Mesh-to-raster based non-rigid registration of multi-modal images

Region of interest (ROI) alignment in medical images plays a crucial role in diagnostics, procedure planning, treatment, and follow-up. Frequently, a model is represented as triangulated mesh while the patient data is provided from CAT scanners as pixel or voxel data. Previously, we presented a 2D method for curve-to-pixel registration. This paper contributes (i) a general mesh-to-raster (M2R) framework to register ROIs in multi-modal images; (ii) a 3D surface-to-voxel application, and (iii) a comprehensive quantitative evaluation in 2D using ground truth provided by the simultaneous truth and performance level estimation (STAPLE) method. The registration is formulated as a minimization problem where the objective consists of a data term, which involves the signed distance function of the ROI from the reference image, and a higher order elastic regularizer for the deformation. The evaluation is based on quantitative light-induced fluoroscopy (QLF) and digital photography (DP) of decalcified teeth. STAPLE is computed on 150 image pairs from 32 subjects, each showing one corresponding tooth in both modalities. The ROI in each image is manually marked by three experts (900 curves in total). In the QLF-DP setting, our approach significantly outperforms the mutual information-based registration algorithm implemented with the Insight Segmentation and Registration Toolkit (ITK) and Elastix

Generalizing the advancing front method to composite surfaces in the context of meshing constraints topology

International audienceBeing able to automatically mesh composite geometry is an important issue in the context of CAD-FEA integration. In some specific contexts of this integration, such as using virtual topology or meshing constraints topology (MCT), it is even a key requirement. In this paper, we present a new approach to automatic mesh generation over composite geometry. The proposed mesh generation approach is based on a generalization of the advancing front method (AFM) over curved surfaces. The adaptation of the AFM to composite faces (composed of multiple boundary representation (B-Rep) faces) involves the computation of complex paths along these B-Rep faces, on which progression of the advancing front is based. Each mesh segment or mesh triangle generated through this progression on composite geometry is likely to lie on multiple B-Rep faces and consequently, it is likely to be associated with a composite definition across multiple parametric spaces. Collision tests between new front segments and existing mesh elements also require specific and significant adaptations of the AFM, since a given front segment is also likely to lie on multiple B-Rep faces. This new mesh generation approach is presented in the context of MCT, which requires being able to handle composite geometry along with non-manifold boundary configurations, such as edges and vertices lying in the interior domain of B-Rep faces

Colliding Interfaces in Old and New Diffuse-interface Approximations of Willmore-flow

This paper is concerned with diffuse-interface approximations of the Willmore flow. We first present numerical results of standard diffuse-interface models for colliding one dimensional interfaces. In such a scenario evolutions towards interfaces with corners can occur that do not necessarily describe the adequate sharp-interface dynamics. We therefore propose and investigate alternative diffuse-interface approximations that lead to a different and more regular behavior if interfaces collide. These dynamics are derived from approximate energies that converge to the $L^1$-lower-semicontinuous envelope of the Willmore energy, which is in general not true for the more standard Willmore approximation

