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.14@ucl.ac.uk wrote:
External Email - Use CautionDear 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:-
- Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
- Platform: Ubuntu 18.04.2 LTS
- 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