Hello,

In our lab, we create a txt file with all the subject names (as they appear on their respective folders).  Name that txt file whatever you want (like "subs.txt") and save it somewhere in one of the paths (we use /Users/Home_User).

Then in terminal, after setting the environments for Freesurfer and the subjects directory, insert the following:

for SubjectName in `cat subs.txt`

do

recon-all -s $SubjectName -all -qcache

done


Make sure you have the ` (not ') on either side of the "cat" command or it won't work.  This works for us and we have 200 subjects.

Good luck,


-David Vazquez, M. A.
Graduate Student, University of California Riverside
NSF Graduate Student Fellow
dvazq002@ucr.edu
951-827-5243 Dept. Office
951-827-3985 Dept. Fax



On Mon, Apr 15, 2013 at 10:10 PM, Anupa AV <av.anupa@yahoo.com> wrote:
Dear FS experts,

I'd like to know about the for loop command for running recon-all for multiple subjects.

But didn't get much info.

Can anyone please tell me how to run recon-all for multiple subjects?
Thanks in advance.


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