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Dear Christian,
 
In the second figure I attached, the normalised T1 is included.
 
I observed that not all brain surface appears to be surrounded by grey matter. I was thinking of a partial volume effect first , but when you look at the corresponding white matter, you see that it seems to "fill" the dark spots in the grey matter segment (first figure).
 
Thanks for any remedy,
 
Franz
 


 
2010/11/17 Christian Gaser <[log in to unmask]>
Dear Franz,

my first guess is that the GM/WM images are normalized, but the T1 image is not. You have to use the normalized T1 image to correctly compare it with its segmented counterparts.

Regards,

Christian

____________________________________________________________________________

Christian Gaser, Ph.D.
Assistant Professor of Computational Neuroscience
Department of Psychiatry
Friedrich-Schiller-University of Jena
Jahnstrasse 3, D-07743 Jena, Germany
Tel: ++49-3641-934752   Fax:   ++49-3641-934755
e-mail: [log in to unmask]
http://dbm.neuro.uni-jena.de
On Tue, 16 Nov 2010 14:44:25 +0100, Franz Riederer <[log in to unmask]> wrote:

>Dear all,
>
>I see there is a lot of effort to support people working with structural MRI
>analyses, and I am grateful for that. Although I got some inspiration from
>the archives of the mailing list, I could not find an answer for the
>following problem:
>In some rare instances grey matter seems classified as white matter (please
>see attachment, blue arrow). In these instances, the dura over the cortex
>appears rather bright (lower image). Changing the bias regularisation to
>"extremely light" instead of the default "very light" seemed to have a minor
>positive effect.
>
>To my surprise, the Unified Segmentation within SPM8 seemed to be less
>sensitive to this artifact.
>
>I also see that this might be a problem of the sequence we used in this
>subject.
>
>I wonder whether there is a way to optimize post processing.
>
>Many thanks in advance,
>
>
>Franz
>