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
