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,


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

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.