Anupa,
If you want to run several subjects at the same time just open different command windows. On each you can run a recon all. You can also run a list of recon on each window. Just put the commands in a text file, name it something like i.e. group1.sh and run the command "sh group1.sh". Each subject will be done in sequence and each command window can have its own sequence. If you add the appropriate linux command you can also receive an email when the list of subjects is done.

Hope helps


2013/9/7 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
it won't handle it. If you gave it multiple inputs each with it's own -i it
would assume that they are different images of the same subject and perform
motion correction and averaging. I don't think that is the case here - you
want to give each instance of recon-all a single nifti volume as input
(unless you acquired multiple T1-weighted images/session)

cheers
Bruce


On Sat, 7 Sep 2013, Watson, Christopher wrote:

> 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
>
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>
>
>
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