Thanks a lot, Jesper.
It's for the "standard" way, I guess, within Feat. Also there is not a whole lot of neck and the "no-neck / no nose" has not been cropped but just masked out (as part of the freesurfer pipe). So I guess it won't make much of a difference but we may as well give it a test.
Best wishes-
Andreas
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Von: FSL - FMRIB's Software Library im Auftrag von Jesper Andersson
Gesendet: Do 18.12.2008 00:38
An: [log in to unmask]
Betreff: Re: [FSL] fnirt
Hi Andreas,
> 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
tight".
Good luck Jesper
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