> quick question: Is fnirt better off when superfluous neck and / or parts
> of the nose / face are removed? Would you expect much of a difference?
It depends. If you are using it in the "standard" way, i.e. registering to
a template in standard-space and with --refmask specified to be a mask
that mask out most extra-cerebral bits, then it will make no difference.
If you are using it to "register some image to some other image", then it
might make a difference. The execution time (and RAM requirements) will
depend on the FOV of the --ref image (the --in image matters very little).
It is therefore a bad idea to use your "typical structural image" with an
FOV that extends almost down to the shoulders in the z-direction. It helps
a lot to crop the image to be "a reasonably tight fit around the brain".
Look at the MNI template to get an idea of what I mean by "reasonably
Good luck Jesper