Hi Allison, This looks like a shell scripting issue. Have you tried escaping the inner quotes? Something as "\"Atlas Name\""? You might as well just drop the for-loop and copy-paste the command for as many atlases you are interested in, and making small edits by hand. The number isn't too large, shouldn't be no more than a handful. All the best, Anderson On 29 August 2017 at 21:11, Allison Jack <[log in to unmask]> wrote: > 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 >