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Problem with the source command

dihia -  
Hello,
to install the freesurfer software I need to execute the two commands:
setenv FREESURFER_HOME usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
but I get an error message for the second one telling me that the file SetUpFreeSurfer.csh does not exist even though it is in freesurfer.
Thank you for sending me your responses.

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26 answers

  1.  Xavstarblues Contributor
    Hello
    Have you checked the rights on the file?

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    1. dihia
      Hi,
      thank you for your response.
      Yes, I checked by running the command ls -l -t and here is what it shows me:
      -rwxr-xr-x 1 root root 1394 2011-12-30 14:48 SetUpFreeSurfer.csh
      1. Xavstarblues Contributor

        just do a
        chmod 777 on the file and retest your command?
        or make sure you run your command as root?
    2. zipe31 Contributor
      Hello,

      setenv FREESURFER_HOME usr/local/freesurfer
      Isn't there a slash missing in front? 

      setenv FREESURFER_HOME /usr/local/freesurfer

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      Do something for the environment, close your windows and adopt a penguin.
      1. dihia
        @Xavstarblues: I executed the command and here's what it returns to me:
        /root> chmod 777 SetUpFreeSurfer.csh
        chmod: cannot access 'SetUpFreeSurfer.csh': Permission denied

        @zip31: I don't know, I copied the command from the FreeSurfer site and it's written like this on all the sites.
        1. zipe31 Contributor
          I copied the command from the freesurfer website
          Do you have a link?

          Is your shell csh?
      3. dihia
        there's this site: http://biowulf.nih.gov/apps/freesurfer.html
        I can't access the freesurferwiki site to give you the link.
        1. zipe31 Contributor 
           bash shell: export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME//SetUpFreeSurfer.sh csh/tcsh shell: setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME//SetUpFreeSurfer.csh

          Whether in bash or csh, both have the slash (the root of the system) at the beginning of the path ;-((
      4. dihia
        and now it shows me this error:
        % source $FREESURFER_HOME//SetUpFreeSurfer.csh
        /usr/local/freesurfer/SetUpFreeSurfer.csh: Too many open files.
        1. dubcek Contributor
          hello
          what does the command 
          limit descriptors
          respond?
          3. dihia
            % limit
            cputime illimité
            filesize illimité
            datasize illimité
            stacksize 8192 ko
            coredumpsize 0 ko
            memoryuse illimité
            memorylocked 64 ko
            maxproc illimité
            openfiles 1024
            2. dihia
              When I run the limit command as root, it gives this:
              /root> limit
              cputime unlimited
              filesize unlimited
              datasize unlimited
              stacksize 8192 kbytes
              coredumpsize 0 kbytes
              memoryuse unlimited
              vmemoryuse unlimited
              descriptors 1024
              memorylocked 64 kbytes
              maxproc unlimited

              And when I execute the command: limit openfiles 2048
              the result: no such limit.
              2. dihia
                the response: limit: descriptors: Can't set limit (Operation not permitted)
                1. dubcek Contributor 
                  ~/tmp/a# limit descriptors descriptors 1024 ~/tmp/a# limit descriptors 2048 ~/tmp/a# limit descriptors descriptors 2048 ~/tmp/a#
                  1. dihia
                    :/root> descriptors 1024
                    descriptors: Command not found.
                    nassima:/root> limit descriptors
                    descriptors 1024
                    :/root> limit descriptors 2048
                    limit: descriptors: Can't set limit (Operation not permitted)
                    2. dihia
                      Hello,

                      the command limit descriptors 2048 worked, but when executing the command: source $FREESURFER_HOME/SetUpFreeSurfer.csh I still get the same error too many open files.
                      1. dubcek Contributor
                        and in bash? 
                        bash export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME//SetUpFreeSurfer.sh
                        1. dihia
                          Thank you, it worked, but I have another issue if you can help me because I now need to execute the command qdec
                          it shows me this error:
                          /usr/local/freesurfer/bin/qdec.bin: Format error for exec(). Binary file not executable.
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