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