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
On Behalf Of Dong, Yilei
Sent: Thursday, March 21, 2024 1:26 PM
To: Freesurfer support list
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
On Behalf Of Dong, Yilei
Sent: Thursday, March 21, 2024 1:26 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] nu_correct: Command not found error
External Email
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Sent: Thursday, March 21, 2024 6:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] nu_correct: Command not found error
It looks like Freesurfer can’t find minc toolkit binaries on your system.
Did
u.mgz --ants-n4 --n 1
--proto-iters 1000 --distance 50"
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Dong, Yilei
Sent: Wednesday, March 20, 2024 2:01 PM
To: Freesurfer support list
Subject: [Freesurfer] nu_correct: Command not found error
External E
External Email - Use Caution
Could you replace this line:
export PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$PATH
with this one and try again:
export PATH=/usr/local/freesurfer/bin:/usr/local/freesurfer/mni/bin:$PATH
Please also paste the output of
Hi Ian, I think I've seen something like this before, and I remember it
relating to how FS was sourced. Are you setting FREESURFER_HOME before or after
you source SetUpFreeSurfer.sh? And after you source FS, what's the output of
`echo $MNI_DIR`?
best,
Andrew
On 3/28/19, 11:02 AM,
External Email - Use Caution
Hello all.
I am attempting to run recon-all in a docker container. I have a set of
commands to set up the system, and on my local machine (Ubuntu) it works
fine. However on the docker container (also Ubuntu) I get
nu_correct: Command not found.
I have encountered this error in the past, and I think it was because I was
not
sourcing SetUpFreeSurfer.sh correctly. That is the the script
that sets up the MNI_DIR I think.
echo $MNI_DIR or whatever it is called and it should show you
if it is being setup properly. It may be pointing to the
Hi Nick,
I had a look in the bin directory and there is a command called
'mri_nu_correct.mni'. Is this the command the script is trying to call?
This is the only nu_correct command I could find. I specify v5.2 in the
script as there are other versions installed on the clusters.
Thanks again for
Sinead,
In your freesurfer directory, is there an 'mni' directory? under that
directory is a 'bin' directory where nu_correct should be.
Nick
Hi Nick,
I had a look in the bin directory and there is a command called
'mri_nu_correct.mni'. Is this the command the script is trying to call?
Sinead,
Is 'nu_correct' in your freesurfer/mni/bin directory? Are you being
careful to run the setup script for just freeview 5.2 and not other
packages or versions which might mess-up the perl paths?
Nick
On Fri, 2013-03-08 at 09:50 +, Sinead Kelly wrote:
Dear all,
I am currently
Dear all,
I am currently running cortical thickness analysis using Freesurfer v5.2 on
a high performance computing cluster however, when I run the 'recon_all'
command I get the following error
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
Current Stamp:
12 matches
Mail list logo
