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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