Hi Kimberly
BET expects a particular data ordering in your images. You can check
whether you have this problem on a file named image.nii by running
bet image image-bet -g -1
This will result in a strongly imbalanced brain extraction in
image-bet.nii. If it removes the base of the brain and leaves the
superior part intact, then your data ordering is okay. If you find
that it is imbalanced in any other direction, you should reorder your
data using fslswapdim, e.g.
fslswapdim image RL PA IS image-reordered
and run BET on the resulting file.
Hope this helps
Rolf
On Mon, Dec 14, 2009 at 04:53:34PM +0000, Kimberly Kontson wrote:
>
> With a fractional intensity threshold of 0.3, the resultant BET images
> still have tissue missing from the cortex. I have changed the
> threshold to 0.2 and 0.1, but now there is unwanted tissue included in
> these images (eyes, etc). Is there a way to manually remove this
> unwanted tissue in the images through FSL?
>
>
>
> Thank you!
>
>
>
> Kimberly
--
Rolf A Heckemann, MD PhD
Médecin chercheur
Fondation Neurodis
CERMEP - Imagerie du Vivant
Hôpital Neurologique Pierre Wertheimer
59 Boulevard Pinel
69003 Lyon
France
1260811029
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