there is a typo: it should be "-autorecon2" not "-autrecon2"
cheers Bruce On Mon, 22 May 2017, Gwang-Won Kim wrote:
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?
FreeSurfer version: 6.0
Platform: CentOS release 6.8
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