Dear Deane,
If the FSLDIR variable is being set but others are not then
that indicates that your .cshrc is being run (to set FSLDIR)
but that the source command is failing.
This assumes that FSLDIR has not been set in any other
way (such as by hand previously in that shell). Also your
.cshrc file should have been created as a pure text file, and
not with Word or TextEdit in any enhanced text mode.
So assuming that it isn't a problem identified above,
what happens if you start a new terminal window, then type
the four lines that you put in your .cshrc? Once you've run
these four commands, let us know of any errors and
also what the output is from the following commands (to be typed):
echo $FSLDIR
echo $FSLCONFDIR
echo $PATH
setenv | grep FSL
ls $FSLDIR
ls -l ${FSLDIR}/etc/fslconf/fsl.csh
This should allow us to figure out what is going wrong.
All the best,
Mark
On 26 Jan 2007, at 20:32, [log in to unmask] wrote:
>
> Mark,
>
> That is the entirety of the .cshrc file.
>
> echo $FSLCONFDIR returns
> tsh: FSLCONFDIR: Undefined variable.
>
> Kind Regards,
>
> Deane
>
>
>
> Quoting Mark Jenkinson <[log in to unmask]>:
>
>> Hi,
>>
>> The lines in you .cshrc look fine but it looks like something is
>> going wrong with the source command.
>> What happens if you echo $FSLCONFDIR in your shell?
>> And does ${FSLDIR}/etc/fslconf/fsl.csh exist with the right
>> permissions?
>>
>> If you still can't identify or fix the problem then send us your
>> full .cshrc file.
>>
>> All the best,
>> Mark
>>
>>
>>
>>
>>
>> On 25 Jan 2007, at 17:36, Deane Aikins wrote:
>>
>>> Hello,
>>>
>>> We are installing FSL 3.3 on Mac Os X 10.4.8. FSLVIEW installed
>>> successfully
>>>
>>> The .cshrc file contains the following:
>>> setenv FSLDIR /usr/local/bin/fsl
>>> source ${FSLDIR}/etc/fslconf/fsl.csh
>>> setenv PATH ${FSLDIR}/bin:${PATH}
>>> setenv DISPLAY localhost:0.0
>>>
>>> The command echo $FSLDIR returns:
>>>
>>> /usr/local/bin/fsl
>>>
>>> When we enter fsl_gui we get:
>>>
>>> You need to source an FSL setup file - either fsl.sh or fsl.csh in
>>> $FSLDIR/etc/fslconf !
>>>
>>> Any help is appreciated.
>>> Thank you
>>>
>>> Delete | Reply |
>>
>>
>
>
> Deane Aikins, PhD
> Director, Cognitive Neuroscience Laboratory
> National Center for PTSD Clinical Neuroscience Division
> Assistant Professor, Department of Psychiatry
> Yale School of Medicine
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