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.

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