Re: [Freesurfer] Freesurfer - issue after installation in Linux

yes, depending on your hardware it can take >12 hours, particularly if you aren't using -openmp On Thu, 3 Oct 2019, Theotonio Pauliquevis wrote:

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Hi,  Thanks for the prompt reply.

After I installed tcsh it did run successfully.

Since this fixing I did run example 2,  and it is still running, continuously, during the last 3h25min.

Is that normal?

Attached it is my screen output in case someone could see any problems in my (intermediary) results.

BTW, it is still running while I write this e-mail to the group.

Regards

Theotonio

Em qui, 3 de out de 2019 às 13:32, Tim Schäfer ts+ml@rcmd.org escreveu:         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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