Documentation/4.0/Modules/OrientScalarVolume - Revision history

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

2013-06-14T07:28:34Z

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

JChris.FillionR at 11:26, 2 February 2012

2012-02-02T11:26:13Z

JChris.FillionR: moved Documentation/4.0/Modules/OrientImage to Documentation/4.0/Modules/OrientScalarVolume

2012-02-02T06:14:47Z

moved Documentation/4.0/Modules/OrientImage to Documentation/4.0/Modules/OrientScalarVolume

Marianna at 20:21, 11 November 2011

2011-11-11T20:21:49Z

Marianna at 20:16, 11 November 2011

2011-11-11T20:16:32Z

Marianna at 19:07, 3 November 2011

2011-11-03T19:07:40Z

Marianna: Created page with ' {{documentation/{{documentation/version}}/module-header}} {{doc…'

2011-11-03T19:04:29Z

Created page with ' {{documentation/{{documentation/version}}/module-header}}   {{doc…'

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}}
{{documentation/{{documentation/version}}/module-acknowledgements|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}}
}}
<br>
Author: Bill Lorensen, Bills Basement<br>
Contact: Bill Lorensen, <email>bill.lorensen@gmail.com</email><br>
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-isomics.png|Isomics, Inc.
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }}


{{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}}
There are currently no tutorials for this module.

{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* See the [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM Module]] for a user interface that allows you to associate your output DICOM files with an existing DICOM Study.


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}}
}}
}}


{{documentation/{{documentation/version}}/module-footer|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}}
}}
}}

← Older revision		Revision as of 07:28, 14 June 2013
Line 1:		Line 1:
		+	<noinclude>{{documentation/versioncheck}}</noinclude>
	<!-- ---------------------------- -->		<!-- ---------------------------- -->
	{{documentation/{{documentation/version}}/module-header}}		{{documentation/{{documentation/version}}/module-header}}

@@ Line 19: / Line 19: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }}
+{{documentation/{{documentation/version}}/module-description}}
 <!-- ---------------------------- -->
@@ Line 83: / Line 83: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-There are currently no tutorials for this module.
+N/A
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Panels and their use}}
 {|
 |[[Image:OrientImage-3-6.png|thumb|280px|Orient Images UI]]
 |}
@@ Line 93: / Line 94: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Similar Modules}}
-* Point to other modules that have similar functionality
+N/A
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|References}}
-Publications related to this module go here. Links to pdfs would be useful.
+N/A
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Information for Developers}}
-{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
+{{documentation/{{documentation/version}}/module-developerinfo}}
 <!-- ---------------------------- -->
-{{documentation/{{documentation/version}}/module-footer|category=
+{{documentation/{{documentation/version}}/module-footer}}
 <!-- ---------------------------- -->

← Older revision	Revision as of 06:14, 2 February 2012
(No difference)

@@ Line 7: / Line 7: @@
 {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
 {{documentation/{{documentation/version}}/module-introduction-row}}
-{{documentation/{{documentation/version}}/module-acknowledgements|xmlurl=
+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>
@@ Line 19: / Line 17: @@
 }}
 {{documentation/{{documentation/version}}/module-introduction-end}}
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}

@@ Line 10: / Line 10: @@
    {{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}}
 }}
-<br>
+Author: Jim Miller, GE<br>
-Author: Bill Lorensen, Bills Basement<br>
+Contact: Jim Miller <email>millerjv@ge.com</email><br>
 {{documentation/{{documentation/version}}/module-introduction-row}}
 {{documentation/{{documentation/version}}/module-introduction-logo-gallery
-|Image:Logo-isomics.png|Isomics, Inc.
+|Image:GE-logo.png|GE
-|Image:Logo-splnew.jpg|Surgical Planning Laboratory
+|Image:Itk-logo.jpg|Itk
 }}
 {{documentation/{{documentation/version}}/module-introduction-end}}