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Problem with the source command

dihia -  
 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

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  1. Xavstarblues Posted messages 10585 Registration date   Status Contributor Last intervention   1 858
     
    Hello
    Have you checked the rights on the file?

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  2. 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
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    1. Xavstarblues Posted messages 10585 Registration date   Status Contributor Last intervention   1 858
       

      just do a
      chmod 777 on the file and retest your command?
      or make sure you run your command as root?
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  3. zipe31 Posted messages 34620 Registration date   Status Contributor Last intervention   6 501
     
    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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  4. 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.
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    1. zipe31 Posted messages 34620 Registration date   Status Contributor Last intervention   6 501
       
      I copied the command from the freesurfer website
      Do you have a link?

      Is your shell csh?
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  6. dihia
     
    there's this site: http://biowulf.nih.gov/apps/freesurfer.html
    I can't access the freesurferwiki site to give you the link.
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    1. zipe31 Posted messages 34620 Registration date   Status Contributor Last intervention   6 501
        
       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 ;-((
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  7. dihia
     
    and now it shows me this error:
    % source $FREESURFER_HOME//SetUpFreeSurfer.csh
    /usr/local/freesurfer/SetUpFreeSurfer.csh: Too many open files.
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  8. dubcek Posted messages 18627 Registration date   Status Contributor Last intervention   5 660
     
    hello
    what does the command 
    limit descriptors
    respond?
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  9. dihia
     
    hello dubcek
    the command responds: no such limit
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  10. dubcek Posted messages 18627 Registration date   Status Contributor Last intervention   5 660
     
    what does the command 
    limit
    return</pre>
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  11. dihia
     
    % limit
    cputime illimité
    filesize illimité
    datasize illimité
    stacksize 8192 ko
    coredumpsize 0 ko
    memoryuse illimité
    memorylocked 64 ko
    maxproc illimité
    openfiles 1024
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  12. dubcek Posted messages 18627 Registration date   Status Contributor Last intervention   5 660
     
    try in root 
    limit openfiles 2048
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  13. 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.
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  14. dubcek Posted messages 18627 Registration date   Status Contributor Last intervention   5 660
     
    try as root 
    limit descriptors 2048
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  15. dihia
     
    the response: limit: descriptors: Can't set limit (Operation not permitted)
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  16. dubcek Posted messages 18627 Registration date   Status Contributor Last intervention   5 660
     
    ~/tmp/a# limit descriptors descriptors 1024 ~/tmp/a# limit descriptors 2048 ~/tmp/a# limit descriptors descriptors 2048 ~/tmp/a#
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  17. 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)
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  18. dubcek Posted messages 18627 Registration date   Status Contributor Last intervention   5 660
     
    what is the limit ? 
    limit -h
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  19. 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.
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  20. dubcek Posted messages 18627 Registration date   Status Contributor Last intervention   5 660
     
    and in bash? 
    bash export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME//SetUpFreeSurfer.sh
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  21. 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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