Random boundaries: quantifying segmentation uncertainty in solutions to boundary-value problems

Engineering simulations using boundary-value partial differential equations often implicitly assume that the uncertainty in the location of the boundary has a negligible impact on the output of the simulation. In this work, we develop a novel method for describing the geometric uncertainty in image-derived models and use a naive method for subsequently quantifying a simulation's sensitivity to that uncertainty. A Gaussian random field is constructed to represent the space of possible geometries, based on image-derived quantities such as pixel size, which can then be used to probe the simulation's output space. The algorithm is demonstrated with examples from biomechanics where patient-specific geometries are often segmented from low-resolution, three-dimensional images. These examples show the method's wide applicability with examples using linear elasticity and fluid dynamics. We show that important biomechanical outputs of these example simulations, namely maximum principal stress and wall shear stress, can be highly sensitive to realistic uncertainties in geometry

Automated modeling of brain bioelectric activity within the 3D Slicer environment

Electrocorticography (ECoG) or intracranial electroencephalography (iEEG) monitors electric potential directly on the surface of the brain and can be used to inform treatment planning for epilepsy surgery when paired with numerical modeling. For solving the inverse problem in epilepsy seizure onset localization, accurate solution of the iEEG forward problem is critical which requires accurate representation of the patient's brain geometry and tissue electrical conductivity. In this study, we present an automatic framework for constructing the brain volume conductor model for solving the iEEG forward problem and visualizing the brain bioelectric field on a deformed patient-specific brain model within the 3D Slicer environment. 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. We use an epilepsy case study to illustrate the workflow of our framework developed and integrated within 3D Slicer

Cell-based maximum entropy approximants for three-dimensional domains: Application in large strain elastodynamics using the meshless total Lagrangian explicit dynamics method

We present the cell-based maximum entropy (CME) approximants in E3 space by constructing the smooth approximation distance function to polyhedral surfaces. CME is a meshfree approximation method combining the properties of the maximum entropy approximants and the compact support of element-based interpolants. The method is evaluated in problems of large strain elastodynamics for three-dimensional (3D) continua using the well-established meshless total Lagrangian explicit dynamics method. The accuracy and efficiency of the method is assessed in several numerical examples in terms of computational time, accuracy in boundary conditions imposition, and strain energy density error. Due to the smoothness of CME basis functions, the numerical stability in explicit time integration is preserved for large time step. The challenging task of essential boundary condition (EBC) imposition in noninterpolating meshless methods (eg, moving least squares) is eliminated in CME due to the weak Kronecker-delta property. The EBCs are imposed directly, similar to the finite element method. CME is proven a valuable alternative to other meshless and element-based methods for large-scale elastodynamics in 3D. A naive implementation of the CME approximants in E3 is available to download at https://www.mountris.org/software/mlab/cme.Fil: Mountris, Konstantinos A.. Universidad de Zaragoza; EspañaFil: Bourantas, George C.. University of Western Australia; AustraliaFil: Millán, Raúl Daniel. Universidad Nacional de Cuyo. Facultad de Ciencias Aplicadas a la Industria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Joldes, Grand R.. University of Western Australia; AustraliaFil: Miller, Karol. Cardiff University; Reino Unido. University of Western Australia; AustraliaFil: Pueyo, Esther. Centro de Investigacion Biomedica En Red.; España. Universidad de Zaragoza; EspañaFil: Wittek, Adam. University of Western Australia; Australi

Suite of Meshless Algorithms for Accurate Computation of Soft Tissue Deformation for Surgical Simulation

The ability to predict patient-specific soft tissue deformations is key for computer-integrated surgery systems and the core enabling technology for a new era of personalized medicine. Element-Free Galerkin (EFG) methods are better suited for solving soft tissue deformation problems than the finite element method (FEM) due to their capability of handling large deformation while also eliminating the necessity of creating a complex predefined mesh. Nevertheless, meshless methods based on EFG formulation, exhibit three major limitations: i) meshless shape functions using higher order basis cannot always be computed for arbitrarily distributed nodes (irregular node placement is crucial for facilitating automated discretization of complex geometries); ii) imposition of the Essential Boundary Conditions (EBC) is not straightforward; and, iii) numerical (Gauss) integration in space is not exact as meshless shape functions are not polynomial. This paper presents a suite of Meshless Total Lagrangian Explicit Dynamics (MTLED) algorithms incorporating a Modified Moving Least Squares (MMLS) method for interpolating scattered data both for visualization and for numerical computations of soft tissue deformation, a novel way of imposing EBC for explicit time integration, and an adaptive numerical integration procedure within the Meshless Total Lagrangian Explicit Dynamics algorithm. The appropriateness and effectiveness of the proposed methods is demonstrated using comparisons with the established non-linear procedures from commercial finite element software ABAQUS and experiments with very large deformations. To demonstrate the translational benefits of MTLED we also present a realistic brain-shift computation.Comment: Accepted for publication in Medical Image Analysi

Three-dimensional reconstruction of coronary arteries and plaque morphology using CT angiography - comparison and registration with IVUS

Background: The aim of this study is to present a new methodology for three-dimensional (3D) reconstruction of coronary arteries and plaque morphology using Computed Tomography Angiography (CTA). Methods: The methodology is summarized in six stages: 1) pre-processing of the initial raw images, 2) rough estimation of the lumen and outer vessel wall borders and approximation of the vessel's centerline, 3) manual adaptation of plaque parameters, 4) accurate extraction of the luminal centerline, 5) detection of the lumen - outer vessel wall borders and calcium plaque region, and 6) finally 3D surface construction. Results: The methodology was compared to the estimations of a recently presented Intravascular Ultrasound (IVUS) plaque characterization method. The correlation coefficients for calcium volume, surface area, length and angle vessel were 0.79, 0.86, 0.95 and 0.88, respectively. Additionally, when comparing the inner and outer vessel wall volumes of the reconstructed arteries produced by IVUS and CTA the observed correlation was 0.87 and 0.83, respectively. Conclusions: The results indicated that the proposed methodology is fast and accurate and thus it is likely in the future to have applications in research and clinical arena

Unusual cardiovascular complications of brucellosis presenting in two men: two case reports and a review of the literature

Introduction: Brucellosis is a zoonosis with worldwide distribution, which is particularly endemic in many countries of the Mediterranean basin. Cardiovascular complications of this disease, such as endocarditis, myocarditis and pericarditis, are very rare, with even fewer cases of myocarditis or asymptomatic pericardial effusion in the absence of concomitant endocarditis being reported. Case presentation: We report two cases of brucellosis in two Caucasian men, aged 17 and 34 years old, with myocarditis and asymptomatic pericardial effusion, respectively. Of note, neither patient had concomitant endocarditis. The disease was confirmed serologically and by blood cultures. Both patients recovered completely after receiving appropriate antibiotic treatment without any sign of relapse during a follow-up of 12 months. Conclusion: These two cases emphasize that in endemic areas Brucella can be considered as a potentially causative agent of idiopathic pericardial effusion or myocarditis, even in the absence of concomitant endocarditis. This possibility could be taken into account particularly in cases where contraction of brucellosis is possible, such as occupational exposure or consumption of unpasteurized dairy products. © 2011 Gatselis et al; licensee BioMed Central Ltd