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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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    0
    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
      0
      1. Xavstarblues Contributor

        just do a
        chmod 777 on the file and retest your command?
        or make sure you run your command as root?
        0
    2. zipe31 Contributor
      Hello,

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

      setenv FREESURFER_HOME /usr/local/freesurfer

      --
      Zen my nuggets ;-)
      Do something for the environment, close your windows and adopt a penguin.
      0
      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.
        0
        1. zipe31 Contributor
          I copied the command from the freesurfer website
          Do you have a link?

          Is your shell csh?
          0
      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.
        0
        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 ;-((
          0
      4. dihia
        and now it shows me this error:
        % source $FREESURFER_HOME//SetUpFreeSurfer.csh
        /usr/local/freesurfer/SetUpFreeSurfer.csh: Too many open files.
        0
        1. dubcek Contributor
          hello
          what does the command 
          limit descriptors
          respond?
          0
          1. dihia
            hello dubcek
            the command responds: no such limit
            0
            1. dubcek Contributor 
              what does the command 
              limit
              return</pre>
              0
              1. dihia
                % limit
                cputime illimité
                filesize illimité
                datasize illimité
                stacksize 8192 ko
                coredumpsize 0 ko
                memoryuse illimité
                memorylocked 64 ko
                maxproc illimité
                openfiles 1024
                0
                1. dubcek Contributor
                  try in root 
                  limit openfiles 2048
                  0
                  1. 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.
                    0
                    1. dubcek Contributor
                      try as root 
                      limit descriptors 2048
                      0
                      1. dihia
                        the response: limit: descriptors: Can't set limit (Operation not permitted)
                        0
                        1. dubcek Contributor 
                          ~/tmp/a# limit descriptors descriptors 1024 ~/tmp/a# limit descriptors 2048 ~/tmp/a# limit descriptors descriptors 2048 ~/tmp/a#
                          0
                          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)
                            0
                            1. dubcek Contributor
                              what is the limit ? 
                              limit -h
                              0
                              1. 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.
                                0
                                1. dubcek Contributor
                                  and in bash? 
                                  bash export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME//SetUpFreeSurfer.sh
                                  0
                                  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.
                                    0
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