Structural Shape Optimization Based On The Use Of Cartesian Grids

Tesis por compendioAs ever more challenging designs are required in present-day industries, the traditional trial-and-error procedure frequently used for designing mechanical parts slows down the design process and yields suboptimal designs, so that new approaches are needed to obtain a competitive advantage. With the ascent of the Finite Element Method (FEM) in the engineering community in the 1970s, structural shape optimization arose as a promising area of application. However, due to the iterative nature of shape optimization processes, the handling of large quantities of numerical models along with the approximated character of numerical methods may even dissuade the use of these techniques (or fail to exploit their full potential) because the development time of new products is becoming ever shorter. This Thesis is concerned with the formulation of a 3D methodology based on the Cartesian-grid Finite Element Method (cgFEM) as a tool for efficient and robust numerical analysis. This methodology belongs to the category of embedded (or fictitious) domain discretization techniques in which the key concept is to extend the structural analysis problem to an easy-to-mesh approximation domain that encloses the physical domain boundary. The use of Cartesian grids provides a natural platform for structural shape optimization because the numerical domain is separated from a physical model, which can easily be changed during the optimization procedure without altering the background discretization. Another advantage is the fact that mesh generation becomes a trivial task since the discretization of the numerical domain and its manipulation, in combination with an efficient hierarchical data structure, can be exploited to save computational effort. However, these advantages are challenged by several numerical issues. Basically, the computational effort has moved from the use of expensive meshing algorithms towards the use of, for example, elaborate numerical integration schemes designed to capture the mismatch between the geometrical domain boundary and the embedding finite element mesh. To do this we used a stabilized formulation to impose boundary conditions and developed novel techniques to be able to capture the exact boundary representation of the models. To complete the implementation of a structural shape optimization method an adjunct formulation is used for the differentiation of the design sensitivities required for gradient-based algorithms. The derivatives are not only the variables required for the process, but also compose a powerful tool for projecting information between different designs, or even projecting the information to create h-adapted meshes without going through a full h-adaptive refinement process. The proposed improvements are reflected in the numerical examples included in this Thesis. These analyses clearly show the improved behavior of the cgFEM technology as regards numerical accuracy and computational efficiency, and consequently the suitability of the cgFEM approach for shape optimization or contact problems.La competitividad en la industria actual impone la necesidad de generar nuevos y mejores diseños. El tradicional procedimiento de prueba y error, usado a menudo para el diseño de componentes mecánicos, ralentiza el proceso de diseño y produce diseños subóptimos, por lo que se necesitan nuevos enfoques para obtener una ventaja competitiva. Con el desarrollo del Método de los Elementos Finitos (MEF) en el campo de la ingeniería en la década de 1970, la optimización de forma estructural surgió como un área de aplicación prometedora. El entorno industrial cada vez más exigente implica ciclos cada vez más cortos de desarrollo de nuevos productos. Por tanto, la naturaleza iterativa de los procesos de optimización de forma, que supone el análisis de gran cantidad de geometrías (para las se han de usar modelos numéricos de gran tamaño a fin de limitar el efecto de los errores intrínsecamente asociados a las técnicas numéricas), puede incluso disuadir del uso de estas técnicas. Esta Tesis se centra en la formulación de una metodología 3D basada en el Cartesian-grid Finite Element Method (cgFEM) como herramienta para un análisis numérico eficiente y robusto. Esta metodología pertenece a la categoría de técnicas de discretización Immersed Boundary donde el concepto clave es extender el problema de análisis estructural a un dominio de aproximación, que contiene la frontera del dominio físico, cuya discretización (mallado) resulte sencilla. El uso de mallados cartesianos proporciona una plataforma natural para la optimización de forma estructural porque el dominio numérico está separado del modelo físico, que podrá cambiar libremente durante el procedimiento de optimización sin alterar la discretización subyacente. Otro argumento positivo reside en el hecho de que la generación de malla se convierte en una tarea trivial. La discretización del dominio numérico y su manipulación, en coalición con la eficiencia de una estructura jerárquica de datos, pueden ser explotados para ahorrar coste computacional. Sin embargo, estas ventajas pueden ser cuestionadas por varios problemas numéricos. Básicamente, el esfuerzo computacional se ha desplazado. Del uso de costosos algoritmos de mallado nos movemos hacia el uso de, por ejemplo, esquemas de integración numérica elaborados para poder capturar la discrepancia entre la frontera del dominio geométrico y la malla de elementos finitos que lo embebe. Para ello, utilizamos, por un lado, una formulación de estabilización para imponer condiciones de contorno y, por otro lado, hemos desarrollado nuevas técnicas para poder captar la representación exacta de los modelos geométricos. Para completar la implementación de un método de optimización de forma estructural se usa una formulación adjunta para derivar las sensibilidades de diseño requeridas por los algoritmos basados en gradiente. Las derivadas no son sólo variables requeridas para el proceso, sino una poderosa herramienta para poder proyectar información entre diferentes diseños o, incluso, proyectar la información para crear mallas h-adaptadas sin pasar por un proceso completo de refinamiento h-adaptativo. Las mejoras propuestas se reflejan en los ejemplos numéricos presentados en esta Tesis. Estos análisis muestran claramente el comportamiento superior de la tecnología cgFEM en cuanto a precisión numérica y eficiencia computacional. En consecuencia, el enfoque cgFEM se postula como una herramienta adecuada para la optimización de forma.Actualment, amb la competència existent en la industria, s'imposa la necessitat de generar nous i millors dissenys . El tradicional procediment de prova i error, que amb freqüència es fa servir pel disseny de components mecànics, endarrereix el procés de disseny i produeix dissenys subòptims, pel que es necessiten nous enfocaments per obtindre avantatge competitiu. Amb el desenvolupament del Mètode dels Elements Finits (MEF) en el camp de l'enginyeria en la dècada de 1970, l'optimització de forma estructural va sorgir com un àrea d'aplicació prometedora. No obstant això, a causa de la natura iterativa dels processos d'optimització de forma, la manipulació dels models numèrics en grans quantitats, junt amb l'error de discretització dels mètodes numèrics, pot fins i tot dissuadir de l'ús d'aquestes tècniques (o d'explotar tot el seu potencial), perquè al mateix temps els cicles de desenvolupament de nous productes s'estan acurtant. Esta Tesi se centra en la formulació d'una metodologia 3D basada en el Cartesian-grid Finite Element Method (cgFEM) com a ferramenta per una anàlisi numèrica eficient i sòlida. Esta metodologia pertany a la categoria de tècniques de discretització Immersed Boundary on el concepte clau és expandir el problema d'anàlisi estructural a un domini d'aproximació fàcil de mallar que conté la frontera del domini físic. L'utilització de mallats cartesians proporciona una plataforma natural per l'optimització de forma estructural perquè el domini numèric està separat del model físic, que podria canviar lliurement durant el procediment d'optimització sense alterar la discretització subjacent. A més, un altre argument positiu el trobem en què la generació de malla es converteix en una tasca trivial, ja que la discretització del domini numèric i la seua manipulació, en coalició amb l'eficiència d'una estructura jeràrquica de dades, poden ser explotats per estalviar cost computacional. Tot i això, estos avantatges poden ser qüestionats per diversos problemes numèrics. Bàsicament, l'esforç computacional s'ha desplaçat. De l'ús de costosos algoritmes de mallat ens movem cap a l'ús de, per exemple, esquemes d'integració numèrica elaborats per poder capturar la discrepància entre la frontera del domini geomètric i la malla d'elements finits que ho embeu. Per això, fem ús, d'una banda, d'una formulació d'estabilització per imposar condicions de contorn i, d'un altra, desevolupem noves tècniques per poder captar la representació exacta dels models geomètrics Per completar la implementació d'un mètode d'optimització de forma estructural es fa ús d'una formulació adjunta per derivar les sensibilitats de disseny requerides pels algoritmes basats en gradient. Les derivades no són únicament variables requerides pel procés, sinó una poderosa ferramenta per poder projectar informació entre diferents dissenys o, fins i tot, projectar la informació per crear malles h-adaptades sense passar per un procés complet de refinament h-adaptatiu. Les millores proposades s'evidencien en els exemples numèrics presentats en esta Tesi. Estes anàlisis mostren clarament el comportament superior de la tecnologia cgFEM en tant a precisió numèrica i eficiència computacional. Així, l'enfocament cgFEM es postula com una ferramenta adient per l'optimització de forma.Marco Alacid, O. (2017). Structural Shape Optimization Based On The Use Of Cartesian Grids [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/86195TESISCompendi

