NA-MIC NCBC Collaboration:Automated FE Mesh Development

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Visualization of mesh quality

Abstract

Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.

Grant#

R01EB005973

Key Personnel

• Musculoskeletal Imaging, Modeling and Experimentation (MIMX) at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan
• NA-MIC: Steve Pieper (Isomics), Curt Lisle (KnowledgeVis)

Funding Duration

09/20/2006-06/30/2011

Projects

An initial version of the meshing tool was recently released as a standalone application called IA-FEMesh. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.

Active projects in this collaboration are:

Meshing Algorithms

1. Voxel Meshing Module (Iowa)
2. Novel Hexahedral Meshing Algorithms (Iowa)
3. Mapped Hexahedral Meshing (Iowa)
4. Hex vs Tet Mesh Comparisons (Iowa/Isomics/BWH)

Automated Segmentation

1. EM Segmentation For Orthopaedic Applications (Iowa)
2. Integration of Neural Network Algorithms (Iowa)

Validation

1. Validation of Defined Regions of Interest Using Surface Scanning (Iowa)
2. FE Mesh Validation (Iowa)

Mesh Quality Visualization

1. FE Mesh Quality Visualization (Iowa/Isomics)
2. Standalone FE Mesh Quality Viewer
3. Mesh Quality Command Line Module

Mesh Improvement

1. Mesh Quality Improvement

Slicer3 Integration

1. Slicer Interactive Module
2. Mesh KWWidgets Interface
3. Slicer3 Mesh Meeting October 2008
4. Completed Module Released in Slicer 3.6

Slicer3 Meshing Tutorial

1. Iowa Meshing Tutorial - Tutorial showing how to mesh the proximal phalanx bone with an example dataset
2. Updated Tutorial along with screencasts here

Publications

1. Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Toward the development of virtual surgical tools to aid orthopaedic FE analyses EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.
2. DeVries N.A., Shivanna K.H., Tadepalli S.C., Magnotta V.A., Grosland N.M. IA-FEMesh: Anatomic Fe Models - A Check of Mesh Accuracy and Validity. Iowa Orthop J. 2009 Jan;29:48-54. PMID: 19742085. PMCID: PMC2723692.
3. Kallemeyn N.A., Tadepalli S.C., Shivanna K.H., Grosland N.M. AAn Interactive Multiblock Approach to Meshing the Spine. Comput Methods Programs Biomed. Comput Methods Programs Biomed. 2009 Sep;95(3):227-35. PMID: 19394107.
4. Grosland N.M., Shivanna K.H., Magnotta V.A., Kallemeyn N.A., DeVries N.A., Tadepalli S.C., Lisle C. http://www.na-mic.org/publications/item/view/1794 IA-FEMesh: An Open-source, Interactive, Multiblock Approach to Anatomic Finite Element Model Development. Comput Methods Programs Biomed.]. Comput Methods Programs Biomed. 2009 Apr;94(1):96-107. PMID: 19157630. PMCID: PMC2712294.
5. Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. Semi-automated Phalanx Bone Segmentation using the Expectation Maximization Algorithm. J Digit Imaging. 2009 Oct;22(5):483-91. PMID: 18769967. PMCID: PMC2745490.
6. Grosland NM, Bafna R, Magnotta VA. Automated Hexahedral Meshing of Anatomic Structures using Deformable Registration. Comput Methods Biomech Biomed Engin. 2009;12(1):35-43.
7. DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. Validation of Phalanx Bone Three-dimensional Surface Segmentation from Computed Tomography Images using Laser Scanning. Skeletal Radiol. 2008 Jan;37(1):35-42. PMID: 17962937.
8. Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. Automated Bony Region Identification using Artificial Neural Networks: Reliability and Validation Measurements. Skeletal Radiol. 2008 Apr;37(4):313-9. PMID: 18172639.
9. Magnotta V, Li W, Grosland N. Comparison of Displacement-Based and Force-Based Mapped Meshing. Int Conf Med Image Comput Comput Assist Interv. 2008 Sep;11(WS). Workshop on Computational Biomechanics for Medicine.
10. Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces. Proceedings of the 2008 Summer Bioengineering Conference, 2008.
11. Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. A Check Of Mesh Quality, American Society of Biomechanics, August 22-27, 2007.
12. Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing, Proceedings of the 16th International Meshing Roundtable, 2007.
13. Shivanna KH, Adams BD, Magnotta VA, Grosland NM. Towards Automating Patient-Specific Finite Element Model Development. Proceedings Computational Biomechanics For Medicine, 2006.

Meetings and Events Specific to this Collaboration

• 2006
  • Vincent Magnotta presented background information about the data acquisitioin and validation at the 2006 NA-MIC AHM (Slides: Validation of Bone Models using 3D Surface Scanning).
  • Orthopaedic Research Society - 2006
    • Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.
  • MICCAI - 2006
    • Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.
  • November 7-8, 2006: Meshing Collaborator Project Visit to BWH
• 2007
  • NA-MIC AHM
    • NA-MIC All Hands Meeting Update 2007
    • 2007 Project Half Week
  • American Society of Biomechanics 2007
    • Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. A check of mesh quality. in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the American Society of Biomechanics 2007, Palo Alto, CA
    • Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.
    • DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.
    • Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.
  • NA-MIC Summer Project Week
    • Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3
    • Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK
• 2008
  • NA-MIC AHM
    • NA-MIC All Hands Meeting Update
    • 2008 Winter Project Week:Finite Element Meshing into NA-MIC
  • Annual BMES Meeting
    • Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.
  • Pre ORS
    • Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.
  • Orthopaedic Research Society
    • Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. Comparison of the EM algorithm and an artifical neural network for automated bone segmentation. in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.
  • ASME Summer Bioengineering Conference
    • Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces. in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.
  • NA-MIC Summer Project Week
    • NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008
  • MICCAI
    • Vincent Magnotta presents at the MICCAI Workshop - Computational Biomechanics for Medicine, New York, NY 2008.
• 2009
  • NA-MIC All Hands Meeting
    • AHM Update
    • Iowa Meshing Tutorial
  • ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.
    • Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.
    • Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.
    • Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.
    • Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.
    • Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.
    • Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.
  • American Society of Biomechanics Annual Meeting
    • Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.
  • NA-MIC Summer Project Week
    • MeshingSummer2009
  • Meshing Tcon September 26

• 2010
  • NA-MIC Update 2010
  • Pre ORS
    • Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.
  • Orthopaedic Research Society
    • Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.

Resource Links

• netget
• tetgen
• libmesh
• Mesquite
• Opt-ms

• Mesh warping project at the SPL - Steve Haker:
  • Haker S., Warfield S.K., Tempany C.M. Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.Int Conf Med Image Comput Comput Assist Interv. 2004;7(Pt 2):267-275.