Difference between revisions of "Modules:BRAINSResample"

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Category: Registration
 
Category: Registration
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===Authors, Collaborators & Contact===
 
===Authors, Collaborators & Contact===
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* Author1: Hans Johnson, University of Iowa
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* Contributor1: Kent WIlliams, University of Iowa
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Author: This tool was developed by Vincent Magnotta, Greg Harris, and Hans Johnson.
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* Contact: Hans Johnson, hans-johson at uiowa.edu
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 +
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. 
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===Module Description===
 
===Module Description===
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BRAINSResample is a program whose purpose is to resample image volumes to a new resolution, optionally applying a transformation.
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{| style="color:green" border="1"
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|Program title || BRAINSResample
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|-
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|Program version || 3.0.0
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|-
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|Program documentation-url || https://www.slicer.org/wiki/Modules:BRAINSResample |-
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|}
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BRAINSResample is a program whose purpose is to resample image volumes to a new resolution, optionally applying a transformation.
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== Usage ==
 
== Usage ==
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In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.
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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).
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<!-- ===Use Cases, Examples===
 
<!-- ===Use Cases, Examples===
  
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This module is especially appropriate for these use cases:
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This module is especially appropriate for these use cases:  
  
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* Use Case 1:
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* Use Case 1:
 
* Use Case 2:
 
* Use Case 2:
  
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{|
 
{|
 
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|
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* <span style="color:blue">'''''Inputs''''' </span> Parameters for specifying the image to warp and resulting image space
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** <span style="color:green">'''Image To Warp'''</span> [<span style="color:orange">--inputVolume</span>]: Image To Warp
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** <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.
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* <span style="color:blue">'''''Outputs''''' </span> Resulting deformed image parameters
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** <span style="color:green">'''Output Image'''</span> [<span style="color:orange">--outputVolume</span>]: Resulting deformed image
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** <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.
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* <span style="color:blue">'''''Warping Parameters''''' </span> Parameters used to define home the image is warped
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** <span style="color:green">'''Deformation Field'''</span> [<span style="color:orange">--deformationVolume</span>]: Deformation Field to be used to warp the image
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** <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
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** <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
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** <span style="color:green">'''Default Value'''</span> [<span style="color:orange">--defaultValue</span>]: Default voxel value
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* <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
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** <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
  
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*Input Image Files
 
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**Image To Warp: Input Image to transform/warp
 
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**Reference Image: Defines the output space into which Image will be warped
 
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**Deformation Field: Vector volume defining voxel transformation
 
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*Warping Parameters
 
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**Warp By Transform: Filename of BRAINSFit Transfrom file to use in place of deformation field
 
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**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.
 
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**Interpolation Mode: Specifies which interpolator is used.
 
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**Invert Linear Transform: Perform transform inversion in ITK physical space before applying linear transform to the image.
 
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*Result File
 
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**Output Image: the input image, transformed/warped and then resampled into the reference image space.
 
 
|[[Image:BRAINSResampleUI.png|thumb|280px|User Interface]]
 
|[[Image:BRAINSResampleUI.png|thumb|280px|User Interface]]
 
|}
 
|}
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===Dependencies===
 
===Dependencies===
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BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
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BRAINSResample depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
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===Tests===
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BRAINSResample depends on BRAINSCommonLib
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TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
 
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===Known bugs===
 
  
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Links to known bugs in the Slicer3 bug tracker
 
  
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* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]
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===Tests===
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http://testing.psychiatry.uiowa.edu
  
  
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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.
 
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.
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<!== ===Source code & documentation===
 
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Links to the module's source code:
 
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Source code:
 
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*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
 
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*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]
 
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Doxygen documentation:
 
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*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]
 
  
 
== More Information ==  
 
== More Information ==  
  
 
===Acknowledgment===
 
===Acknowledgment===
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Include funding and other support here.
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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.
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===References===
 
===References===
 
Publications related to this module go here. Links to pdfs would be useful.
 
Publications related to this module go here. Links to pdfs would be useful.
 
-->
 
-->

Latest revision as of 13:18, 27 November 2019

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Module Name

BRAINSResample

User Interface

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

Program title BRAINSResample
Program version 3.0.0
Program documentation-url -

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).

Quick Tour of Features and Use

  • Inputs Parameters for specifying the image to warp and resulting image space
    • Image To Warp [--inputVolume]: Image To Warp
    • Reference Image [--referenceVolume]: 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.
  • Outputs Resulting deformed image parameters
    • Output Image [--outputVolume]: Resulting deformed image
    • Pixel Type [--pixelType]: 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.
  • Warping Parameters Parameters used to define home the image is warped
    • Deformation Field [--deformationVolume]: Deformation Field to be used to warp the image
    • Warp By Transform [--warpTransform]: Filename for the BRAINSFit transform used in place of the deformation field
    • Interpolation Mode [--interpolationMode]: Type of interpolation to be used when applying transform to moving volume. Options are Linear, NearestNeighbor, BSpline, or WindowedSinc
    • Default Value [--defaultValue]: Default voxel value
  • Advanced Options 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
    • Add Grids [--gridSpacing]: 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
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 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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