Difference between revisions of "Modules:EMSegmentBatch-Documentation-3.4"

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[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 
[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 +
 +
[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]
 
__NOTOC__
 
__NOTOC__
 
===Module Name===
 
===Module Name===
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Register Images BatchMake
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EM Segment BatchMake
 +
{|
 +
|[[Image:EMSegmentBatchMakeModule.png|thumb|580px|EM Segment BatchMake module GUI ]]
 +
|}
  
 
== General Information ==
 
== General Information ==
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===Authors, Collaborators & Contact===
 
===Authors, Collaborators & Contact===
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* Authors: Julien Finet, Stephen Aylward
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* Authors: Stephen Aylward, Julien Finet
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* Contact: julien.finet at kitware.com
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* Contact: stephen.aylward at kitware.com
  
 
===Module Description===
 
===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 [[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.
  
 
== Usage ==
 
== Usage ==
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Fixed Image = the fixed image <br>
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MRML Scene = the mrml file name that contains all the parameters previously defined with EMSegment Template Builder module<br>
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Moving Image Directory = the directory the moving images share with each others<br>
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Data directory = where the patients images are ( T1, T2 images )
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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.
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Directory mask = to be a valid input, the patients directories located in "Data directory" must match the mask
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Resampled Image Directory = the output directory where the registered images will be saved
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Target 1 mask = T1 image mask that must be matched inside the patients directories
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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.
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Target 2 mask = T2 image mask that must be matched inside the patients directories
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Output directory = where the results are saved
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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===
 
===Examples, Use Cases & Tutorials===
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For the following file tree:<br>
 
For the following file tree:<br>
 
* Images
 
* Images
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** Target.mha
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** EMSegmentParameters.mrml
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** Atlas
 +
*** ...
 
** Patient1
 
** Patient1
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*** 00001.txt
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*** Patient1.txt
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*** 00001.mha  
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*** Patient1-T1.mha
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*** Patient1-T2.mha
 
** Patient2
 
** Patient2
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*** 00001.txt
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*** Patient2.txt
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*** 00001.mha  
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*** Patient2-T1.mha
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*** Patient2-T2.mha
 
** Patient3
 
** Patient3
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*** 00001.txt
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*** Patient3.txt
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*** 00001.mha
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*** Patient3-T1.mha
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* Result
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*** Patient3-T2.mha
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Parameters could be:<br>
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* Results
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Fixed Image: "Images/Target.mha"<br>
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Parameters are:<br>
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Moving Image Directory: "Images"<br>
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MRMLScene: "Images/EMSegmentParameters.mrml"<br>
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Moving Image Mask: "Patient*/*.mha"<br>
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Data Directory: "Images"<br>
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Resampled Image Directory: "Result"<br>
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Directory Mask: Patient*<br>
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Resampled Image Mask: "Resampled-{movingImage}"<br>
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Target 1 Mask: *T1.mha<br>
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Target 2 Mask: *T2.mha<br>
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Output directory: "Results"<br>
  
 
===Quick Tour of Features and Use===
 
===Quick Tour of Features and Use===
  
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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>
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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.  
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Input directory = Moving Image directory (probably on the network)<br>
 
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Output directory = Resampled Image directory (probably on the network)<br>
 
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Executable directory = directory where all your applications are: bmGridStore, bmGridSend, RegisterImages...). This directory shall be the same for all of your condor machines.<br>
 
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Working directory = directory where the BatchMake and condor scripts will be written (probably on the network)<br>
 
  
 
== Development ==
 
== Development ==
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===Dependencies===
 
===Dependencies===
  
−
Register Images module
+
EMSegment Simple module
  
 
===Known bugs===
 
===Known bugs===
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===Source code & documentation===
 
===Source code & documentation===
  
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Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/BatchMakeApplications/GenericBatchMakeModule/BatchMakeModule.cxx?view=annotate BatchMakeModule.cxx]
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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]
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XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/BatchMakeApplications/EMSegmentBatchMakeModule/EMSegmentBatchMakeModule.xml?view=co EMSegmentBatchMakeModule.xml]
  
 
Documentation:
 
Documentation:

Latest revision as of 02:16, 27 November 2019

Home < Modules:EMSegmentBatch-Documentation-3.4

Return to Slicer 3.4 Documentation

Gallery of New Features

Module Name

EM Segment BatchMake

EM Segment BatchMake module GUI

General Information

Module Type & Category

Type: CLI

Category: Batch Processing

Authors, Collaborators & Contact

  • Authors: Stephen Aylward, Julien Finet
  • Contact: stephen.aylward at kitware.com

Module Description

This module is the BatchMake version of 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

EMSegment Simple module

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Source Code: EMSegmentBatchMakeModule.cxx

XML Description: EMSegmentBatchMakeModule.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 National Centers for Biomedical Computing.

References

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