Difference between revisions of "2011 Winter Project Week:NAMICShapeAnalysis"

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(Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…')
 
 
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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]]
−
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
+
Image:mrml_group.png| Mrml scene for a group test.
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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:mrml_interaction.png|Mrml scene for an interaction test.
 +
Image:shapeAnalysisMANCOVA_Wizard-screenshot.png | shapeAnalysisMANCOVA_Wizard-screenshot
 
</gallery>
 
</gallery>
  
 
==Key Investigators==
 
==Key Investigators==
−
* UNC: Lucile Bompard, Martin Styner  
+
* UNC: Lucile Bompard, Clement Vachet, Martin Styner  
 
* Utah: Chris Gloschat
 
* Utah: Chris Gloschat
  
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<h3>Objective</h3>
 
<h3>Objective</h3>
−
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
+
Statistical shape analysis methods have emerged within the last decade to allow for a localized analysis of shape.The UNC shapeAnalysisMANCOVA pipeline is a unified method for local shape analysis that can accommodate different number of variates and contrasts. Unlike current shape analysis frameworks,it also allows to include any number of associated variables in the statistical analysis of the data.
 +
This tool has been designed to interact seamlessly with the existing UNC SPHARM-PDM based shape analysis toolbox. Indeed, the point-based models computed with the SPHARM-PDM tool can be used in combination with this pipeline to perform quantitative morphological assessment of structural changes at specific locations.
 +
The aim is to  improve this UNC pipeline by integrating the Particle-based Shape Correspondence, and using SPHARM as an initialization.
  
  
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
 +
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.
 +
The point-based models will be analyzed with methods using multivariate analysis of covariance (MANCOVA).
 +
The steps performed in order to obtain the statistical analysis are the following, for each iteration:
  
−
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
+
computing a General Linear Model (GLM) to test group differences at every surface location,
  
−
Our plan for the project week is to first try out <bar>,...
+
doing the Metric computation thanks to the Multivariate analysis of covariance (MANCOVA),
 +
 
 +
computing the P-values and controlling for the mutliple testing problem,
 +
 
 +
doing the permutations tests (considering the linear varibles).
 +
 
 +
The data scenes (MRML scene) are created and can be displayed within 3D Slicer.
 +
 
 +
Our plan for the project week is to:
 +
* try to get rid of boost library - find similar method in Slicer libraries if possible
 +
* use GenerateCLP to integrate shapeAnalysisMANCOVA_Wizard directly within Slicer3
 +
* Load MRML scenes created for quality control directly within Slicer
 +
* improve the shapeAnalysisMANCOVA_Wizard
  
 
</div>
 
</div>
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<h3>Progress</h3>
 
<h3>Progress</h3>
−
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
+
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.  
 +
The shapeAnalysisMANCOVA_Wizard's window is now resizable.
  
  
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==Delivery Mechanism==
 
==Delivery Mechanism==
  
−
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
+
This work will be delivered to the NA-MIC Kit as a  
  
 
#ITK Module
 
#ITK Module
 
#Slicer Module
 
#Slicer Module
 
##Built-in
 
##Built-in
−
##Extension -- commandline
+
##Extension -- commandline YES
−
##Extension -- loadable
+
##Extension -- loadable YES
−
#Other (Please specify)
+
#Other shapeAnalysisMANCOVA_Wizard
−
 
 
−
==References==
 
−
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
 
−
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
 
−
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
 
−
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
 
−
 
 
−
</div>
 

Latest revision as of 15:16, 14 January 2011

Home < 2011 Winter Project Week:NAMICShapeAnalysis

  • Mrml scene for a group test.

  • Mrml scene for an interaction test.

  • shapeAnalysisMANCOVA_Wizard-screenshot

Key Investigators

  • UNC: Lucile Bompard, Clement Vachet, Martin Styner
  • Utah: Chris Gloschat

Objective

Statistical shape analysis methods have emerged within the last decade to allow for a localized analysis of shape.The UNC shapeAnalysisMANCOVA pipeline is a unified method for local shape analysis that can accommodate different number of variates and contrasts. Unlike current shape analysis frameworks,it also allows to include any number of associated variables in the statistical analysis of the data. This tool has been designed to interact seamlessly with the existing UNC SPHARM-PDM based shape analysis toolbox. Indeed, the point-based models computed with the SPHARM-PDM tool can be used in combination with this pipeline to perform quantitative morphological assessment of structural changes at specific locations. The aim is to improve this UNC pipeline by integrating the Particle-based Shape Correspondence, and using SPHARM as an initialization.




Approach, Plan

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. The point-based models will be analyzed with methods using multivariate analysis of covariance (MANCOVA). The steps performed in order to obtain the statistical analysis are the following, for each iteration:

computing a General Linear Model (GLM) to test group differences at every surface location,

doing the Metric computation thanks to the Multivariate analysis of covariance (MANCOVA),

computing the P-values and controlling for the mutliple testing problem,

doing the permutations tests (considering the linear varibles).

The data scenes (MRML scene) are created and can be displayed within 3D Slicer.

Our plan for the project week is to:

  • try to get rid of boost library - find similar method in Slicer libraries if possible
  • use GenerateCLP to integrate shapeAnalysisMANCOVA_Wizard directly within Slicer3
  • Load MRML scenes created for quality control directly within Slicer
  • improve the shapeAnalysisMANCOVA_Wizard

Progress

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. The shapeAnalysisMANCOVA_Wizard's window is now resizable.


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 YES
    3. Extension -- loadable YES
  3. Other shapeAnalysisMANCOVA_Wizard
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