PaCER - A fully automated method for electrode trajectory and contact reconstruction in deep brain stimulation

in NeuroImage: Clinical (2018), 17

Abstract Deep brain stimulation (DBS) is a neurosurgical intervention where electrodes are permanently implanted into the brain in order to modulate pathologic neural activity. The post-operative ... [more ▼]

Abstract Deep brain stimulation (DBS) is a neurosurgical intervention where electrodes are permanently implanted into the brain in order to modulate pathologic neural activity. The post-operative reconstruction of the DBS electrodes is important for an efficient stimulation parameter tuning. A major limitation of existing approaches for electrode reconstruction from post-operative imaging that prevents the clinical routine use is that they are manual or semi-automatic, and thus both time-consuming and subjective. Moreover, the existing methods rely on a simplified model of a straight line electrode trajectory, rather than the more realistic curved trajectory. The main contribution of this paper is that for the first time we present a highly accurate and fully automated method for electrode reconstruction that considers curved trajectories. The robustness of our proposed method is demonstrated using a multi-center clinical dataset consisting of N=44 electrodes. In all cases the electrode trajectories were successfully identified and reconstructed. In addition, the accuracy is demonstrated quantitatively using a high-accuracy phantom with known ground truth. In the phantom experiment, the method could detect individual electrode contacts with high accuracy and the trajectory reconstruction reached an error level below 100 μm (0.046 ± 0.025 mm). An implementation of the method is made publicly available such that it can directly be used by researchers or clinicians. This constitutes an important step towards future integration of lead reconstruction into standard clinical care. [less ▲]

A parallel and efficient multi-split XFEM for 3-D analysis of heterogeneous materials

in Computer Methods in Applied Mechanics and Engineering (2018)

We propose a parallel and computationally efficient multi-split XFEM approach for 3-D analysis of heterogeneous materials. In this approach, multiple discontinuities (pores and reinforcement particles ... [more ▼]

We propose a parallel and computationally efficient multi-split XFEM approach for 3-D analysis of heterogeneous materials. In this approach, multiple discontinuities (pores and reinforcement particles) may intersect any given element (we call those elements multi-split elements). These discontinuities are modeled by imposing additional degrees of freedom at the nodes. The main advantage of the proposed scheme is that the mesh size remains independent of the relative distance among the heterogeneities/discontinuities. The pores and reinforcement particles are assumed to be spherical. The simulations are performed for uniform and non-uniform heterogeneity distribution. The Young’s modulus of the heterogeneous material is evaluated for different amount of pores and reinforcement particles. To demonstrate the computational efficiency of the multi-split XFEM, elastic damage analysis is performed for the unit cell with 5% pores and 5% reinforcement particles under uniaxial tensile loading. These simulations show that the Young’s modulus decreases linearly with the increase in the volume fraction of the pores and increases linearly with the increase in volume fraction of reinforcement particles. The multi-split XFEM is found to be at least 1.8 times computationally efficient than standard XFEM and at least 6.7 times computationally efficient than FEM. [less ▲]

A Parallel Multiscale DEM-VOF Method For Large-Scale Simulations Of Three-Phase Flows

in Proceedings of ECCM-ECFD 2018 (2018)

A parallel dual-grid multiscale DEM-VOF coupling is here investigated. Dual- grid multiscale couplings have been recently used to address different engineering problems involving the interaction between ... [more ▼]

A parallel dual-grid multiscale DEM-VOF coupling is here investigated. Dual- grid multiscale couplings have been recently used to address different engineering problems involving the interaction between granular phases and complex fluid flows. Nevertheless, previous studies did not focus on the parallel performance of such a coupling and were, therefore, limited to relatively small applications. In this contribution, we propose an insight into the performance of the dual-grid multiscale DEM-VOF method for three- phase flows when operated in parallel. In particular,we focus on a famous benchmark case for three-phase flows and assess the influence of the partitioning algorithm on the scalability of the dual-grid algorithm. [less ▲]

Parameter identification problem in bimaterial human skin and sensitivity analysis : Uncertainties in biomechanics of skin

Scientific Conference (2019, December 09)

The proposed paper concerns the prediction of the numerical response of a biomechanical structure submitted to an unknown external loading state. The methodology is based on homogeneous and then ... [more ▼]

The proposed paper concerns the prediction of the numerical response of a biomechanical structure submitted to an unknown external loading state. The methodology is based on homogeneous and then heterogeneous structures such as healthy or pathological cutaneous tissues that can be mechanically tested in vivo under a patchy knowledge of boundary conditions. Experimental data corresponding to the extension of a piece of skin located between two pads with displacement enslavement, represent input data to the numerical model. Data are reaction force on one pad and displacement field between the two pads and all around. The numerical model consists of a representation of the bi-material domain geometry with neo-hookean behaviors. The boundary conditions and loadings of the experimental extension test are imposed. The materials parameters have been identified by inverse method starting from a constrained cost function minimizing the difference between the calculated displacements field and experimental displacements field obtained by digital image correlation and taking into account the reaction force as a constraint. An analysis of the model sensitivity to material parameters is presented. [less ▲]

