Modules:EMSegmentBatch-Documentation-3.4 - Revision history

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2019-11-27T02:16:19Z

Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Marianna at 20:20, 26 May 2009

2009-05-26T20:20:01Z

Finetjul: /* Authors, Collaborators & Contact */

2009-04-06T18:02:27Z

Authors, Collaborators & Contact

Finetjul: /* Authors, Collaborators & Contact */

2009-04-06T18:01:57Z

Authors, Collaborators & Contact

Finetjul: /* Module Name */

2009-04-06T17:59:27Z

Module Name

Finetjul: Add EMSegmentBatchMake module documentation

2009-04-06T17:57:50Z

Add EMSegmentBatchMake module documentation

Finetjul: Add Register Images BatchMake Module documentation

2009-04-06T17:30:57Z

Add Register Images BatchMake Module documentation

New page

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
Register Images BatchMake

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

Type: CLI

Category: Batch Processing

===Authors, Collaborators & Contact===
* Authors: Julien Finet, Stephen Aylward
* Contact: julien.finet at kitware.com

===Module Description===
This Module is the BatchMake version of [http://wiki.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.4 Register Images module], an integrated framework providing access to ITK registration technologies. N moving images can be registered with a single fixed image on a computational grid. The moving images are the images filenames that match a mask in a directory.

== Usage ==
Fixed Image = the fixed image 
Moving Image Directory = the directory the moving images share with each others 
Moving Image Mask = a mask (concatenated to the Moving Image Directoy) that is used to select only the moving images. If the moving images are in sub directories, separate the sub directories with the '/' character.
Resampled Image Directory = the output directory where the registered images will be saved
Resampled Image Mask = the name of the resampled images created by Register Images. To ensure uniqueness of the name, you can use the ${movingImage} BatchMake variable that contains the name of each moving image.

For the other parameters, please see the [http://wiki.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.4 Register Images module documentation].

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

For the following file tree: 
* Images
** Target.mha
** Patient1
*** 00001.txt
*** 00001.mha
** Patient2
*** 00001.txt
*** 00001.mha
** Patient3
*** 00001.txt
*** 00001.mha
* Result
Parameters could be: 
Fixed Image: "Images/Target.mha" 
Moving Image Directory: "Images" 
Moving Image Mask: "Patient*/*.mha" 
Resampled Image Directory: "Result" 
Resampled Image Mask: "Resampled-{movingImage}" 

===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. Set the Input, Output, Executable and Working directories. 
Input directory = Moving Image directory (probably on the network) 
Output directory = Resampled Image directory (probably on the network) 
Executable directory = directory where all your applications are: bmGridStore, bmGridSend, RegisterImages...). This directory shall be the same for all of your condor machines. 
Working directory = directory where the BatchMake and condor scripts will be written (probably on the network) 

== Development ==

===Dependencies===

Register Images 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://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/BatchMakeApplications/GenericBatchMakeModule/BatchMakeModule.cxx?view=annotate BatchMakeModule.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/BatchMakeApplications/RegisterImagesBatchMakeModule/RegisterImagesBatchMakeModule.xml?view=co RegisterImagesBatchMakeModule.xml]

Documentation:

== 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===

@@ Line 21: / Line 21: @@
 ===Module Description===
-This module is the BatchMake version of [http://wiki.slicer.org/slicerWiki/index.php/Modules:EMSegment-Simple-Documentation-3.4 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-Documentation-3.4|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 15: / Line 15: @@
 ===Authors, Collaborators & Contact===
-* Authors: Julien Finet, Brad Davis and Julien Jomier
+* Authors: Stephen Aylward, Julien Finet
 * Contact: julien.finet at kitware.com

@@ Line 4: / Line 4: @@
 EM Segment BatchMake
 {|
-|[Image:RegisterImagesBatchMakeModule.png|thumb|580px|EM Segment BatchMake module GUI ]]
+|[[Image:EMSegmentBatchMakeModule.png|thumb|580px|EM Segment BatchMake module GUI ]]
 |}

