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

From NAMIC Wiki
Jump to: navigation, search
 
(3 intermediate revisions by the same user not shown)
Line 23: Line 23:
 
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
+
* explain the ShapeWorks command line tools to optimize and analyze correspondences
 
* discuss next steps toward making these tools accessible to UIowa team
 
* discuss next steps toward making these tools accessible to UIowa team
  
Line 31: Line 31:
  
 
<h3>Progress</h3>
 
<h3>Progress</h3>
* preliminary results look promising
+
preliminary results look promising
* ITKv4 module for mixed-effects model available
+
 
** ITKv4 module tested on Linux system
+
[https://github.com/joshcates/ITKParticleShapeModeling ITKv4] module for mixed-effects model available on GitHub
** Mixed-effects model for shapes from a single structure from the HD data (in progress). This should result in:
+
* tested on Windows and Linux
*** application (source code) to run mixed-effects shape model for HD data
+
* application to run mixed-effects model on single component shapes (90%)
*** an example parameter file
+
 
* To Do
+
To Do
** get working code for shape complexes (multiple structures per shape)
+
* get working code for shape complexes (multiple structures per shape)
** work on extracting labels from input labelmap (various components in the shape) - possibly add a tool to the preprocessing stage ?
+
* 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
  
  

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