Hi Mike

mri_pretess that is causing this behavior. I guess we delete the pretess output after ceating the surfaces, which makes it harder to diagnose this kind of thing. I ran (which I got from the recon-all.log):

mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz

it's hard to visualize what pretess is doing, particularly when there is diagonal connectivity, but it determined that these voxels would have resulted in topological pathological configurations, and so decides to fill or erase. I would erase a bit more wm around those voxels and you should be all set

cheers Bruce

On Tue, 11 Mar 2014, Harms, Michael wrote:

Hi guys, I was wondering if someone could take a look at a subject that I just uploaded (L217_100908.zip). An RA was editing wm.mgz to attempt to fix a topology problem in the LH visual cortex.  The edited wm.mgz that she created looks fine to me, but after re-running FS, the surfaces still aren't accurate.  So, I ran 'defect-seg', which still showed a defect in that area.  What I then noticed is that lh.orig.nofix doesn't seem to completely respect the borders of wm.mgz.

e.g.,  see volume indexes 141 135 50 141 136 50 140 136 50 140 137 50 139 135 48 139 136 48 138 136 48 138 137 48

For each volume index, wm.mgz has value 1 (indicating that it was edited to "off"), but lh.orig.nofix does not seem to be respecting that setting when the initial white surface is constructed.

thanks, -MH

--  Michael Harms, Ph.D.

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Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mharms@wustl.edu

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