Modules:EMSegmenter-3.6 - Revision history

Pohl: /* References */

2011-12-10T02:09:48Z

References

2011-11-23T19:16:32Z

Step 7: Specify Intensity Distribution

2011-08-03T19:46:35Z

2011-05-03T17:11:24Z

2011-04-26T22:09:21Z

2011-04-21T18:59:25Z

Step 2: Define Input Channels

2011-04-01T17:36:46Z

Usage

2011-04-01T17:29:10Z

2011-03-07T02:34:30Z

Use Cases, Examples & Tutorials

2011-02-17T03:53:31Z

Use Cases, Examples & Tutorials

← Older revision		Revision as of 02:09, 10 December 2011
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	===References===		===References===
−	* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.
−
−	* Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. [http://www.spl.harvard.edu/publications/item/view/58 A Bayesian model for joint segmentation and registration.] Neuroimage. 2006 May 15;31(1):228-39.
−
	*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]]		*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]]

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 ==== Step 7: Specify Intensity Distribution ====
-Refining the intensity distribution for each structure of interest is often a critical step in the parameterization of the segmentation algorithm. Slicer 3.6 includes an overview window that shows the distribution in a 1D and 2D graph (press "Plot Distributions" to view the graph). By placing the mouse cursor in the 2D viewers the corresponding intensity value is shown in the graph.
+Refining the intensity distribution for each structure of interest is often a critical step in the parameterization of the segmentation algorithm. The panel includes an overview window that shows the distribution in a 1D and 2D graph (press "Plot Distributions" to view the graph). By placing the mouse cursor in the 2D viewers the corresponding intensity value is shown in the graph.
 ==== Step 8: Edit Node-based Parameters ====

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 ===Authors, Collaborators & Contact===
 * Dominique Belhachemi, UPenn
 * Kilian Pohl: UPenn

← Older revision		Revision as of 17:11, 3 May 2011
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		+	[[EMSegmenter-Overview\|Return to EMSegmenter Overview Page]]
		+
	[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]		[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]
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−	~~[[EMSegmenter-Overview\|Return to EMSegmenter Overview Page]]~~

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

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 ===EMSegmenter===
 EMSegmenter
 == General Information ==
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 ===Module Description===
 This module is designed for users who perform atlas based medical image segmentation. The module can be operated in <B>two</B> modes: <br>
 An <B>advanced mode (Button: Adjust Parameters)</B> that allows users to parameterize the tool to specific segmentation tasks and a <B>simple mode (Button: Use Existing Setting)</B> which is designed for users who would like to apply the predefined parameterization to new data with a minimal amount of user interaction. One can also apply the parameterization to medical scans via the command-line executable <B>EMSegmentCommandLine</B>. The remainder of this sections describes the work flow of the two modes in further detail:

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 ==== Step 2: Define Input Channels  ====
 In this step the user specifies the scans to be segmented as well as the check list associated with the preprocessing.
 === Advanced Mode ===

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 re-run.
-One important aspect of the project is the workflow wizard.  This
+One important aspect of the project is the workflow wizard. This wizard simplifies the module by dividing the complicated template specification task into a number of smaller, intuitive steps. The wizard allows to [[EMSegmenter-CreateTask|create tasks]] and to use them to analyze data sets.
-The wizard allows to record tasks and to use them to [[EMSegmenter-Tasks|analyze data sets]]
+There are multiple [[EMSegmenter-Tasks|'''predefined tasks''']] which are ready to use.
 === Simple Mode ===

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 The wizard allows to record tasks and to use them to [[EMSegmenter-Tasks|analyze data sets]]
 === Advanced Mode ===
-The work flow is defined by nine steps which one can navigate via the "Back", "Next", or "Segment" button. The Segment button jumps right away to the last step of the work flow and segments the medical scans into the structures of interests.
+Unlike the Simple mode, the advanced mode is defined by nine steps which one can navigate via the "Back", "Next", or "Segment" button. The Segment button jumps right away to the last step of the work flow and segments the medical scans into the structures of interests.
 ==== Step 1: Define Task ====
 Select an already existing task or define a new one. Click on the button "Adjust Parameters" for the advanced mode in the pop up window. A MRML file defining parameters of the algorithm specific to the task as well atlas data are automatically downloaded for existing Tasks.
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 ==== Step 9: Define Miscellaneous Parameters ====
 This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.
 ===Use Cases, Examples & Tutorials ===

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 * EMSegmenter Tutorial for 3D Slicer 3.6.3
-in preparation - will be ready on Fri, Feb 18 2011
+** [[Media:EMSegmenterTutorialSimpleMode-Slicer-3.6.3-1.pdf | Simple Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]
-<br>
+** [[Media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf | Advanced Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]
 * A full Tutorial for all two EMSegment modules