afni.nimh.nih.gov

That suggests that FSL is leaving the tranformation
in the dataset header, rather than applying it to the
data. But AFNI will not apply those internally when
performing some group comparison, so maybe you will
indeed need to run 3dWarp -gridset.

When applying such a transformation, there is no need
to keep the original grid. afni_proc.py would use
isotropic voxels that are basically the minimum edge
size.

- rick