Difference between revisions of "2011 Summer Project Week Shape Analysis UNC"

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<gallery>
 
<gallery>
 
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:SPHARMPDM_Logo.gif|SOME OUTPUTS: Triangular mesh representation of the input segmentation - The first triangular mesh,mapped in the sphere - Spherical representation of the harmonic representation of the input parameterization - DistanceMap colorMap(after MANCOVA) and Particle
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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Image:MANCOVA.jpg|shapeAnalysisMANCOVA -- Pvalues
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Image:shapeAnalysisMANCOVA_Wizard-screenshot.png | shapeAnalysisMANCOVA_Wizard-screenshot
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</gallery>
 
</gallery>
  
 
==Key Investigators==
 
==Key Investigators==
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* UNC: Lucile Bompard, Clement Vachet,Beatriz Paniagua,Martin Styner  
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* UNC: Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner  
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* ......
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* Utah: Josh Cates, Manasi Datar, Ross Whitaker
 +
 
 +
 
 +
The UNC shape analysis framework is an automatic shape correspondence methodology that uses spherical harmonics for sampling (SPHARM-PDM). ShapeAnalysisModule computes point-based models using a parametric boundary description. The point-based models computed with this tool are used to perform statistical studies (within shapeAnalysisMANCOVA) or to get correspondence point Models(within ParticleModule). The ParticleModule is already part of the ShapeAnalysisModule. You can choose to run it or not. Nevertheless, some triangulation of spherical harmonics are not preserved, not surprisingly.  
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
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The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). ShapeAnalysisModule computes point-based models using a parametric boundary description. The goal is to be able to use the point-based models computed with this tool to perform statistical studies (within shapeAnalysisMANCOVA) or to get correspondence point Models(within ParticleModule).  
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The goal is to improve the Particle Module. We need to set template population that not change their correspondence. That is to say, we have to know how to fix a template for the Particle study.
  
  
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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The developed shapeAnalysisMANCOVA is a C++ program that can be run both with shapeAnalysisMANCOVA_Wizard as well as a command line tool. In order to compile shapeAnalysisMANCOVA, ITK, VTK, GenerateCLP and Boost Libraries for C (v 0.39.1) must already be installed.
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Our plan for the project week is to:
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The point-based models will be analyzed with methods using multivariate analysis of covariance (MANCOVA).
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* Meet with all interested parties
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The steps performed in order to obtain the statistical analysis are the following, for each iteration:
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* Decided how we are going to fix the template 
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computing a General Linear Model (GLM) to test group differences at every surface location,
 
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doing the Metric computation thanks to the Multivariate analysis of covariance (MANCOVA),
 
  
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computing the P-values and controlling for the mutliple testing problem,
 
  
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doing the permutations tests (considering the linear varibles).
 
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The data scenes (MRML scene) are created and can be displayed within 3D Slicer.
 
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Our plan for the project week is to:
 
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* try to get rid of boost library - find similar method in Slicer libraries if possible
 
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* use GenerateCLP to integrate shapeAnalysisMANCOVA_Wizard directly within Slicer3
 
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* Load MRML scenes created for quality control directly within Slicer
 
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* improve the shapeAnalysisMANCOVA_Wizard
 
  
 
</div>
 
</div>
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<h3>Progress</h3>
 
<h3>Progress</h3>
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shapeAnalysisMANCOVA_Wizard can be use either though command line or within Slicer and whatever the choise, the mrml scene will be displayed in Slicer3 at the end.  
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The shapeAnalysisMANCOVA_Wizard's window is now resizable.
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A template has been set.  
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We are still testing the improvement of this add on our results.
  
  
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==Delivery Mechanism==
 
==Delivery Mechanism==
  
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This work will be delivered to the NA-MIC Kit as a  
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This work will be delivered to the NAMIC Kit as a  
  
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#ITK Module
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#NITRIC distribution
 
#Slicer Module
 
#Slicer Module
 
##Built-in
 
##Built-in
 
##Extension -- commandline  YES
 
##Extension -- commandline  YES
 
##Extension -- loadable  YES
 
##Extension -- loadable  YES
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#Other shapeAnalysisMANCOVA_Wizard
 

Latest revision as of 21:07, 23 June 2011

Home < 2011 Summer Project Week Shape Analysis UNC

  • SOME OUTPUTS: Triangular mesh representation of the input segmentation - The first triangular mesh,mapped in the sphere - Spherical representation of the harmonic representation of the input parameterization - DistanceMap colorMap(after MANCOVA) and Particle

  • shapeAnalysisMANCOVA -- Pvalues

  • shapeAnalysisMANCOVA_Wizard-screenshot

Key Investigators

  • UNC: Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
  • Utah: Josh Cates, Manasi Datar, Ross Whitaker


The UNC shape analysis framework is an automatic shape correspondence methodology that uses spherical harmonics for sampling (SPHARM-PDM). ShapeAnalysisModule computes point-based models using a parametric boundary description. The point-based models computed with this tool are used to perform statistical studies (within shapeAnalysisMANCOVA) or to get correspondence point Models(within ParticleModule). The ParticleModule is already part of the ShapeAnalysisModule. You can choose to run it or not. Nevertheless, some triangulation of spherical harmonics are not preserved, not surprisingly.

Objective

The goal is to improve the Particle Module. We need to set template population that not change their correspondence. That is to say, we have to know how to fix a template for the Particle study.


Approach, Plan

Our plan for the project week is to:

  • Meet with all interested parties
  • Decided how we are going to fix the template


Progress

A template has been set. We are still testing the improvement of this add on our results.


Delivery Mechanism

This work will be delivered to the NAMIC Kit as a

  1. NITRIC distribution
  2. Slicer Module
    1. Built-in
    2. Extension -- commandline YES
    3. Extension -- loadable YES
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