Difference between revisions of "NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008"

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__NOTOC__
 
__NOTOC__
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===Instructions for Use of this Template===
 
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#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/Project-Name
 
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#Copy the entire text of this page into the page created above
 
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#Link the created page into the list of projects for the project event
 
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#Delete this section from the created page
 
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#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
===Key Investigators===
 
===Key Investigators===
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<h1>Approach, Plan</h1>
 
<h1>Approach, Plan</h1>
  
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Work during the project week will continue much of the work that we have undertaken over the past year. Several integration projects will be tackled.
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Work during the project week will continue much of the work that we have undertaken over the past year. Several integration projects are planned:
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#Update existing voxel meshing execution model code. Bring it up to date with the changes that have taken place over the past six months with the base meshing code. Support now exists within Slicer3 for handling of unstructured grids and this should be propagated into this module.
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*Update existing voxel meshing execution model code. Bring it up to date with the changes that have taken place over the past six months with the base meshing code. Support now exists within Slicer3 for handling of unstructured grids and this should be propagated into this module.
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#Work with Steve and Curt on changes to the meshing workflow.
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*Work with Steve and Curt on changes to the meshing workflow.
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#Work with Curt on unifying stand-alone and Slicer3 meshing code base.
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*Work with Curt on unifying stand-alone and Slicer3 meshing code base.
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#Discuss with KWWidgets developers some of the issues that exist in this toolkit
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*Discuss some issues with KWWidgets developers: Multi-column list box scrolling issues, and Notebook widget and potential for constant size tabs and scrolling tabs
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#*Multi-column list box scrolling issues
 
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#*Notebook widget and potential for constant size tabs and scrolling tabs
 
 
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<h1>Progress</h1>
 
<h1>Progress</h1>
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*Much progress was made adding support for VTK Unstructured Grid datatypes as a subclass of models in Slicer3.  Slicer's Model Hierarchy module was modified to include control over unstructured grids.  This work is currently in the meshing branch of Slicer, but will be merged into the trunk in the next few weeks, after completing and testing what we developed this week.
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*The mesh generation interface has stabilized now that all the desired features for creating meshes have been implemented and partially tested.  These new editing functions will be integrated with Slicer and tested during the next few months.
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*Several user interface bugs were fixed in mesh generation. Initial support for node and element set definitions have been added.
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*Created a initial mesh from an Aneurysm as provided by Luca. Testing also being done on data provided by Adam Wittek.
  
 
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{|
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|[[Image:AneurysmMesh.png|thumb|320px|Initial Hex mesh generated from an aneurysm]]
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|[[Image:Summer08-mesh-in-slicer.png|thumb|320px|Unstructured Grid Mesh in Slicer Model Editor]]
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|[[Image:PatrioticMesh.png|thumb|320px|Holiday Spirit or a Mesh showing material properties depending on the time of year]]
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|}
  
  
 
===References===
 
===References===
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* Fletcher, P.T., Tao, R., Jeong, W.-K., Whitaker, R.T., "A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI," to appear Information Processing in Medical Imaging (IPMI) 2007.
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* Grosland NM, Brown TD. A voxel-based formulation for contact finite element analysis. Comput Methods Biomech Biomed Engin. 5(1):21-32, 2002.
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* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore, J.H., and Gerig, G., "Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis," Medical Image Analysis 10 (2006), 786--798.
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* Grosland NM, Bafna R, Magnotta VA. Automated Hexahedral Meshing of Anatomical structures using Deformable Registration. Computer Methods  in Biomechanics and Biomedical Engineering. Accepted.
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* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore J.H., and Gerig, G., Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis, Lecture Notes in Computer Science LNCS, James S. Duncan and Guido Gerig, editors, Springer Verlag, Vol. 3749, Oct. 2005, pp. 131 -- 138
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* Grosland NM, Shivanna KH, Magnotta VM, Kallemeyn NA, DeVries NA, Tadepalli SC. IA-FEMesh: An open-source, interactive, multiblock approach to musculoskeletal finite element model development. Submitted.
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* C. Goodlett, I. Corouge, M. Jomier, and G. Gerig, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39
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* P. P. P'ebay and D. C. Thompson and J. Shepherd and P. Knupp and C. Lisle and V. A. Magnotta and N. M. Grosland, New Applications of the Verdict Library for Standardized Mesh Verification. Pre, Post, and End-to-End Processing, Proc. 16th International Meshing Roundtable,Seattle, WA, 2007
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===Text from Adam's Previous Page===
 
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Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]], [[Algorithm:Site1|Site1 Algorithms]], [[DBP1:Site2|Site2 DBP 1]]
 
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__NOTOC__
 
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= '''Computing the Brain Deformation for Image-Guided Neurosurgery''' (The Intelligent Systems of Medicine Laboratory  [http://www.mech.uwa.edu.au/ISML/ link title]
 
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School of Mechanical Engineering, The University of Western Australia)=
 
  
 
=Description=
 
=Description=
  
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The Intelligent Systems of Medicine Laboratory  (ISML) mission is to work towards improving clinical outcomes through appropriate use of technology. We are interested in biomechanics (both engineering biomechanics and sport biomechanics), biomedical engineering, computer integrated surgery, medical robotics and related fields. We run exciting research projects in these areas, generously funded by The Australian Research Council and other agencies.
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The Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX) Program is a collaborative effort directed at computational modeling of anatomic structures. A primary objective is to automate the development of patient-/subject- specific models using a combination of imaging and modeling techniques, with particular emphasis on finite element modeling.
  
