Elastic Registration Tools

Simple Elastic (Multiple) Image Warping: SimpleWarp

  • Regional mutual information driven image warping tool. Used for approximate spatial normalization of brain anatomy and geometric distortion estimation.
  • Command line example estimating warp from reference image to floating image:
  • SimpleWarp  refImage.gipl refImageMask.gipl floatImage.gipl warpOut.gipl -dofin ref2float.dof -Quiet -NoLog
  • Here each of the .gipl files can also be analyze, or nifti format images in stored either 16 or 32 bit integer or 32 bit floating point data format.
  • The "refImageMask.gipl" should have the same dimensions as "refim.gipl" but contain a mask of the region to be warped (e.g., set to 100 inside and -1 outside).
  • The optional "-dofin ref2float.dof" option specifies the initial linear transformation from reference to floating coordinates (calculated using mmvreg). This can be as a ".dof" file format or a midas transformation file format.
  • The final warp is saved in a 4D floating point image "warpOut.gipl" and can be applied to images using the warpimF command.
  • The "-Quiet" and "-NoLog" options prevent printing of debugging information and the creation of log files for the program execution.


Program to apply simple linear elastic deformation fields (created by SimpleWarp) to images using specified interpolation.


warpimF  warpIn.gipl refImage.gipl floatImage.gipl float2ref.gipl -dofin ref2float.dof -InterpC3

This applies the transformation field stored as a 4D image file "warpIn.gipl" to bring "floatImage.gipl" into the coordinates and sampling resolution of "refImage.gipl" using Cubic Interpolation (-InterpC3 option). Alternative interpolation schemes are -InterpNN for nearest neighbour, -InterpL3 for trilinear, etc. An additional linear transformation is compounded onto the deformation field using "-dofin ref2float.dof" to floating image coordinates (as in the SimpleWarp command).