Hi Ajna
Do you have intensity inhomogeneity in your images? In addition to
setting the initial position of the T1 to be close to the template,
you can also try using segment to write out a bias-corrected version
of your T1, and then running segmentation on that bias-corrected
image...
Good luck,
Jonathan
On Wed, Dec 17, 2008 at 4:03 PM, Ajna <[log in to unmask]> wrote:
> Dear SPMers,
> I am having difficult time segmenting MPRAGE acquired on 3T with SPM5, and
> am running out ideas of what might be the problem. Segmentation tends to
> miss-classify the external cortical gray matter as CSF. Problem is
> persistent if no manual coregistration of MPRAGE to T1 template is not first
> performed, but even after manual coregistration, segmentation still
> classifies significant amount of GM as CSF at the brain surfaces. Also, the
> normalized MPRAGE tends to be imperfectly coregistered to the MNI template,
> but the fit is only slightly off... My MPRAGE images appear to be high
> quality, with clear intensity distinction between tissue types. Any advice
> on how to trouble-shoot this problem would be greatly appreciated.
>
> Thank you,
> -Ajna Borogovac, Columbia University, NY
>
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