Hi FS experts,
I'm encountering an error in the Skull Strip routine with one brain that the FreeSurferWiki site and FS list don't seem to address. The error message is "mri_watershed Error: indices out of bounds" and results in an exit with errors (I've attached the recon-all.log). If I run "recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas " or "recon-all -skullstrip -clean-bm -no-wsgcaatlas -gcut" on this brian the skull strip routine does finish but very little of the skull is removed and large chunks of the brain are removed in the brainmask file. I've checked the Talairach transform and it looks good but I did notice that the WM in the T1.mgz is not in the 110 range but more like 90. Do you think the problem is in the mri_normalize output and could be correct with control points? Your advice is greatly appreciated.
Thanks,
Tim Holden
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