Difference between revisions of "Automatic SPHARM Shape Analysis in 3D Slicer"

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Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
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Image: http://www.na-mic.org/Wiki/index.php/File:UNCShape_OverviewAnalysis_MICCAI06.gif| Shape Analysis Overview.
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Image: UNCShape_OverviewAnalysis_MICCAI06.gif|[http://www.na-mic.org/Wiki/index.php/Algorithm:UNC:Shape_Analysis SPHARM-PDM  Overview]
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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:Slicer1.png|Quality Control within Slicer.
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Image:Spharm-correspondance.jpg‎|Quality Control visualization of the SPHARM correspondence using the color map Phi. Same color represent the same Φ parameter value of the spherical parameterization.
 
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==Instructions for Use of this Template==
 
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#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
 
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#Copy the entire text of this page into the page created above
 
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#Link the created page into the list of projects for the project event
 
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#Delete this section from the created page
 
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#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
==Key Investigators==
 
==Key Investigators==
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The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via  BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.
 
The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via  BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.
  
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Our plan for the project week is make this module as part of Slicer3 <bar>,...
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Our plan for the project week is to make ShapeAnalysisModule directly available as a 3D Slicer extension <bar>,...
  
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
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This week, I developed a quality control based on MRML scene for our statistic tool shapeAnalysisMANCOVA.
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Latest revision as of 13:49, 25 June 2010

Home < Automatic SPHARM Shape Analysis in 3D Slicer

  • Quality Control within Slicer.

  • Quality Control visualization of the SPHARM correspondence using the color map Phi. Same color represent the same Φ parameter value of the spherical parameterization.

Key Investigators

  • UNC: Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner

Objective

Statistical shape analysis is emerging as an important tool for understanding anatomical structures from medical images. The UNC shape analysis framework is an automatic approach employing sampled spherical harmonics (SPHARM-PDM). In order to facilitate shape analysis study using our framework, we developed a 3D Slicer module called ShapeAnalysisModule that, unlike current shape analysis frameworks, allows the user to perform shape analysis via straightforward and efficient user interface including intuitive quality control visualizations.


Approach, Plan

The developed ShapeAnalysisModule is a C++ program that can be run both as part of 3D Slicer as well as a command line tool. The tool computes the shape analysis via BatchMake (Kitware Inc) script that allows the use of a computational grid. The processing first fills interior holes, performs minimal smoothing operation and ensure spherical topology. The processed binary segmentations are converted to raw surface meshes, and a spherical parametrization is computed. The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Via icosahedron subdivision of the spherical parametrization, triangulated surfaces with correspondences are computed next (SPHARM-PDM). The SPHARM-PDM meshes are then ready for surface vertex-by-vertex analysis using the statistical analysis module ShapeAnalysisMANCOVA. For quality control, data scenes (MRML scene) are created and can be displayed within 3D Slicer. These scenes allow the user to visualize the surface reconstruction and established correspondence in an intuitive fashion.<foo>.

Our plan for the project week is to make ShapeAnalysisModule directly available as a 3D Slicer extension <bar>,...

Progress

This week, I developed a quality control based on MRML scene for our statistic tool shapeAnalysisMANCOVA.


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 (Please specify)


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