[VoxBo] normalization using SPM procedures (taking skull into account)

[Joonkoo Park]

Hello,

As recommended by VoxBo wiki, I'm trying to normalize images using SPM5.
I first convert the (anatomical) .cub files into .hdr and .img (using 
vb2img) and use SPM procedures to calculate *_sn.mat and eventually 
warp the original .img image to a normalized one. I used T1.nii file in 
spm/template folder as a template for calculating parameters for 
anatomical images.

One problem I see here (well, it would be the same case if I were to 
use VoxBo norm) is that my anatomical images (i guess functional images 
too) do not include skull, but the template includes skull and other 
parts of the head. I am worried that my anatomical image will assume 
that even the skull part of the template is part of the brain, and this 
seems to the case when I look at the normalized images.

The skull part of my images are eliminated during the preprocessing 
procedure at the scanner site. Is there a way to solve this problem?

Thanks!