2009 Winter Project Week UtahPlugins

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Screen shot of the segmentation plugin.
Output of the segmentation plugin, showing the bias corrected image and the probabilities for white and gray matter.

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Key Investigators

  • Marcel Prastawa, Utah 2
  • Steve Pieper, Isomics, Inc.


itkEMS is a brain MRI segmentation software that combines registration and bias correction. It is currently in use at UNC-CH and Utah as a general purpose segmentation tool, and has also been applied as a method for skull stripping structural and DT MRI. It is currently available as a stand-alone software that uses ITK and FLTK.

The goal of this project is to develop Slicer plugins that incorporate different components of the segmentation software to provide the NA-MIC community with the capability of developing their own custom segmentation pipelines.

Approach, Plan

We plan to develop different plugins using CLP that can be combined together to form a segmentation pipeline. We will explore the use of the module chaining mechanism developed by Marco.


We have implemented and tested a preliminary version of a registration and segmentation plugins using CLP.

The multi-channel MRI bias correction scheme with spatial probabilistic constraints have been implemented as a separate Slicer plugin and is available through NITRC

Remaining task: Better integration with Slicer by having MRML outputs that can be used for subsequent processing within Slicer.