Hi Varina
I have similar problems frequently, even with adult images. Still, I
haven't found an alternative to BET that is reasonably fast. Here are
some tricks you can try individually or in combination:
Due to a bug, BET trusts the data ordering instead of the NIfTI header
to determine the vertical axis. If your data ordering is
non-standard, It can help to apply fslreorient2std to your image
before bet.
Your specific problem may be due to large amounts of face and neck
data in the image. Sometimes it helps to use -R to make bet estimate
the centre of gravity recursively.
You can try pre-masking with standard_space_roi -b. This is best used
after fslreorient2std and generates a much more generous mask than
bet, but it is more robust. If you determine the voxel coordinates of
the centre of gravity on the output (fslstats -C) and feed them to bet
via the -c parameter, you may get a better extraction. You've got a
choice of applying bet to the original image or to the
standard_space_roi output. I have found no hard and fast rule as to
which is better, just that if you bet the premasked output you
probably need to use the -f parameter with a low value (0.2-0.4) to
avoid undersegmentation (cut-off gyri).
Finally, if you have a T2-weighted image acquired in the same scanning
session, try providing it to bet via -A2.
To apply a mask named mask.nii, use 'fslmaths image -mas mask masked'.
'fslmaths' entered by itself tells you about this and other options.
Hope this helps,
Rolf
On 1 October 2011 19:39, Varina Wolf <[log in to unmask]> wrote:
> GreyMatterMask Image Upload: 283825
>
> Hello FSL experts,
>
> I never could get BET to strip my pediatric structural T1 images well. Just left huge chunks of tissue infront of the brainstem, and if I adjusted the f upward, it ended up chopping off cortex to correct for this.
>
> Alternatively, I am looking for a way to subtract out the skull and nonbrain using this greymatter mask that is uploaded. Does fslmaths or any other such program have this capability?
>
> Gratefully,
> Varina
>
--
Rolf A Heckemann, MD PhD
Médecin chercheur
Fondation Neurodis
CERMEP - Imagerie du Vivant
Hôpital Neurologique Pierre Wertheimer
59 Boulevard Pinel
69003 Lyon
France
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