Difference between revisions of "Mapped Hexahedral Meshing"

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(New page: '''Objective:''' * Develop a tool for mapped meshing that will warp a template mesh onto a surface for a new subject * Determine the limits that the warping algorithm will succeed and fai...)
 
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'''Progress:'''
 
'''Progress:'''
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* Previous work on this project was performed at the 2007 AHM -  [https://na-mic.org/w/images/3/34/2007_AHM_Programming_Half_Week_MappedMesh.ppt Mapped Mesh 4 Block]
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* Warped meshing framework has been developed using VTK and ITK.
+
* Warped meshing framework has been developed using VTK and ITK using a finite element approach
 
**VTK
 
**VTK
 
***Support the reading and writing of meshes (vtkUnstructuredGrid) and surfaces (vtkPolyData)
 
***Support the reading and writing of meshes (vtkUnstructuredGrid) and surfaces (vtkPolyData)
 
***Distance measures between the deforming mesh and the subject surface
 
***Distance measures between the deforming mesh and the subject surface
 
***Initial registration - [http://www.vtk.org/doc/nightly/html/classvtkIterativeClosestPointTransform.html Iterative Closest Point] or [http://www.vtk.org/doc/nightly/html/classvtkProcrustesAlignmentFilter.html Procrustes]  
 
***Initial registration - [http://www.vtk.org/doc/nightly/html/classvtkIterativeClosestPointTransform.html Iterative Closest Point] or [http://www.vtk.org/doc/nightly/html/classvtkProcrustesAlignmentFilter.html Procrustes]  
 +
**ITK
 +
***Finite element framework used to warped the template mesh onto the subject surface
 +
*Registration made hierarchical to speed up the registration process
 +
**Requires multiple template meshes to exist
 +
**This is readily supported using the interactive meshing tools by changing the average edge length
 +
**Subsequent meshes are initialized using a thin plate splines
 +
*Parameters allowed to vary at each level of the registration
 +
**Iterations
 +
**Young's Modulus
 +
*Convergence based on distance between the warped template and the subject surface
 +
**User specified convergence threshold in mm
 +
**Convergence can be based on average or maximum distance
 +
*Boundary conditions can be applied
 +
**Center of the mesh - Holds the eight nodes closest to the center of the mesh fixed
 +
**External - Applies boundary conditions to the mesh as they fall within a user specified tolerance of the subject surface
 +
* Initial testing done by warping a cube mesh onto a sphere
 +
**Evaluation:
 +
***Distance between warped mesh and subject surface
 +
***Mesh quality
  
−
 
+
'''Publications:'''
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* Meshing module is now built by default with Slicer3
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*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.
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'''To Do:'''
 
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* We should remove the need for the surface extraction when Slicer3 supports the loading of unstructured grids.
 
  
 
'''Key Investigators:'''
 
'''Key Investigators:'''
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'''Links:'''
 
'''Links:'''
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*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modelling and Experimentation (MIMX)]
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*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)]
  
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'''Description:'''
 
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This program will convert an image into a hexahedral mesh using
 
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the voxels as the hexahedral elements. This is is typically done
 
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for only a portion of the image and thus a binary image from a
 
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segmentation may be used to define the region for meshing.
 
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Since these meshes may be fairly large the user is allowed
 
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to downsample the image by an integer value. Currently this
 
−
must be odd.
 
