It looks like Freesurfer can’t find minc toolkit binaries on your system.

Did your recon-all finish fine? I think FS 7.2 recon-all is configured to use ANTS N4BiasFieldCorrection for nu correct by default.

This is from your log:

“mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50”

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dong, Yilei
Sent: Wednesday, March 20, 2024 2:01 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] nu_correct: Command not found 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, called EXPANSE. I get an error file that says "nu_correct: Command not found. FREESURFER: Undefined variable." The sample error file and the output file I have attached for one of the subjects are recon-all-slurm.29376886.exp-5-44.err & recon-all-slurm.29376886.exp-5-44.out respectively. The script I used to submit the job via slurm is called recon-all-slurm.sb. 

I googled the error and found that someone else who had a similar situation did not source their Freesurfer environment correctly. Would this be the same thing for us as well? The main thing for us is Freesurfer/7.2.0 already has been available as a module for us on EXPANSE. 

Sincerely,

Yilei