Surely there is a simple fix to my problem, but I've been unable to succesfully run Freesurfer commands after many attempts (with my very basic bash knowledge) and searching prior archives.
I'm running Freesurfer on a 64-bit machine, Ubuntu 18.04 LTS.
No Freesurfer commands work (files not found), except the "freesurfer" command. I've included some pertinent output below. All of the installation files seem to be in the right place and the path seems to
be correct, so I'm perplexed. Any help very much appreciated.
Ashesh Thaker, MD |
Assistant Professor
School of Medicine, Department of Radiology
University of Colorado Anschutz Medical Campus
ashesh@ashesh-gpu:~$ export FREESURFER_HOME=/usr/local/freesurfer
ashesh@ashesh-gpu:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/subjects
MNI_DIR /usr/local/freesurfer/mni
FSL_DIR /usr/local/fsl
ashesh@ashesh-gpu:~$ recon-all
bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory
ashesh@ashesh-gpu:~$ freeview
bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: bad interpreter: No such file or directory
ashesh@ashesh-gpu:~$ freesurfer
FreeSurfer is a set of tools for the analysis and visualization
of structural and functional brain imaging data. FreeSurfer
also refers to the structural imaging stream within the
FreeSurfer suite.
Users should consult the online documentation available at:
http://surfer.nmr.mgh.harvard.edu
Alternatively, the 'recon-all' command help-text provides
adequate information to begin processing subject data, such
as the sample subject 'bert' found in the 'freesurfer/subjects'
directory. Type 'recon-all --help' to view this help-text.
Direct comments and questions to:
freesurfer@nmr.mgh.harvard.edu
You are running this version of FreeSurfer:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ashesh@ashesh-gpu:~$ echo $PATH
/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin