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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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Answer 1 / 26
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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Answer 2 / 26
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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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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Answer 3 / 26
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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Answer 4 / 26
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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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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Answer 5 / 26
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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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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Answer 6 / 26
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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Answer 7 / 26
dubcek Posted messages 18702 Registration date   Status Contributor Last intervention   5 658
 
hello
what does the command 
limit descriptors
respond?
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Answer 8 / 26
dihia
 
hello dubcek
the command responds: no such limit
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Answer 9 / 26
dubcek Posted messages 18702 Registration date   Status Contributor Last intervention   5 658
 
what does the command 
limit
return</pre>
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Answer 10 / 26
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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Answer 11 / 26
dubcek Posted messages 18702 Registration date   Status Contributor Last intervention   5 658
 
try in root 
limit openfiles 2048
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Answer 12 / 26
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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Answer 13 / 26
dubcek Posted messages 18702 Registration date   Status Contributor Last intervention   5 658
 
try as root 
limit descriptors 2048
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Answer 14 / 26
dihia
 
the response: limit: descriptors: Can't set limit (Operation not permitted)
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Answer 15 / 26
dubcek Posted messages 18702 Registration date   Status Contributor Last intervention   5 658
 
~/tmp/a# limit descriptors descriptors 1024 ~/tmp/a# limit descriptors 2048 ~/tmp/a# limit descriptors descriptors 2048 ~/tmp/a#
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Answer 16 / 26
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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Answer 17 / 26
dubcek Posted messages 18702 Registration date   Status Contributor Last intervention   5 658
 
what is the limit ? 
limit -h
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Answer 18 / 26
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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Answer 19 / 26
dubcek Posted messages 18702 Registration date   Status Contributor Last intervention   5 658
 
and in bash? 
bash export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME//SetUpFreeSurfer.sh
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Answer 20 / 26
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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