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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 imagine there is some software that is required that I haven't installed on the container image - does anyone have any idea what it might be?
1. I have run these commands:
source /usr/local/freesurfer/SetUpFreeSurfer.sh export PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$PATH
2. I have set FREESURFER_HOME
Attached at the end is some output from both failing and successful runs.
3. nu_correct exists in freesurfer/mni/bin
4. Perl is present and correct on both systems.
Thank you in advance, Ian
FAILING OUTPUT:
#-------------------------------------------- #@# Talairach Thu Mar 28 14:12:31 UTC 2019 /subjects/FS_subj_001/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 40ed7e79aa5d 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 GNU/Linux Thu Mar 28 14:12:32 UTC 2019 nu_correct: Command not found.
SUCCESSFUL OUTPUT:
#-------------------------------------------- #@# Talairach Thu Mar 28 14:33:45 GMT 2019 /home/ian/subjects/FS_subj_001/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/home/ian/subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux ian-Sabre-17WV8 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 28 14:33:45 GMT 2019 Program nu_correct, built from:
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 $MNI_DIR`?
best, Andrew
On 3/28/19, 11:02 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ian Hardingham" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ian@omroth.com> wrote:
External Email - Use Caution
Hello all.
I am attempting to run recon-all in a docker container. I have a set of commands to set up the system, and on my local machine (Ubuntu) it works fine. However on the docker container (also Ubuntu) I get
nu_correct: Command not found.
I imagine there is some software that is required that I haven't installed on the container image - does anyone have any idea what it might be?
1. I have run these commands:
source /usr/local/freesurfer/SetUpFreeSurfer.sh export PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$PATH
2. I have set FREESURFER_HOME
Attached at the end is some output from both failing and successful runs.
3. nu_correct exists in freesurfer/mni/bin
4. Perl is present and correct on both systems.
Thank you in advance, Ian
FAILING OUTPUT:
#-------------------------------------------- #@# Talairach Thu Mar 28 14:12:31 UTC 2019 /subjects/FS_subj_001/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 40ed7e79aa5d 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 GNU/Linux Thu Mar 28 14:12:32 UTC 2019 nu_correct: Command not found.
SUCCESSFUL OUTPUT:
#-------------------------------------------- #@# Talairach Thu Mar 28 14:33:45 GMT 2019 /home/ian/subjects/FS_subj_001/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/home/ian/subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux ian-Sabre-17WV8 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 28 14:33:45 GMT 2019 Program nu_correct, built from:
-- Ian Hardingham
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 the following command:
echo $PATH
Best,
Tim
On March 28, 2019 at 4:00 PM Ian Hardingham ian@omroth.com wrote:
External Email - Use CautionHello all.
I am attempting to run recon-all in a docker container. I have a set of commands to set up the system, and on my local machine (Ubuntu) it works fine. However on the docker container (also Ubuntu) I get
nu_correct: Command not found.
I imagine there is some software that is required that I haven't installed on the container image - does anyone have any idea what it might be?
- I have run these commands:
source /usr/local/freesurfer/SetUpFreeSurfer.sh export PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$PATH
- I have set FREESURFER_HOME
Attached at the end is some output from both failing and successful runs.
nu_correct exists in freesurfer/mni/bin
Perl is present and correct on both systems.
Thank you in advance, Ian
FAILING OUTPUT:
#-------------------------------------------- #@# Talairach Thu Mar 28 14:12:31 UTC 2019 /subjects/FS_subj_001/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 40ed7e79aa5d 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 GNU/Linux Thu Mar 28 14:12:32 UTC 2019 nu_correct: Command not found.
SUCCESSFUL OUTPUT:
#-------------------------------------------- #@# Talairach Thu Mar 28 14:33:45 GMT 2019 /home/ian/subjects/FS_subj_001/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/home/ian/subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux ian-Sabre-17WV8 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 28 14:33:45 GMT 2019 Program nu_correct, built from:
-- Ian Hardingham
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
freesurfer@nmr.mgh.harvard.edu
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Hoopes, Andrew -
Ian Hardingham -
Tim Schäfer