It looks like seg2recon is also looking for FREESURFER. Set it to your Freesurfer install directory, same as FREESURFER_HOME.
From: Maya Yablonski mayay@stanford.edu Sent: Tuesday, October 31, 2023 7:08 PM To: Huang, Yujing YHUANG43@mgh.harvard.edu Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
External Email - Use Caution Thanks! That seems to do the trick and it started running, but crashed after a few minutes. The log file shows the last thing that ran was this command: seg2recon --s sub-xx --seg PATH/sub-xx/mri/synthseg.rca.mgz --i /PATH/sub-xx/mri/orig.mgz --threads 1 followed by this error: FREESURFER: Undefined variable.
Should I define this variable in addition to FREESURFER_HOME and SUBJECTS_DIR? Where should it point to? Thanks for the help! Maya