2008 Winter Project Week:Geodesic Tractography Segmentation

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Home < 2008 Winter Project Week:Geodesic Tractography Segmentation
The Cingulum Bundle Anchor Tract
Many Fiber Bundles

Key Investigators

  • Georgia Tech: John Melonakos, Vandana Mohan
  • Kitware: Luis Ibanez
  • BWH: Marc Niethammer, Marek Kubicki


We have developed techniques for finding the optimal geodesic path (or anchor tract) between two regions of interest in DWMRI data.

The objectives of this project is to enable the command-line execution of a Matlab executable.

See our Project Page for more details.

Approach, Plan

Our approach is described by the references below. Our challenge is to link the Matlab executable with the Slicer3 command line module.


Jan 2008 Project Week

We have been exploring two options of creating plugins from MATLAB code: 1. Create intermediate C code using MATLAB compiler, and modifying this code with the GenerateCLP procedure to generate the plugin. 2. Create an executable directly from MATLAB and then invoke it within a C wrapper function which we then convert to the pluginfor slicer.

Progress this week: 1. Learned how to create plugins for slicer from C code and the mapping from slicer params to variables for C code... Tried a few examples with this. 2. Explored the MATLAB compiler generated C code towards modifying it with GenerateCLP.

June 2007 Project Week

During this Project Week, we did a lot of algorithmic design work, focusing on leveraging optimal or geodesic path information to provide for volumetric segmentations of fiber bundles. Working with Marek Kubicki and the Harvard DBP, we were able to begin the process of applying our algorithm to the full cingulum bundle with new labelmaps and to a new fiber bundle - Arcuate. We have recently achieved significant results in volumetric segmentations using a locally-constrained region-based technique (see the images above).

Jan 2007 Project Half Week

We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.


NA-MIC Publications Database