Hi - you could posisbly use a standard-space mask (look for example at
$FSLDIR/etc/standard/avg152T1_strucseg )along with registration using
FLIRT to remove cerebellum and brainstem, but the accuracy of this will
depend on how well the particular image fits the standard under FLIRT's
12DOF affince transform.
Cheers.
On Tue, 16 Nov 2004, NL wrote:
> Hi
>
> I am new to the world of FMRI and would really appreciate any help on the
> following. I am dealing with lesioned pediatric Brains. I need to use an
> effective skull stripping algorithm and then use a segmentation algorithm to
> find lesion volumes, CSF, white matter, Grey matter etc. I am using AFNI to
> look at the lesions. I did look up BET and FAST. The problem I am facing
> with BET is that the Brain stem and cerebellum also comes into the picture.
> So then I tried using Freesurfer. The problem I faced there was with very
> large lesions extending from the ventricle to the cortex, Freesurfer did get
> rid of the brainstem for me but also got rid of a part of the cortex (didnt
> give very accurate Results). I then used FAST on these outputs and I got
> volumes for CSF, white matter and grey matter. But obviously it is not
> accurate. Could anyone please suggest a method for stripping off the skull
> for these lesioned brains? I guess after that it is just a matter of using
> FAST. Or could anyone suggest an entire new way to look at volumes? Any help
> would be appreciated. thank you
>
> NL
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
|