GPU accelerated FEM for simulation and segmentation

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Home < GPU accelerated FEM for simulation and segmentation

Key Investigators

  • Megumi Nakao and Nobuhiko Hata


We are developing a fast FEM-based mesh deformation library for interactive simulation and segmentation. The goal in this project week is summarized as

  • integrate linear FEM-based deformation algo into the slicer
  • perform deformation on specific data
  • implement GPU-based acceleration for real-time deformation

Approach, Plan

  • integrate a liner FEM solver(original C++ source) into the 3D slicer framework.
  • make tetrahedral meshes from medical images and set up physical conditions. Other mesh formats, points and surface models will be probablly accepted.
  • evaluate some deformation results qualitatively and improve the simulation.
  • try GPU-based acceleration by modifying the linear equation solver using CUBLAS library.


We have got the following results through this project week

  • The FEM-based deformation library was implemented on the Slicer framework.
  • Elastic deformation results were confirmed using sample data.
  • CUBLAS library enables interactive update of the stiffness matrix for tetrahedral meshes with 2000 vertices


  • M. Nakao and K. Minato, "Physics-based Interactive Volume Manipulation for Sharing Surgical Process", IEEE Trans. on Information Technology in Biomedicine, 2009. (in press)
  • H. K. W. Cecilia, M. Nakao and K. Minato, "Automated Volume Sampling Optimization for Direct Volume Manipulation in Patient-specific Surgical Simulation", IEEE International Symposium on Biomedical Imaging, June 2009. (To appear)
  • M. Nakao, S. Yano, T. Matsuyuki, T. Kawamoto and M. Kotaro, "Interactive Volume Manipulation for Supporting Preoperative Planning", Stud. Health Tech. Inform. (MMVR), Vol. 125, pp. 316-321, Jan. 2008.
  • M. Nakao, A. Kawashima, K. Minato, M. Kokubo, "Simulating Lung Tumor Motion for Dynamic Tumor-Tracking Irradiation", IEEE Nuclear Science Symposium and Medical Imaging Conference, pp. 4549-4551, Oct. 2007.
  • M. Nakao, T. Kuroda, M. Komori, H. Oyama, K. Minato and T. Takahashi, "Transferring Bioelasticity Knowledge through Haptic Interaction", IEEE Multimedia, Vol. 13, No. 3, pp.50-60, Jul. 2006.
  • (My homepage)