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The result is a registered image which will be saved to the location specified in the Output image box.
All other options/boxes can be left at their default values.
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Reference image mode in the top box, then filling in the Reference image and Input image boxes with the appropriate images.
Weighting volumes can be specified using -refweight, -inweight (or both).
This allows the cost function to have a different weighting at each voxel, which is useful for excluding areas (weight=0) of no interest, or increasing the weighting around important structures such as the ventricles.
The two resulting transformations are concatenated and then applied to the original low res image to create an Output image that is a version of the low res image transformed (resliced) to the reference image space. For 3D to 3D mode the DOF can be set to 12 (affine), 9 (traditional), 7 (global rescale) or 6 (rigid body).
In addition, there is the BBR cost function which utilises a segmentation of the reference image to define a boundary, and it is the intensity differences in the input image, across the transformed boundary, that contribute to the cost.
Note that this is different from masking the original images, as masking introduces artificial boundaries whereas weighting does not.
Choose from 6,7,9 or 12 Degrees of Freedom (DOF) for full 3D registrations.
More flexible DOF options are provided by the specific schedule files provided in This includes Nearest Neighbour, a family of Sinc-based methods (three window types - rectangular, Hanning and Blackman) with configurable window width, and spline (a highly efficient method, with similar output characteristics to sinc).
The interpolation is only used for the final transformation (and in applyxfm), not in the registration calculations.
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