[Freesurfer] Skull Stripping Corrections

Hello-

I've been working through the Skull Stripping checking/corrections tutorial and have a question. So far, I have found no problems akin to the tutorial, where skull is left behind or brain parts are missing. However, I do see remnants of eyeballs/eye sockets, arteries, and dura/pia/meninges. They don't seem too bad: http://www.tc.umn.edu/~norb0062/skull_strip_leftovers.bmp

But I'm wondering how much trouble such remnants can cause down the pipeline. That is to say, when performing these checks should I only be concerned with making sure that all skull has been stripped away without taking away any brain, or should I also be concerned with making sure that all non-brain bits have been stripped away?