Hello Ashesh,
You need someone with admin or root privileges to install tcsh (and I would do csh as well) shells on your machine so those scripts can run, i.e.
$ sudo apt-get install tcsh $ sudo apt-get install csh
On Oct 25, 2018, at 13:35, Thaker, Ashesh A <ASHESH.THAKER@ucdenver.edumailto:ASHESH.THAKER@ucdenver.edu> wrote:
External Email - Use Caution
Dear Freesurfer team,
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.
Kind regards,
Ashesh Thaker, MD | Assistant Professor School of Medicine, Department of Radiology University of Colorado Anschutz Medical Campus 720 848 6568 (office) | ashesh.thaker@ucdenver.edumailto:ashesh.thaker@ucdenver.edu
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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.eduhttp://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.edumailto: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
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