Procedures for finite element mesh generation from medical imaging: application to the intervertebral disc

Dissertação de mestrado integrado em Engenharia BiomédicaThe paramount goal of this ‘half-year’ work is the development of a set of methodologies and procedures for the geometric modelling by a finite element (FE) mesh of the bio-structure of a motion segment (or functional spinal unit), i.e., two vertebrae and an intervertebral disc, from segmented medical images (processed from medical imaging). At an initial stage, a three-dimensional voxel-based geometric model of a goat motion segment was created from magnetic resonance imaging (MRI) data. An imaging processing software (ScanIP/Simplewire) was used for imaging segmentation (identification of different structures and tissues), both in images with lower (normal MRI) and higher (micro-MRI) resolutions. It shall be noticed that some soft-tissues, such as annulus fibrosus or nucleus pulposus, are very hard to isolate and identify given that the interface between them is not clearly defined. At the end of this stage, images with different resolutions allowed to generate different 3D voxel-based geometric models. Thereafter, a procedure for the FE mesh generation from the aforementioned voxelized data should be studied and applied. However, as the original geometry was only approximately known from real medical imaging, it was difficult to objectively quantify the quality of the FE meshing procedure and the accuracy between source geometry and target FE mesh. In order to overcome such difficulties, and due to the lack of quality of the available medical imaging, a “virtualization” procedure was developed to create a set of segmented 2D medical images from a well-defined geometry of a motion segment. The main idea was to create the conditions to quantify the quality and the accuracy of the developed FE meshing procedure, as well to study the effect of imaging resolution. Starting from the virtually generated 2D segmented images, a 3D voxel-based structure was achieved. Given that initial domains are now clearly defined, there is no need for further image processing. Then, a two-step FE mesh generation procedure (generation followed by simplification) allows to create an optimized tetrahedral FE mesh directly from 3D voxelized data. Finally, because the virtualization procedure allowed to know the initial geometry, one is able to objectively quantify the quality and the accuracy of the final simplified tetrahedral FE mesh, and thus to understand and quantify: a) the role of the medical image resolution on the FE geometrical reconstruction, b) the procedure and parameters of the FE mesh generation step, and c) the procedure and parameters of the FE mesh simplification step, and thus to give a clear contribution in the definition of the procedure for the FE mesh generation from medical imaging in case of an intervertebral disc.O objetivo fundamental deste trabalho de seis meses é o desenvolvimento de um conjunto de metodologias e procedimentos para a modelação geométrica, através de uma malha de elementos finitos (EF) de uma bio-estrutura de um motion segment (ou unidade funcional da coluna), ou seja, duas vértebras e um disco intervertebral, a partir de imagens médicas segmentadas (processadas a partir de imagiologia médica). Numa fase inicial, um modelo geométrico tridimensional baseado em voxels de um motion segment de uma cabra foi criado a partir de informação de imagens médicas de ressonância magnética (RM). Um software de processamento de imagem (ScanIp/Simplewire) foi usado para segmentação de imagens (identificação de diferentes estruturas e tecidos), em imagens de menor (RM normal) e maior (micro-RM) resolução. Deve ser referido que alguns tecidos moles, como o anel fibroso e o núcleo pulposo são muito difíceis de isolar e identificar, dado que as fronteiras destes não estão claramente definidas. No final desta etapa, as imagens com diferentes resoluções permitiram gerar diferentes modelos geométricos 3D baseados em voxels. Posteriormente, um procedimento para geração de malha de EF, a partir da informação voxelizada acima mencionada, deveria ser estudado e aplicado. No entanto, como a geometria original era aproximadamente conhecida a partir de imagens médicas reais, foi difícil quantificar objetivamente a qualidade do procedimento de geração de malha de EF e a precisão entre a geometria de origem e a malha de EF de destino. A fim de superar tais dificuldades, e devido à falta de qualidade de imagens médicas disponíveis, um procedimento de “virtualização” foi desenvolvido para criar um conjunto de imagens médicas 2D segmentadas a partir de uma geometria de um motion segment bem conhecida. A principal ideia foi criar as condições para quantificar a qualidade e a precisão do procedimento de geração de malha de EF desenvolvido, bem como estudar o efeito da resolução da imagem médica. A partir das imagens 2D segmentadas, geradas virtualmente, uma estrutura de voxels 3D pode ser conseguida. Dado que os domínios iniciais estão agora claramente definidos, não há necessidade de processamento de imagem adicional. Por conseguinte, um procedimento de geração de malha de EF de duas etapas (geração seguida por simplificação) permite criar uma malha de EF tetraédrica otimizada diretamente a partir de informação 3D voxelizada. Por fim, como o procedimento de virtualização permitiu conhecer a geometria inicial, é possível quantificar objetivamente a qualidade e exatidão da malha de EF tetraédrica final simplificada, e assim, compreender e quantificar: a) o papel da resolução da imagem médica na reconstrução geométrica de EF; b) o procedimento e os parâmetros da etapa de geração de malha de EF; c) o procedimento e os parâmetros da etapa de simplificação de malhas de EF, e assim, dar uma contribuição clara na definição do procedimento para a geração de malha de EF a partir de imagem médica, no caso de um disco intervertebral.European Project : NP Mimetic - Biomimetic Nano-Fiber Based Nucleus Pulposus Regeneration for the Treatment of Degenerative Disc Disease, funded by the European Commission under FP7 (grant NMP3-SL-2010-246351

