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. > > > _______________________________________________ > 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. > >
_______________________________________________ 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.
