mesh generation; Patient-Specific Modelling; biomechanics; Finite Element Method
Abstract :
[en] Thanks to advances in medical imaging technologies and numerical methods, Patient-Specific Modelling is more and more used to improve diagnosis and to estimate the outcome of surgical interventions. It requires the extraction of the domain of interest from the medical scans of the patient, as well as the discretisation of this geometry. However, extracting smooth multi-material meshes that conform to the tissue boundaries described in the segmented image is still an active field of research. We propose to solve this issue by combining an implicit surface reconstruction method with a multi-region mesh extraction scheme. The surface reconstruction algorithm is based on multi-level partition of unity implicit surfaces which we extended to the multi-material case. The mesh generation algorithm consists in a novel multidomain version of the marching tetrahedra. It generates multi-region meshes as a set of triangular surface patches consistently joining each other at material junctions. This paper presents this original meshing strategy, starting from boundary points extraction from the segmented data, to heterogeneous implicit surface definition, multi-region surface triangulation and mesh adaptation. Results indicate that the proposed approach produces smooth and high-quality triangular meshes with a reasonable geometric accuracy. Hence, the proposed method is well suited for subsequent volume mesh generation and Finite Element simulations.
Research Center/Unit :
Non Linear Computational Mechanics LTAS-MN2L
Disciplines :
Engineering, computing & technology: Multidisciplinary, general & others
Author, co-author :
D'Otreppe, Vinciane ; Université de Liège - ULiège > Département d'aérospatiale et mécanique > LTAS-Mécanique numérique non linéaire
Boman, Romain ; Université de Liège - ULiège > Département d'aérospatiale et mécanique > LTAS-Mécanique numérique non linéaire
Ponthot, Jean-Philippe ; Université de Liège - ULiège > Département d'aérospatiale et mécanique > LTAS-Mécanique numérique non linéaire
Language :
English
Title :
Generating smooth surface meshes from multi-region medical images
Publication date :
2012
Journal title :
International Journal for Numerical Methods in Biomedical Engineering
Gibson S. Constrained elastic surface nets: generating smooth surfaces from binary segmented data. In Medical Image Computing and Computer-Assisted Intervention MICCAI'98, Vol. 1496, Wells W, Colchester A, Delp S (eds), Lecture Notes in Computer Science. Springer: Berlin Heidelberg, 888-898. DOI: 10.1007/BFb0056277.
Nielson GM. Dual marching cubes. In Proceedings of the Conference on Visualization '04, VIS '04, IEEE Computer Society: Washington, DC, USA, 2004; 489-496. DOI: 10.1109/VISUAL.2004.28.
Wang SW, Kaufman AE. Volume sampled voxelization of geometric primitives. In Proceedings of the 4th Conference on Visualization '93, VIS '93. IEEE Computer Society: Washington, DC, USA, 1993; 78-84. DOI: 10.1109/VISUAL.1993.398854.
Alexa M, Behr J, Cohen-Or D, Fleishman S, Levin D, Silva CT. Point set surfaces. In Proceedings of the Conference on Visualization '01, VIS '01. IEEE Computer Society: Washington, DC, USA, 2001; 21-28. DOI: 10.1109/VISUAL.2001.964489.
Guennebaud G, Gross M. Algebraic point set surfaces. ACM Transactions on Graphics 2007; 26: 23. DOI: 10.1145/1276377.1276406.
Zhao HK, Osher S, Fedkiw R. Fast surface reconstruction using the level set method. IEEE Workshop on Variational and Level Set Methods in Computer Vision 2001; 0: 194-201. DOI: 10.1109/VLSM.2001.938900.
Carr JC, Beatson RK, Cherrie JB, Mitchell TJ, Fright WR, McCallum BC, Evans TR. Reconstruction and representation of 3D objects with radial basis functions. In Proceedings of the 28th Annual Conference on Computer Graphics and Interactive Techniques, SIGGRAPH '01, ACM, New York, NY, USA, 2001; 67-76. DOI: 10.1145/383259.383266.
Ohtake Y, Belyaev A, Alexa M, Turk G, Seidel HP. Multi-level partition of unity implicits. ACM Transactions on Graphics 2003; 22: 463-470. DOI: 10.1145/882262.882293.
Franke R, Nielson G. Smooth interpolation of large sets of scattered data. International Journal for Numerical Methods in Engineering 1980; 15(11): 1691-1704. DOI: 10.1002/nme.1620151110.
Hege H, Seebass M, Stalling D, Zöckler M. A generalized marching cubes algorithm based on non-binary classifications. ZIB Report SC 97-05, Berlin, 1997.
Wu Z, Sullivan J Jr. Multiple material marching cubes algorithm. International Journal for Numerical Methods in Engineering 2003; 58(2): 189-207. DOI: 10.1002/nme.775.
Bertram M, Reis G, Van Lengen R, Köhn S, Hagen H. Non-manifold mesh extraction from time-varying segmented volumes used for modeling a human heart. In Eurographics/IEEE VGTC Symposium on Visualization, Ken Brodlie DD, Joy K (eds). Citeseer, Eurographics Association, 2005; 199-206.
Bischoff S, Kobbelt L. Extracting consistent and manifold interfaces from multi-valued volume data sets. In Bildverarbeitung für die Medizin 2006, Brauer W, Handels H, Ehrhardt J, Horsch A, Meinzer HP, Tolxdorff T (eds), Informatik aktuell, Springer: Berlin Heidelberg, 2006; 281-285. DOI: 10.1007/3-540-32137-3_57.
