Patient-specific solution of the electrocorticography forward problem in deforming brain.

Invasive intracranial electroencephalography (iEEG), or electrocorticography (ECoG), measures electric potential directly on the surface of the brain and can be used to inform treatment planning for epilepsy surgery. Combined with numerical modeling it can further improve accuracy of epilepsy surgery planning. Accurate solution of the iEEG forward problem, which is a crucial prerequisite for solving the iEEG inverse problem in epilepsy seizure onset zone localization, requires accurate representation of the patient's brain geometry and tissue electrical conductivity after implantation of electrodes. However, implantation of subdural grid electrodes causes the brain to deform, which invalidates preoperatively acquired image data. Moreover, postoperative magnetic resonance imaging (MRI) is incompatible with implanted electrodes and computed tomography (CT) has insufficient range of soft tissue contrast, which precludes both MRI and CT from being used to obtain the deformed postoperative geometry. In this paper, we present a biomechanics-based image warping procedure using preoperative MRI for tissue classification and postoperative CT for locating implanted electrodes to perform non-rigid registration of the preoperative image data to the postoperative configuration. We solve the iEEG forward problem on the predicted postoperative geometry using the finite element method (FEM) which accounts for patient-specific inhomogeneity and anisotropy of tissue conductivity. Results for the simulation of a current source in the brain show large differences in electric potential predicted by the models based on the original images and the deformed images corresponding to the brain geometry deformed by placement of invasive electrodes. Computation of the lead field matrix (useful for solution of the iEEG inverse problem) also showed significant differences between the different models. The results suggest that rapid and accurate solution of the forward problem in a deformed brain for a given patient is achievable.

Is There a Relationship Between Stress in Walls of Abdominal Aortic Aneurysm and Symptoms?

BACKGROUND: Abdominal aortic aneurysm (AAA) is a permanent and irreversible dilation of the lower region of the aorta. It is typically an asymptomatic condition that if left untreated can expand to the point of rupture. In simple mechanical terms, rupture of an artery occurs when the local wall stress exceeds the local wall strength. It is therefore understandable that numerous studies have attempted to estimate the AAA wall stress and investigate the relationship between the AAA wall stress and AAA symptoms. MATERIALS AND METHODS: We conducted computational biomechanics analysis for 19 patients with AAA (a proportion of these patients were classified as symptomatic) to investigate whether the AAA wall stress fields (both the patterns and magnitude) correlate with the clinical definition of symptomatic and asymptomatic AAAs. For computation of AAA wall stress, we used a very efficient method recently presented by the Intelligent Systems for Medicine Laboratory. The Intelligent Systems for Medicine Laboratory's method uses geometry from computed tomography images and mean arterial pressure as the applied load. The method is embedded in the software platform BioPARR-Biomechanics based Prediction of Aneurysm Rupture Risk, freely available from http://bioparr.mech.uwa.edu.au/. The uniqueness of our stress computation approach is three-fold: i) the results are insensitive to unknown patient-specific mechanical properties of arterial wall tissue; ii) the residual stress is accounted for, according to Y.C. Fung's Uniform Stress Hypothesis; and iii) the analysis is automated and quick, making our approach compatible with clinical workflows. RESULTS: Symptomatic patients could not be identified from the plots (pattern) of AAA wall stress and stress magnitude. Although the largest stress was predicted for a patient who suffered from AAA symptoms, the three patients with the smallest stress were also symptomatic. CONCLUSIONS: The results demonstrate, contrary to the common view, that neither the wall stress magnitude nor the stress distribution appears to be associated with the presence of clinical symptoms.

Efficient inverse isoparametric mapping algorithm for whole-body computed tomography registration using deformations predicted by nonlinear finite element modeling.

Biomechanical modeling methods can be used to predict deformations for medical image registration and particularly, they are very effective for whole-body computed tomography (CT) image registration because differences between the source and target images caused by complex articulated motions and soft tissues deformations are very large. The biomechanics-based image registration method needs to deform the source images using the deformation field predicted by finite element models (FEMs). In practice, the global and local coordinate systems are used in finite element analysis. This involves the transformation of coordinates from the global coordinate system to the local coordinate system when calculating the global coordinates of image voxels for warping images. In this paper, we present an efficient numerical inverse isoparametric mapping algorithm to calculate the local coordinates of arbitrary points within the eight-noded hexahedral finite element. Verification of the algorithm for a nonparallelepiped hexahedral element confirms its accuracy, fast convergence, and efficiency. The algorithm's application in warping of the whole-body CT using the deformation field predicted by means of a biomechanical FEM confirms its reliability in the context of whole-body CT registration.

