Modules:EM-Segmenter-Documentation

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Module Name

MyModule

EMSegmenter Applied to MR T1 & T2 tutorial data

Segmentation of brain structures using EMSegmenter

Caption 3

General Information

Module Type & Category

Type: Interactive (Template Builder) and CLI (EMSegment Simple)

Category: Segmentation

Authors, Collaborators & Contact

• Kilian Pohl: Harvard
• Brad Davis: Kitware, Inc.
• Sebastien Barre: Kitware, Inc.
• Yumin Yuan: Kitware, Inc.
• Polina Golland: MIT
• Contact: Brad Davis, brad.davis@kitware.com

Module Description

The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.

As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.

Usage

Examples, Use Cases & Tutorials

• Note use cases for which this module is especially appropriate, and/or link to examples.
• Link to examples of the module's use
• Link to any existing tutorials

Quick Tour of Features and Use

List all the panels in your interface, their features, what they mean, and how to use them. For instance:

• Input panel:
• Parameters panel:
• Output panel:
• Viewing panel:

Development

Dependencies

Slicer base modules.

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Customize following links for your module.

Links to documentation generated by doxygen.

More Information

For more information about the EM Segmenter project in Slicer3 see the old EMSegment Wiki page here

Acknowledgment

Funding for the EMSegmenter module was provided by NAMIC.

References

Kilian TMI Paper