Claudio Lobos

Mixed-Element Mesh for an Intra-Operative Modeling of the Brain Tumor Extraction

This paper presents a modified-octree technique that generates a mixed-element mesh. The final output mesh consider cubes, prisms, pyramids and tetrahedra. This technique is optimized for brain tumor extraction simulation in a real-time application. The proposed technique is based on the octree algorithm with a specific constraint: elements will be split only if they intersects a certain region of interest. With this approach we pursued a refined mesh only in the path from the skull opening point to the tumor. Fast computation by the Finite Element Method (FEM) is achieve thanks to the local refinement. Examples are given and comparison with other approaches are presented.

Finite element modelling of nearly incompressible materials and volumetric locking: a case study

The purpose of this paper is to illustrate the influence of the choice of the finite element technology on the occurrence of locking and hourglass instabilities. We chose to focus on the case study of the activation of the posterior genio-glossus (GGp) that is a lingual muscle located at the root of the tongue and inserts in the front to the mandible. The activation of this muscle compresses the tongue in the lower part and generates a forward and upward movement of the tongue body, because of the incompressibility of tongue tissues (for example during the production of the phonemes /i/ or /s/).

Jacobian-based repair method for finite element meshes after registration

Registration methods are used in the meshing field to “adapt” a given mesh to a target domain. Finite element method (FEM) is applied to the resulting mesh to compute an approximate solution to the system of partial differential equations (PDE) representing the physical phenomena under study. Prior to FE analysis the Jacobian matrix determinant must be checked for all mesh elements. The value of this Jacobian depends on the configuration of the element nodes. If it is negative for a given node, the element is invalid and therefore the FE analysis cannot be carried out. Similarly, some elements, although valid, can present poor quality regarding Jacobian-based indicator values, such as the Jacobian ratio. Mesh registration procedures are likely to produce invalid and/or poor quality elements if the Jacobian parameter is ignored. To repair invalid and poor quality elements after mesh registration, we propose a relaxation procedure driven by specific validity and quality energy formulations derived from the Jacobian value. The algorithm first recovers mesh validity and further improves elements quality, focusing primarily on nodes that make the elements invalid or of poor quality. Our novel approach has been developed in the context of non-rigid mesh registration and validated on a data set of 60 clinical cases in the context of orthopaedic and orthognathic hard and soft tissues modelling studies. The proposed repair method achieves a valid state of the mesh and also raises the quality of the elements to a level suitable for commercial FE solvers.

The Isochronal Fibration: Characterization and Implication in Biology

Limit cycles, because they are constituted of a periodic succession of states (discrete or continuous) constitute a good manner to store information. From any points of the state space reached after a perturbation or stimulation of the cognitive system storing this information, one can aim to join through a more or less long return trajectory a precise neighbourhood of the asymptotic trajectory at a specific moment (or a specific place) on the limit cycle, i.e. where the information of interest stands. We propose that the isochronal fibration, initially imagined and described by A. T. Winfree may be an excellent way to connect directly those two locations. Each isochron is indeed the set of points in temporal phase with one single point of the attractor. The characterisation of the isochronal fibration of various dynamical systems is not easy and until now has principally only been done numerically but not analytically. By integrating the homogeneous solutions of the dynamical system we can solve this fibration in the case of the well known anharmonic pendulum. Other isochronal fibration on classical examples such as the van der Pol system and the non-symmetrical PFK limit cycle are obtained numerically and we also provide the first numerical study on 3-dimentional systems like the anharmonic pendulum with a linear relaxation on its third variable and the Lorenz attractor. The empirical approach seems us useful for dealing with the isochronal fibration which could constitute a powerful tool for understanding and controlling the dynamics of biological or biological-inspired systems.

Patient-specific finite element model of the buttocks for pressure ulcer prevention – linear versus non-linear modelling

Currently available techniques and/or protocols designed to prevent pressure sore formation in persons with spinal cord injury and wheelchair users are mainly based on the improvement of the skin/support interface and on postural and behavioural education. These techniques, however, seem to lack efficiency as the prevalence and incidence of pressure sores still remains very high. This study outlines a methodology aiming at the definition of an individual and personalised pressure ulcer risk assessment scale based on patient-specific Finite Element modelling of the buttocks.

