Documentation/Nightly/Modules/BRAINSResample

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For the stable Slicer documentation, visit the 4.8 page.


Introduction and Acknowledgements

This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website.
Author: Hans Johnson, UIOWA
Contributor1: Vincent Magnotta, UIOWA
Contact: Hans Johnson,

University of Iowa  
Surgical Planning Laboratory  


Module Description

This program 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). Full documentation available here: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSResample.


Use Cases

Most frequently used for these scenarios:

  1. Change an image's resolution and spacing.
  2. Apply a transformation to an image (using an ITK transform IO mechanisms)
  3. Warping an image (using a vector image deformation field).

Tutorials

Links to tutorials that use this module

Panels and their use

Parameters:

  • 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
    • Displacement Field (deprecated) (deformationVolume): Displacement Field to be used to warp the image (ITKv3 or earlier)
    • Transform file (warpTransform): Filename for the BRAINSFit transform (ITKv3 or earlier) or composite transform file (ITKv4)
    • Interpolation Mode (interpolationMode): Type of interpolation to be used when applying transform to moving volume. Options are Linear, ResampleInPlace, NearestNeighbor, BSpline, or WindowedSinc
    • Compute inverse transform of given transformation? (inverseTransform): True/False is to compute inverse of given transformation. Default is false
    • Default Value (defaultValue): Default voxel value
  • Advanced Options:
    • 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
  • Multiprocessing Control:
    • Number Of Threads (numberOfThreads): Explicitly specify the maximum number of threads to use.


List of parameters generated transforming this XML file using this XSL file. To update the URL of the XML file, edit this page.


Similar Modules

References

Publications related to this module go here. Links to pdfs would be useful. For extensions: link to the source code repository and additional documentation

Information for Developers