Difference between revisions of "MeshingSummer2009"

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__NOTOC__
 
__NOTOC__
 
<gallery>
 
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
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Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:Femesh-in-trunk-120808.png|First Release of IA-FEMesh module
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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Image:MeshingSummerProjectWeek2009.png| IA-FEMesh release 2 alpha with MRML transform
 
</gallery>
 
</gallery>
  
==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 Project/<Project Name>
 
#Copy the entire text of this page into the page created above
 
#Link the created page into the list of projects for the project event
 
#Delete this section from the created page
 
#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
==Key Investigators==
 
==Key Investigators==
* UIowa: Nicole Grosland, Vince Magnotta, Kiran Shivanna
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* 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>
We are integrating finite element mesh creation tools developed at the University of Iowa into Slicer.  The result will be that Slicer models can be further processed into meshes for analysis using external finite element programs, such as ABAQUS.  
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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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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
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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Standalone mesh creation tools exist in the standalone application IA-FEMesh found  [http://www.ccad.uiowa.edu/mimx/IA-FEMesh by clicking here.]
  
Our plan for the project week is to first try out <bar>,...
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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 doesn't allow MRML saves & restores.   The second implementation will use MRML display nodes to display the meshes and will support interactive exploration and editing using VTK 3D widgets.  
  
 
</div>
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
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The rendering and data storage methods have been modified to conform to Slicer's MRML architecture for separate model and display nodes. The three major classes of objects managed by IA-FEMesh (surfaces, building blocks, and meshes) are currently rendering in slicer using custom MRMLDisplayNode subclasses.  
  
 +
We have some minor remaining rendering issues, but Meshing module objects are now stored in MRML successfully.  Over the next few months, we will complete the integration and testing of this approach and  propagate changes back to the standalone code version of IA-FEMesh so future development of the standalone and integrated versions can continue from a single code base.
 +
 +
This recent work will remain in the Slicer Meshing-V-2-1 branch for now.  The IA_FEMesh module  V1, which matches the tutorial, is currently in the Slicer trunk and Slicer V3.4.
  
 
</div>
 
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==References==
 
==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
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*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.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
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*Shivanna KH, Grosland NM, Russell ME, Pedersen DR, Diarthrodial  Joint Contact Models: A finite element analysis of the human hip, Engineering with Computers (accepted).
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
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* Goodlett C, Corouge I, Jomier M, Gerig G, 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 .
 
  
 
</div>
 
</div>

Latest revision as of 14:35, 26 June 2009

Home < MeshingSummer2009


Key Investigators

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

Objective

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.




Approach, Plan

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

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 doesn't allow MRML saves & restores. The second implementation will use MRML display nodes to display the meshes and will support interactive exploration and editing using VTK 3D widgets.

Progress

The rendering and data storage methods have been modified to conform to Slicer's MRML architecture for separate model and display nodes. The three major classes of objects managed by IA-FEMesh (surfaces, building blocks, and meshes) are currently rendering in slicer using custom MRMLDisplayNode subclasses.

We have some minor remaining rendering issues, but Meshing module objects are now stored in MRML successfully. Over the next few months, we will complete the integration and testing of this approach and propagate changes back to the standalone code version of IA-FEMesh so future development of the standalone and integrated versions can continue from a single code base.

This recent work will remain in the Slicer Meshing-V-2-1 branch for now. The IA_FEMesh module V1, which matches the tutorial, is currently in the Slicer trunk and Slicer V3.4.

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).