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 the following command: echo $PATH Best, Tim > On March 28, 2019 at 4:00 PM Ian Hardingham <i...@omroth.com> wrote: > > > External Email - Use Caution > > Hello all. > > I am attempting to run recon-all in a docker container. I have a set of > commands to set up the system, and on my local machine (Ubuntu) it works > fine. However on the docker container (also Ubuntu) I get > > nu_correct: Command not found. > > I imagine there is some software that is required that I haven't > installed on the container image - does anyone have any idea what it > might be? > > 1. I have run these commands: > > source /usr/local/freesurfer/SetUpFreeSurfer.sh > export > PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
