I'm afraid that BET does not usually work well with mouse brains and this causes problems for all the other tools. However, this has been discussed on the list before so have a search through the archive and see if some posts there might be of help to you.
All the best,
On 6 Feb 2012, at 09:22, Maxim Bester wrote:
> hi all,
> in an EAE mouse model we measure the ventricular enlargement to assess volume changes due to neurodegeneration. As we do have hi-res T1/T2 data, ,measuring brain volume directly (better: white/gray matter fraction) would be more accurate.
> Is there any possibility using fsl to solve this problem without outlining the brain manually ?
> might there even be a possibility to use siena with rodent images to measure individual volume changes?
> thanks for any hint in advance,