Modules:BRAINSResample - Revision history

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Usage

KentWilliams at 21:01, 6 May 2010

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KentWilliams: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features NOTOC ===Module Name=== BRAINSResample {| |[[Image:…'

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[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSResample

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

== General Information ==
===Module Type & Category===

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSResample is a program whose purpose is to resample image volumes to a new resolution, optionally applying a transformation.
== Usage ==
In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.

===Quick Tour of Features and Use===

{|
|

*Input Image Files
**Image To Warp: Input Image to transform/warp
**Reference Image: Defines the output space into which Image will be warped
**Deformation Field: Vector volume defining voxel transformation
*Warping Parameters
**Warp By Transform: Filename of BRAINSFit Transfrom file to use in place of deformation field
**Pixel Type: Specifies pixel type for input & output image. "binary" pixel type uses a modified algorithm whereby the image is read as unsigned char voxels, a signed distance map is created, te signed distance map is resampled, and the thresholded image is written to disk.
**Interpolation Mode: Specifies which interpolator is used.
**Invert Linear Transform: Perform transform inversion in ITK physical space before applying linear transform to the image.
|[[Image:BRAINSResampleUI.png|thumb|280px|User Interface]]
|}

== Development ==

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

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===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===
Include funding and other support here.

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

@@ Line 38: / Line 38: @@
 |-
-|Program documentation-url || http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSResample
+|Program documentation-url || https://www.slicer.org/wiki/Modules:BRAINSResample |-
 |}

@@ Line 17: / Line 17: @@
 Category: Registration
 ===Authors, Collaborators & Contact===
-* Author1: Hans Johnson, University of Iowa
-* Contributor1: Kent WIlliams, University of Iowa
+Author: This tool was developed by Vincent Magnotta, Greg Harris, and Hans Johnson.
-* Contact: Hans Johnson, hans-johson at uiowa.edu
 ===Module Description===
-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).
@@ Line 51: / Line 71: @@
 {|
+|
 |[[Image:BRAINSResampleUI.png|thumb|280px|User Interface]]
 |}
@@ Line 71: / Line 93: @@
 ===Dependencies===
-BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
+BRAINSResample depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
-===Tests===
+BRAINSResample depends on BRAINSCommonLib
-* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]
+===Tests===
@@ Line 84: / Line 104: @@
 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 ==
-   --outputVolume <std::string>
+===Acknowledgment===
-     Resulting deformed image
+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.
 -->

@@ Line 26: / Line 26: @@
 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, Rigid transformation (using an ITK transform) and Warping (using a deformation field volume).
+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:

@@ Line 60: / Line 60: @@
 **Interpolation Mode: Specifies which interpolator is used.
 **Invert Linear Transform: Perform transform inversion in ITK physical space before applying linear transform to the image.
 |[[Image:BRAINSResampleUI.png|thumb|280px|User Interface]]
 |}