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Module Name


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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

Module Description

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


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.
  • Result File
    • Output Image: the input image, transformed/warped and then resampled into the reference image space.
User Interface


Notes from the Developer(s)


BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.


TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.

Known bugs

Links to known bugs in the Slicer3 bug tracker

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

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