Letter to the editor: Current progress in patient-specific modeling by Neal and Kerckhoffs (2010).

A recent review article on 'Current progress in patient-specific modeling' in Briefings in Bioinformatics contains the statement summarizing the results of our previous study 'On the unimportance of constitutive models in computing brain deformation for image-guided surgery' published in Biomechanics and Modeling in Mechanobiology as confirmation of adequacy of linear elastic model for such computation. The purpose of this Letter to the Editor is to clarify this statement by informing the Readers of Briefings in Bioinformatics that our study indicates the following: (i) a simple linear elastic constitutive model for the brain tissue is sufficient when used with an appropriate finite deformation solution (i.e. geometrically non-linear analysis); and (ii) Linear analysis approach that assumes infinitesimally small brain deformations leads to unrealistic results.

Computation for biomechanical analysis of aortic aneurysms: the importance of computational grid.

Aortic wall stress is the most common variable of interest in abdominal aortic aneurysm (AAA) rupture risk assessment. Computation of such stress has been dominated by finite element analysis. However, the effects of finite element (FE) formulation, element quality, and methods of FE mesh construction on the efficiency, robustness, and accuracy of such computation have attracted little attention. In this study, we fill this knowledge gap by comparing the results of the calculated aortic wall stress for ten AAA patients using tetrahedral and hexahedral meshes when varying the FE formulation (displacement-based and hybrid), FE shape functions, spatial integration scheme, and number of elements through the wall thickness.

Image data and computational grids for computing brain shift and solving the electrocorticography forward problem.

This article describes the dataset applied in the research reported in NeuroImage article "Patient-specific solution of the electrocorticography forward problem in deforming brain" [1] that is available for download from the Zenodo data repository (https://zenodo.org/record/7687631) [2]. Preoperative structural and diffusion-weighted magnetic resonance (MR) and postoperative computed tomography (CT) images of a 12-year-old female epilepsy patient under evaluation for surgical intervention were obtained retrospectively from Boston Children's Hospital. We used these images to conduct the analysis at The University of Western Australia's Intelligent Systems for Medicine Laboratory using SlicerCBM [3], our open-source software extension for the 3D Slicer medical imaging platform. As part of the analysis, we processed the images to extract the patient-specific brain geometry; created computational grids, including a tetrahedral grid for the meshless solution of the biomechanical model and a regular hexahedral grid for the finite element solution of the electrocorticography forward problem; predicted the postoperative MRI and DTI that correspond to the brain configuration deformed by the placement of subdural electrodes using biomechanics-based image warping; and solved the patient-specific electrocorticography forward problem to compute the electric potential distribution within the patient's head using the original preoperative and predicted postoperative image data. The well-established and open-source file formats used in this dataset, including Nearly Raw Raster Data (NRRD) files for images, STL files for surface geometry, and Visualization Toolkit (VTK) files for computational grids, allow other research groups to easily reuse the data presented herein to solve the electrocorticography forward problem accounting for the brain shift caused by implantation of subdural grid electrodes.

SlicerCBM: automatic framework for biomechanical analysis of the brain.

PURPOSE: Brain shift that occurs during neurosurgery disturbs the brain's anatomy. Prediction of the brain shift is essential for accurate localisation of the surgical target. Biomechanical models have been envisaged as a possible tool for such predictions. In this study, we created a framework to automate the workflow for predicting intra-operative brain deformations. METHODS: We created our framework by uniquely combining our meshless total Lagrangian explicit dynamics (MTLED) algorithm for computing soft tissue deformations, open-source software libraries and built-in functions within 3D Slicer, an open-source software package widely used for medical research. Our framework generates the biomechanical brain model from the pre-operative MRI, computes brain deformation using MTLED and outputs results in the form of predicted warped intra-operative MRI. RESULTS: Our framework is used to solve three different neurosurgical brain shift scenarios: craniotomy, tumour resection and electrode placement. We evaluated our framework using nine patients. The average time to construct a patient-specific brain biomechanical model was 3 min, and that to compute deformations ranged from 13 to 23 min. We performed a qualitative evaluation by comparing our predicted intra-operative MRI with the actual intra-operative MRI. For quantitative evaluation, we computed Hausdorff distances between predicted and actual intra-operative ventricle surfaces. For patients with craniotomy and tumour resection, approximately 95% of the nodes on the ventricle surfaces are within two times the original in-plane resolution of the actual surface determined from the intra-operative MRI. CONCLUSION: Our framework provides a broader application of existing solution methods not only in research but also in clinics. We successfully demonstrated the application of our framework by predicting intra-operative deformations in nine patients undergoing neurosurgical procedures.

