View source for Modules:BRAINSResample

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__NOTOC__
===Module Name===
BRAINSResample

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|[[Image:BRAINSResampleUI.png|thumb|280px|User Interface]]
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== General Information ==
===Module Type & Category===

Type: CLI

Category: Registration



===Authors, Collaborators & Contact===

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

Contributors: The development of this tool was supported by funding from grants NS050568 and NS40068 from the National Institute of Neurological Disorders and Stroke and grants MH31593, MH40856, from the National Institute of Mental Health.  



===Module Description===

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|Program title || BRAINSResample

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|Program version || 3.0.0

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|Program documentation-url || http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSResample

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BRAINSResample is a program whose purpose is to resample image volumes to a new resolution, optionally applying a transformation.

== Usage ==
BRAINSResample collects together three common image processing tasks that all involve resampling an image volume: Resampling to a new resolution and spacing, applying a transformation (using an ITK transform IO mechanisms) and Warping (using a vector image deformation field).

<!-- ===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===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1
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===Quick Tour of Features and Use===

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* <span style="color:blue">'''''Inputs''''' </span> Parameters for specifying the image to warp and resulting image space
** <span style="color:green">'''Image To Warp'''</span> [<span style="color:orange">--inputVolume</span>]: Image To Warp
** <span style="color:green">'''Reference Image'''</span> [<span style="color:orange">--referenceVolume</span>]: Reference image used only to define the output space. If not specified, the warping is done in the same space as the image to warp.
* <span style="color:blue">'''''Outputs''''' </span> Resulting deformed image parameters
** <span style="color:green">'''Output Image'''</span> [<span style="color:orange">--outputVolume</span>]: Resulting deformed image
** <span style="color:green">'''Pixel Type'''</span> [<span style="color:orange">--pixelType</span>]: Specifies the pixel type for the input/output images.  The "binary" pixel type uses a modified algorithm whereby the image is read in as unsigned char, a signed distance map is created, signed distance map is resampled, and then a thresholded image of type unsigned char is written to disk.
* <span style="color:blue">'''''Warping Parameters''''' </span> Parameters used to define home the image is warped
** <span style="color:green">'''Deformation Field'''</span> [<span style="color:orange">--deformationVolume</span>]: Deformation Field to be used to warp the image
** <span style="color:green">'''Warp By Transform'''</span> [<span style="color:orange">--warpTransform</span>]: Filename for the BRAINSFit transform used in place of the deformation field
** <span style="color:green">'''Interpolation Mode'''</span> [<span style="color:orange">--interpolationMode</span>]: Type of interpolation to be used when applying transform to moving volume.  Options are Linear, NearestNeighbor, BSpline, or WindowedSinc
** <span style="color:green">'''Default Value'''</span> [<span style="color:orange">--defaultValue</span>]: Default voxel value
* <span style="color:blue">'''''Advanced Options''''' </span> Add warped grid to output image to help show the deformation that occured with specified spacing.   A spacing of 0 in a dimension indicates that grid lines should be rendered to fall exactly (i.e. do not allow displacements off that plane).  This is useful for makeing a 2D image of grid lines from the 3D space 
** <span style="color:green">'''Add Grids'''</span> [<span style="color:orange">--gridSpacing</span>]: Add warped grid to output image to help show the deformation that occured with specified spacing.   A spacing of 0 in a dimension indicates that grid lines should be rendered to fall exactly (i.e. do not allow displacements off that plane).  This is useful for makeing a 2D image of grid lines from the 3D space 

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

== Development ==

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

===Dependencies===
BRAINSResample depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
BRAINSResample depends on BRAINSCommonLib


===Tests===
http://testing.psychiatry.uiowa.edu


===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.

== More Information == 

===Acknowledgment===
The development of this tool was supported by funding from grants NS050568 and NS40068 from the National Institute of Neurological Disorders and Stroke and grants MH31593, MH40856, from the National Institute of Mental Health.  


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