Hello,
Im having trouble to generate a correct aseg.mgz for one volume of mine. The nu_noneck.mgz is also incorrect and therefore I think the -careg stage of autorecon2 might fail. Is there a way to do some kind quality check, like the tal-check during autorecon1, to see whether the talairach.m3z is incorrect? Are there some kind of instructions like fixing the bad output from the talairach registration? Or are there some parameters which can be adjusted to get better results?
If none of this is possible in some way, would it be advisable to use the -noaseg flag? Im actually in no need for the subcortical segmentation, it would just be a plus, but the aseg.mgz is needed during the -segmentation stage to remove the cerebellum and brain stem. Maybe there even is another way to remove these structures automatically?
Thanks in advance,
Regards,
Falk