Documentation/Nightly/Modules/OrientScalarVolume

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For the stable Slicer documentation, visit the 4.8 page.


Introduction and Acknowledgements

This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website.
Author: Jim Miller, GE
Contact: Jim Miller

GE  
Itk  
NA-MIC  

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 Slicer 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.


Use Cases

  • 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

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

Tutorials

N/A

Panels and their use

Parameters:
  • IO: Input/output parameters
    • Input Volume 1 (inputVolume1): Input volume 1
    • Output Volume (outputVolume): The oriented volume
  • Orientation Parameters: Orientation of output
    • Orientation (orientation): Orientation choices


List of parameters generated transforming this XML file using this XSL file. To update the URL of the XML file, edit this page.

Orient Images UI

Similar Modules

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References

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Information for Developers