Hi,
Did the image before you ran BET on it look to be
in the same orientation in FSLView? The orientation
shown is always that dictated by the scanning protocol
(e.g. axial, coronal, etc) and so it is normal to see data
in different orientations than the standard-space templates.
However, if your output from BET was in a very different
orientation from the input to BET, then this is very serious
and we need to know more.
All the best,
Mark
On 11 Nov 2009, at 15:11, *Shal Hat* wrote:
> Hi,
>
> I use BET to extract the brain. However when I looked at it using
> FSLVIEW, the brain was
> inverted (cortex on bottom, anterior is where Right should be and
> posterior is where Left
> should be). How would I be able to resolve this issue? What caused
> it? How will it affect my
> GLM or ICA analysis?
>
> Thanks a million :)
>
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