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Thanks for your advise! On Tue, Feb 19, 2013 at 4:56 PM, Mark Jenkinson < [log in to unmask]> wrote: > 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 > -- Hoi Fong, Chan, MD En Chu Kong hospital, Department of neurology National Taiwan University , Department of anatomy and cell biology Taipei