Dear Hima,
Use some image viewing software (such as fslview) to find the
co-ordinate (in mm, not voxels) of the approximate centre of the brain.
Say this is 50, 60, 70. Then, run bet from the command line as follows
bet <input fileroot> <output fileroot> -c 50 60 70
bet will then initialise the sphere from the coordinates you specify
Heidi
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.
>>>
>>>__________________________________
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>>
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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
>>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
>
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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
Headington
Oxford OX3 9DU
http://www.fmrib.ox.ac.uk/~heidi
Tel: 01865 222782
Fax: 01865 222717
email: [log in to unmask]
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