Hi Krishna,

how does your brainmask look? In my experience, if you use bet to create a brainmask for monkeys, occasionally the brain center is positioned to far posterior. This seems to cause to a loss of frontal gray & white matter in the brainmask. That in turn, would "crop" these parts away from what is considered for the reconstruction. Then since I have no clue about your workflow an procedere this might not actually be helpful...

Nevertheless Best Regards Sebastian

On Apr 7, 2010, at 1:05 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:

Message: 2 Date: Wed, 7 Apr 2010 16:06:31 -0400 From: "Srihasam, Krishna" Krishna_Srihasam@hms.harvard.edu Subject: [Freesurfer] Problems segmenting monkey brain To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 97172F7B8A916A44BF05EA8D13905ECE50C293CA0F@ITCCRMAIL02.MED.HARVARD.EDU

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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