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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