On stress in abdominal aortic aneurysm: Linear versus non-linear analysis and aneurysm rupture risk.

We present comprehensive biomechanical analyses of abdominal aortic aneurysms (AAA) for 43 patients. We compare stress magnitudes and stress distributions within arterial walls of abdominal aortic aneurysms (AAA) obtained using two simulation and modelling methods: (a) Fully automated and computationally very efficient linear method embedded in the software platform Biomechanics based Prediction of Aneurysm Rupture Risk (BioPARR), freely available from https://bioparr.mech.uwa.edu.au/; (b) More complex and much more computationally demanding Non-Linear Iterative Stress Analysis (Non-LISA) that uses a non-linear inverse iterative approach and strongly non-linear material model. Both methods predicted localised high stress zones with over 90% of AAA model volume fraction subjected to stress below 20% of the 99th percentile maximum principal stress. However, for the non-linear iterative method, the peak maximum principal stress (and 99th percentile maximum principal stress) was higher and the stress magnitude in the low stress area lower than for the automated linear method embedded in BioPARR. Differences between the stress distributions obtained using the two methods tended to be particularly pronounced in the areas where the AAA curvature was large. Performance of the selected characteristic features of the stress fields (we used 99th percentile maximum principal stress) obtained using BioPARR and Non-LISA in distinguishing between the AAAs that would rupture and remain intact was for practical purposes the same for both methods.

Should anthropometric differences between the commonly used pedestrian computational biomechanics models and Chinese population be taken into account when predicting pedestrian head kinematics and injury in vehicle collisions in China?

Computational biomechanics models play a key role in predicting/evaluating pedestrian head kinematics and injury risk in car-to-pedestrian collisions. The human multibody models most commonly used in car-to-pedestrian collision reconstruction, such as pedestrian model by The Netherlands Organisation for Applied Scientific Research TNO, are built using the anthropometry of Western European population as defined in TNO (2013) human multibody model database. In this study, we investigate the effects of the anthropometric differences between the Western European and Chinese populations on the pedestrian head kinematics and injury responses predicted using multibody models. The comparison was conducted through car-to-pedestrian collision simulations using pedestrian multibody models representing anthropometric characteristics of Western European and Chinese populations, three typical vehicle shapes (sedan, SUV and minivan), five initial vehicle impact speeds (30, 35, 40, 45, 50 km/h), and six pedestrian walking postures. The results indicate that the change of pedestrian model anthropometry (from Western European to Chinese) exerts appreciable effects on both the predicted initial boundary conditions of the head-to-windscreen impact (in particular the head-to-windscreen impact angle) and the head injury indices in the impact with the road surface (secondary impact).

Evaluation of the head protection effectiveness of cyclist helmets using full-scale computational biomechanics modelling of cycling accidents.

INTRODUCTION: Cycling is a popular choice for urban transportation. Helmets are important and the most popular means of head protection for cyclists. However, a debate about the effectiveness of helmets in protecting a cyclist's head from injury continues. METHOD: We employed computational biomechanics methods to analyze the head protection effectiveness of nine off-the-shelf-helmets for two typical impact scenarios that occur in cycling accidents: cyclist's head impacting a kerb (kerb-impact) and cyclist skidding (skidding impact) on the road surface. We conducted drop tests for all nine analyzed helmets, and used the test data for validation of the corresponding helmet finite element (FE) models created in this study. The validated helmet models were then used in the full-scale computer simulations (FE analysis for the skull, brain and helmet, and multibody dynamics for the remaining segments of the cyclist's body) of the cycling accidents for cyclists wearing a helmet and without a helmet. RESULTS: The results indicate that helmets can reduce both the peak linear acceleration of the cyclist head center of gravity (COG) and the risk of cyclist skull fracture. However, higher rotational acceleration of the head COG was predicted for cyclists wearing helmets. The results obtained using the injury criteria that rely on the brain deformations (maximum shear strain MPS and cumulative strain damage measure CSDM) suggest that helmets may offer protection in all the analyzed cyclist impact scenarios. However, the predicted level of protection varies for different helmets and impact scenarios with appreciable variations in the predictions obtained using different injury criteria. Reduction in the maximum principal strain (MPS0.98) for helmeted cyclists was predicted for both impact scenarios. In contrast, wearing the helmet reduced the CSDM only for the skidding impact scenario. For the kerb-impact scenario, no clear influence of the helmet on the predicted CSDM was observed.

