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My experience is with only structural rat MRI  and microPET, but I
think the basic process applies. 
I like to start by realigning using Check Reg->re-Orient until the images are close
to my template, so that the brains are reasonably aligned and overlap the template
fairly well.

I follow this by (SPM) Realigning the images to the template.  There is an advantage
over human mri in that variability between rat brains is less, which allows this
realignment process to work fairly well.   The
disadvantage is that there is a much higher percentage of voxels coming from
outside the brain.   If my hand realignment is reasonably close, I use a large mask
as a weighting image in the realignment.   My large mask comes from ROIs of
the brain of the template, which I enlarged using Check Reg.

This last step won't be perfect because the template and MRI are from different
animals, but it should be good enough to get the MRI to fall underneath a tighter
mask of the template brain.
At this point you should be able to proceed with normalization.  You could mask
out non-brain, or specify the template mask as a weighting image for the template
or rat MRIs.

My basic approach is to take smaller steps than I would in processing human brains,
verify constantly, and try to prevent far out solutions using brain masks as weighting images.

The problem becomes harder and trickier the closer the nuisance activation is to the
brain.  Eliminating signal from around the eyes isn't too bad.

Hope this helps some.


dave
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On Thu, Mar 19, 2009 at 12:41 PM, Joensuu, Raimo <[log in to unmask]> wrote:
Hello,

I am doing fMRI with rats. My fMRI images contain a lot of signal from eyes and extracranial muscles and matching them to the segmented anatomical images (which contain only the brain) fails badly. I wonder if anybody anybody has succeeded in this type of normalization?

Cheers,
Raimo

Raimo Joensuu, PhD
Senior Research Scientist
AstraZeneca R&D Molndal, DECS - Imaging
S-43183 Mölndal, Sweden
phone: +46 (0)31 706 5993
fax: +46 (0)31 776 3758