Sorry about that - I read your email too quickly and didn't notice that you were not just doing a straight subsampling. There is a section on this in the FLIRT FAQ (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ), particularly the last paragraph of Can I register to an image but use higher/lower resolution (voxel size)?" section.

If you have access to freesurfer, you may find that this is easier to do with mri_convert, in that case you can do it like this:

mri_convert -vs 2 2 2 -oni 92 -onj 92 -onk 56 INPUT.nii.gz OUTPUT.nii.gz

Regarding your other question, it's difficult to say without knowing more about exactly what you're trying to do but in general, you would do something like an affine registration with FLIRT and then a nonlinear registration with FNIRT. There are some basic examples of this on the FNIRT webpage.

Hope this helps,

Niels