you'll need to either add control points and/or edit the wm.mgz On Tue, 17 Nov 2009, Dana W. Moore wrote:

Hi Bruce,

Thanks for the suggestion. Which function should I use to fix segmentation/topology errors?

Thanks, Dana

At 10:24 AM 11/17/2009, Bruce Fischl wrote:

...

Hi Dana,

what's the bright stuff out near the pial surface? Is it dura? It's hard to tell from just a single slice. If it is, then you could try erasing it. Looks like there were also segmentation/topology fixing errors in the right superior temporal gyrus, which you could fix. Finally, you can try putting some control points near the base of some off the wm strands in the left temporal white matter.

cheers Bruce

On Tue, 17 Nov 2009, Dana W. Moore wrote:

...

Hi everyone,

I have an image in which the pial surface left out portions of the cortex (see left temporal lobe below). I am not sure how to go about editing this. I tried adding control points to the brainmask.mgz volume and running -autorecon2-cp -autorecon3, but the result seems unchanged (see control points in picture below). Did I do something wrong? The edit voxels tool I believe would help if the problem was that these voxels had been removed during skull-stripping, but this is not the case--they were just excluded from the pial boundary.

Thanks, Dana

Emacs!

Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003@med.cornell.edu

Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003@med.cornell.edu