View source for GtractCopyImageOrientation

__NOTOC__
===Copy Image Orientation===
Copy Image Orientation

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|[[Image:screenshotBlank.png|thumb|280px|Output]]
|[[Image:screenshotBlank.png|thumb|280px|Caption]]
|}
== General Information ==

===Module Type & Category===

Type: CLI

Category: Diffusion.GTRACT



===Authors, Collaborators & Contact===

Author: This tool was developed by Vincent Magnotta and Greg Harris.

Contributors: 

Contact: name, email


===Module Description===

{| style="color:green" border="1"

|Program title || Copy Image Orientation

|-
|Program description || This program will copy the orientation from the reference image into the moving image. Currently, the registration process requires that the diffusion weighted images and the anatomical images have the same image orientation (i.e. Axial, Coronal, Sagittal). It is suggested that you copy the image orientation from the diffusion weighted images and apply this to the anatomical image. This image can be subsequently removed after the registration step is complete. We anticipate that this limitation will be removed in future versions of the registration programs.

|-
|Program version || 4.0.0

|-
|Program documentation-url || https://www.slicer.org/wiki/Modules:GTRACT |-
|}

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1:
* Example 2:

===Tutorials===

* Tutorial 1
** Data Set 1

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them.

{|
|
* <span style="color:blue">'''''Input Parameters''''' </span> 
** <span style="color:green">'''Input Image Volume'''</span> [<span style="color:orange">--inputVolume</span>] : Required: input file containing the signed short image to reorient without resampling.
** <span style="color:green">'''Input Reference Image Volume'''</span> [<span style="color:orange">--inputReferenceVolume</span>] : Required: input file containing orietation that will be cloned.


* <span style="color:blue">'''''Output File''''' </span> 
** <span style="color:green">'''Output Code Image Volume'''</span> [<span style="color:orange">--outputVolume</span>] : Required: name of output NRRD or Nifti file containing the reoriented image in reference image space.


|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] 

===Usability issues===

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.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information == 

===Acknowledgment===

Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

===References===

Publications related to this module go here. Links to pdfs would be useful.