Difference between revisions of "Voxel Meshing Module"

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**[[Coordinate System Conversion Between ITK and Slicer3]]
 
**[[Coordinate System Conversion Between ITK and Slicer3]]
 
* Extraction of surfaces nodes has been implemented to view results in Slicer3
 
* Extraction of surfaces nodes has been implemented to view results in Slicer3
 +
* Material properties can be assigned to the elements using the Voxel data signal intensity and converting this into a modulus value. The user can specify the number of unique values to use for the modulus.
 +
**Rebinning can be done based on the minimum and maximum value and then divide this into equal steps between these values
 +
**A user specified histogram can also be done using a user specified histogram
 +
*Output formats
 +
**VTK
 +
**[http://www.simulia.com/ Abaqus]
 +
* Source code updated to support VTK 5.0 instead of VTK 5.1. This change required that the histogram bin data is written as Field Data in a VTK file.
 +
* Meshing module is now built by default with Slicer3
 +
* This code was updated to integrate with the new meshing module. This should be available in Slicer3.4 release
  
−
'''To Do:'''
 
−
* Slicer3 needs to add support for loading and manipulating VTK Unstructured Grids
 
  
 
'''Key Investigators:'''
 
'''Key Investigators:'''
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'''Links:'''
 
'''Links:'''
−
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modelling and Experimentation (MIMX)]
+
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)]
 +
 
 +
'''Description:'''
 +
This program will convert an image into a hexahedral mesh using
 +
the voxels as the hexahedral elements. This is is typically done
 +
for only a portion of the image and thus a binary image from a
 +
segmentation may be used to define the region for meshing.
 +
Since these meshes may be fairly large the user is allowed
 +
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.
 +
 
 +
'''Program Usage:'''
 +
VoxelMeshingModule
 +
 +
  --imagefilename      Input image File Name
 +
  --maskfilename      Input mask File Name
 +
  --abaqusfilename    Output Abaqus Filename
 +
  --vtkfilename        Output mesh VTK filename
 +
  --vtksurfacefilename Output mesh surface VTK filename (Hack required for slicer3)
 +
  --resamplesize      The image resample downsampling factor - Must be odd
 +
  --meshindexoffset    The mesh index offset for nodes and elements
 +
  --poissonratio      Poisson Ratio for the mesh
 +
  --abaqustitle        Abaqus title for generated mesh
 +
  --numberofbins      The number of histogram bins in the mesh
 +
  --histogamlowerbound The lower bound for the mesh histogram
 +
  --histogamupperbound The upper bound for the mesh histogram
 +
  --histogambinfile    Mesh material properties histogram bin filename
 +
 
 +
'''Figures:'''
 +
 
 +
[[Image:Slicer3Surface.png|left|thumb|300px|Surface of proximal phalanx generated via Slicer3]]
 +
 
 +
[[Image:VoxelMesh.png|left|thumb|300px|Voxel mesh generated via Slicer3 execution Model]]
 +
 
 +
[[Image:Mimx.png|left|thumb|300px|Slicer3 Voxel Mesh Module]]

Latest revision as of 21:05, 9 December 2008

Home < Voxel Meshing Module

Objective:

  • Develop an initial framework for integration of Meshing modules into the NA-MIC kit

Progress:

  • Base code has been developed as an Execution Model for Slicer3
  • Orientatation issues wrt Slicer3 and ITK coordinate systems have been determined
  • Extraction of surfaces nodes has been implemented to view results in Slicer3
  • Material properties can be assigned to the elements using the Voxel data signal intensity and converting this into a modulus value. The user can specify the number of unique values to use for the modulus.
    • Rebinning can be done based on the minimum and maximum value and then divide this into equal steps between these values
    • A user specified histogram can also be done using a user specified histogram
  • Output formats
  • Source code updated to support VTK 5.0 instead of VTK 5.1. This change required that the histogram bin data is written as Field Data in a VTK file.
  • Meshing module is now built by default with Slicer3
  • This code was updated to integrate with the new meshing module. This should be available in Slicer3.4 release


Key Investigators:

  • Iowa: Nicole Grosland, Vincent Magnotta, Ritesh Bafna

Links:

Description: This program will convert an image into a hexahedral mesh using the voxels as the hexahedral elements. This is is typically done for only a portion of the image and thus a binary image from a segmentation may be used to define the region for meshing. Since these meshes may be fairly large the user is allowed 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.

Program Usage: 

VoxelMeshingModule 

 --imagefilename      Input image File Name
 --maskfilename       Input mask File Name
 --abaqusfilename     Output Abaqus Filename
 --vtkfilename        Output mesh VTK filename
 --vtksurfacefilename Output mesh surface VTK filename (Hack required for slicer3)
 --resamplesize       The image resample downsampling factor - Must be odd
 --meshindexoffset    The mesh index offset for nodes and elements
 --poissonratio       Poisson Ratio for the mesh
 --abaqustitle        Abaqus title for generated mesh
 --numberofbins       The number of histogram bins in the mesh
 --histogamlowerbound The lower bound for the mesh histogram
 --histogamupperbound The upper bound for the mesh histogram
 --histogambinfile    Mesh material properties histogram bin filename

Figures:

Surface of proximal phalanx generated via Slicer3
Voxel mesh generated via Slicer3 execution Model
Slicer3 Voxel Mesh Module
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