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The Linear Registration module is a CLI module using the ITK...

If you want a resampled data set to be created from the moving data set, then use the pull-down menus to generate a new output volume and a new transform

If you do not want to resample the data, then:

  1. Tell the Linear or Affine plugin to generate an output transform
  2. Do not tell the Linear or Affine plugin to generate an output volume
  3. After running the module, go to the Data module and drag the moving image under the calculated transform.
  4. Go to the transform module, select the transform you just created (even if it shows up), at the bottom of the module click on the invert transform button