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We intend to contribute to Na-MIC by providing algorithms for computing the intra-operative brain deformations for image-guided neurosurgery. We treat the brain shift as a continuum mechanics problem involving finite deformations and solve it using non-linear finite element procedures. We use the procedures (non-linear explicit dynamics with Total Lagrangian formulation) that do not require iterations even when applied to non-linear problems and are, therefore, amenable to computing the intra-operative brain deformations in real time (under 150 s) on a standard PC.
 
  
  
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= Key Investigators =
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= [http://www.ccad.uiowa.edu/mimx/publications/ Publications]=
  
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* Prof. Karol Miller (kmiller@mech.uwa.edu.au), Dr Adam Wittek, Grand Joldes
 
  
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= Publications [http://www.mech.uwa.edu.au/ISML/publications.htm link title]=
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= Links =
  
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*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line at [http://www3.interscience.wiley.com/cgi-bin/jissue/109075715 link title].
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* [http://www.ccad.uiowa.edu/mimx/ MIMX Group]
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*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line at [http://www.sciencedirect.com/ link title].
 
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*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
 
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*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
 
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*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
 
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*[6] Horton, A., Wittek, A. and K. Miller  (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40 [http://www.mech.uwa.edu.au/ISML/publications.htm link title].
 
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*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63 [http://www.mech.uwa.edu.au/ISML/ publications.htm link title].
 
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*[8] Joldes, G., Wittek, A. and Miller, K.  (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
 
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*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
 
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*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
 
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*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12 [http://www.mech.uwa.edu.au/ISML/ publications.htm link title].
 
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*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.
 
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''In Press''
 
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*[13] AWittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
 
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*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.
 
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= Links =
 
  
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* Link1
 
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* Link2
 
  
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  Project Week Results:  [[blah|Jan 2006]], [[blah|Jun 2007]]
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  Project Week Results:  [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week:Meshing_Techniques_into_NA-MIC_Toolkit Winter 2008], [http://www.na-mic.org/Wiki/index.php/Collaboration/Iowa/Meshing/Adding_VTK_Interactive_WWidgets_to_Slicer3 June 2007]

Latest revision as of 14:27, 27 June 2008

Home < NA-MIC < Projects < External Collaboration < Mesh Generation Summer 2008
Return to Project Week Main Page
Building Block shown with number of mesh seeds color coded.
Mesh quality visualization.



Key Investigators

  • Iowa: Nicole Grosland, Kiran Shivanna, Vincent Magnotta
  • Isomics: Steve Piper
  • Knowledge Vis: Curt Lisle


Objective

We are developing methods generation of finite element meshes. This includes both semi-automated techniques using building blocks that can be manipulated with a number of new VTK widgets, and fully automated mapped meshing techniques. Our group is focused around the application of these tools to study orthopaedic biomechanics, but there are several other potential applications.


Approach, Plan

Work during the project week will continue much of the work that we have undertaken over the past year. Several integration projects are planned:

  • Update existing voxel meshing execution model code. Bring it up to date with the changes that have taken place over the past six months with the base meshing code. Support now exists within Slicer3 for handling of unstructured grids and this should be propagated into this module.
  • Work with Steve and Curt on changes to the meshing workflow.
  • Work with Curt on unifying stand-alone and Slicer3 meshing code base.
  • Discuss some issues with KWWidgets developers: Multi-column list box scrolling issues, and Notebook widget and potential for constant size tabs and scrolling tabs

Progress

  • Much progress was made adding support for VTK Unstructured Grid datatypes as a subclass of models in Slicer3. Slicer's Model Hierarchy module was modified to include control over unstructured grids. This work is currently in the meshing branch of Slicer, but will be merged into the trunk in the next few weeks, after completing and testing what we developed this week.
  • The mesh generation interface has stabilized now that all the desired features for creating meshes have been implemented and partially tested. These new editing functions will be integrated with Slicer and tested during the next few months.
  • Several user interface bugs were fixed in mesh generation. Initial support for node and element set definitions have been added.
  • Created a initial mesh from an Aneurysm as provided by Luca. Testing also being done on data provided by Adam Wittek.


Initial Hex mesh generated from an aneurysm
Unstructured Grid Mesh in Slicer Model Editor
Holiday Spirit or a Mesh showing material properties depending on the time of year


References

  • Grosland NM, Brown TD. A voxel-based formulation for contact finite element analysis. Comput Methods Biomech Biomed Engin. 5(1):21-32, 2002.
  • Grosland NM, Bafna R, Magnotta VA. Automated Hexahedral Meshing of Anatomical structures using Deformable Registration. Computer Methods in Biomechanics and Biomedical Engineering. Accepted.
  • Grosland NM, Shivanna KH, Magnotta VM, Kallemeyn NA, DeVries NA, Tadepalli SC. IA-FEMesh: An open-source, interactive, multiblock approach to musculoskeletal finite element model development. Submitted.
  • P. P. P'ebay and D. C. Thompson and J. Shepherd and P. Knupp and C. Lisle and V. A. Magnotta and N. M. Grosland, New Applications of the Verdict Library for Standardized Mesh Verification. Pre, Post, and End-to-End Processing, Proc. 16th International Meshing Roundtable,Seattle, WA, 2007

Description

The Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX) Program is a collaborative effort directed at computational modeling of anatomic structures. A primary objective is to automate the development of patient-/subject- specific models using a combination of imaging and modeling techniques, with particular emphasis on finite element modeling.


Publications

Links


Project Week Results:  Winter 2008, June 2007
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