Optimized FE mesh generation based on medical imaging and on a user-defined spatial refinement gradient. Application to a motion segment

In general, the starting point for the 3D geometrical modelling by finite elements of an anatomical structure is the generation of a 3D voxel-based geometrical model, obtained after denoising, smoothing and segmentation of a set of 2D medical images. The accuracy of the FE computation increases if the geometry of model resembles, for instance, the natural smoothness of real anatomical structure. Usually, the lack of detailed data in conventional imaging techniques causes further problems in the IVD finite element mesh generation and analysis. Difficulties arise mainly due to the complexity and the dimension of the IVD constituent structures and the lower resolution of medical imaging. After the 3D voxelized model has been defined, a specific isotropic tetrahedral FE meshing procedure is applied and, generally, a too dense and highly refined FE mesh is obtained. Therefore, it is necessary to decrease its size by diminishing the total number of nodes and elements while maintaining both geometrical accuracy and a physically compatible FE mesh refinement. Generally, after this procedure, the smaller elements are located at the internal and external boundaries, while larger elements are located inside the FE mesh. However, this is not always acceptable. There may be situations where this accuracy may be required simultaneously in structures outside and inside the FE mesh. In a motion segment, the FE mesh should be more refined at the IVD and coarser at the vertebrae (nearly incompressible medium). On the other hand, since the annulus fibrosus (AF) is a stiff ring-shaped structure made up of concentric lamellae [1], an optimized FE mesh should be more refined at the annulus fibrosus than at the nucleus pulposus (NP)The aims of this study are: - to study the impact of medical imaging resolution in the FE mesh accuracy; - to develop a refinement gradient, where in this case the elements should be smaller in the outer annulus (where lamellae are denser and combined) than the ones in the inner annulus (less dense lamellae)

3D reconstruction of a spinal motion segment from 2D medical images: objective quantification of the geometric accuracy of the FE mesh generation procedure

The Finite Element (FE) Analysis is an essential tool to study the biomechanical behaviour of the spine, and particularly of the intervertebral disc (IVD). The 3D reconstruction of a patient-oriented IVD has numerous obstacles. Difficulties arise mainly due to the complexity and dimensions of the IVD’s constituent structures. The lack of detailed data in conventional imaging techniques causes further problems in the IVD finite element mesh generation and analysis. The accuracy of the FE computation increases if the geometry of model resembles, for instance, the natural smoothness of real anatomical structure. Accounting to this, the main idea of this work is to evaluate the impact of the reconstruction parameters by comparing the final 3D geometrical reconstruction by finite elements with an initial well-defined geometry of a given anatomical structure, and to develop the procedures for the 3D mesh generation from 2D medical imaging

Optimized FE mesh generation procedure based on a user-defined spatial refinement gradient. Application to a motion segment

Finite Element (FE) meshes are usually highly refined and dense and, consequently, computationally very expensive. Therefore, after the preliminary FE mesh generation, it is necessary to decrease its size by diminishing the total number of nodes and elements while maintaining both geometrical accuracy and a physically-meaningful FE mesh refinement. The aim of this work is to describe an optimized FE mesh simplification procedure based on edge contraction and on a user-defined spatial refinement gradient criterion. The main idea is that, for normal mechanical loadings applied to a motion segment, the vertebrae shall behave almost as an incompressible medium, and only the intervertebral disc (IVD) should undergo relevant strains. In this case, it is acceptable (and desirable) to attain a problem-functional FE mesh, in which the FE mesh should be more refined at the IVD and coarser at vertebrae. On the other hand, an optimized FE mesh should be more refined at the annulus fibrosus than at the nucleus pulposus. In summary, the proposed FE mesh generation and simplification procedure, being based on a user-definable spatial FE mesh refinement gradient, allows the user to define precisely the required refinement and thus to reduce drastically the number of elements in the final FE mesh and consequently to diminish the computation time required for the FE analysis, while keeping the necessary physical meaning on the FE mesh. The aforesaid procedure will be applied to the FE mesh generation (based on [1]) of a motion segment initially characterized by medical imaging

