Hi Laura,
what version of FS are you running? The ICV is estimated using the
talairach xform, and there were some problems with it in 5.1.
cheers
Bruce
On Mon, 13 Aug 2012, Wisse, L.E.M.
wrote:
Dear freesurfers,
I tried to calculate ICV with FreeSurfer, but I encountered some problems. I
first ran autorecon 1, 2 and 3, but I noticed afterwards that a few ICV
values were really off. The values were really high and when I looked at
brain.finalsurfs.mgz, the segmentation also included skull, eyes and
sometimes even the nose and ears. (I am not sure that I should look at the
brainfinal.surfs.mgz for ICV segmentation, but the segmentations seemed to
correlate with the ICV values.)
So, I decided to try adjusting the watershed parameters and I also tried
using gcut. I noticed that the segmentation brain.finalsurfs improved a lot,
however in aseg.stats the ICV values did not change at all!
Can anyone help me with this problem?
Kind regards,
Laura Wisse
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