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.edumailto:YHUANG43@mgh.harvard.edu> Date: Monday, March 2, 2026 at 12:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:ryan.wales@mssm.edu> Sent: Sunday, March 1, 2026 7:26 PM To: freesurfer@nmr.mgh.harvard.edumailto: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://secure-web.cisco.com/1Q1rusbYeN6Pge_tcWF7yHke48QvUFi6yzO0GiKdtmW3dWR...https://secure-web.cisco.com/1O8k9p6IS7uLUjZ06OABt9WCVWBkTWN6l288ThbE0v8H0j33-Av_RSD_eSjsrdt3JFbWPFxAn3Q7fMm2_E1vzV74nxtaUy3pWWz8i2lCo10ZmC6URbblWmWZEf1Eq18sxrRzYbj3vpWcOCcauRhNEZGXzs6Hzu6EFOntK9Xm0LubHtmDv_kVgh70RjzlDC55iTIsv42Dn9BT2mUcPp2oRBpar6Ql_aAOZZ5qAMBApjte1ol0CO5cecD_osAXsX-cDs3aCqBVFyZzcRSYO_HYwti_Uju1ST1B-JVEFltgfa6-U-tucHPExhbPwMEuWhlPNweuL_jiQykUWQ71cOVMDcA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1KfETP9AssoehTvJ3VhjCNZJJg3rReFE0UsHzbxBF1de4xGTUNpeFsLLK0GXlkaifVOAnnjXP0RnwLdnVzXal-2D00na-5Figsf3pd-5FmENhSfiNV2NeGJlYN-2Df0DD4r8-2DGTdC39N-5FoG5VkfkSLSNl-5FrhI94SLOcuPw5e-2D3MDd6nXX3tHD-5FV3dmGPIweVJ7eiTIOGwW-5F3BP3ygjuI48GKHZe-5F0d4zCv9yhCD-2Dt5G9-5FnF0ytz8bONPAgHgqLrNUnIztQwMa2-5FwKmmIQCbQxQUM7VpximrARTImzgMX35-2DizOLs-2DE-2DluWfEVmgGCw-2DQyBOOFCgsm8Ubeb2pslf8pCfWVkzKqpA_https-253A-252F-252Fwww.mail-2Darchive.com-252Ffreesurfer-2540nmr.mgh.harvard.edu-252Fmsg76646.html%26d%3DDwMFAg%26c%3DshNJtf5dKgNcPZ6Yh64b-ALLUrcfR-4CCQkZVKC8w3o%26r%3Dda1OysULLVt4-104__5UCZgndjKV6BfO7U4feeDo510%26m%3DGAasydl5JCuok5N_tiIPDcQhX6tD3IrZoHdntNliGdbkwkv-WBXJBGIR8E8267pf%26s%3DozoO8sSI8mberJJurnpV-b5SXvCWw5BRZqdFgpnravM%26e%3D
Can’t figure this one out. Thanks all!
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