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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 >