@@ Line 1: / Line 1: @@
 [[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 __NOTOC__
 ===Module Name===

@@ Line 2: / Line 2: @@
 __NOTOC__
 ===Module Name===
-Register Images BatchMake
+EM Segment BatchMake
 == General Information ==
@@ Line 12: / Line 15: @@
 ===Authors, Collaborators & Contact===
-* Authors: Julien Finet, Stephen Aylward
+* Authors: Julien Finet, Brad Davis and Julien Jomier
 * Contact: julien.finet at kitware.com
 ===Module Description===
-This Module is the BatchMake version of [http://wiki.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.4 Register Images module], an integrated framework providing access to ITK registration technologies. N moving images can be registered with a single fixed image on a computational grid. The moving images are the images filenames that match a mask in a directory.
+This module is the BatchMake version of [http://wiki.slicer.org/slicerWiki/index.php/Modules:EMSegment-Simple-Documentation-3.4 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.
 == Usage ==
-Fixed Image = the fixed image <br>
+MRML Scene = the mrml file name that contains all the parameters previously defined with EMSegment Template Builder module<br>
-Moving Image Directory = the directory the moving images share with each others<br>
+Data directory = where the patients images are ( T1, T2 images )
-Moving Image Mask = a mask (concatenated to the Moving Image Directoy) that is used to select only the moving images. If the moving images are in sub directories, separate the sub directories with the '/' character.
+Directory mask = to be a valid input, the patients directories located in "Data directory" must match the mask
-Resampled Image Directory = the output directory where the registered images will be saved
+Target 1 mask = T1 image mask that must be matched inside the patients directories
-Resampled Image Mask = the name of the resampled images created by Register Images. To ensure uniqueness of the name, you can use the ${movingImage} BatchMake variable that contains the name of each moving image.
+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===
@@ Line 31: / Line 34: @@
 For the following file tree:<br>
 * Images
-** Target.mha
+** EMSegmentParameters.mrml
 ** Patient1
-*** 00001.txt
+*** Patient1.txt
-*** 00001.mha
+*** Patient1-T1.mha
 ** Patient2
-*** 00001.txt
+*** Patient2.txt
-*** 00001.mha
+*** Patient2-T1.mha
 ** Patient3
-*** 00001.txt
+*** Patient3.txt
-*** 00001.mha
+*** Patient3-T1.mha
-* Result
+*** Patient3-T2.mha
-Parameters could be:<br>
+* Results
-Fixed Image: "Images/Target.mha"<br>
+Parameters are:<br>
-Moving Image Directory: "Images"<br>
+MRMLScene: "Images/EMSegmentParameters.mrml"<br>
-Moving Image Mask: "Patient*/*.mha"<br>
+Data Directory: "Images"<br>
-Resampled Image Directory: "Result"<br>
+Directory Mask: Patient*<br>
-Resampled Image Mask: "Resampled-{movingImage}"<br>
+Target 1 Mask: *T1.mha<br>
 ===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. Set the Input, Output, Executable and Working directories.<br>
+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 ==
@@ Line 61: / Line 66: @@
 ===Dependencies===
-Register Images module
+EMSegment Simple module
 ===Known bugs===
@@ Line 73: / Line 78: @@
 ===Source code & documentation===
-Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/BatchMakeApplications/GenericBatchMakeModule/BatchMakeModule.cxx?view=annotate BatchMakeModule.cxx]
+Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/BatchMakeApplications/EMSegmentBatchMakeModule/EMSegmentBatchMakeModule.cxx?view=annotate EMSegmentBatchMakeModule.cxx]
-XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/BatchMakeApplications/RegisterImagesBatchMakeModule/RegisterImagesBatchMakeModule.xml?view=co RegisterImagesBatchMakeModule.xml]
+XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/BatchMakeApplications/EMSegmentBatchMakeModule/EMSegmentBatchMakeModule.xml?view=co EMSegmentBatchMakeModule.xml]
 Documentation: