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Hi all, I'm trying to get recon-all to adjust white matter boundary after making a deletion from wm.mgz. What I'm finding is that, apparently in only some of my brains, the surface doesn't seem to get adjusted. Here is T1.mgz with the edit overlay to show where I have made a deletion (in this case, because there is a hyper-intensity on the surface of the middle temporal gyrus which is getting read as WM): [image: image.png] and here is wm.mgz: [image: image.png] (adjacent slices have been similarly edited).
I've tried a few recon-all commands, but the one I expected to work was: recon-all -s 1062_1 -autorecon2-wm -autorecon3 -gca-dir (gcadir) -gca (gca volume) -gca-skull (gca-withskull volume) -3T -mprage -nowmsa -xopts-overwrite -expert ../expert.opts
(expert opts just has "mri_segment -wlo 92")
recon-all outputs no errors, and both surf/lh.white and surf/rh.white show that they have been modified in the filesystem. I'm happy to attach log files if it would be helpful. Thank you, -Matt
