Hi Jeff,
> I have been running FSL VBM analyses and many times I have
> my most
> significant results appear to fall outside of the actual
> brain
> (somewhere the skull should be according to an overlapped
> standard
> MNI152 brain). Why would this be? Is it possible that
> fslvbm_3_proc is
> not scaling my nifti files appropriately? or is it finding
> a
> difference in skull density? or maybe something else is
> happening?
At this stage of the analysis, there should not be any skull in your images. If there is, it means that you have not followed the fslvbm protocol or you have not checked properly your images after the fslvbm_1_bet.
A good thing might be to look at the GM_mod_merg 4D image in fslview and check each volume to see if the registration is correct, which I suspect is not... If this is indeed the registration that has failed, you will need to determine why by checking each step of the protocol up until the registration.
Cheers,
Gwenaelle
--------------------------------------------------------------------
Gwenaëlle Douaud, PhD
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/~douaud
--------------------------------------------------------------------
|