Hi Brian, the 5 mm cutoff is indeed to prevent ridiculously large thickness values in the brainstem and the ventricles. It shouldn't cause you any problems, because the cortex should never be that thick, except in some pathologies, which aren't terribly subtle.
Bruce On Mon, 22 Oct 2001, Brian C. Schweinsburg wrote: > Hi users, > > Check the register.csh code. At the end, there is a line that I believe needs >changed. It starts out as mri_convert -raw 256 256 256 ... The latest mri_convert >does not support the -raw option (check mri_convert -u). I changed the -raw to "-it >afni" and it ran. When I ran mri_average ont the registered set of images, I got a >message stating I had a mirror image, and the data did not look good. > > Also, mris_convert -c thickness ... seems to use a cutoff of 5mm. This is different >than my previous version of freesurfer, and was wondering why this is the case. Is it >assumed that anything over 5mm is likely incorrect or extra brainstem with overlay? > > Brian > > > _______________________ > Brian C. Schweinsburg > University of California, San Diego > San Diego State University > Office: (858) 642-3736 > Pager: (619) 290-2659 > Fax: (858) 552-7432 > http://mednmr3.ucsd.edu/brian/home.htm > _______________________ > > >
