Documentation/Nightly/Modules/EMSegment Command-line

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Introduction and Acknowledgements

This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the NAC website. Author: Kilian Pohl, UPenn Contributor1: Daniel Haehn, UPENN Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email>

University of Pennsylvania   Surgical Planning Laboratory

Use Cases

The primary function of the EMSegmenter module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images by using those parameters collected from the calibration process in EMSegmenter module. The EMSegment Command-line module which wraps the EMSegmentCommandLine executable provides this batch processing capability. The EMSegment Command-line module is automatic generated from the EMSegmentCommandLine executable using the --xml option.

This module is especially appropriate for segmenting large quantity of data by scripted/batch processing. It requires predefined parameter set, and new target/atlas images can be specified on command line. A list of predefined task is given here.

Tutorials

These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use.

Slides - Data

Panels and their use

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

Parameters:

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     * ': 
     
       ** ': 
       
        *** ': 
       
     
   
 

List of parameters generated transforming [ this XML file] using this XSL file. To update the URL of the XML file, edit this page.

References

Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. A Hierarchical Algorithm for MR Brain Image Parcellation. IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.