Hi as a short addition to Heidi's reply: if a different centre does not help, you might also want to simply remove some bottom slices (in case they don't contain only brain stem) or use the -f option as described in http://www.fmrib.ox.ac.uk/fslfaq/#bet_notwork good luck christian On 20 Feb 2004, at 18:05, Himachandra Chebrolu wrote: > Mr.Heidi, > Thanks for your reply.My Images do contain a lot of > neck.If you don't mind can you specify more details > about managing the coordinates of the brain centre. > Thanks! > -Hima. > --- Heidi Johansen-Berg <[log in to unmask]> wrote: >> 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] > > > ===== > Himachandra Chebrolu > University Of Kentucky > Lexington,KY-40506 > > __________________________________ > Do you Yahoo!? > Yahoo! Mail SpamGuard - Read only the mail you want. > http://antispam.yahoo.com/tools > -- Christian F. Beckmann Oxford University Centre for Functional Magnetic Resonance Imaging of the Brain, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/ Phone: +44(0)1865 222782 Fax: +44(0)1865 222717