Hi all,
I have a few quick questions about the vbm scripts for spm2b (presumably
applicable for spm2)
Based on previous emails, I understand script number 1 to be doing the
following steps
1) Normalize (affine - to a T1 template)
2) Segment
3) Normalize (nonlinear - to a GM template)
4) Segment
5) Modulate
The Good et al optimized vbm also calls for a cleanup step which John has
indicated would work well if one did brain extraction and then created new
gray or white matter images by using ImCalc. As far as I can tell from
previous emails, this cleanup step is happening in the vbm script, but I
couldn't tell where it's coded. Is it explicitly in the vbm script or is it
buried in the brain segmentation in spm2 (whereas it had to be done
separately in spm99).
If this cleanup step is not in the script now, would it be easy to insert
the code to do this? I've seen other code for segmentation and brain
extraction, but I wouldn't know how to integrate this into the vbm script?
Lastly, in trying to do brain extraction using pulldown menus, I noticed
that saving the extracted brain is no longer an option, as it was in spm99.
If the vbm script or segmentation doesn't do the cleanup operation, how
would one save the extracted brain mask for this purpose?
Thanks very much for the clarification.
HOWIE ROSEN
Howard Rosen
UCSF Department of Neurology
Memory and Aging Center
350 Parnassus Ave., Box 1207, Suite 706
San Francisco, CA 94143
Phone: 415-476-1895
Fax: 415-476-4800
email: [log in to unmask]
http://memory.ucsf.edu
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