Hi FSL experts,
I'm trying to use autoaq with a for loop that cycles through a couple different atlases. Right now I'm just going off of the usage text for autoaq; I couldn't find any documentation for the tool on the wiki and I didn't see an answer on the listserv--apologies if I've missed something.
Basically, I'm looking for an example of correct usage of the -u option. Everything works great when I run it outside of a loop, e.g.,
autoaq -i thresh_tstat1.nii.gz -a "Juelich Histological Atlas" -t .0001 -p -u -o test.txt
But then I tried this:
for ATLAS in '"Juelich Histological Atlas"' '"Harvard-Oxford Cortical Structural Atlas"'; do
autoaq -i thresh_tstat1.nii.gz -a $ATLAS -t .0001 -p -u -o test_loop.txt
done
and I got the following errors:
/Applications/fsl/bin/autoaq: line 69: ${OUT}: ambiguous redirect
/Applications/fsl/bin/autoaq: line 76: ${NEWOUT}: ambiguous redirect
And then it dumped the usage for cluster.
Help?
Thanks!
A
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