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
