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