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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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