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



2017-07-07 15:23 GMT+02:00 Gabor Perlaki <petzinger.gabor@gmail.com>:
Dear all,

Freesurfer 6 creates pial and white matter surfaces around the optic chiasm in some of my subjects (see the attached pictures). When I check the aparc.DKTatlas+aseg.mgz, sometimes these places are segmented as optic chiasm or nothing (which seems to be good), but sometimes this region is segmented as white matter or medialorbitofrontal cortex. Could somebody please confirm that these surface inacuracies don't matter as long as the area is not segmented as a cortical region or white matter in the aparc.DKTatlas+aseg.mgz file, and I should correct it if missegmented as a cortical region or white matter?
I suspect that I should correct the wm.mgz. However, all of the brainmask, aseg and wm corrections are done on my subjects and I'd like to correct this new error without loosing those corrections. How should I correct this new wm inaccuracy without loosing my earlier aseg corrections?

Best Regards,
Gabor



2017-06-30 14:11 GMT+02:00 Gabor Perlaki <petzinger.gabor@gmail.com>:
Dear all,


I use Freesurfer 6. In some of my subjects the surfaces (both pial and white) intruding into the optic chiasm. However, when I check the aparc.DKTatlas+aseg.mgz it seems that although the surfaces are wrong, the region is segmented as optic chiasm. Can I ignore this type of surface inaccuracies similarly to surface inacurracies around the amygdala and hippocampus?

Best Regards,
Gabor



--
Gabor Perlaki
research associate
Diagnostic Center of Pécs
H-7623 Pécs, Rét str. 2.
Tel.: 0036-30-2084367
E-mail: petzinger.gabor@gmail.com