Modules:EMSegmentBatch-Documentation-3.6 - Revision history

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2010-04-02T20:38:30Z

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2010-04-02T20:35:06Z

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2010-04-02T20:07:58Z

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

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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 BatchMake
{|
|[[Image:EMSegmentBatchMakeModule.png|thumb|580px|EM Segment BatchMake module GUI ]]
|}

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

Type: CLI

Category: Batch Processing

===Authors, Collaborators & Contact===
* Authors: Stephen Aylward, Julien Finet, Julien Jomier
* Contact: stephen.aylward at kitware.com

===Module Description===
This module is the BatchMake version of [http://wiki.slicer.org/slicerWiki/index.php/Modules:EMSegment-Simple EM Segment Simple], 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.
The batch processing feature allows the user to run the EMSegment module on multiple patients. By defining a patient root directory and a mask to iterate through the patients, EMSegment simple will be run for each images found in the matched images.

== Usage ==
MRML Scene = the mrml file name that contains all the parameters previously defined with EMSegment Template Builder module 
Data directory = where the patients images are ( T1, T2 images )
Directory mask = to be a valid input, the patients directories located in "Data directory" must match the mask
Target 1 mask = T1 image mask that must be matched inside the patients directories
Target 2 mask = T2 image mask that must be matched inside the patients directories
Output directory = where the results are saved

===Examples, Use Cases & Tutorials===

For the following file tree: 
* Images
** EMSegmentParameters.mrml
** Atlas
*** ...
** Patient1
*** Patient1.txt
*** Patient1-T1.mha
*** Patient1-T2.mha
** Patient2
*** Patient2.txt
*** Patient2-T1.mha
*** Patient2-T2.mha
** Patient3
*** Patient3.txt
*** Patient3-T1.mha
*** Patient3-T2.mha
* Results
Parameters are: 
MRMLScene: "Images/EMSegmentParameters.mrml" 
Data Directory: "Images" 
Directory Mask: Patient* 
Target 1 Mask: *T1.mha 
Target 2 Mask: *T2.mha 
Output directory: "Results" 

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

To run the module on a condor grid, open the BatchMake parameter group and choose "condor" as running mode. Make sure your data are accessible by all the condor machines.

== Development ==

===Dependencies===

[http://wiki.slicer.org/slicerWiki/index.php/Modules:EMSegment-Simple EMSegment Simple module]

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

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===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/BatchMakeApplications/EMSegmentBatchMakeModule/EMSegmentBatchMakeModule.cxx EMSegmentBatchMakeModule.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/BatchMakeApplications/EMSegmentBatchMakeModule/EMSegmentBatchMakeModule.xml EMSegmentBatchMakeModule.xml]

Documentation: http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/BatchMakeApplications/EMSegmentBatchMakeModule

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

← Older revision		Revision as of 20:35, 2 April 2010
Line 94:		Line 94:

	===References===		===References===
		+	[http://batchmake.org/Wiki/Batchmake_slicer batchmake.org]

@@ Line 19: / Line 19: @@
 ===Module Description===
-This module is the BatchMake version of [http://wiki.slicer.org/slicerWiki/index.php/Modules:EMSegment-Simple EM Segment Simple], 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.
+This module is the BatchMake version of [[Modules:EMSegment-Simple|EM Segment Simple]], 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.
 The batch processing feature allows the user to run the EMSegment module on multiple patients. By defining a patient root directory and a mask to iterate through the patients, EMSegment simple will be run for each images found in the matched images.
@@ Line 66: / Line 66: @@
 ===Dependencies===
-[http://wiki.slicer.org/slicerWiki/index.php/Modules:EMSegment-Simple EMSegment Simple module]
+[[Modules:EMSegment-Simple|EMSegment Simple module]]
 ===Known bugs===

@@ Line 82: / Line 82: @@
 XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/BatchMakeApplications/EMSegmentBatchMakeModule/EMSegmentBatchMakeModule.xml EMSegmentBatchMakeModule.xml]
-Documentation: http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/BatchMakeApplications/EMSegmentBatchMakeModule
+Documentation: [http://batchmake.org/Wiki/Batchmake_slicer batchmake.org]
 == More Information ==
@@ Line 94: / Line 94: @@
 ===References===