Computer simulation of tumour resection-induced brain deformation by a meshless approach.

Tumour resection requires precise planning and navigation to maximise tumour removal while simultaneously protecting nearby healthy tissues. Neurosurgeons need to know the location of the remaining tumour after partial tumour removal before continuing with the resection. Our approach to the problem uses biomechanical modelling and computer simulation to compute the brain deformations after the tumour is resected. In this study, we use meshless Total Lagrangian explicit dynamics as the solver. The problem geometry is extracted from the patient-specific magnetic resonance imaging (MRI) data and includes the parenchyma, tumour, cerebrospinal fluid and skull. The appropriate non-linear material formulation is used. Loading is performed by imposing intra-operative conditions of gravity and reaction forces between the tumour and surrounding healthy parenchyma tissues. A finite frictionless sliding contact is enforced between the skull (rigid) and parenchyma. The meshless simulation results are compared to intra-operative MRI sections. We also calculate Hausdorff distances between the computed deformed surfaces (ventricles and tumour cavities) and surfaces observed intra-operatively. Over 80% of points on the ventricle surface and 95% of points on the tumour cavity surface were successfully registered (results within the limits of two times the original in-plane resolution of the intra-operative image). Computed results demonstrate the potential for our method in estimating the tissue deformation and tumour boundary during the resection.

Automatic framework for patient-specific modelling of tumour resection-induced brain shift.

Our motivation is to enable non-biomechanical engineering specialists to use sophisticated biomechanical models in the clinic to predict tumour resection-induced brain shift, and subsequently know the location of the residual tumour and its boundary. To achieve this goal, we developed a framework for automatically generating and solving patient-specific biomechanical models of the brain. This framework automatically determines patient-specific brain geometry from MRI data, generates patient-specific computational grid, assigns material properties, defines boundary conditions, applies external loads to the anatomical structures, and solves differential equations of nonlinear elasticity using Meshless Total Lagrangian Explicit Dynamics (MTLED) algorithm. We demonstrated the effectiveness and appropriateness of our framework on real clinical cases of tumour resection-induced brain shift.

Simulation of intracranial hemodynamics by an efficient and accurate immersed boundary scheme.

We use computational fluid dynamics (CFD) to simulate blood flow in intracranial aneurysms (IAs). Despite ongoing improvements in the accuracy and efficiency of body-fitted CFD solvers, generation of a high quality mesh appears as the bottleneck of the flow simulation and strongly affects the accuracy of the numerical solution. To overcome this drawback, we use an immersed boundary method. The proposed approach solves the incompressible Navier-Stokes equations on a rectangular (box) domain discretized using uniform Cartesian grid using the finite element method. The immersed object is represented by a set of points (Lagrangian points) located on the surface of the object. Grid local refinement is applied using an automated algorithm. We verify and validate the proposed method by comparing our numerical findings with published experimental results and analytical solutions. We demonstrate the applicability of the proposed scheme on patient-specific blood flow simulations in IAs.

Real-Time Nonlinear Finite Element Computations on GPU - Application to Neurosurgical Simulation.

Application of biomechanical modeling techniques in the area of medical image analysis and surgical simulation implies two conflicting requirements: accurate results and high solution speeds. Accurate results can be obtained only by using appropriate models and solution algorithms. In our previous papers we have presented algorithms and solution methods for performing accurate nonlinear finite element analysis of brain shift (which includes mixed mesh, different non-linear material models, finite deformations and brain-skull contacts) in less than a minute on a personal computer for models having up to 50.000 degrees of freedom. In this paper we present an implementation of our algorithms on a Graphics Processing Unit (GPU) using the new NVIDIA Compute Unified Device Architecture (CUDA) which leads to more than 20 times increase in the computation speed. This makes possible the use of meshes with more elements, which better represent the geometry, are easier to generate, and provide more accurate results.

Prediction of pedestrian brain injury due to vehicle impact using computational biomechanics models: Are head-only models sufficient?

