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This can occur if your structural images contain lots of neck. By default, BET assumes that the centre of the brain is in the centre of the field of view. If this is not the case then you can tell it the co-ordanates of the brain centre is by adding -c x y z to your command line. (type bet with no arguments to get full usage for bet). Heidi Himachandra Chebrolu wrote: >Hi, >I'm a newbie to this software.I've started using it >only a couple of weeks back.I'm trying to extract the >brain.But the problem I'm having is it is picking up >the tongue and other fat matter present in the >brain.Is there any way I control the algorithm so that >it will also remove the fat(high intensity) and also >recognize the morphological structure(i.e.low >intensity parts like tongue etc which are >connected).Hope someone will be able to help. >Thanks is advance! >-Hima. > >__________________________________ >Do you Yahoo!? >Yahoo! Mail SpamGuard - Read only the mail you want. >http://antispam.yahoo.com/tools > > -- Dr Heidi Johansen-Berg Wellcome Trust Training Fellow Oxford Centre for Functional Magnetic Resonance Imaging of the Brain John Radcliffe Hospital Headington Oxford OX3 9DU http://www.fmrib.ox.ac.uk/~heidi Tel: 01865 222782 Fax: 01865 222717 email: [log in to unmask]