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2019-11-27T02:12:48Z

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Finetjul: Created page with 'Return to Slicer 3.6 Documentation NOTOC ===Module Name=== Register Images BatchMake {| |[[Image:RegisterImagesBatchMakeModule.png|thumb|580px|Register …'

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[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
Register Images BatchMake
{|
|[[Image:RegisterImagesBatchMakeModule.png|thumb|580px|Register Images BatchMake]]
|}

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

Type: CLI

Category: Batch Processing

===Authors, Collaborators & Contact===
* Authors: Julien Finet and Stephen Aylward at Kitware Inc.
* 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-3.6 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-3.6 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}" 
 
RegisterImages would then be run 3 times with the following parameters: 
RegisterImages ... Images/Target.mha Images/Patient1/00001.mha --resampledImage Resampled-Patient1/00001.mha 
RegisterImages ... Images/Target.mha Images/Patient2/00001.mha --resampledImage Resampled-Patient2/00001.mha 
RegisterImages ... Images/Target.mha Images/Patient3/00001.mha --resampledImage Resampled-Patient3/00001.mha 

===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===

[http://wiki.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Register Images module]

===Known bugs===
Don't use paths with space characters.

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/GenericBatchMakeModule/BatchMakeModule.cxx?view=annotate BatchMakeModule.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/BatchMakeApplications/RegisterImagesBatchMakeModule/RegisterImagesBatchMakeModule.xml?view=co RegisterImagesBatchMakeModule.xml]

Documentation: [http://batchmake.org/Wiki/Batchmake_slicer batchmake.org]
== 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 19: / Line 19: @@
 ===Module Description===
-This Module is the BatchMake version of [http://wiki.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 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 [[Modules:RegisterImages-Documentation-3.6|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 ==
@@ Line 28: / Line 28: @@
 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.<br>
-For the other parameters, please see the [http://wiki.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Register Images module documentation].
+For the other parameters, please see the [[Modules:RegisterImages-Documentation-3.6|Register Images module documentation]].
 ===Examples, Use Cases & Tutorials===
@@ Line 69: / Line 69: @@
 ===Dependencies===
-[http://wiki.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Register Images module]
+[[Modules:RegisterImages-Documentation-3.6|Register Images module]]
 ===Known bugs===

Modules:RegisterImagesBatch-Documentation-3.6 - Revision history

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

Finetjul: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== Register Images BatchMake {| |[[Image:RegisterImagesBatchMakeModule.png|thumb|580px|Register …'

Finetjul: Created page with 'Return to Slicer 3.6 Documentation NOTOC ===Module Name=== Register Images BatchMake {| |[[Image:RegisterImagesBatchMakeModule.png|thumb|580px|Register …'