Difference between revisions of "Modules:OrientImages-Documentation-3.6"

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[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
 
[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
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[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]
 
 
__NOTOC__
 
__NOTOC__
 
===Module Name===
 
===Module Name===
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Type: CLI
 
Type: CLI
  
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Category: Base or (Filtering, Registration, ''etc.'')
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Category: Converters
  
 
===Authors, Collaborators & Contact===
 
===Authors, Collaborators & Contact===
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===Module Description===
 
===Module Description===
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Overview of what the module does goes here.
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Orients an output volume. Rearranges the slices in a volume according to the selected orientation. The slices are not interpolated. They are just reordered and/or permuted. The resulting volume will cover the original volume. NOTE: since Slicer3 takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume, To see the difference, save the volume and display it with a system that either ignores the orientation of the image (e.g. Paraview) or displays individual images.
  
 
== Usage ==
 
== Usage ==
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===Examples, Use Cases & Tutorials===
 
===Examples, Use Cases & Tutorials===
  
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* Note use cases for which this module is especially appropriate, and/or link to examples.
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* This module is useful for transforming volume from its original orientation to a given orientation. Note, that the module does not align the voxel space axes with the physical space axes. If your input image is not axis-aligned, the output will preserve the direction cosines of the input image. It does not change the spatial position and orientation of the volume in the physical space.
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* Link to examples of the module's use
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* Link to any existing tutorials
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When combined with "Create a Dicom Series" module, one can synthesize a sagittal acquisition from an axially acquired volume.
 +
 
 +
* A command line example of the module is
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 +
  OrientImage
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    --orientation Axial
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    ${MRML_DATA}/fixed.nrrd
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    ${TEMP}/OrientImageTestAxial.nrrd
  
 
===Quick Tour of Features and Use===
 
===Quick Tour of Features and Use===
 
List all the panels in your interface, their features, what they mean, and how to use them. For instance:
 
List all the panels in your interface, their features, what they mean, and how to use them. For instance:
  
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* '''Input panel:'''
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* '''Input/output panel:'''
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[[Image:OrientImage-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
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User specifies the input volume and creates an output volume.
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* '''Parameters panel:'''
 
* '''Parameters panel:'''
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* '''Output panel:'''
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[[Image:OrientImage-OrientationPanels-3-6.png|thumb|right|280px|Orientation panels]]
 +
User selects the desired orientation.
 +
 
 
* '''Viewing panel:'''
 
* '''Viewing panel:'''
 +
 +
Since Slicer3 takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume.
  
 
Note, that the module does not align the voxel space axes with the physical space axes. If your input image is not axis-aligned, the output will preserve the direction cosines of the input image.
 
Note, that the module does not align the voxel space axes with the physical space axes. If your input image is not axis-aligned, the output will preserve the direction cosines of the input image.
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===Dependencies===
 
===Dependencies===
  
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Other modules or packages that are required for this module's use.
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Depends only on Slicer3's core IO and display functionalities.
  
 
===Known bugs===
 
===Known bugs===
  
−
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.  
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None.
  
 
===Usability issues===
 
===Usability issues===
  
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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.
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None.
  
 
===Source code & documentation===
 
===Source code & documentation===
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XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/OrientImage.xml?view=co Orient orientImage.xml]
 
XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/OrientImage.xml?view=co Orient orientImage.xml]
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Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/OrientImageTest.cxx?rev=11535&view=log OrientImageTest.cxx]
  
 
Usage:
 
Usage:
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===References===
 
===References===
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 +
Internally, the module uses itk::OrientImageFilter. More details on algorithm can be found [http://public.kitware.com/Insight/Doxygen/html/classitk_1_1OrientImageFilter.html here].

Latest revision as of 15:18, 30 April 2010

Home < Modules:OrientImages-Documentation-3.6

Return to Slicer 3.6 Documentation

Module Name

Orient Images

Orient Images UI

General Information

Module Type & Category

Type: CLI

Category: Converters

Authors, Collaborators & Contact

  • Author: Bill Lorensen
  • Contact: bill.lorensen at gmail.com

Module Description

Orients an output volume. Rearranges the slices in a volume according to the selected orientation. The slices are not interpolated. They are just reordered and/or permuted. The resulting volume will cover the original volume. NOTE: since Slicer3 takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume, To see the difference, save the volume and display it with a system that either ignores the orientation of the image (e.g. Paraview) or displays individual images.

