View source for GtractAnisotropyMap

__NOTOC__
===Anisotropy Map===
Anisotropy Map

{|
|[[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 || Anisotropy Map

|-
|Program description || This program will generate a scalar map of anisotropy, given a tensor representation. Anisotropy images are used for fiber tracking, but the anisotropy scalars are not defined along the path. Instead, the tensor representation is included as point data allowing all of these metrics to be computed using only the fiber tract point data. The images can be saved in any ITK supported format, but it is suggested that you use an image format that supports the definition of the image origin. This includes NRRD, NifTI, and Meta formats. These images can also be used for scalar analysis including regional anisotropy measures or VBM style analysis.

|-
|Program version || 4.0.0

|-
|Program documentation-url || http://wiki.slicer.org/slicerWiki/index.php/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 Tensor Image Volume'''</span> [<span style="color:orange">--inputTensorVolume</span>] : Required: input file containing the diffusion tensor image
** <span style="color:green">'''Type Code for Anisotropy Map'''</span> [<span style="color:orange">--anisotropyType</span>] : Anisotropy Mapping Type: ADC, FA, RA, VR, AD, RD, LI ''Default value: ADC''


* <span style="color:blue">'''''Output File''''' </span> 
** <span style="color:green">'''Output Anisotropy Image Volume'''</span> [<span style="color:orange">--outputVolume</span>] : Required: name of output NRRD file containing the selected kind of anisotropy scalar.


|[[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.