External Email - Use Caution There is a misconfiguration in your system. It seems that various important Linux directories (like /bin/) are not in your PATH environment variable, and thus your shell is not functional anymore because required standard software (tr, sed, grep, cp, ...) cannot be found.
I can only suspect that you have set something like this in a config file (like ~/.profile, ~/.bash_profile, or ~/.bashrc): PATH=/some/path/here where the line should read: PATH=$PATH:/some/path/here and thus removed all the standard directories from your PATH. You need to find the broken config file and fix that line. Most likely you will not be able to start a text editor from the command line due to the issue, so I would recommend to start an editor from the GUI. If you have no GUI on the machine, you can do something like this: PATH=$PATH:/bin/:/usr/bin/ to get a text editor and other tools back onto your PATH first. You can try the following command to find candidates for the broken config file: fgrep -r "PATH=" ~/.* Best, Tim > On August 15, 2019 at 2:03 PM "Collins Jones, Liam" <liam.jones...@ucl.ac.uk> > wrote: > > > External Email - Use Caution > > Dear FreeSurfer developers, > > I am having trouble with FreeSurfer set up and configuration on Linux. The > installation appears to have completed without any problems, though when > pasting the lines > > export FREESURFER_HOME=/usr/local/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > into the terminal command window I am seeing the following:- > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer > FSFAST_HOME /usr/local/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer/subjects > MNI_DIR /usr/local/freesurfer/mni > bash: tr: No such file or directory > bash: grep: No such file or directory > bash: tr: No such file or directory > bash: sed: No such file or directory > FSL_DIR /usr/share/fsl/5.0 > > Following this, when running the first command from the "Test your FreeSurfer > installation" section of the Download website, I'm seeing this error:- > > Command 'cp' is available in '/bin/cp' > The command could not be located because '/bin' is not included in the PATH > environment variable. > > I am not sure why this error is occurring and have been through the archive > but could not find a similar problem. In addition to this I'm unable to run > basic Linux commands (eg ls) in the same terminal window. > > Is there a way to overcome this so that I can run FreeSurfer functions? Any > help would be greatly appreciated. > > Here are some background details:- > 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 > 2) Platform: Ubuntu 18.04.2 LTS > 3) uname -a: Linux bodhi 4.15.0-55-generic #60-Ubuntu SMP Tue Jul 2 18:22:20 > UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > > Many thanks, > Liam Collins-Jones. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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
