Hi Yilei,
I think "nu_correct: Command not found. FREESURFER: Undefined variable." is unrelated to your recon-all didn't finish. That error happens in the beginning of recon-all and recon-all uses ANTS N4BiasFieldCorrection for nu correct instead. We have addressed this error in our dev version.
I'm wondering if your cluster computer enforces some time, memory ... limit on your job.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Dong, Yilei Sent: Thursday, March 28, 2024 2:18 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all nu_correct error
External Email - Use Caution Hi Freesurfer support,
Recently, I submitted a script to run recon-all on 100 MRI images on UCSD's computing cluster. I get an error file that says "nu_correct: Command not found. FREESURFER: Undefined variable." I previously emailed this problem and was told to send my recon-all.log if running the recon-all did not work a 2nd time. I was also told previously that my cluster's Freesurfer can't locate the minc toolkit binaries on my system. How can this error be troubleshooted? Please let me know if you need any other information.
Freesurfer version: 7.2.0, but already available as module
Platform: Rocky Linux release 8.8 (Green Obsidian)
uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Recon-all log: see attached
Sincerely,
Yilei