Try putting:
set FSLDIR [ exec sh -c "echo \$FSLDIR" ]
At the top of the fsf file, and then use the ${FSLDIR} in your settings.
Cheers
Eugene
--
Eugene Duff, Phd
Analysis Group, Centre for Functional MRI of the Brain (FMRIB)
Nuffield Department of Clinical Neurosciences
John Radcliffe Hospital
University of Oxford, OX3 9DU
Ph: +44 (0) 1865 222 523
--
On 30 September 2011 14:39, Christine Zakrzewski <
[log in to unmask]> wrote:
> You should be able to redirect output from FEAT to be the input to the
> script where you define this variable with a pipe, |.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Benjamin A Philip
> Sent: Thursday, September 29, 2011 8:27 PM
> To: [log in to unmask]
> Subject: [FSL] Unix $ variables in .fsf files
>
> Is there any way to get a FSL .fsf file to read a $ variable set
> outside the file? Specifically, I'd love to let my FEAT parameters call
> $FSLDIR, to make sure they can run (and find the standard brain files)
> on any computer. Obviously, I have tried setting the path names to
> $FSLDIR/restofpath and the running the .fsf file from the command line,
> but that leads to FSL looking for a directory starting with "$FSLDIR"
> rather than the contents thereof.
>
> Thanks,
>
> --
> Benjamin Philip, Ph.D.
> Postdoctoral Fellow - Freylab
> 1227 Department of Psychology
> University of Oregon
> Eugene, OR 97403-1227
> (541) 346-4953
> [log in to unmask]
> Office: 307 Straub Hall
>
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