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[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
EM Segment Simple
{|
|[[Image:EMSegment-Simple.png|thumb|580px|EM Segment Simple module GUI and Result]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Sebastien Barre: Kitware, Inc.
* Brad Davis: Kitware, Inc.
* Polina Golland: MIT
* Kilian Pohl: IBM
* Yumin Yuan: Kitware, Inc.
* Contact: Kilian Pohl, pohl@csail.mit.edu

===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.

===Use Cases, Examples, 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.

[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]

===Quick Tour of Features and Use===

* '''Parameters panel:''' [[Image:EMSegment-Simple-Panel.png|300px|thumb|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.

===Notes from the Developer(s)===

===Dependencies===

Slicer3 base modules.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php 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 [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

[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]
*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]

== More Information ==

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

The old [[Modules:EM-Segmenter-Documentation:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.

There is also an old [http://www.na-mic.org/Wiki/index.php/EMSegmenter_Mini-Tutorials 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. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]

@@ Line 88: / Line 88: @@
 == 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 [[EMSegmenter-Overview| see the EMSegment Wiki page here]]
 The old [[Modules:EM-Segmenter-Documentation:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.
 ===Acknowledgment===

Modules:EMSegment-Simple3.6 - Revision history

Belhachemi: /* More Information */

Pohl: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== EM Segment Simple {| |[[Imag…'

Pohl: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features NOTOC ===Module Name=== EM Segment Simple {| |[[Imag…'