Difference between revisions of "2010 Summer Project Week Primate image analysis using the standard Slicer pipeline"

From NAMIC Wiki
Jump to: navigation, search
(Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List </gallery> ==Key Investigators== * University of Iowa: Nicole Grosland, Vince Magno…')
 
Line 6: Line 6:
  
 
==Key Investigators==
 
==Key Investigators==
−
* University of Iowa: Nicole Grosland, Vince Magnotta, Kiran Shivanna
+
* UNC: Yundi Shi, Martin Styner
−
* Isomics: Steve Pieper, Curtis Lisle
+
* Emory: Mar Sanchez
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
Line 13: Line 13:
  
 
<h3>Objective</h3>
 
<h3>Objective</h3>
−
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.
+
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis.  This is part of a longitudinal study of rhesus macaque monkeys
−
 
 
−
Standalone mesh creation tools exist in the standalone application IA-FEMesh found  [http://www.ccad.uiowa.edu/mimx/IA-FEMesh by clicking here.]
 
  
  
Line 26: Line 24:
 
<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
−
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.  
+
* Skull stripping and Tissue segmentation
 +
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
 +
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys
 +
 
 +
* Affine alignment
 +
RVIEW is currently used for affine alignment of the monkey images. Affine registration in Slicer was tested but not producing very satisfying results.  We need to work with ?? for the special challenge in registration of the monkey brains.
  
−
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.  
+
* Atlas building
 +
Atlaswerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH).  We would like to start using open source tools like the deamons registration in Slicer for the same task.
  
  
Line 36: Line 40:
  
 
<h3>Progress</h3>
 
<h3>Progress</h3>
−
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 [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.
 
  
 
</div>
 
</div>

Revision as of 20:56, 16 June 2010

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


Key Investigators

  • UNC: Yundi Shi, Martin Styner
  • Emory: Mar Sanchez

Objective

To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys



Approach, Plan

  • Skull stripping and Tissue segmentation

ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images. Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

  • Affine alignment

RVIEW is currently used for affine alignment of the monkey images. Affine registration in Slicer was tested but not producing very satisfying results. We need to work with ?? for the special challenge in registration of the monkey brains.

  • Atlas building

Atlaswerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.


Progress


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).


Retrieved from "https://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Primate_image_analysis_using_the_standard_Slicer_pipeline&oldid=54269"