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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__NOTOC__ | __NOTOC__ | ||
===Module Name=== | ===Module Name=== | ||
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{| | {| | ||
− | |[[Image: | + | |[[Image:OrientImage-3-6.png|thumb|280px|Orient Images UI]] |
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|} | |} | ||
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Type: CLI | Type: CLI | ||
− | Category: | + | Category: Converters |
===Authors, Collaborators & Contact=== | ===Authors, Collaborators & Contact=== | ||
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===Module Description=== | ===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 == | == Usage == | ||
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===Examples, Use Cases & Tutorials=== | ===Examples, Use Cases & Tutorials=== | ||
− | * Note | + | * 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=== | ===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: | ||
− | * '''Input panel:''' | + | * '''Input/output panel:''' |
+ | [[Image:OrientImage-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]] | ||
+ | User specifies the input volume and creates an output volume. | ||
+ | |||
* '''Parameters panel:''' | * '''Parameters panel:''' | ||
− | + | [[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=== | ||
− | + | Depends only on Slicer3's core IO and display functionalities. | |
===Known bugs=== | ===Known bugs=== | ||
− | + | None. | |
===Usability issues=== | ===Usability issues=== | ||
− | + | 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] | ||
+ | |||
+ | 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=== | ||
+ | |||
+ | 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-3.6Return to Slicer 3.6 Documentation
Module Name
Orient Images
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:
User specifies the input volume and creates an output volume.
- Parameters panel:
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.