the three principal axes of a patient's premolar. Our results indicate that similar patterns can be obtained for the CRot positions of different patients and teeth if the same load conditions are used. Moreover, equally rotating the direction of the couple about the three principal axes results in different patterns for the CRot positions, especially in labiolingual direction. The CRot trajectories follow similar patterns in the corresponding teeth, but any changes in the direction of the force and couple cause misalignment of the CRot trajectories, seen as rotations about the long axis of the tooth.

Chunked Bounding Volume Hierarchies for Fast Digital Prototyping Using Volumetric Meshes.

We present a novel approach to using Bounding Volume Hierarchies (BVHs) for collision detection of volumetric meshes for digital prototyping based on accurate simulation. In general, volumetric meshes contain more primitives than surface meshes, which in turn means larger BVHs. To manage these larger BVHs, we propose an algorithm for splitting meshes into smaller chunks with a limited-size BVH each. Limited-height BVHs make guided, all-pairs testing of two chunked meshes well-suited for GPU implementation. This is because the dynamically generated work during BVH traversal becomes bounded. Chunking is simple to implement compared to dynamic load balancing methods and can result in an overall two orders of magnitude speedup on GPUs. This indicates that dynamic load balancing may not be a well suited scheme for the GPU. The overall application timings showed that data transfers were not the bottleneck. Instead, the conversion to and from OpenCL friendly data structures was causing serious performance impediments. Still, a simple OpenMP acceleration of the conversion allowed the GPU solution to beat the CPU solution by 20 percent. We demonstrate our results using rigid and deformable body scenes of varying complexities on a variety of GPUs.

A numerical strategy for finite element modeling of frictionless asymmetric vocal fold collision.

Analysis of voice pathologies may require vocal fold models that include relevant features such as vocal fold asymmetric collision. The present study numerically addresses the problem of frictionless asymmetric collision in a self-sustained three-dimensional continuum model of the vocal folds. Theoretical background and numerical analysis of the finite-element position-based contact model are presented, along with validation. A novel contact detection mechanism capable to detect collision in asymmetric oscillations is developed. The effect of inexact contact constraint enforcement on vocal fold dynamics is examined by different variational methods for inequality constrained minimization problems, namely, the Lagrange multiplier method and the penalty method. In contrast to the penalty solution, which is related to classical spring-like contact forces, numerical examples show that the parameter-independent Lagrange multiplier solution is more robust and accurate in the estimation of dynamical and mechanical features at vocal fold contact. Furthermore, special attention is paid to the temporal integration schemes in relation to the contact problem, the results suggesting an advantage of highly diffusive schemes. Finally, vocal fold contact enforcement is shown to affect asymmetric oscillations. The present model may be adapted to existing vocal fold models, which may contribute to a better understanding of the effect of the nonlinear contact phenomenon on phonation. Copyright © 2016 John Wiley & Sons, Ltd.

Multiphase flow of immiscible fluids on unstructured moving meshes.

In this paper, we present a method for animating multiphase flow of immiscible fluids using unstructured moving meshes. Our underlying discretization is an unstructured tetrahedral mesh, the deformable simplicial complex (DSC), that moves with the flow in a Lagrangian manner. Mesh optimization operations improve element quality and avoid element inversion. In the context of multiphase flow, we guarantee that every element is occupied by a single fluid and, consequently, the interface between fluids is represented by a set of faces in the simplicial complex. This approach ensures that the underlying discretization matches the physics and avoids the additional book-keeping required in grid-based methods where multiple fluids may occupy the same cell. Our Lagrangian approach naturally leads us to adopt a finite element approach to simulation, in contrast to the finite volume approaches adopted by a majority of fluid simulation techniques that use tetrahedral meshes. We characterize fluid simulation as an optimization problem allowing for full coupling of the pressure and velocity fields and the incorporation of a second-order surface energy. We introduce a preconditioner based on the diagonal Schur complement and solve our optimization on the GPU. We provide the results of parameter studies as well as a performance analysis of our method, together with suggestions for performance optimization.