Somehow, my last email didn't appear on the Freesurfer forum. I'm resending it without the attachments.
Dear Bruce,
I'm not interested in the chiasm, but the medialorbitofrontal cortex would be interesting. In most of the subjects pial and white surfaces intrude into the area around the optic chiasm, which is clearly not a cortical region. However, I think that until this region is segmented as a subcortical label (i.e. opic chiasm) or nothing in the aparc.DKTatlas+aseg.mgz file my cortical measures won't be affected, but if it's labeled as medialorbitofrontal cortex or wm then I should correct it. 1. Could you please confirm that these surface inacuracies don't matter as long as the area is not segmented as a cortical region (i.e. medialorbitofrontal) or white matter in the aparc.DKTatlas+aseg.mgz file? 2. I think I should correct the wm.mgz, but I'm not sure about how to correct it without loosing my earlier corrections. I'm ready with all of the other corrections inclding wm, brainmask and aseg corrections as well?
I'm trying to resend some images showing the missegmented area.
Best Regards, Gabor