This normalise uses intensity differences. It can be adjusted to only do affine.
SPM Batch GUI
SPM, Tools, Old Normalise
“Estimate” calculates spatial normalisation and saves the parameters (*_sn.mat and *_inv_sn.mat files), but does not warp any images
“Write” uses saved parameters to write a warped (normalised) file at a specified voxel size and bounding box.
“Estimate and Write” does both steps; options are same as separate steps.
Set “Affine Regularisation” to “No regularisation"
For affine only, set “Nonlinear Frequency Cutoff” to “Inf”
