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

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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