An experimental and numerical study on aluminum alloy tailor heat treated blanks

Information is presented on the conceptualization, experimental study, and numerical process simulation of tailor heat treated aluminum alloy blanks. This concept is intended to improve the forming behavior of aluminum parts in challenging conditions. The implementation requires precise control of laser heat treatment parameters within a suitable industrial framework. The study details material properties, heat treatment parameters, and experimental results for the strength and elongation properties of an AA6063-T6 aluminum alloy. Constitutive modeling is applied using the Hocket–Sherby equation, which allowed us to establish a correlation between laser heat treatment maximum temperature and the corresponding material softening degree. Based on the generated flow stress–strain curves, a numerical simulation of a representative case study was performed with Abaqus finite element software highlighting potential improvements of tailor heat treated blanks (THTB). The influence and effectiveness of heat-affected zone (HAZ) dimensions and material softening were analyzed.This research was funded by Projects I&DT SIT—Softening in Tool, grant number CENTRO02-0853-FEDER-045419 and METRICS (UID/EMS/04077/2020)

Influence of porosity and cell density on tissue engineering of mandibular condylar cartilage

One of the major problems of the cartilage tissue engineering is to produce materials with similar biomechanical properties to those in the native tissue. Some parameters of the solid matrix such as the porosity of the scaffold and the number of cells may limit physiologically the nutrient supply and tissue growth. This work aims to simulate the impact of the porosity and the initial cell seeding in condylar chondrocytes-seeded agarose scaffolds on the nutrient supply, cell density and the solid volume fraction. A finite element tool was developed in a home-developed code and a free swelling culture period of 1 week was simulated. The results of the mathematical analysis revealed that porosity of the scaffold affects the solid volume fraction, reducing the diffusivity of the solutes and, consequently, delaying the cell proliferation.The first author is grateful to FCT (Fundação para a Ciência e Tecnologia) for the PhD grant (SFRH/BD/87933/2012). This work is supported by FCT with the reference projects UID/EEA/04436/2013, PEst C/EME/UI0481/2013, FCOMP-01-0124-FEDER 015191, and by FEDER funds through the COMPETE 2020 – Programa Operacional Competitividade e Internacionalização (POCI) with the reference projects POCI-01-0145-FEDER-006941 and COMPETE 2020 PTDC/ EMSTEC/ 3263/ 201

NEOTROPICAL ALIEN MAMMALS: a data set of occurrence and abundance of alien mammals in the Neotropics

Biological invasion is one of the main threats to native biodiversity. For a species to become invasive, it must be voluntarily or involuntarily introduced by humans into a nonnative habitat. Mammals were among first taxa to be introduced worldwide for game, meat, and labor, yet the number of species introduced in the Neotropics remains unknown. In this data set, we make available occurrence and abundance data on mammal species that (1) transposed a geographical barrier and (2) were voluntarily or involuntarily introduced by humans into the Neotropics. Our data set is composed of 73,738 historical and current georeferenced records on alien mammal species of which around 96% correspond to occurrence data on 77 species belonging to eight orders and 26 families. Data cover 26 continental countries in the Neotropics, ranging from Mexico and its frontier regions (southern Florida and coastal-central Florida in the southeast United States) to Argentina, Paraguay, Chile, and Uruguay, and the 13 countries of Caribbean islands. Our data set also includes neotropical species (e.g., Callithrix sp., Myocastor coypus, Nasua nasua) considered alien in particular areas of Neotropics. The most numerous species in terms of records are from Bos sp. (n = 37,782), Sus scrofa (n = 6,730), and Canis familiaris (n = 10,084); 17 species were represented by only one record (e.g., Syncerus caffer, Cervus timorensis, Cervus unicolor, Canis latrans). Primates have the highest number of species in the data set (n = 20 species), partly because of uncertainties regarding taxonomic identification of the genera Callithrix, which includes the species Callithrix aurita, Callithrix flaviceps, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Callithrix penicillata, and their hybrids. This unique data set will be a valuable source of information on invasion risk assessments, biodiversity redistribution and conservation-related research. There are no copyright restrictions. Please cite this data paper when using the data in publications. We also request that researchers and teachers inform us on how they are using the data