Difference between revisions of "Linear Mixed-effects shape model to explore Huntington's Disease Data"

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<gallery>
 
<gallery>
 
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:fixedEffects01.png|fixed-effects (slope) [blue denotes expansion, yellow denotes contraction]
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Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:fixedEffects02.png|fixed-effects (slope) [blue denotes expansion, yellow denotes contraction]
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Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
 
</gallery>
 
</gallery>
  
 
==Key Investigators==
 
==Key Investigators==
 
* UIowa: Hans Johnson, Dave Welch
 
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Ross Whitaker
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* Utah: Manasi Datar, Josh Cates, Ross Whitaker
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
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Meet with UIowa team to:
 
Meet with UIowa team to:
 
* give an overview of results from the linear mixed-effects shape model
 
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
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* explain the ShapeWorks command line tools to optimize and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team, to facilitate further exploration of the Huntington's disease Data
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* discuss next steps toward making these tools accessible to UIowa team
  
 
</div>
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
* preliminary results look promising
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preliminary results look promising
* ITKv4 module for mixed-effects model (Josh) available for Manasi to test
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* Once tested, this module can be used by UIowa team on a larger cohort of cases
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[https://github.com/joshcates/ITKParticleShapeModeling ITKv4] module for mixed-effects model available on GitHub
 +
* tested on Windows and Linux
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* application to run mixed-effects model on single component shapes (90%)
 +
 
 +
To Do
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* get working code for shape complexes (multiple structures per shape)
 +
* example parameter file for preprocessing shapes, initializing correspondences and applying mixed-effects model
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* extracting labels from input labelmap (various components in the shape) - clarify and possibly add a tool to the preprocessing stage
  
  

Latest revision as of 14:00, 21 June 2013

Home < Linear Mixed-effects shape model to explore Huntington's Disease Data

Key Investigators

  • UIowa: Hans Johnson, Dave Welch
  • Utah: Manasi Datar, Josh Cates, Ross Whitaker

Objective

Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

Approach, Plan

Meet with UIowa team to:

  • give an overview of results from the linear mixed-effects shape model
  • explain the ShapeWorks command line tools to optimize and analyze correspondences
  • discuss next steps toward making these tools accessible to UIowa team

Progress

preliminary results look promising

ITKv4 module for mixed-effects model available on GitHub

  • tested on Windows and Linux
  • application to run mixed-effects model on single component shapes (90%)

To Do

  • get working code for shape complexes (multiple structures per shape)
  • example parameter file for preprocessing shapes, initializing correspondences and applying mixed-effects model
  • extracting labels from input labelmap (various components in the shape) - clarify and possibly add a tool to the preprocessing stage


References

M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy, STIA 2012