Automatic SPHARM Shape Analysis in 3D Slicer

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Key Investigators

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


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>,...


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)