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
dvazq...@ucr.edu
951-827-5243 Dept. Office
951-827-3985 Dept. Fax
On Mon, Apr 15, 2013 at 10:10 PM, Anupa AV av.an...@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.html
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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