2010 Summer Project Week Mouse Brain Cortical Thickness Analysis

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Home < 2010 Summer Project Week Mouse Brain Cortical Thickness Analysis

Key Investigators

  • UNC: Ipek Oguz, Martin Styner


Cortical thickness measurement is an important tool in investigating animal models of neurodegenarative diseases. However, the difference between human and rodent models necessitates adaptation of automated image analysis tools to the rodent scale. This project aims to provide tools for mouse and rat brains equivalent to state-of-the-art human brain analysis software.

Approach, Plan

  • Segmentation
    • Provides the neo-cortex separation from other brain structures
    • Uses atlas-based segmentation, such that the structural segmentation
    • Source and destination boundaries are manually defined over the atlas by our expert.
  • The thickness measurement step:
    • Computes a Laplacian field from the source boundary toward the destination boundary.
    • Using measureThicknessFilter by Marc Niethammer
  • Statistical Analysis
    • Use particle correspondence algorithm minimizing entropy between dynamically moving sample points
    • ShapeAnalysis tools by Beatriz Paniagua


  • My goal for this project was to convert the pipeline into Slicer3 wizard module
  • It was done with need of more improvements (with help of Clement):
    • Text editor or CSV editor to process streams of line data
    • Result visualization
  • I learned here:
    • Slicer/QT superbuild: a great playground for better module creation
    • CTest: the most impressive one to build robust tools
    • GIT: helpful for collaboration and maintenance

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)

  1. ITK Module
  2. Slicer Module: Thickness measurement filter developed by Marc Niethammer
    1. Built-in
    2. Extension -- python module for whole analysis pipeline
    3. Extension -- loadable
  3. Other (Please specify)