External Email - Use Caution       

You need to install the tcsh shell:

  sudo apt-get install tcsh

Best,

Tim


> On October 3, 2019 at 6:30 PM Tim Schäfer <tim@rcmd.org> wrote:
>
>
> You need to install the tcsh shell:
>
>   sudo apt-get install tcsh
>
> Best,
>
> Tim
>
> > On October 3, 2019 at 6:26 PM Theotonio Pauliquevis <theotonio@gmail.com> wrote:
> >
> >
> >         External Email - Use Caution       
> >
> > Hi,
> >
> > I just installed freesurfer in Linux Ubuntu 14.04, and I got a critical
> > (and strange) problem in the earlier tests of freesurfer  (Example 2). Any
> > help would be appreciated. Basically, when trying example 2 in instructions
> > homepage I got the following error:
> >
> > theo@theo-Inspiron-5457:~$ recon-all -i sample-001.nii.gz -s bert -all
> > bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No
> > such file or directory
> >
> > But the fact is that recon-all is there and apparently it is well
> > configured, because 1) the recon-all does exist, and 2) permissions are ok:
> >
> > theo@theo-Inspiron-5457:~$ ls -l /usr/local/freesurfer/bin/recon-all
> > -rwxrwxr-x 1 8481 1590 327555 Jan 18  2017
> > /usr/local/freesurfer/bin/recon-all
> >
> > and the command is promptly recognized :
> >
> > theo@theo-Inspiron-5457:~$ which recon-all
> > /usr/local/freesurfer/bin/recon-all/
> >
> > Any ideas? Anybody got this issue before? It seems to be some (not obvious)
> > permission problem.
> >
> > Below I type the whole procedure to install, so one can see that I followed
> > all installation instructions.
> >
> > History:
> >
> > 1) Successfully downloaded and unzipped the files at /usr/loca/freesurfer
> >
> > 2) Successful set up of environment variables after including the following
> > lines in .bashrc:
> >
> > ##############################################
> > #Software FREESURFER - Enviroment variables
> > #
> > export FREESURFER_HOME=/usr/local/freesurfer
> > source $FREESURFER_HOME/SetUpFreeSurfer.sh
> > export SUBJECTS_DIR=/home/theo/freesurfer/subjects
> > ##############################################
> >
> > BTW, "theo" is my userID
> >
> > 3) File license.txt copied to /usr/local/freesurfer
> >
> > 4) message after open a  terminal window confirms that Enviroment variables
> > were correctly set:
> >
> > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME   /usr/local/freesurfer
> > FSFAST_HOME       /usr/local/freesurfer/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR      /usr/local/freesurfer/subjects
> > MNI_DIR           /usr/local/freesurfer/mni
> > (base) theo@theo-Inspiron-5457:~$ echo $SUBJECTS_DIR
> > /home/theo/freesurfer/subjects
> > (base) theo@theo-Inspiron-5457:~$
> >
> >
> >  Any help is welcome
> > Regards
> >
> > Theotonio
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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