View source for GtractTensor

__NOTOC__
===Tensor Estimation===
Tensor Estimation

{|
|[[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 || Tensor Estimation

|-
|Program description || This step will convert a b-value averaged diffusion tensor image to a 3x3 tensor voxel image. This step takes the diffusion tensor image data and generates a tensor representation of the data based on the signal intensity decay, b values applied, and the diffusion difrections. The apparent diffusion coefficient for a given orientation is computed on a pixel-by-pixel basis by fitting the image data (voxel intensities) to the Stejskal-Tanner equation. If at least 6 diffusion directions are used, then the diffusion tensor can be computed. This program uses itk::DiffusionTensor3DReconstructionImageFilter. The user can adjust background threshold, median filter, and isotropic resampling.

|-
|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 Image Files''''' </span> 
** <span style="color:green">'''Input Image Volume'''</span> [<span style="color:orange">--inputVolume</span>] : Required: input image 4D NRRD image. Must contain data based on at least 6 distinct diffusion directions. The inputVolume is allowed to have multiple b0 and gradient direction images. Averaging of the b0 image is done internally in this step. Prior averaging of the DWIs is not required.


* <span style="color:blue">'''''Output Image Files''''' </span> 
** <span style="color:green">'''Output Tensor Image Volume'''</span> [<span style="color:orange">--outputVolume</span>] : Required: name of output NRRD file containing the Tensor vector image


* <span style="color:blue">'''''Tensor Conversion Parameters''''' </span> 
** <span style="color:green">'''Median Filter Size'''</span> [<span style="color:orange">--medianFilterSize</span>] : Median filter radius in all 3 directions ''Default value: 0,0,0''
** <span style="color:green">'''B0 Image Threshold'''</span> [<span style="color:orange">--backgroundSuppressingThreshold</span>] : Image threshold to suppress background. This sets a threshold used on the b0 image to remove background voxels from processing. Typically, values of 100 and 500 work well for Siemens and GE DTI data, respectively. Check your data particularly in the globus pallidus to make sure the brain tissue is not being eliminated with this threshold. ''Default value: 100''
** <span style="color:green">'''Resample To Isotropic Voxels'''</span> [<span style="color:orange">--resampleIsotropic</span>] : Flag to resample to isotropic voxels. Enabling this feature is recommended if fiber tracking will be performed. ''Default value: 0''
** <span style="color:green">'''Isotropic Voxel Size'''</span> [<span style="color:orange">--size</span>] : Isotropic voxel size to resample to ''Default value: 2.0''
** <span style="color:green">'''Vector Image B0 Index'''</span> [<span style="color:orange">--b0Index</span>] : Index in input vector index to extract ''Default value: 0''
** <span style="color:green">'''Apply Measurement Frame'''</span> [<span style="color:orange">--applyMeasurementFrame</span>] : Flag to apply the measurement frame to the gradient directions ''Default value: 0''
** <span style="color:green">'''Ignore Indices'''</span> [<span style="color:orange">--ignoreIndex</span>] : Ignore diffusion gradient index. Used to remove specific gradient directions with artifacts.


|[[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.