Hi Russ,
If you use 3dzeropad, an afni function, to cut off the very top, bottom
and sides of the image (non-brain stuff), this problem goes away. For
example:
3dZeropad -S -30 -I -65 -A -35 -P -30 -prefix filename inputfile will
remove the 30 most superior slices, the 65 most inferior slices, etc.
Best
Jen
Jennifer Bramen
UCLA Brain Mapping Center
660 Charles Young Dr. So
Los Angeles, CA 90095
On May 18, 2004, at 4:26 PM, Russ Poldrack wrote:
> hi - we're having some trouble getting BET to work properly with
> MP-RAGE data from a Siemens Allegra. The problem is that the carotids
> are very bright, and BET consistently includes a chunk of neck tissue
> within the segmented brain, leading to bad registration errors with the
> standard for some subjects. We have tried a wide range of BET
> parameters but have not been able to prevent this. We've solved the
> problem so far by trying to optimize BET for the rest of the brain and
> then removing the offending sections by hand, but clearly it would be
> nice if BET could deal with these images more adequately. Do you have
> any suggestions about tricks that we might try (other than getting a
> new anatomical sequence)?
>
> cheers,
> russ
>
> ---
> Russell A. Poldrack, Ph.D.
> Assistant Professor of Psychology, UCLA
> Franz Hall, Box 951563
> Los Angeles, CA 90095-1563
> email: [log in to unmask]
> phone: 310.794.1224
> fax: 310.206.5895
> web: http://www.poldracklab.org/
>
>
Jennifer Bramen
UCLA Brain Mapping Center
660 Charles Young Dr. So
Los Angeles, CA 90095
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