Usage

Examples, Use Cases & Tutorials

  • This module is useful for transforming volume from its original orientation to a given orientation. Note, that the module does not align the voxel space axes with the physical space axes. If your input image is not axis-aligned, the output will preserve the direction cosines of the input image. It does not change the spatial position and orientation of the volume in the physical space.

When combined with "Create a Dicom Series" module, one can synthesize a sagittal acquisition from an axially acquired volume.

  • A command line example of the module is
 OrientImage
   --orientation Axial 
   ${MRML_DATA}/fixed.nrrd 
   ${TEMP}/OrientImageTestAxial.nrrd

Quick Tour of Features and Use

List all the panels in your interface, their features, what they mean, and how to use them. For instance:

  • Input/output panel:
Input/Output panels

User specifies the input volume and creates an output volume.

  • Parameters panel:
Orientation panels

User selects the desired orientation.

  • Viewing panel:

Since Slicer3 takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume.

Note, that the module does not align the voxel space axes with the physical space axes. If your input image is not axis-aligned, the output will preserve the direction cosines of the input image.

Development

Dependencies

Depends only on Slicer3's core IO and display functionalities.

Known bugs

None.

Usability issues

None.

Source code & documentation

Source Code: OrientImage.cxx

XML Description: Orient orientImage.xml

Test: OrientImageTest.cxx

Usage: 

./OrientImage  [--processinformationaddress <std::string>] [--xml]
               [--echo] [-o <Axial|Coronal|Sagittal|RIP|LIP|RSP|LSP|RIA
               |LIA|RSA|LSA|IRP|ILP|SRP|SLP|IRA|ILA|SRA|SLA|RPI|LPI|RAI
               |LAI|RPS|LPS|RAS|LAS|PRI|PLI|ARI|ALI|PRS|PLS|ARS|ALS|IPR
               |SPR|IAR|SAR|IPL|SPL|IAL|SAL|PIR|PSR|AIR|ASR|PIL|PSL|AIL
               |ASL>] [--] [--version] [-h] <std::string> <std::string>


Where: 

--processinformationaddress <std::string>
  Address of a structure to store process information (progress, abort,
  etc.). (default: 0)

--xml
  Produce xml description of command line arguments (default: 0)

--echo
  Echo the command line arguments (default: 0)

-o <Axial|Coronal|Sagittal|RIP|LIP|RSP|LSP|RIA|LIA|RSA|LSA|IRP|ILP|SRP
   |SLP|IRA|ILA|SRA|SLA|RPI|LPI|RAI|LAI|RPS|LPS|RAS|LAS|PRI|PLI|ARI|ALI
   |PRS|PLS|ARS|ALS|IPR|SPR|IAR|SAR|IPL|SPL|IAL|SAL|PIR|PSR|AIR|ASR|PIL
   |PSL|AIL|ASL>,  --orientation <Axial|Coronal|Sagittal|RIP|LIP|RSP|LSP
   |RIA|LIA|RSA|LSA|IRP|ILP|SRP|SLP|IRA|ILA|SRA|SLA|RPI|LPI|RAI|LAI|RPS
   |LPS|RAS|LAS|PRI|PLI|ARI|ALI|PRS|PLS|ARS|ALS|IPR|SPR|IAR|SAR|IPL|SPL
   |IAL|SAL|PIR|PSR|AIR|ASR|PIL|PSL|AIL|ASL>
  Orientation choices (default: LPS)

--,  --ignore_rest
  Ignores the rest of the labeled arguments following this flag.

--version
  Displays version information and exits.

-h,  --help
  Displays usage information and exits.

<std::string>
  (required)  Input volume 1

<std::string>
  (required)  The oriented volume


Description: Orients an output volume. Rearranges the slices in a volume
accoording to the selected orientation. The resulting volume will cover
the original volume.

Author(s): Bill Lorensen

Acknowledgements: 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.

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

Internally, the module uses itk::OrientImageFilter. More details on algorithm can be found here.

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