The problem here is that SZ*.nii presumably refers to a list of files due to shell expansion. I don't know how recon-all handles that (e.g. if it will take only the first file in the list, or all files), but that command probably won't do what you want it to.
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anupa AV [av.anupa@yahoo.com] Sent: Saturday, September 07, 2013 5:56 AM To: KOOL; Freesurfer Subject: [Freesurfer] recon-all for multiple subjects
Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that?
I've tried using the following command lines
cd /home/john/Anu (where I kept all the .nii files)
for x in * do recon-all -i SZ*.nii -s $x -all done
But this is not working