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[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 
[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
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[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]
 
__NOTOC__
 
__NOTOC__
 
===Module Name===
 
===Module Name===
 
EM Segment Simple
 
EM Segment Simple
 
{|
 
{|
−
|[[Image:EMSegment-Workflow.png|thumb|580px|EM Segment Workflow]]
 
 
|[[Image:EMSegment-Simple.png|thumb|580px|EM Segment Simple module GUI and Result]]
 
|[[Image:EMSegment-Simple.png|thumb|580px|EM Segment Simple module GUI and Result]]
 
|}
 
|}
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===Authors, Collaborators & Contact===
 
===Authors, Collaborators & Contact===
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* Kilian Pohl: Harvard/BWH
 
 
* Brad Davis: Kitware, Inc.
 
* Brad Davis: Kitware, Inc.
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* Kilian Pohl: IBM
 
* Sebastien Barre: Kitware, Inc.
 
* Sebastien Barre: Kitware, Inc.
 
* Yumin Yuan: Kitware, Inc.
 
* Yumin Yuan: Kitware, Inc.
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===Examples, Use Cases & Tutorials===
 
===Examples, Use Cases & Tutorials===
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* A full Tutorial for all three EMSegment modules
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These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use.  A recent (later than 7Jan08) version of Slicer3 is required to run the test data.
  
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* Note use cases for which this module is especially appropriate, and/or link to examples.
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[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]
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* Link to examples of the module's use
 
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* Link to any existing tutorials
 
  
 
===Quick Tour of Features and Use===
 
===Quick Tour of Features and Use===
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List all the panels in your interface, their features, what they mean, and how to use them. For instance:
 
  
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* '''Input panel:'''
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* '''Parameters panel:''' [[Image:EMSegment-Simple-Panel.png|300px|thumb|EMSegment Simple Parameters Panel]]
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* '''Parameters panel:'''
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** MRML Scene: Select the mrml scene for the tutorial parameter set
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* '''Output panel:'''
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** Result Labelmap: Select a new image filename for output labelmap
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* '''Viewing panel:'''
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** Target Volumes: Select input target volumes (Note: target volume order is important)
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** Click `Apply’, wait (~30 minutes for full size images)
  
 
== Development ==
 
== Development ==
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The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]
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The module is implemented as a very simple programmatic Slicer3 module, whose purpose is to offer simple interface for segmenting new data
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with predefined parameter set. The module GUI interacts with the Logic classes, which are solely responsible for maintaining and accessing MRML nodes. The
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The module is implemented as a programmatic Slicer3 module because it
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Logic class provides APIs that the GUI code uses to access and modify data.  The Logic class also wraps the algorithm code itself.
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requires a large degree of interaction with the user, the data stored
 
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in the MRML tree, and the Slicer3 GUI itself.  Because the MRML node
 
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structure is rather complicated (for example the anatomical tissue
 
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hierarchy and a large number of interdependent nodes) the Logic class
 
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is solely responsible for maintaining and accessing these nodes. The
 
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Logic class provides an API that the GUI code uses to access and
 
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modify data.  The Logic class also wraps the algorithm code itself.
 
  
 
===Dependencies===
 
===Dependencies===
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Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.
 
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.
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*2008: Working on a single channel T1 version of the parameter set. See [[media:EM-T1.zip|'''here''']] for the Data and such (20meg).
 
  
 
===Source code & documentation===
 
===Source code & documentation===
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[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.
 
[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.
 
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
 
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
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*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]
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*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkEMSegmentGUI.html Module GUI]
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== More Information ==  
 
== More Information ==  
  
 
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]
 
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]
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The old [[Modules:EM-Segmenter-Documentation:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.
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There is also an old [http://www.na-mic.org/Wiki/index.php/EMSegmenter_Mini-Tutorials EMSegmenter Mini-Tutorials]
  
 
===Acknowledgment===
 
===Acknowledgment===

Latest revision as of 15:08, 19 August 2010

Home < Modules:EMSegment-Simple-3.4

Return to Slicer 3.4 Documentation

Gallery of New Features

Module Name

EM Segment Simple

EM Segment Simple module GUI and Result

General Information

Module Type & Category

Type: CLI

Category: Segmentation

Authors, Collaborators & Contact

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

Module Description

This module provide a simplified "one-click" GUI interface for the EMSegment Command-line Executable. The interface is simple because the number of required command-line parameters is minimized, and it is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.

Usage

Similar to the EMSegment Command-line Executable, once a set of parameters for segmentation algorithm is deemed satisfactory through the process of calibrating in the Template Builder module, the user will commonly want to bypass this detailed calibration process when segmenting new images. This module provides a simple interface to specify a small number of required command-line parameters --- a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image --- , and to allow any EM algorithm parameters to be modified, within the MRML scene, via the EMSegment GUI interface.

Examples, Use Cases & Tutorials

  • A full Tutorial for all three EMSegment modules

These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use. A recent (later than 7Jan08) version of Slicer3 is required to run the test data.

Slides - Data

Quick Tour of Features and Use

  • Parameters panel:
    EMSegment Simple Parameters Panel
    • MRML Scene: Select the mrml scene for the tutorial parameter set
    • Result Labelmap: Select a new image filename for output labelmap
    • Target Volumes: Select input target volumes (Note: target volume order is important)
    • Click `Apply’, wait (~30 minutes for full size images)

Development

The module is implemented as a very simple programmatic Slicer3 module, whose purpose is to offer simple interface for segmenting new data with predefined parameter set. The module GUI interacts with the Logic classes, which are solely responsible for maintaining and accessing MRML nodes. The Logic class provides APIs that the GUI code uses to access and modify data. The Logic class also wraps the algorithm code itself.

Dependencies

Slicer3 base modules.

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems.

  • Atlas-to-target registration and intensity normalization are very important; it will be most effective to apply these steps using algorithms that are customized to your data. Defaults are provided but they may perform poorly for your data---this will lead to poor segmentation results.

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

Source code & documentation

Links for the module.

More Information

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

The old EMSegmenter FAQ contains frequently asked questions about the EMSegment interfaces in Slicer3.

There is also an old EMSegmenter Mini-Tutorials

Acknowledgment

Funding for the EMSegmenter module was provided by NAMIC.

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. [bib]

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