Difference between revisions of "2010 NAMIC Project week:IA-FEMesh"

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(final progress update for Summer project week 2010)
 
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Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
 
Image:Femesh-in-trunk-120808.png|First Release of IA-FEMesh module
 
Image:Femesh-in-trunk-120808.png|First Release of IA-FEMesh module
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Image:IA-FEMesh-image-material-properties.png|Assigning materials from an image
 
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* University of Iowa: Nicole Grosland, Vince Magnotta, Kiran Shivanna
 
* University of Iowa: Nicole Grosland, Vince Magnotta, Kiran Shivanna
 
* Isomics: Steve Pieper, Curtis Lisle
 
* Isomics: Steve Pieper, Curtis Lisle
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<h3>Objective</h3>
 
<h3>Objective</h3>
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We are integrating finite element mesh creation tools developed at the University of Iowa into 3D Slicer.  The result will be that 3D Slicer models can be further processed into meshes for analysis using external finite element programs, such as ABAQUS.  
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We have integrated finite element mesh creation tools developed at the University of Iowa into 3D Slicer.  The result is that 3D Slicer models can now be further processed into meshes for analysis using external finite element programs, such as ABAQUS.  
  
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Standalone mesh creation tools exist in the standalone application IA-FEMesh found  [http://www.ccad.uiowa.edu/mimx/IA-FEMesh  by clicking here.]
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The original mesh creation tools exist in the standalone application IA-FEMesh found  [http://www.ccad.uiowa.edu/mimx/IA-FEMesh  by clicking here.]
  
  
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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The first integration of the IA-FEMesh module was released at the NA-MIC All Hands Meeting in January 2009. The module's first release functions in 3D Slicer for creating meshes interactively, but didn't support import or save with MRML scenes.    Since this time, we have developed a direct import of MRML Models and Volumes into the IA-FEMesh workflow and improved integration with Slicer internals.  
 
The first integration of the IA-FEMesh module was released at the NA-MIC All Hands Meeting in January 2009. The module's first release functions in 3D Slicer for creating meshes interactively, but didn't support import or save with MRML scenes.    Since this time, we have developed a direct import of MRML Models and Volumes into the IA-FEMesh workflow and improved integration with Slicer internals.  
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<h3>Progress</h3>
 
<h3>Progress</h3>
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IA-FEMesh now creates and registers four specialized MRML node classes. We completed MRML volume import to IA-FEMesh and are storing the IJ2RAS matrix. We are ready to adapt the material properties algorithm to work with the imported Slicer3 volume.  
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Image-based material properties for mesh elements can be assigned from volumes in the MRML scene. This was implemented during the Project Week!
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IA-FEMesh creates and registers four specialized MRML node classes. We completed MRML volume import to IA-FEMesh and are storing the IJ2RAS matrix. We adapted the material properties algorithm to extract image properties from the imported Slicer MRML volume.
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An updated [http://wiki.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010 tutorial for the module] including screencasts of module operations was recently completed.  The tutorial complements the existing module [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]  to provide multiple documentation methods for using IA-FEMesh to new problems in finite element mesh development.  
 +
 
  
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An updated tutorial for the module including screencasts of module operations was recently comopleted. The tutorial complements the existing module Users Guide to provide multiple documentation methods for using IA-FEMesh to new problems in finite element mesh development.
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[[Media:Meshing-image-materials-best.mov|SCREENCAST: Assigning mesh material categories from a MRML volume]]
  
 
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==Delivery Mechanism==
 
==Delivery Mechanism==
  
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This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
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This work will be delivered to the NA-MIC Kit as a  
  
 
#ITK Module
 
#ITK Module
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##Built-in
 
##Built-in
 
##Extension -- commandline
 
##Extension -- commandline
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##Extension -- loadable  YES
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##Extension -- loadable  '''YES'''
 
#Other (Please specify)
 
#Other (Please specify)
  

Latest revision as of 11:12, 25 June 2010

Home < 2010 NAMIC Project week:IA-FEMesh

  • First Release of IA-FEMesh module

  • Assigning materials from an image


Key Investigators

  • University of Iowa: Nicole Grosland, Vince Magnotta, Kiran Shivanna
  • Isomics: Steve Pieper, Curtis Lisle


Objective

We have integrated finite element mesh creation tools developed at the University of Iowa into 3D Slicer. The result is that 3D Slicer models can now be further processed into meshes for analysis using external finite element programs, such as ABAQUS.

The original mesh creation tools exist in the standalone application IA-FEMesh found by clicking here.



Approach, Plan

The first integration of the IA-FEMesh module was released at the NA-MIC All Hands Meeting in January 2009. The module's first release functions in 3D Slicer for creating meshes interactively, but didn't support import or save with MRML scenes. Since this time, we have developed a direct import of MRML Models and Volumes into the IA-FEMesh workflow and improved integration with Slicer internals.

During the project week, we plan to resolve image orientation issues in the algorithm which extracts mesh material properties automatically from the source volume. The volume IJK2RAS matrix will be used to orient the image in the material properties algorithm. We also expect to improve MRML integration and code cleanliness during the week.


Progress

Image-based material properties for mesh elements can be assigned from volumes in the MRML scene. This was implemented during the Project Week!

IA-FEMesh creates and registers four specialized MRML node classes. We completed MRML volume import to IA-FEMesh and are storing the IJ2RAS matrix. We adapted the material properties algorithm to extract image properties from the imported Slicer MRML volume.

An updated tutorial for the module including screencasts of module operations was recently completed. The tutorial complements the existing module Users Guide to provide multiple documentation methods for using IA-FEMesh to new problems in finite element mesh development.


SCREENCAST: Assigning mesh material categories from a MRML volume

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a

  1. ITK Module
  2. Slicer Module
    1. Built-in
    2. Extension -- commandline
    3. Extension -- loadable YES
  3. Other (Please specify)

References

  • Grosland Nicole M; Shivanna Kiran H; Magnotta Vincent A; Kallemeyn Nicole A; DeVries Nicole A; Tadepalli Srinivas C; Lisle Curtis R; IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development. Computer methods and programs in biomedicine 2009;94(1):96-107.
  • Shivanna KH, Grosland NM, Russell ME, Pedersen DR, Diarthrodial Joint Contact Models: A finite element analysis of the human hip, Engineering with Computers (accepted).


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