Funny, I was having the same problem when I got your email.
I tried various things, and what worked in my case was to increase the
number of Gaussians per class for CSF from 2 to 4.
So that variable will now be 2 2 4 4 instead of 2 2 2 4.
Maybe the CSF + skull is too variable to be well modeled with only 2
Gaussians?
Philip Kohn
Ajna 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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