Hi Stefano, hi Bruce,
sorry to partly high-jack your thread Stafano. In my experience with NHPs I often encounter problems like included cerebellum, so I routinely check the filled.mgz before actually running the surface recon, to confirm that the cerebellum (or other non-white matter) is NOT part of either hemisphere. (In my cases typically I then have to either edit the wm.mgz, the brain mask, or the pons cutting plane, but I guess that is NHP specific). Now wouldn't that filled.mgz check not also work for human recons?
best Sebastian
On May 26, 2013, at 21:13 , Bruce Fischl wrote:
Hi Stefano
a defect with over 60K vertices is more than 1/2 the size of a typical hemisphere, so something has gone badly wrong. Have you checked the skull stripping? The aseg? The talairach? There shouldn't be a defect that big - you will need to figure out why
cheers Bruce On Sun, 26 May 2013, stdp82@virgilio.it wrote:
Hi list, I'm running recon-all on two T1 but the command is for two days on CORRECTING DEFECT 11 (vertices=55538, convex hull=7811). Is it ok? What's happen? Thanks, Stefano
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