Hi, thanks for sending the data. Yes, this is a fairly tricky image
as the slices are thick and the brain tissue quite dark.
However you can get pretty good results just using the -f and -g
options, for example
bet 116_1 116_1_brain -f 0.2 -g 0.4
You might want to further fine tune these.
You might also want to remove bright CSF/eyes using the -uthr option
in avwmaths++
Cheers.
On 7 Jun 2007, at 10:23, Ed Gronenschild wrote:
> Hi,
>
> Using BET (v1.2) on axial (transversal) T2 stacks I get very bad
> results: only part of
> the brain is extracted. Using different settings with the -f and -g
> options does not
> produce much better results (btw, no other options were used).
> Therefore, a few questions arise:
>
> 1.
> The stacks measures 512 * 512 pixels with 24 slices.The voxel size is
> 0.4492 * 0.4492 * 5.0 mm.
> The fact that the voxels are not cubic could that be a problem?
>
> 2.
> If I inverse Y (flip the stack vertically) the results become even
> worse.
> Is BET sensitive to spatial orientation of the stack?
>
> Ed Gronenschild, PhD
> Maastricht University
> Dept. of Medical Informatics
> Maastricht, The Netherlands
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