I think it is related to this issue - https://github.com/freesurfer/freesurfer/issues/892

The bug has been fixed since FS 7.3.2. See this PR to fix your local recon-all - https://github.com/freesurfer/freesurfer/pull/886/changes

I think you can also workaround the bug by setting FREESURFER environment variable to FREESURFER_HOME before submitting recon-all.

From: Wales, Ryan <ryan.wales@mssm.edu>
Sent: Monday, March 2, 2026 5:16 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: FREESURFER: undefined variable

        External Email - Use Caution        

For some reason, the error didn’t show up in the log. When I ran the command in my terminal, the very next line (after the end of the log) said “FREESURFER: undefined variable”.

From: Huang, Yujing <YHUANG43@mgh.harvard.edu>
Date: Monday, March 2, 2026 at 4:41 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: FREESURFER: undefined variable

I don’t see the error in the recon-all.log.

From: Wales, Ryan <ryan.wales@mssm.edu>
Sent: Monday, March 2, 2026 2:13 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: FREESURFER: undefined variable

        External Email - Use Caution        

Hi Yujing,

It is attached. Let me know if there’s any other data I can provide. Thanks!

Ryan

From: Huang, Yujing <YHUANG43@mgh.harvard.edu>
Date: Monday, March 2, 2026 at 12:12 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: FREESURFER: undefined variable

USE CAUTION: External Message.

It is not clear which command caused that error. Can you send your recon-all.log?

From: Wales, Ryan <ryan.wales@mssm.edu>
Sent: Sunday, March 1, 2026 7:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FREESURFER: undefined variable

        External Email - Use Caution        

Hi,

I’m trying to run FreeSurfer (v. 7.2.0) longitudinally, first creating the base template for my sample subject across both timepoints, using:

recon-all -base sub_01-tp sub-01_ses-01_t1 -tp sub-01_ses-02_t1 -all

Both cross-sectional timepoints were previously run separately. Just after ‘mri_pretess’ finishes, I encounter the error:

“FREESURFER: Undefined variable”. 

I’m running FreeSurfer on my organization’s HPC, and I’ve ensured that SUBJECTS_DIR and FREESURFER_HOME are both set appropriately. 

I found another post with the same error, but they also had “nu_correct: Command not found”, unlike me. Both of us are using v. 7.2.0.

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg76646.html

Can’t figure this one out. Thanks all!

Best,

Ryan Wales

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