Thank you!

But then it sounds like my approach is correct.

I wanted my varying native resolution data to all have the same resolution (192,224,192) and that the brains are placed at the center of the volumes so that they all somewhat overlap.

But a simple 3dresample command gives me the correct grid but the brains are not moved to the center (of course)

And a simple 3dresampel command with the template as -master sometimes results in that the brain ends up at the corner of the image. It is important that the brains are centred in the volume an all somewhat overlap (not aligned to each other but basically occupies the same space).

So I re sampled the MNI-template (actually zero-padded since the template dims where very close to the wanted res) and used 3dAllineate with the template with the wanted resolution as a base. But I don't want it to actually align my brains to it (no rotation or scaling), just move them to where the MNI brain is and the -cmass -warp shift_only options seems to only preform the "shift". The individual brains seem to keep their angulations etc which is what I want. Does that seem about right?