External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, March 21, 2024 6:11 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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
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