Dear Jiansong,
A word of caution beforehand. It's be more than 2 years now since I have
done this cerebellum/brainstem removal, and my memory of the exact step may
be not very accurate. But the general steps are correct.
The procedure below applies to a template brain, i.e. one for which masks
of these areas exist. If you want to do it for individual brains, you are
back to drawing ROIs in some software package (e.g. MRIcro). This can be
tedious.
So here is basic outline for for the removal of the cerebellum/brainstem
from a template brain. For instance I did this for the colin template (I
think it's available with the other ICBM templates at
http://www.loni.ucla.edu/ but I am not sure). This was also the brain on
which the AAL regional templates were drawn.
(1) CREATE A MASK FOR BRAINSTEM AND CEREBELLUM
take wfu_pickatlas and load all AAL regional masks that cover the brainstem
and/or cerebellum (or any other region for that matter that you want to
remove). Save this combined mask as e.g. colin_no_cereb_bs_mask.img IN
REVERSE POLARITY, i.e. 0's in the brainstem and cerebellum, and 1's elsewhere
(2) REMOVE CEREBELLUM/BRAINSTEM FROM IMAGE
use spm_imcalc and multiply your T1 image (e.g., colin.img) with your newly
create mask (colin_no_cereb_bs_mask.img). The result is your template brain
without the cerebellum/brainstem
(3) CREATE RENDER.MAT FILE FOR 3D RENDERING
Now I assume that you might want to render inferior temporal activation on
a 3D brain (e.g. with the Overlay/Render button). In order to do so, you
need a render_xxx.mat file. You can create this by using the Render/Xtract
Brain button (in SPM2). Then the render_xxx.mat file will be created for
which you are prompted when you want to do the 3D rendering.
Cheers,
Jan
Jiansong Xu wrote:
> Dear Friends:
>
> Are there any methods or tools which allow me to remove cerebellum and/or
> brain stem from the whole brain images, either T1 or EPI T2 high resolution
> images?
>
> Thanks
>
> Jiansong
>
--
Jan Gläscher, Ph.D. Caltech Brain Imaging Center
+1 (626) 395-4976 (office) Caltech, Broad Center, M/C 114-96
+1 (626) 395-2000 (fax) 1200 California Blvd
[log in to unmask] Pasadena, CA 91125
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