Reitinger B, Bornik E, Beichel R. Constructing smooth nonmanifold meshes of multi-labeled volumetric datasets. In The 13th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision, WSCG, Press, 2005; 227-234.
Dillard S, Bingert J, Thoma D, Hamann B. Construction of simplified boundary surfaces from serial-sectioned metal micrographs. IEEE Transactions on Visualization and Computer Graphics 2007; 13: 1528-1535. DOI: 10.1109/TVCG.2007.70543.
Müller H. Boundary extraction for rasterized motion planning. In Modelling and Planning for Sensor Based Intelligent Robot Systems, Horst Bunke TK, Noltemeier H (eds), 1995; 41-50.
Nielson GM, Franke R. Computing the separating surface for segmented data. In Proceedings of the 8th Conference on Visualization '97, VIS '97, IEEE Computer Society Press, Los Alamitos, CA, USA, 1997; 229-233. DOI: 10.1109/VISUAL.1997.663887.
Bonnell KS, Joy KI, Hamann B, Schikore DR, Duchaineau M. Constructing material interfaces from data sets with volume-fraction information. In Proceedings of the Conference on Visualization '00, VIS '00, IEEE Computer Society Press, Los Alamitos, CA, USA, 2000; 367-372. DOI: 10.1109/VISUAL.2000.885717.
Zhang Y, Hughes TJ, Bajaj CL. An automatic 3D mesh generation method for domains with multiple materials. Computer Methods in Applied Mechanics and Engineering 2010; 199(5-8): 405-415. DOI: 10.1016/j.cma.2009.06.007.
Liu Y, Fedorov A, Kikinis R, Chrisochoides N. Non-rigid registration for brain MRI: faster and cheaper. International Journal of Functional Informatics and Personalised Medicine 2010; 3(1): 48-57. DOI: 10.1504/IJFIPM.2010.033245.
Pons J, Ségonne F, Boissonnat J, Rineau L, Yvinec M, Keriven R. High-quality consistent meshing of multi-label datasets. In Information Processing in Medical Imaging, Vol. 4584, Karssemeijer N, Lelieveldt B (eds), Lecture Notes in Computer Science, Springer: Berlin Heidelberg, 2007; 198-210. DOI: 10.1007/978-3-540-73273-0_17.
Meyer M, Whitaker R, Kirby RM, Ledergerber C, Pfister H. Particle-based sampling and meshing of surfaces in multimaterial volumes. IEEE Transactions on Visualization and Computer Graphics November 2008; 14: 1539-1546. DOI: 10.1109/TVCG.2008.154.
Boltcheva D, Yvinec M, Boissonnat JD. Mesh generation from 3D multi-material images. In Medical Image Computing and Computer-Assisted Intervention - MICCAI 2009, Vol. 5762, Yang GZ, Hawkes D, Rueckert D, Noble A, Taylor C (eds), Lecture Notes in Computer Science, Springer: Berlin Heidelberg, 2009; 283-290. DOI: 10.1007/978-3-642-04271-3_35.
Lorensen WE, Cline HE. Marching cubes: a high resolution 3D surface construction algorithm. SIGGRAPH Computer Graphics 1987; 21: 163-169. DOI: 10.1145/37402.37422.
Si H. Tetgen: a quality tetrahedral mesh generator and three-dimensional Delaunay triangulator. Technical Report I.4, Weierstrass-Institute, Berlin, 2006.
Geuzaine C, Remacle JF. Gmsh: A 3-D finite element mesh generator with built-in pre- and post-processing facilities. International Journal for Numerical Methods in Engineering 2009; 79(11): 1309-1331. DOI: 10.1002/nme.2579.
Sazonov I, Nithiarasu P. Semi-automatic mesh generation and cosmetics for subject-specific biomedical geometries. CMBE11: 2nd International Conference on Computational & Mathematical Biomedical Engineering, Washington DC, USA, 2011; 209-212.
Taubin G. Estimation of planar curves, surfaces, and nonplanar space curves defined by implicit equations with applications to edge and range image segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence 1991; 13: 1115-1138. DOI: 10.1109/34.103273.
Yoshizawa S, Belyaev AG, Seidel HP. A simple approach to interactive free-form shape deformations. Pacific Conference on Computer Graphics and Applications 2002; 0: 471. DOI: 10.1109/PCCGA.2002.1167905.
Braude I, Marker J, Museth K, Nissanov J, Breen D. Contour-based surface reconstruction using MPU implicit models. Graphical Models 2007; 69(2): 139-157. DOI: 10.1016/j.gmod.2006.09.007.
Gibson SFF. Using distance maps for accurate surface representation in sampled volumes. In Proceedings of the 1998 IEEE Symposium on Volume Visualization, VVS '98, ACM: New York, NY, USA, 1998; 23-30. DOI: 10.1145/288126.288142.
Wang MY, Wang X. A level-set based variational method for design and optimization of heterogeneous objects. Computer-Aided Design 2005; 37(3): 321-337. DOI: 10.1016/j.cad.2004.03.007.
Ning P, Bloomenthal J. An evaluation of implicit surface tilers. IEEE Computer Graphics and Applications 1993; 13: 33-41. DOI: 10.1109/38.252552.
Pieper S, Halle M, Kikinis R. 3D slicer. IEEE International Symposium on Biomedical Imaging: Nano to Macro 2004; 1: 632-635. DOI: 10.1109/ISBI.2004.1398617.
