Hi,
I have a (0.35 mm)^3 resolution monkey brain which I am trying to segment. I am unable to get the frontal cortex to segment properly. My WM.mgz looks good ( I think), but after I do "recon-all -autorecon2-wm ", the surf that gets created has no frontal cortex. I have attached two pictures of one slice, with generated surface overlaid on WM.mgz ( WM_Surf133.jpg) and the same generated surface on T1 image (NU-Surf133.jpg). I tried adding control points, I manually edited the WM.mgz and nothing works. Any help will be appreciated..
regards, Krishna Srihasam Postdoctoral Fellow Livingstone Lab 220 Longwood Avenue, WAS 232 Boston, MA 02115
Krishna, How have you processed this data? Have you used any of the suggested flags and/or parameters for monkeys?
See: https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData
freesurfer@nmr.mgh.harvard.edu
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Allison Stevens -
Srihasam, Krishna