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
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
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-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
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
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
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Thursday, March 21, 2024 6:11 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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
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-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
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Thursday, March 21, 2024 6:11 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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
External Email - Use Caution
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
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-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
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Thursday, March 21, 2024 6:11 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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
freesurfer@nmr.mgh.harvard.edu
-
Dong, Yilei -
Huang, Yujing