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Hi Yujing, 

I re-ran the recon-all script on the 100 subjects and once again, I have the same "nu_correct: Command not found. FREESURFER: Undefined variable." Attached is a recon-all.log from one of my subjects. If indeed my Freesurfer cannot locate the minc toolkit binaries, how would I fix the error? 
Sincerely,
Yilei 


From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Dong, Yilei <yid025@health.ucsd.edu>
Sent: Friday, March 22, 2024 10:20 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] nu_correct: Command not found error
 
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It looks like starting with Freesurfer v7.0.0, bias field correction is done with ANTS N4 instead of the MINC software. ANTS installation apparently is also not required. Would it make a difference if I re-ran recon-all after installing minc toolkit binaries? I'm going to go ahead and rerun it again for now.

Sincerely, 
Yilei
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Friday, March 22, 2024 4:58 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] nu_correct: Command not found error
 

You can re-run it. Send the recon-all.log if you still have problems.

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dong, Yilei
Sent: Thursday, March 21, 2024 1:26 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] nu_correct: Command not found error

 

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Hi Yujing, 

 

My recon-all just ended at that point. It didn't make it through the entire processing stream. Should I rerun the entire process or make any additional adjustments when I submit my script again? 

 

Sincerely,

Yilei

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Thursday, March 21, 2024 6:11 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] nu_correct: Command not found error

 

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

 

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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