2009 Winter Project Week UtahPlugins

Return to Project Week Main Page

Screen shot of the segmentation plugin.

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

Insert non-formatted text here

Key Investigators

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

Objective

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.

Progress

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.