It looks like -autrecon2 is misspelled. It should be -autorecon2 I hope this is helpful.
Best regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Gwang-Won Kim Sent: Monday, May 22, 2017 7:44 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all error: -autrecon2 unrecognized Hello FreeSurfer Developers, I saw UserContributions/FAQ of FreeSurfer as following: Q. I have already skull-stripped data. Can I submit it to recon-all? A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit differently. First you must run only -autorecon1 like this: recon-all -autorecon1 -noskullstrip -s <subjid> Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this brainmask.mgz file and check that it looks okay (there is no skull, cerebellum is intact; use the sample subject bert that comes with your FreeSurfer installation to make sure it looks comparable). From there you can run the final stages of recon-all: recon-all -autrecon2 -autorecon3 -s <subjid> I tried to process recon-all -autrecon2 -autorecon3 -s <subjid>. But I have a problem. Error message: Flag -autrecon2 unrecognized. What is the problem? 1) FreeSurfer version: 6.0 2) Platform: CentOS release 6.8
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