I have 3T epi data for which I don't have field maps and am trying to
achieve the best registration possible by using an initial highres (6DOF
to an epi obtained during rest) and the subject's structural T1 en route
to the template.
Mark has previously suggested to me that my best bet is to use cost
function masking. I've tried following the tips provded by Matthew Brett
on the CBU page, although these are designed for SPM. In tyring to
extrapolate them for the purposes of FEAT analysis,a few issues have

1 - Would I have to mask just the initial highres, or both the initial
highres and task epi? If the latter, would I just mask the middle volume,
as this is what is used in the registration? If so, my 4D file contains
160 volumes. Would the middle correspond to the 79th, or the 80th?

2 - The CBU page recommends co-registering the epi to the structural and
using the "yoke" function in MRIcro to identify points where there is
signal dropout in the epi relative to the structural. These are the
portions that should be masked out. If I register the unmasked epi to the
structural, wouldn't this yield a (relatively) poor correspondance between
the images, so that using this as the basis for identifying signal dropout
would not be the best way to go about it? Are there any alternative ways
for idetifying which areas to mask out?

3 - Following from 2, would there be any problems in doing a straight
image subtraction to identify the areas to be masked? It seems to me that
this would be plagued by the same problems as in 2, but that it would be a
quicker way to go about it?

4 - The CBU page recommends smoothing the mask image (8mm in accordance
with the SPM default). Would I also need to do this with FEAT? Would I use
5mm, as this is the FEAT default (or alternatively, whatever level I set
it to)?

5 - As an aside, can someone tell me why the average epi template in SPM
would be a poor choice as an intial highres? Does the fact that it's not
the same brain as your subject introduce more problems than the advantage
of having the added contrast?

Sorry if some of these questions seem a bit basic - still trying to get my
head around all of this!
Thanks heaps, I really appreciate your ongoing help!