I had some subjects processed through the standard recon-all pipeline that had some remaining skull just below the frontal lobe (superior part of the orbit). The segmentation as checked in tkmedit appeared to be ok, i.e. it was not considering the skull parts as white matter. The reconstructed cortical surfaces also appeared to be good in tksurfer. Playing with the watershed value did not provide much improvement, and I assume that to clean up the images adequately I would have to do so by hand.

My question is: should I be concerned about improving skull stripping for these subjects, given the good segmentation and cortical reconstruction obtained?

Thank you.

Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Rm 2140 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 moana@email.unc.edu