Hi Binyam,
don't worry about the subcortical regions in the wm.mgz (they were actually classified as white matter, but it won't matter)
Bruce
On Wed, 21 Mar 2007, Binyam Nardos wrote:
Dear Freesurfers, after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes? appreciate any help,
Binyam
Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601
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