Try "chmod 755 autoaq" and then run the script again.
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Sandra Petris [[log in to unmask]]
Sent: Sunday, February 17, 2013 3:56 PM
To: [log in to unmask]
Subject: Re: [FSL] Reporting p-value, cluster size and percentage of tract involved all in one
Dear Anderson,
I followed your instructions. However I got the following error message, when running:
./autoaq -i cluster_index_t3_090 -a "JHU White-Matter Tractography Atlas" -t 0.90 -o try.txt
bash: ./autoaq: Permission denied
Do you know what this error means..
Thanks a lot
sandra
2013/2/15 Anderson M. Winkler <[log in to unmask]<mailto:[log in to unmask]>>
Dear Sandra, dear Mingxia,
To make it executable, the simplest way is:
chmod +x ./autoaq
Then the "sh" at the beginning won't be needed. Also, the error related to the lines 45 and 51 should disappear.
The reason why this error happens is because when "sh" is invoked to interpret the script, the script's first line, which begins with the shebang "#!" is interpreted not as a directive to call a program to interpret the script (in this case, /bin/bash), but as a comment, and so, it is ignored. This causes the script to be read and executed by sh instead of bash. In many systems, this makes no difference. However, in some systems, including Debian/Ubuntu, sh is a symlink to /bin/dash, which is a lighter, mostly compatible, but less feature-rich than bash. The autoaq uses some features that are exclusive of bash, hence the replacement for sh (or dash), fails.
So, in short, just make it executable, drop the sh, and it should work just fine (unless you don't have bash, but this is unlikely).
Hope this helps!
All the best,
Anderson
2013/2/14 Chris Watson <[log in to unmask]<mailto:[log in to unmask]>>
What if you change the double equals sign on lines 43 and 46 to a single equals sign?
On 02/14/2013 05:42 PM, zhang mingxia wrote:
-a "JHU White-Matter Tractography Atlas" -t 0.90 -o try.txt
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