Do you mean you're using Normalise:Est+Write, and for the source image you choose "mT1.nii" (or whatever it is named)? The reason that works just fine is because it's a different way to normalise your data.
You should do as Dr. Ashburner suggested and align your T1 so that the origin (0 0 0) is at the anterior commissure, and coregister the BOLD images to that. Then try segmentation again.
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From: SPM (Statistical Parametric Mapping) [[log in to unmask]] On Behalf Of Asaf Kaftory [[log in to unmask]]
Sent: Wednesday, December 08, 2010 2:05 AM
To: [log in to unmask]
Subject: Re: [SPM] segmentation product
Hello both John and Chris,
thanks for your replies.
First, Chris -
I am talking about FMRI data, and i've co-registered the EPI images (coreg: reference image=mean unwarped EPI, source image=T1 image).
Second, Chris and John -
If the problem lies in the co-reg (as Chris suggested) or in poor segmentation due to what John mentioned, how come using the segmented image (as opposed to the segmented parameter file) seems to work just fine?
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