View source for GtractCoRegAnatomy

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===Coregister B0 to Anatomy B-Spline===
Coregister B0 to Anatomy B-Spline

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|[[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 B0 to Anatomy B-Spline

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|Program description || This program will register a Nrrd diffusion weighted 4D vector image to a fixed anatomical image. Two registration methods are supported for alignment with anatomical images: Rigid and B-Spline. The rigid registration performs a rigid body registration with the anatomical images and should be done as well to initialize the B-Spline transform. The B-SPline transform is the deformable transform, where the user can control the amount of deformation based on the number of control points as well as the maximum distance that these points can move. The B-Spline registration places a low dimensional grid in the image, which is deformed. This allows for some susceptibility related distortions to be removed from the diffusion weighted images. In general the amount of motion in the slice selection and read-out directions direction should be kept low. The distortion is in the phase encoding direction in the images. It is recommended that skull stripped (i.e. image containing only brain with skull removed) images shoud be used for image co-registration with the B-Spline transform.

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|Program version || 4.0.0

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

{|
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* <span style="color:blue">'''''Input Image Parameters''''' </span> 
** <span style="color:green">'''Input Image Volume'''</span> [<span style="color:orange">--inputVolume</span>] : Required: input vector image file name. It is recommended that the input volume is the skull stripped baseline image of the DWI scan.
** <span style="color:green">'''Input Anatomical Image Volume'''</span> [<span style="color:orange">--inputAnatomicalVolume</span>] : Required: input anatomical image file name. It is recommended that that the input anatomical image has been skull stripped and has the same orientation as the DWI scan.
** <span style="color:green">'''Vector Image Index'''</span> [<span style="color:orange">--vectorIndex</span>] : Vector image index in the moving image (within the DWI) to be used for registration. ''Default value: 0''
** <span style="color:green">'''Input Rigid Transform'''</span> [<span style="color:orange">--inputRigidTransform</span>] : Required (for B-Spline type co-registration): input rigid transform file name. Used as a starting point for the anatomical B-Spline registration.


* <span style="color:blue">'''''Output Files''''' </span> 
** <span style="color:green">'''Output Transform'''</span> [<span style="color:orange">--outputTransformName</span>] : Required: filename for the  fit transform.


* <span style="color:blue">'''''Registration Parameters''''' </span> 
** <span style="color:green">'''Transform Type'''</span> [<span style="color:orange">--transformType</span>] : Transform Type: Rigid|Bspline ''Default value: Rigid''
** <span style="color:green">'''Number Of Iterations'''</span> [<span style="color:orange">--numberOfIterations</span>] : Number of iterations in the selected 3D fit ''Default value: 1000''
** <span style="color:green">'''Grid Size'''</span> [<span style="color:orange">--gridSize</span>] : Number of grid subdivisions in all 3 directions ''Default value: 12,4,12''
** <span style="color:green">'''Border Size'''</span> [<span style="color:orange">--borderSize</span>] : Size of border ''Default value: 3''
** <span style="color:green">'''Number of Histogram Bins'''</span> [<span style="color:orange">--numberOfHistogramBins</span>] : Number of histogram bins ''Default value: 50''
** <span style="color:green">'''Spatial Scale'''</span> [<span style="color:orange">--spatialScale</span>] : Scales the number of voxels in the image by this value to specify the number of voxels used in the registration ''Default value: 100''
** <span style="color:green">'''Convergence Factor'''</span> [<span style="color:orange">--convergence</span>] : Convergence Factor ''Default value: 10000000''
** <span style="color:green">'''Gradient Tolerance'''</span> [<span style="color:orange">--gradientTolerance</span>] : Gradient Tolerance ''Default value: 0.0001''
** <span style="color:green">'''Maximum Step Size'''</span> [<span style="color:orange">--maximumStepSize</span>] : Maximum permitted step size to move in the selected 3D fit ''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 the selected 3D fit 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">--translationScale</span>] : How much to scale up changes in position compared to unit rotational changes in radians -- decrease this to put more translation in the fit ''Default value: 1000.0''
** <span style="color:green">'''Relaxation Factor'''</span> [<span style="color:orange">--relaxationFactor</span>] : Fraction of gradient from Jacobian to attempt to move in the selected 3D fit ''Default value: 0.5''
** <span style="color:green">'''Number Of Samples'''</span> [<span style="color:orange">--numberOfSamples</span>] : Number of voxels sampled for mutual information computation in the selected 3D fit ''Default value: 100000''
** <span style="color:green">'''Initialize with MomentsAlign registration phase'''</span> [<span style="color:orange">--useMomentsAlign</span>] : MomentsAlign assumes that the center of mass of the images represent similar structures.  Perform a MomentsAlign registration as part of the sequential registration steps.   This option MUST come first, and CAN NOT be used with either CenterOfHeadLAlign, GeometryAlign, or initialTransform file.  This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
** <span style="color:green">'''Initialize with GeometryCenterAlign registration phase'''</span> [<span style="color:orange">--useGeometryAlign</span>] : GeometryAlign on assumes that the center of the voxel lattice of the images represent similar structures. Perform a GeometryCenterAlign registration as part of the sequential registration steps.   This option MUST come first, and CAN NOT be used with either MomentsAlign, CenterOfHeadAlign, or initialTransform file.  This family of options superceeds the use of transformType if any of them are set. ''Default value: false''
** <span style="color:green">'''Initialize with CenterOfHeadAlign registration phase'''</span> [<span style="color:orange">--useCenterOfHeadAlign</span>] : CenterOfHeadAlign attempts to find a hemisphere full of foreground voxels from the superior direction as an estimate of where the center of a head shape would be to drive a center of mass estimate.  Perform a CenterOfHeadAlign registration as part of the sequential registration steps.   This option MUST come first, and CAN NOT be used with either MomentsAlign, GeometryAlign, or initialTransform file.  This family of options superceeds the use of transformType if any of them are set. ''Default value: false''


|[[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.