Difference between revisions of "Documentation/Nightly/Modules/MeshCompression"

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Extension: [[Documentation/{{documentation/version}}/Extensions/ImageToMeshConversion|Image To Mesh Conversion]]<br>
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Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC 3D I2MConversion]]<br>
 
Acknowledgments:
 
Acknowledgments:
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*This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.
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*This work was partially supported by NIH R44 OD018334-03A, grant CCF-1439079 and by the Richard T.Cheng Endowment.
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<br>
 
  
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Author:Fotis Drakopoulos<br>
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Author: Fotis Drakopoulos<br>
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Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)<br>
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Contributors: Joi Best (CRTC), Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)<br>
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Contact: Nikos Chrisochoides, <email>npchris@gmail.com</email><br>
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Contact: Nikos Chrisochoides: <email>npchris@gmail.com</email> , Joi Best: <email>jbest002@odu.edu</email><br>
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Website: http://crtc.wm.edu/html_output/index.htm<br>
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Website: https://crtc.cs.odu.edu <br>
 
License: BSD<br>
 
License: BSD<br>
 
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{|
 
{|
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|[[File:brain_before.jpg|thumb|280px|Brain BCC mesh before MC]]
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|[[File:brain_before.jpg|thumb|300px|Brain BCC mesh before MC]]
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|[[File:brain_after.jpg|thumb|280px|Brain BCC mesh after MC]]<br>
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|[[File:brain_after.jpg|thumb|300px|Brain BCC mesh after MC]]
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|[[File:brain_after_section.jpg|thumb|300px|Brain BCC mesh after MC (cross-section)]]
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|}
  
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|[[File:nidus_before.jpg|thumb|280px|Nidus BCC mesh before MC]]
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{|
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|[[File:nidus_after.jpg|thumb|280px|Nidus BCC mesh after MC]]<br>
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|[[File:nidus_before.jpg|thumb|300px|Nidus BCC mesh before MC]]
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|[[File:nidus_after.jpg|thumb|300px|Nidus BCC mesh after MC]]<br>
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|[[File:nidus_after_section.jpg|thumb|300px|Nidus BCC mesh after MC (cross-section)]]
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|}
  
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|[[File:ventricles_before.jpg|thumb|280px|Ventricles BCC mesh before MC]]
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{|
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|[[File:ventricles_after.jpg|thumb|280px|Ventricles BCC mesh after MC]]
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|[[File:ventricles_before.jpg|thumb|300px|Ventricles BCC mesh before MC]]
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|[[File:ventricles_after.jpg|thumb|300px|Ventricles BCC mesh after MC]]
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|[[File:ventricles_after_section.jpg|thumb|300px|Ventricles BCC mesh after MC (cross-section)]]
 
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{|
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|[[File:target_points.jpg|thumb|960px|How the non-connectivity parameter influences the number of the extracted target points]]
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* '''Mesh Generation Parameters:'''
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* '''Mesh Compression Parameters:'''
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** '''Size:'''  Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).
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** '''Flexibility:'''  Controls the trade-off between the regularization energy defined by the stress energy of a linear bio-mechanical elastic model, and the similarity energy. Value should be between [0.1,1] (default: 1).
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** '''Fidelity:'''  Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).
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** '''Number of Iterations:'''  Controls the number of iterations for the compressor. The larger the value the closer the boundaries of the input mesh to the boundaries of the input image. A large number of iterations might cause distorted poor-quality elements. Value should be between [1,10] (default: 3).
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** '''Resample Resolution:'''  Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).
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** '''Non Connectivity:'''  Controls the density of the extracted target points via a prohibited connectivity between adjacent blocks of voxels. The larger the value the denser the target point set. 0 is vertex non-connectivity (26 neighbors), 1 is edge non-connectivity (18 neighbors), 2 is face non-connectivity (6 neighbors) and 3 is no non-connectivity. Value should be 0 or 1 or 2 or 3. (default: 0).
 
