Hi,
I'm afraid that the brain extraction tool in FSL is designed and optimised for human brains.
In our experience it does not work well for rat brains.
So you can either create a brain mask manually in FSLView or try and use non-linear registration between the image you are dealing with an a template or example image where a brain mask has already been created, then transform that brain mask back into the original image space once you have the registration transformation.
All the best,
Mark
On 17 Feb 2013, at 12:56, "subscribe FSL Hoi Fong, Chan" <[log in to unmask]> wrote:
> FSL expert,
> I am trying to do the VBM analysis on T2W image of Rat Brain. However, when i try to do the BET, all the structure seem to be deleted and shows black screen only. I am wondering is it possible to do the analysis of Rat 's brain on FSL ?
> thanks!!
> best,
> hoifong
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