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

[Charan Ranganath]

Hi, I think I can suggest two potential solutions:
(1) Take the t1.nii image and skull strip it using the brain extraction 
tool (BET). The program is described at: 
http://www.fmrib.ox.ac.uk/analysis/research/bet/

(2) Normalize your EPIs to the EPI template included in SPM.

We have found that we get better across-participant registration with 
approach #2. However, if your EPIs have a lot of dropout and distortion 
or if they only cover part of the brain, you will have to use #1.

Good luck. CR

Joonkoo Park wrote:
> 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!
> 

-- 
Charan Ranganath, Ph.D.
Associate Professor
Center for Neuroscience and Dept. of Psychology
University of California at Davis
1544 Newton Ct.
Davis, CA 95616

phone: 530-757-8750
fax: 530-757-8640

http://DynamicMemoryLab.org