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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Hi Tim
that's a new error - congratulations! If you upload the dataset I'll take a look, but I suspect if you add some control points it will work fine.
cheers Bruce
On Wed, 11 Jan 2012, Holden, Timothy wrote:
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
{Confidentiality Notice} The materials in this email are private and may contain Protected Healthcare Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.
Office Ph# (314) 362-7596 Program Office Ph# (314) 362-7245 Fax# (314) 362-7346
Timothy A. Holden, B.S.E. Research Scientist Cochlear Implant Program http://oto.wustl.edu/implant/ Washington University Medical School Department of Otolaryngology 660 S. Euclid Ave St. Louis, MO 63110-1007
The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Holden, Timothy