It looks like -autrecon2 is misspelled.

It should be -autorecon2

I hope this is helpful.

Best regards,

Don

Don Krieger, Ph.D.

Department of Neurological Surgery

University of Pittsburgh

(412)648-9654 Office

(412)521-4431 Cell/Text

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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