Hi FreeSurfers,

As the subcortical segmentation fails fairly often on my high resolution data I want to skip it by using the –noaseg flag, but I’m currently encountering another issue.

1.) During the –fix stage of –autorecon2 I receive following error during mris_euler_numbers (also if I want to view the lh.orig or rh.orig in tksurfer):

rh.orig: face[233615].v[2] = 119048, but face 233615 not in vertex 119048 face list

lh.orig: face[196300].v[1] = 100366, but face 196300 not in vertex 100366 face list

2.) Normally the subcortical segmentation is also used to cut both hemisphere and to remove the cerebellum. The cutting plane between the hemispheres is done very well, but I have never been able to remove the cerebellum. Do I need to remove it manually or are there some ways to remove it automatically? Is it required to be removed?

3.) I’m interested in measuring cortical thickness only. But do I need to keep something else in mind while not using the subcortical segmentation to process my data?

Thanks in advance,

Regards,

Falk