View source for GtractCoregBvalues

__NOTOC__
===Coregister B-Values===
Coregister B-Values

{|
|[[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 || Coregister B-Values

|-
|Program description || This step should be performed after converting DWI scans from DICOM to NRRD format. This program will register all gradients in a NRRD diffusion weighted 4D vector image (moving image) to a specified index in a fixed image. It also supports co-registration with a T2 weighted image or field map in the same plane as the DWI data. The fixed image for the registration should be a b0 image. A mutual information metric cost function is used for the registration because of the differences in signal intensity as a result of the diffusion gradients. The full affine allows the registration procedure to correct for eddy current distortions that may exist in the data. If the eddyCurrentCorrection is enabled, relaxationFactor (0.25) and maximumStepSize (0.1) should be adjusted.

|-
|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 Parameters''''' </span> 
** <span style="color:green">'''Moving Image Volume'''</span> [<span style="color:orange">--movingVolume</span>] : Required: input moving image file name. In order to register gradients within a scan to its first gradient, set the movingVolume and fixedVolume as the same image.
** <span style="color:green">'''Fixed Image Volume'''</span> [<span style="color:orange">--fixedVolume</span>] : Required: input fixed image file name. It is recommended that this image should either contain or be a b0 image.
** <span style="color:green">'''Fixed Image Index'''</span> [<span style="color:orange">--fixedVolumeIndex</span>] : Index in the fixed image for registration. It is recommended that this image should be a b0 image. ''Default value: 0''


* <span style="color:blue">'''''Output Files''''' </span> 
** <span style="color:green">'''Output Image Volume'''</span> [<span style="color:orange">--outputVolume</span>] : Required: name of output NRRD file containing moving images individually resampled and fit to the specified fixed image index.
** <span style="color:green">'''Output Transform'''</span> [<span style="color:orange">--outputTransform</span>] : Registration 3D transforms concatenated in a single output file.  There are no tools that can use this, but can be used for debugging purposes.


* <span style="color:blue">'''''Registration Parameters''''' </span> 
** <span style="color:green">'''Eddy Current Correction'''</span> [<span style="color:orange">--eddyCurrentCorrection</span>] : Flag to perform eddy current corection in addition to motion correction (recommended) ''Default value: 0''
** <span style="color:green">'''Number Of Iterations'''</span> [<span style="color:orange">--numberOfIterations</span>] : Number of iterations in each 3D fit ''Default value: 1000''
** <span style="color:green">'''Number Of Samples'''</span> [<span style="color:orange">--numberOfSpatialSamples</span>] : Number of voxels sampled for mutual information computation in each 3D fit step ''Default value: 100000''
** <span style="color:green">'''Relaxation Factor'''</span> [<span style="color:orange">--relaxationFactor</span>] : Fraction of gradient from Jacobian to attempt to move in each 3D fit step (adjust when eddyCurrentCorrection is enabled; suggested value = 0.25) ''Default value: 0.5''
** <span style="color:green">'''Maximum Step Size'''</span> [<span style="color:orange">--maximumStepSize</span>] : Maximum permitted step size to move in each 3D fit step (adjust when eddyCurrentCorrection is enabled; suggested value = 0.1) ''Default value: 0.2''
** <span style="color:green">'''Minimum Step Size'''</span> [<span style="color:orange">--minimumStepSize</span>] : Minimum required step size to move in each 3D fit step without converging -- decrease this to make the fit more exacting ''Default value: 0.0001''
** <span style="color:green">'''Translation Scale'''</span> [<span style="color:orange">--spatialScale</span>] : How much to scale up changes in position compared to unit rotational changes in radians -- decrease this to put more rotation in the fit ''Default value: 1000.0''
** <span style="color:green">'''B0 Only Registration'''</span> [<span style="color:orange">--registerB0Only</span>] : Register the B0 images only ''Default value: 0''
** <span style="color:green">'''Debug option'''</span> [<span style="color:orange">----debugLevel</span>] : Display debug messages, and produce debug intermediate results.  0=OFF, 1=Minimal, 10=Maximum debugging. ''Default value: 0''


|[[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.