Speech biomechanics: What have we learned and modeled since Joseph Perkell’s tongue model In 1974?

With his “physiologically oriented, dynamic model of the tongue, Joseph Perkell introduced in 1974 a new methodological approach to understanding the “relationships among phonetic models and the properties and capabilities of the speech-production mechanism.” This approach has guided a large part of our studies in the two last decades. In order to investigate how mechanical properties of the orofacial motor system constrain the degrees of freedom of speech articulation and contribute to shaping the speech signals exchanged between speakers and listeners, we, among other research groups, have developed increasingly more realistic 2D, and then 3D, finite element(FE) biomechanical models of the human vocal tract and face. After summarizing some of our modeling and simulation results that shed light on some basic characteristics of speech production, we present recent developments which aim to improve the realism of the models: evaluation of the links between the FE mesh structure (based either on tetrahedra, hexahedra, or mixed elements) and simulation accuracy; development of an active 3D element that simulates muscle mechanics and muscle force generation mechanisms; use of Diffusion Tensor Imaging to investigate muscle anatomy; design of an Atlas-based method (i.e., without manual image segmentation) for the automatic generation of subject-specific models.

Mixed-element Octree: a meshing technique toward fast and real-time simulations in biomedical applications

This article introduces a meshing technique focused on fast and real-time simulation in a biomedical context. We describe in details our algorithm, which starts from a basic Octree regarding the constraints imposed by the simulation, and then, mixed-element patterns are applied over transitions between coarse and fine regions. The use of surface patterns, also composed by mixed elements, allows us to better represent curved domains decreasing the odds of creating invalid elements by adding as few nodes as possible. In contrast with other meshing techniques, we let the user define regions of greater refinement, and as a consequence of that refinement, we add as few nodes as possible to produce a mesh that is topologically correct. Therefore, our meshing technique gives more control on the number of nodes of the final mesh. We show several examples where the quality of the final mesh is acceptable, even without using quality filters. We believe that this new meshing technique is in the correct direction toward real-time simulation in the biomedical field.

Techniques on mesh generation for the brain shift simulation

Neurosurgery interventions involve complex tracking systems because a tissue deformation takes place. The neuronavigation system relies only on pre-operative images. In order to overcome the soft tissue deformations and guarantee the accuracy of the navigation a biomechanical model can be used during surgery to simulate the deformation of the brain. Therefore, a mesh generation for an optimal real-time Finite Element Model (FEM) becomes crucial. In this work we present different alternatives from a mesh generation point of view that were evaluated to optimize the process in terms of elements quantity and quality as well as constraints of a intraoperative application and patient specific data.

Camarón: An Open-source Visualization Tool for the Quality Inspection of Polygonal and Polyhedral Meshes

The numerical simulation of phenomena requires a good quality discretization (mesh) of the domain. Depending on the problem to be simulated, the mesh has to fulfil different quality criteria. Because of geometry restrictions or point density requirements, several mesh elements might not satisfy the required quality criteria and sometimes it is also not required that all elements fulfil them. Then, it would be helpful to know where unwanted elements are located in order to see if they need to be repaired or not. That is why a visualization tool that allows the user to inspect a mesh before a simulation is performed can be useful to prevent simulation problems. Moreover, if data from simulations is available, the visualization of geometrical properties together with simulation data could be also helpful to understand not expected results. These challenges have motivated us to develop Camar´on, a visualization tool for large surface and volume meshes described in this paper. The surface meshes can be composed any polygonal cell and the 3D meshes can include any convex polyhedral cell. This tool was implemented in C++ and the OpenGL Shading Language (GLSL). We discuss the design and implementation issues that make our software portable, extensible and different from other visualization tools. We also compare the performance between Camar´on and GeomView, TetView and MeshLab.