* '''Input/Output:'''
 
* '''Input/Output:'''
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** '''Labeled Image:''' The input labeled image.
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** '''Input Labeled Image:''' The input labeled image.
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** '''Output Mesh:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)
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** '''Input Mesh File:''' The input tetrahedral mesh in vtk file format.
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|[[Image:BCCPanel.jpg|thumb|380px|User Interface]]
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** '''Output Mesh File:''' The output deformed mesh in vtk file format (optional) (default: deformedMesh.vtk).
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** '''Output Source Points File:''' The extracted source points in vtk file format (optional). The source points are the surface vertices of the input mesh.
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** '''Output Target Points File:''' The extracted target points in vtk file format (optional). The target points are the surface edge points of the input labeled image.
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** '''Output Surface Triangles File:''' The extracted surface triangles of the input mesh in vtk file format (optional).
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|[[Image:MCPanel.jpg|thumb|380px|User Interface]]
 
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'''Note: this module will only work if the input image has identity orientation!'''
  
 
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
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N/A
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*[[Documentation/Nightly/Modules/BodyCentricCubicMesh]]
  
  

Latest revision as of 14:08, 7 August 2018

Home < Documentation < Nightly < Modules < MeshCompression


For the latest Slicer documentation, visit the read-the-docs.


Introduction and Acknowledgements

Extension: CBC 3D I2MConversion
Acknowledgments:

  • This work was partially supported by NIH R44 OD018334-03A, grant CCF-1439079 and by the Richard T.Cheng Endowment.

Author: Fotis Drakopoulos
Contributors: Joi Best (CRTC), Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)
Contact: Nikos Chrisochoides: <email>npchris@gmail.com</email> , Joi Best: <email>jbest002@odu.edu</email>
Website: https://crtc.cs.odu.edu
License: BSD

Center for Real-time Computing  


Module Description

The Mesh Compression (MC) module deforms the input tetrahedral mesh towards the boundaries of the input labeled image. Two point sets are extracted for the mesh deformation. The first (source point set) consists of the surface vertices in the input mesh. The second (target point set) consists of the surface edge points in the input labeled image. After the extraction of the two point sets, the input mesh is deformed by registering the source to the target point set using a Physics-Based Non-Rigid Registration method. The current version of the module supports a single-tissue labeled image and mesh.

Use Cases

Brain BCC mesh before MC
Brain BCC mesh after MC
Brain BCC mesh after MC (cross-section)
Nidus BCC mesh before MC
Nidus BCC mesh after MC
Nidus BCC mesh after MC (cross-section)
Ventricles BCC mesh before MC
Ventricles BCC mesh after MC
Ventricles BCC mesh after MC (cross-section)
How the non-connectivity parameter influences the number of the extracted target points


Tutorials

N/A

Panels and their use

  • Mesh Compression Parameters:
    • Flexibility: Controls the trade-off between the regularization energy defined by the stress energy of a linear bio-mechanical elastic model, and the similarity energy. Value should be between [0.1,1] (default: 1).
    • Number of Iterations: Controls the number of iterations for the compressor. The larger the value the closer the boundaries of the input mesh to the boundaries of the input image. A large number of iterations might cause distorted poor-quality elements. Value should be between [1,10] (default: 3).
    • Non Connectivity: Controls the density of the extracted target points via a prohibited connectivity between adjacent blocks of voxels. The larger the value the denser the target point set. 0 is vertex non-connectivity (26 neighbors), 1 is edge non-connectivity (18 neighbors), 2 is face non-connectivity (6 neighbors) and 3 is no non-connectivity. Value should be 0 or 1 or 2 or 3. (default: 0).
  • Input/Output:
    • Input Labeled Image: The input labeled image.
    • Input Mesh File: The input tetrahedral mesh in vtk file format.
    • Output Mesh File: The output deformed mesh in vtk file format (optional) (default: deformedMesh.vtk).
    • Output Source Points File: The extracted source points in vtk file format (optional). The source points are the surface vertices of the input mesh.
    • Output Target Points File: The extracted target points in vtk file format (optional). The target points are the surface edge points of the input labeled image.
    • Output Surface Triangles File: The extracted surface triangles of the input mesh in vtk file format (optional).
User Interface

Note: this module will only work if the input image has identity orientation!

Similar Modules


References

  • Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, "Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images", Engineering with Computers, Volume 28, pages 305-318, 2012.

Information for Developers

Work in progress
 Section under construction.


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