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 2^nd 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