Hi Simon, In 7.3.2, as you mentioned if you split recon-all into multi stages, '-careg' needs to be specified on the command line for autorecon2. This has been fixed in dev version. Best, Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Simon Jones Sent: Monday, March 13, 2023 6:30 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer v. 7.3.2 careg error

External Email - Use Caution Dear Freesurfer Support, Under older versions of Freesurfer such as 7.2.0 I can split recon-all into two stages: recon-all -autorecon1 -noskullstrip -s sub -i sub.nii.gz Manually create brainmask.mgz recon-all -autorecon2 -autorecon3 -s sub Using freesurfer v. 7.3.2 this fails. I looked at the log file and in the -autorecon2 stage the steps go straight from mri_ca_normalize to mri_ca_label missing out mri_ca_register so no transforms/talairach.m3z file is created. I modified the second part to recon-all -autorecon2 -autorecon3 -careg -s sub and then it completed without error. Maybe this is intentional and there is another recommended way to do this multistage pipeline. Thanks, Simon