A PAS-state constrained optimization formulation for the anticipatory network traffic control problem

Scientific Conference (2016, September)

A perspective on urban economics and geographical agent-based models. (Keynote Speech)

Scientific Conference (2015, September)

In this presentation, we will argue that there are many benefits to further liaise urban economic models and geographically -aware agent-based simulation models for further understanding the structure and ... [more ▼]

In this presentation, we will argue that there are many benefits to further liaise urban economic models and geographically -aware agent-based simulation models for further understanding the structure and dynamics of cities, especially at the scale of city regions but also, eventually, for contributing micro understanding of changes in a system of cities. At first sight it appears that these two fields of urban research are very separated: urban economics relies mostly on mathematical proofs, a parsimonious set of interactions, static equilibria and a rather homogeneous space and set of agents; while geographical agent-based models emphasize the dynamics and complexity of cities, the heterogeneity of agents and space, and rely solely on computational methods. The presentation will showcase a series of theoretical and applied research to stress the idea that the two can fruitfully be combined and that results are then palatable to both urban economists and geographers and can therefore participate to consolidating a wider and formalised urban theory. The geographical turn towards agent-based approaches, compared to more aggregate models and behaviourally-blind geocomputational methods, is actually a chance for geographers to formalise market as well as non-market interactions in a manner that is consistent with urban economic theory and enhance the treatment of space in this theory. Relying on a formal description of agents utility permits to discuss normative instruments where environmental and welfare impacts can be traded-off by policy makers. Furthermore,, land or housing market outcomes of the models and the analytical efforts actually help to reduce parametric space and calibrate or validate models against independent data. [less ▲]

PIV study of the effect of piston position on the in-cylinder swirling flow during the scavenging process in large two-stroke marine diesel engines

in Journal of Marine Science and Technology (2013), 18(1), 133-143

A simplified model of a low speed large two- stroke marine diesel engine cylinder is developed. The effect of piston position on the in-cylinder swirling flow during the scavenging process is studied ... [more ▼]

A simplified model of a low speed large two- stroke marine diesel engine cylinder is developed. The effect of piston position on the in-cylinder swirling flow during the scavenging process is studied using the stereo- scopic particle image velocimetry technique. The mea- surements are conducted at different cross-sectional planes along the cylinder length and at piston positions covering the air intake port by 0, 25, 50 and 75 %. When the intake port is fully open, the tangential velocity profile is similar to a Burgers vortex, whereas the axial velocity has a wake- like profile. Due to internal wall friction, the swirl decays downstream, and the size of the vortex core increases. For increasing port closures, the tangential velocity profile changes from a Burgers vortex to a forced vortex, and the axial velocity changes correspondingly from a wake-like profile to a jet-like profile. For piston position with 75 % intake port closure, the jet-like axial velocity profile at a cross-sectional plane close to the intake port changes back to a wake-like profile at the adjacent downstream cross-sectional plane. This is characteristic of a vortex breakdown. The non-dimensional velocity profiles show no significant variation with the variation in Reynolds number. [less ▲]

POD-based model order reduction for the simulation of strong nonlinear evolutions in structures: Application to damage propagation

in IOP Conference Series: Materials Science and Engineering (2014), 10(1),

In this paper, we develop a bridge between POD-based model order reduction techniques and the classical Newton-Krylov solvers to derive an efficient solution procedure for highly nonlinear problems ... [more ▼]

In this paper, we develop a bridge between POD-based model order reduction techniques and the classical Newton-Krylov solvers to derive an efficient solution procedure for highly nonlinear problems undergoing strong topological changes. [less ▲]

POD-based reduction methods, the Quasicontinuum Method and their Resemblance

Scientific Conference (2016, June 27)

Poroelastic model parameter identification using artificial neural networks: on the effects of heterogeneous porosity and solid matrix Poisson ratio

in Computational Mechanics (2020), 66

Predictive analysis of poroelastic materials typically require expensive and time-consuming multiscale and multiphysics approaches, which demand either several simplifications or costly experimental tests ... [more ▼]

Predictive analysis of poroelastic materials typically require expensive and time-consuming multiscale and multiphysics approaches, which demand either several simplifications or costly experimental tests for model parameter identification. This problem motivates us to develop a more efficient approach to address complex problems with an acceptable computational cost. In particular, we employ artificial neural network (ANN) for reliable and fast computation of poroelastic model parameters. Based on the strong-form governing equations for the poroelastic problem derived from asymptotic homogenisation, the weighted residuals formulation of the cell problem is obtained. Approximate solution of the resulting linear variational boundary value problem is achieved by means of the finite element method. The advantages and downsides of macroscale properties identification via asymptotic homogenisation and the application of ANN to overcome parameter characterisation challenges caused by the costly solution of cell problems are presented. Numerical examples, in this study, include spatially dependent porosity and solid matrix Poisson ratio for a generic model problem, application in tumour modelling, and utilisation in soil mechanics context which demonstrate the feasibility of the presented framework. [less ▲]