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Publications (40)
Numerical simulations rely on constructing accurate and detailed models to produce reliable results - a task that is often challenging. This task becomes notably more difficult when the model is of the human brain, the most complex organ of the human body. We create an anatomically comprehensive hexahedral mesh of the human brain using an open-sour...
Computational biomechanics models of the brain have become an important tool for investigating the brain responses to mechanical loads. The geometry, loading conditions, and constitutive properties of such brain models are well-studied and generally accepted. However, there is a lack of experimental evidence to support models of the layers of tissu...
Cerebral aneurysm rupture, leading to subarachnoid hemorrhage with a high mortality rate, disproportionately affects younger populations, resulting in a significant loss of productive life years. A significant proportion of these deaths is due to aneurysmal re-bleeding within the first three days following the initial bleed, prior to treatment. Whi...
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 forwar...
We present an efficient and accurate immersed boundary (IB) finite element (FE) method for internal flow problems with complex geometries (e.g., blood flow in the vascular system). In this study, we use a voxelized flow domain (discretized with hexahedral and tetrahedral elements) instead of a box domain, which is frequently used in IB methods. The...
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...
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-operati...
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 reson...
Our motivation is to enable non-specialists to use sophisticated biomechanical models in the clinic. To further this goal, in this study, we constructed a framework within 3D Slicer for automatically generating and solving patient-specific biomechanical models of the brain. This framework allows determining automatically patient-specific geometry f...
In this study we develop a fast (less than 30 s) method to compute the quantitative flow ratio (QFR) from angiographic images. We evaluate its diagnostic accuracy in patients with intermediate coronary stenosis through comparison with invasively measured fractional flow reserve (FFR). Our method uses a single angiographic view with minimal vessel f...
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...
We present a strong form meshless solver for numerical solution of the non‐stationary, incompressible, viscous Navier–Stokes (N‐S) equations in two (2D) and three dimensions (3D). We solve the flow equations in their stream function–vorticity (in 2D) and vector potential–vorticity (in 3D) formulation, by extending to 3D flows the Boundary Condition...
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 forwar...
A new recovery technique based on discretization corrected particle strength exchange (DC PSE) operators is developed in this paper. DC PSE is a collocation method that can be used to compute derivatives directly at nodal points, instead of by projection from Gauss points as is done in many finite element-based recovery techniques. The proposed met...
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-spe...
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 simulati...
Invasive intracranial electroencephalography (iEEG) or electrocorticography (ECoG) measures electrical potential directly on the surface of the brain, and, combined with numerical modeling, can be used to inform treatment planning for epilepsy surgery. Accurate solution of the iEEG or ECoG forward problem, which is a crucial prerequisite for solvin...
We present an efficient and accurate immersed boundary (IB) finite element (FE) method for numerically solving the incompressible Navier–Stokes equations. Particular emphasis is given to internal flows with complex geometries (blood flow in the vasculature system). IB methods are computationally costly for internal flows, mainly due to the large pe...
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 dra...
Our motivation is to enable non-specialists to use sophisticated biomechanical modelsBiomechanical model in the clinic. To further this goal, in this study, we constructed a framework within 3D Slicer for automatically generating and solving patient-specific biomechanical models of the brain. This framework allows determining automatically patient-...
In this paper, we present a meshless method belonging to the family of element-free Galerkin (EFG) methods. The presented meshless method allows accurate enforcement of essential boundary conditions. The method uses total Lagrangian formulation with explicit time integration to facilitate code simplicity and robust computations in applications that...
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 ki...
We present a flux-conservative finite difference (FCFD) scheme for solving inhomogeneous anisotropic bioelectric problems. The method applies directly on the raw medical image data without the need for sophisticated image analysis algorithms to define interfaces between materials with different electrical conductivities. We demonstrate the accuracy...
Computational fluid dynamics (CFD) studies have been increasingly used for blood flow simulations in intracranial aneurysms (ICAs). However, despite the continuous progress of body-fitted CFD solvers, generating a high quality mesh is still the bottleneck of the CFD simulation, and strongly affects the accuracy of the numerical solution. To overcom...
We present an efficient and accurate immersed boundary (IB) finite element (FE) solver for numerically solving incompressible Navier--Stokes equations. Particular emphasis is given to internal flows with complex geometries (blood flow in the vasculature system). IB methods are computationally costly for internal flows, mainly due to the large perce...
In this paper, we present a meshless method belonging to the family of element-free Galerkin (EFG) methods. The distinguishing feature of the presented meshless method is that it allows accurate enforcement of essential boundary conditions. The method uses total Lagrangian formulation with explicit time integration to facilitate code simplicity and...
In this study we present a kinematic approach to 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 kin...
We present a strong form, meshless point collocation explicit solver for the numerical solution of the transient, incompressible, viscous Navier-Stokes (N-S) equations in two dimensions. We numerically solve the governing flow equations in their stream function-vorticity formulation. We use a uniform Cartesian embedded grid to represent the flow do...
We present a strong form, meshless point collocation explicit solver for the numerical solution of the transient, incompressible, viscous Navier-Stokes (N-S) equations in two dimensions. We numerically solve the governing flow equations in their stream function-vorticity formulation. We use a uniform Cartesian embedded grid to represent the flow do...
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 ha...
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 ha...
This paper describes a new method for simulating tissue growth which can handle anisotropic changes in volume. The method takes advantage of the total Lagrangian formulation which allows the computation of nodal forces for each element in a finite element mesh based on a theoretical stress-free configuration, obtained by considering the unconstrain...
We present an algorithm for modelling swelling and shrinking of soft tissues based on the total Lagrangian formulation of the finite element (FE) method. Explicit time integration with adaptive dynamic relaxation is used to compute the steady state solution. The algorithm can easily handle geometric and material nonlinearities, and is very efficien...
Intra-operative images acquired during brain surgery do not provide sufficient detail to confidently locate brain internal
structures that have been identified in high-resolution pre-operative images. However, the pre-operative images can be warped
to the intra-operative position of brain using predicted deformation field. While craniotomy-induced...