Dear Bruce and Freesurfer Experts,
Thanks for the quick answer, Bruce, to previous post.
As I work my way through all the checks on output I had a couple of other
quick questions
1) I noticed by skull-stripping was poor (too aggerssive at the back of the
brain with part of the occipital lobe and
1. A linear transform isn't always good enough to describe brain/skull
variability. It helps more often than it hurts, but sometimes it does
worse.
2-3. I'll leave these for Nick except to say I think 3g/recon should be
fine and you might be able to get away with a bit less. So 4 would be safe
the documentation is a bit ahead of the release, so
talairach_with_skull_2.lta doesnt exist in a 5.1 run. however, it is the
same file as that produced during the -skull-lta stage (so its file date
will be newer than talairach.lta), so if it is newer, then you can try
rerunning skullstrip and it w
