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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.