Hi Greg, I would suggest that you only do it with either autorecon2 or autorecon3. With autorecon1, it will fail because it won't find aseg.mgz. You should still be able to run autorecon2 after this mistake, but I wouldn't do it (why let the software exit with an error without need?). If you do it both with both autorecon2 and autorecon3, I believe that the code will be run twice. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Gregory Kirk" gkirk@wisc.edu To: "free" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 7, 2014 5:05:27 PM Subject: [Freesurfer] -hippo-subfields
we have freesurfer set up on our big condor cluster, i asked that the
-hippo-subfields be added. they have it set up to run in 3 stages autorecon1 autorecon2 autorecon3 they added the flag to all 3, i think it would only be needed on autorecon3, but don't think it would cause harm, just be ignored in the first 2 ?
thanks
greg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.