When the images are of the same subject then 6 DOF is appropriate for large FOV and 3 DOF is appropriate for small FOV/single slice.
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To apply saved transformations, the GUI Apply XFM can also be used which provides the option of specifying the number of voxels and voxel size directly.
There are two main types of cost function: intra-modal (least squares and normalised correlation) and inter-modal (correlation ratio and mutual information-based options).
The recommended options (to try first) are: correlation ratio (which is the default) for inter-modal and normalised correlation for intra-modal.
The choice of DOF (Degrees of Freedom) depends largely on whether the images to be registered are intra/inter-subject and small/large FOV.
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