Hi.
WRT registering your few EPI slices with a gap in the middle - you are
right in suspecting that there is not nearly enough information in these
few slices to register directly to a full 3D volume - in particular the
rotation will be very poorly conditioned. You will therefore need to
ideally take a whole-brain EPI which includes the few slices which you
have here - you then pretty much know the registration for this pair of
images. Then you can register the whole-brain EPI to a structural. Note
that this problem is quite similar to that covered here:
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0107&L=fsl&F=&S=&P=1453
Alternatively, you will have to work out which parts of the structural are
roughly equivalent to the functional slices and just use those in the
registration, to help constrain the rotation search....
ttfn, Steve :)
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