An extension of shape sensitivity analysis to an immersed boundary method based on Cartesian grids

[EN] Gradient-based shape optimization processes of mechanical components require the gradients (sensitivity) of the magnitudes of interest to be calculated with sufficient accuracy. The aim of this study was to develop algorithms for the calculation of shape sensitivities considering geometric representation by parametric surfaces (i.e. NURBS or T-splines) using 3D Cartesian h-adapted meshes independent of geometry. A formulation of shape sensitivities was developed for an environment based on Cartesian meshes independent of geometry, which implies, for instance, the need to take into account the special treatment of boundary conditions imposed in non body-fitted meshes. The immersed boundary framework required to implement new methods of velocity field generation, which have a primary role in the integration of both the theoretical concepts and the discretization tools in shape design optimization. Examples of elastic problems with three-dimensional components are given to demonstrate the efficiency of the algorithms.The authors wish to thank the Spanish Ministerio de Economia y Competitividad for the financial support received through the project DPI2013-46317-R and the FPI program (BES-2011-044080), and the Generalitat Valenciana through the Project PROMETEO/2016/007.Marco, O.; Ródenas, JJ.; Fuenmayor Fernández, F.; Tur Valiente, M. (2018). An extension of shape sensitivity analysis to an immersed boundary method based on Cartesian grids. Computational Mechanics. 62(4):701-723. https://doi.org/10.1007/s00466-017-1522-0S701723624Abel JF, Shephard MS (1979) An algorithm for multipoint constraints in finite element analysis. Int J Numer Methods Eng 14(3):464–467Akgün MA, Garcelon GH, Haftka RT (2001) Fast exact linear and nonlinear structural reanalysis and the sherman-morrison-woodbury formulas. 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Geometry Modeling for Unstructured Mesh Adaptation

The quantification and control of discretization error is critical to obtaining reliable simulation results. Adaptive mesh techniques have the potential to automate discretization error control, but have made limited impact on production analysis workflow. Recent progress has matured a number of independent implementations of flow solvers, error estimation methods, and anisotropic mesh adaptation mechanics. However, the poor integration of initial mesh generation and adaptive mesh mechanics to typical sources of geometry has hindered adoption of adaptive mesh techniques, where these geometries are often created in Mechanical Computer- Aided Design (MCAD) systems. The difficulty of this coupling is compounded by two factors: the inherent complexity of the model (e.g., large range of scales, bodies in proximity, details not required for analysis) and unintended geometry construction artifacts (e.g., translation, uneven parameterization, degeneracy, self-intersection, sliver faces, gaps, large tolerances be- tween topological elements, local high curvature to enforce continuity). Manual preparation of geometry is commonly employed to enable fixed-grid and adaptive-grid workflows by reducing the severity and negative impacts of these construction artifacts, but manual process interaction inhibits workflow automation. Techniques to permit the use of complex geometry models and reduce the impact of geometry construction artifacts on unstructured grid workflows are models from the AIAA Sonic Boom and High Lift Prediction are shown to demonstrate the utility of the current approach