> Is there a way I can control the degree of transformation parameter with
> spm_realign.m?
>
> For example, instead of realignment using rigid body transformation using 6
> transformation parameters, can I realign the images with rigid body
> transformation plus x shear?
It will involve some additional coding. Basically, there is a structure that
gets passed to spm_realign.m, which has an undocumented field ('lkp'). If
this field is set to [1:6, 12], then it may induce SPM to have the desired
behaviour. I suspect that it won't do exactly what you want it to do though.
Try working through the matrices generated by spm_matrix.m and those used by
the registration and you'll see why (the order of the parameterisation is
important, and you'll also need to account for shear in the reference
image).
Best regards,
-John
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