Hi Mark, it looks like the pial surface is extending too far. When mris_make_surfaces starts it prints out a bunch of information about detected intentis limits. The interesting ones for your purposes will be max_gray_at_csf_border, min_gray_at_csf_border, and max_csf. It seems like it thinks gray matter should be darker than it is. If that's the case, you can explicitly set these bounds on the command line of mris_make_surfaces with (e.g.) -max_csf <max csf val>. Pretty much all the intensity bounds can be set manually in this way.
cheers, Bruce p.s. it is beautiful looking data. -------------------------------------------------------- Bruce Fischl email: [EMAIL PROTECTED] Mass. General Hosp. NMR Center. tel:(617)-726-4897 Rm. 2328, Building 149, 13th Street fax:(617)-726-7422 Charlestown, MA 02129 USA On Mon, 2 Jun 2003, Mark A. Pinsk wrote: > i had a beautiful white matter surface of a monkey brain, all fixed up and ready > for final surface creation. For some reason, after I ran "Make final surface", the > pial surface made some strange mistakes that ruined the entire thing. How can I fix > this, or prevent this from happening? I will try to attach snapshots of a few > coronal slices so you can see what I'm referring to. > > thanks! > Mark > > _______________________________________________ > Join Excite! - http://www.excite.com > The most personalized portal on the Web! >