Objectives: Accident reconstruction using computational biomechanics models plays an important role in research and prevention of human brain injury caused by car-to-pedestrian impacts. Finite element (FE) "head-only" models (that represent only the pedestrian head and brain) used in such reconstruction do not account for the influence of the rest of the pedestrian body on the head kinematics due to the accident and, consequently, on the brain injury risk prediction. Application of full-scale FE pedestrian models, on the other hand, is limited by their high computational cost and, more importantly, by the time-consuming preprocessing when repositioning the model to represent the pedestrian posture and location in relation to the impacting car. The objective of this study is to propose a computational biomechanics modeling approach to overcome these challenges.Methods: First, we couple a validated commercial FE head-neck complex model and a multibody (MB) pedestrian model. This coupled FE-MB model is evaluated through application in reconstruction of a real-world car-to-pedestrian impact accident and comparison of the pedestrian kinematics predicted using this model with the results obtained from the established full-scale MB pedestrian model. Finally, we compare the results obtained using the coupled FE-MB model proposed in this study and FE head-only model in terms of both the head kinematics and brain injury risk predicted using the two models.Results: The results of analysis of head injury criterion (HIC15) and brain deformation-based injury criteria (instantaneous value of cumulative strain damage measure iCSDM and maximum shear strain of the brain tissue) indicate substantial differences in the head kinematics and brain injury risk predicted using the two models. The coupled FE-MB model predicts a high risk of the brain injury which is consistent with the database record of the analyzed accident, in particular for the impact between the pedestrian head and road surface. In contrast, the head-only model did not predict that such impact can occur. The FE head head-only model with rigid skull and prescribed acceleration-time history of the head center of gravity determined from accident reconstruction using the purely MB pedestrian model, predicted appreciably lower iCSDM than the coupled FE-MB model that accounts for skull deformations using the linear elastic-plastic material model.Conclusions: This study suggests that the FE head-only models may be deficient for car-to-pedestrian impact accident reconstruction and estimation of risk of the pedestrian brain injury. In particular, this applies to the models that simplify the pedestrian skull as a rigid body.

Mathematical modeling and computer simulation of needle insertion into soft tissue.

In this study we present a kinematic approach for modeling needle insertion into soft tissues. The kinematic approach allows the presentation of the problem as Dirichlet-type (i.e. driven by enforced motion of boundaries) and therefore weakly sensitive to unknown properties of the tissues and needle-tissue interaction. The parameters used in the kinematic approach are straightforward to determine from images. Our method uses Meshless Total Lagrangian Explicit Dynamics (MTLED) method to compute soft tissue deformations. The proposed scheme was validated against experiments of needle insertion into silicone gel samples. We also present a simulation of needle insertion into the brain demonstrating the method's insensitivity to assumed mechanical properties of tissue.

Image, geometry and finite element mesh datasets for analysis of relationship between abdominal aortic aneurysm symptoms and stress in walls of abdominal aortic aneurysm.

These datasets contain Computed Tomography (CT) images of 19 patients with Abdominal Aortic Aneurysm (AAA) together with 19 patient-specific geometry data and computational grids (finite element meshes) created from these images applied in the research reported in Journal of Surgical Research article "Is There A Relationship Between Stress in Walls of Abdominal Aortic Aneurysm and Symptoms?"[1]. The images were randomly selected from the retrospective database of University Hospitals Leuven (Leuven, Belgium) and provided to The University of Western Australia's Intelligent Systems for Medicine Laboratory. The analysis was conducted using our freely-available open-source software BioPARR (Joldes et al., 2017) created at The University of Western Australia. The analysis steps include image segmentation to obtain the patient-specific AAA geometry, construction of computational grids (finite element meshes), and AAA stress computation. We use well-established and widely used data file formats (Nearly Raw Raster Data or NRRD for the images, Stereolitography or STL format for geometry, and Abaqus finite element code keyword format for the finite element meshes). This facilitates re-use of our datasets in practically unlimited range of studies that rely on medical image analysis and computational biomechanics to investigate and formulate indicators and predictors of AAA symptoms.

Computation of intra-operative brain shift using dynamic relaxation.

Many researchers have proposed the use of biomechanical models for high accuracy soft organ non-rigid image registration, but one main problem in using comprehensive models is the long computation time required to obtain the solution. In this paper we propose to use the Total Lagrangian formulation of the Finite Element method together with Dynamic Relaxation for computing intra-operative organ deformations. We study the best ways of estimating the parameters involved and we propose a termination criteria that can be used in order to obtain fast results with prescribed accuracy. The simulation results prove the accuracy and computational efficiency of the method, even in cases involving large deformations, nonlinear materials and contacts.