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.

I went thru this link, https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2006-November/004083.h... 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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