2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

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  Projects List

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.

Standalone 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

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.

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.

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).