UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

2013-06-14T07:25:40Z

Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

JChris.FillionR: 4.0 -> 4.1

2012-04-12T04:41:07Z

4.0 -> 4.1

New page

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
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 [http://www.na-mic.org/ NA-MIC website].<br>
Author: Jim Miller, GE<br>
Contact: Jim Miller <email>millerjv@ge.com</email><br>
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:GE-logo.png|GE
|Image:Itk-logo.jpg|Itk
|Image:NAMIC 380x463.jpg|NA-MIC
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description}}


{{documentation/{{documentation/version}}/module-section|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:
<pre>
./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
</pre>


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{|
|{{documentation/{{documentation/version}}/module-parametersdescription}}
|[[Image:OrientImage-3-6.png|thumb|280px|Orient Images UI]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
N/A


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

← Older revision		Revision as of 07:25, 14 June 2013
Line 1:		Line 1:
		+	<noinclude>{{documentation/versioncheck}}</noinclude>
	<!-- ---------------------------- -->		<!-- ---------------------------- -->
	{{documentation/{{documentation/version}}/module-header}}		{{documentation/{{documentation/version}}/module-header}}

Documentation/4.1/Modules/OrientScalarVolume - Revision history

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

JChris.FillionR: 4.0 -> 4.1