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 <t...@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 <theoto...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
