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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.