Documentation/4.3/Modules/BRAINSResample

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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, <email>(hans-johnson@uiowa.edu</email>

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).


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: Image To Warp
    • Reference Image: 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: Resulting deformed image
    • Pixel Type: Specifies the pixel type for the input/output images. If the type is "input", then infer from the input image. 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): Displacement Field to be used to warp the image (ITKv3 or earlier)
    • Transform file: Filename for the BRAINSFit transform (ITKv3 or earlier) or composite transform file (ITKv4)
    • Interpolation Mode: 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?: True/False is to compute inverse of given transformation. Default is false
    • Default Value: Default voxel value
  • Advanced Options:
    • Add Grids: 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: Explicitly specify the maximum number of threads to use.


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