  
−
This tool was developed as part of an NIH NA-MIC Collaboration Grant EB005973.
+
'''Figures:'''
  
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'''Program Usage:'''
+
[[Image:MappedHexMeshSquareSphereInit.jpg|left|thumb|300px|Initial position of the cube template mesh and the sphere surface prior to registration using the itk::FEM mapped meshing algorithm]]
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VoxelMeshingModule
 
−
 
−
  --imagefilename      Input image File Name
 
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  --maskfilename      Input mask File Name
 
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  --abaqusfilename    Output Abaqus Filename
 
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  --vtkfilename        Output mesh VTK filename
 
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  --vtksurfacefilename Output mesh surface VTK filename (Hack required for slicer3)
 
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  --resamplesize      The image resample downsampling factor - Must be odd
 
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  --meshindexoffset    The mesh index offset for nodes and elements
 
−
  --poissonratio      Poisson Ratio for the mesh
 
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  --abaqustitle        Abaqus title for generated mesh
 
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  --numberofbins      The number of histogram bins in the mesh
 
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  --histogamlowerbound The lower bound for the mesh histogram
 
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  --histogamupperbound The upper bound for the mesh histogram
 
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  --histogambinfile    Mesh material properties histogram bin filename
 
−
 
 
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'''Figures:'''
 
  
−
[[Image:Slicer3Surface.png|left|thumb|300px|Surface of proximal phalanx generated via Slicer3]]
+
[[Image:MappedMeshCubeSphereQuality.jpg|left|thumb|325px|Mesh quality evaluation of the warped cube]]
  
−
[[Image:VoxelMesh.png|left|thumb|300px|Voxel mesh generated via Slicer3 execution Model]]
+
[[Image:MappedMeshSquareSphere.jpg|left|thumb|300px|a)Position of the template cube mesh and surface after ICP registration. b) Resulting warped cube after itk::FEM mapped meshing. c) Distance map between the warped cube and the sphere surface]]
  
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[[Image:Mimx.png|left|thumb|300px|Slicer3 Voxel Mesh Module]]
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[[Image:MappedMeshProximalPhalanxTrial.jpg|left|thumb|300px|Initial attempt to apply mapped meshing algorithm to the proximal phalanx]]

Latest revision as of 18:27, 10 July 2017

Home < Mapped Hexahedral Meshing

Objective:

  • Develop a tool for mapped meshing that will warp a template mesh onto a surface for a new subject
  • Determine the limits that the warping algorithm will succeed and fail
  • Apply these techniques to a sample of data to determine the reliability of the algorithm with respect to mesh quality

Progress:

  • Previous work on this project was performed at the 2007 AHM - Mapped Mesh 4 Block
  • Warped meshing framework has been developed using VTK and ITK using a finite element approach
    • VTK
      • Support the reading and writing of meshes (vtkUnstructuredGrid) and surfaces (vtkPolyData)
      • Distance measures between the deforming mesh and the subject surface
      • Initial registration - Iterative Closest Point or Procrustes
    • ITK
      • Finite element framework used to warped the template mesh onto the subject surface
  • Registration made hierarchical to speed up the registration process
    • Requires multiple template meshes to exist
    • This is readily supported using the interactive meshing tools by changing the average edge length
    • Subsequent meshes are initialized using a thin plate splines
  • Parameters allowed to vary at each level of the registration
    • Iterations
    • Young's Modulus
  • Convergence based on distance between the warped template and the subject surface
    • User specified convergence threshold in mm
    • Convergence can be based on average or maximum distance
  • Boundary conditions can be applied
    • Center of the mesh - Holds the eight nodes closest to the center of the mesh fixed
    • External - Applies boundary conditions to the mesh as they fall within a user specified tolerance of the subject surface
  • Initial testing done by warping a cube mesh onto a sphere
    • Evaluation:
      • Distance between warped mesh and subject surface
      • Mesh quality

Publications:

Key Investigators:

  • Iowa: Nicole Grosland, Vincent Magnotta, Ritesh Bafna

Links:


Figures:

Initial position of the cube template mesh and the sphere surface prior to registration using the itk::FEM mapped meshing algorithm
Mesh quality evaluation of the warped cube
a)Position of the template cube mesh and surface after ICP registration. b) Resulting warped cube after itk::FEM mapped meshing. c) Distance map between the warped cube and the sphere surface
Initial attempt to apply mapped meshing algorithm to the proximal phalanx
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