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…')
 
 
(17 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
<gallery>
 
<gallery>
−
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
+
Image:Slide1.png
 +
Image:snapshot0001.png
 
</gallery>
 
</gallery>
  
  
 
==Key Investigators==
 
==Key Investigators==
−
* University of Iowa: Nicole Grosland, Vince Magnotta, Kiran Shivanna
+
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
−
* Isomics: Steve Pieper, Curtis Lisle
+
* Emory: Mar Sanchez
 +
* BWH: Andriy Fedorov
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
Line 13: Line 15:
  
 
<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 26:
 
<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
 +
 
 +
* Cortical thickness analysis
 +
Will work with Clement Vachet and adapt the tools for human data to primate data
 +
 
 +
* Affine alignment
 +
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them.  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 45:
  
 
<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.  
+
* Attended the DTI breakout session, and identified the problem/challenge of the commonly used tools in the pipeline used by people in the community and the tools we usually use (DicomtoNrrdConvert...)
 +
 
 +
* Work with Hans, and tested BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template using affine registration. Parameters were selected for monkey data with good results.
  
−
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.  
+
* Testing Demons for warping the subjects to atlas, instead of fWarp.   
 +
 
 +
* Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.
  
 
</div>
 
</div>
Line 47: Line 60:
 
==Delivery Mechanism==
 
==Delivery Mechanism==
  
−
This work will be delivered to the NA-MIC Kit as a
+
This work will be delivered as open-source software and open dataset
−
 
 
−
#ITK Module
 
−
#Slicer Module 
 
−
##Built-in
 
−
##Extension -- commandline
 
−
##Extension -- loadable  '''YES'''
 
−
#Other (Please specify)
 
  
 
==References==
 
==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.
+
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.
−
*Shivanna KH, Grosland NM, Russell ME, Pedersen DR, Diarthrodial  Joint Contact Models:  A finite element analysis of the human hip, Engineering with Computers (accepted).
 
  
  
 
</div>
 
</div>

Latest revision as of 14:32, 25 June 2010

Home < 2010 Summer Project Week Primate image analysis using the standard Slicer pipeline
  • Slide1.png
  • Snapshot0001.png


Key Investigators

  • UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
  • Emory: Mar Sanchez
  • BWH: Andriy Fedorov

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

  • Cortical thickness analysis

Will work with Clement Vachet and adapt the tools for human data to primate data

  • Affine alignment

RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. 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

  • Attended the DTI breakout session, and identified the problem/challenge of the commonly used tools in the pipeline used by people in the community and the tools we usually use (DicomtoNrrdConvert...)
  • Work with Hans, and tested BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template using affine registration. Parameters were selected for monkey data with good results.
  • Testing Demons for warping the subjects to atlas, instead of fWarp.
  • Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.

Delivery Mechanism

This work will be delivered as open-source software and open dataset

References

  • M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.


Retrieved from "https://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Primate_image_analysis_using_the_standard_Slicer_pipeline&oldid=55415"