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
On 20 Feb 2004, at 18:05, Himachandra Chebrolu wrote:
> 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.
> --- 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).
>> Himachandra Chebrolu wrote:
>>> I'm a newbie to this software.I've started using it
>>> only a couple of weeks back.I'm trying to extract
>>> brain.But the problem I'm having is it is picking
>>> the tongue and other fat matter present in the
>>> brain.Is there any way I control the algorithm so
>>> it will also remove the fat(high intensity) and
>>> 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!
>>> Do you Yahoo!?
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>> Dr Heidi Johansen-Berg
>> Wellcome Trust Training Fellow
>> Oxford Centre for Functional Magnetic Resonance
>> Imaging of the Brain
>> John Radcliffe Hospital
>> Oxford OX3 9DU
>> Tel: 01865 222782
>> Fax: 01865 222717
>> email: [log in to unmask]
> Himachandra Chebrolu
> University Of Kentucky
> Do you Yahoo!?
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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