Dear All,
This worked for me...
for x in SZ1 SZ2 SZ3
do
recon-all -i $x.nii -s $x -all -hippo-subfileds
done
Thanks for your valuable inputs...
________________________________
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
To: "Watson, Christopher" <christopher.wat...@childrens.harvard.edu>
Cc: Anupa AV <av.an...@yahoo.com>; KOOL <p.c.m.p.koolsch...@uva.nl>; Freesurfer
<freesurfer@nmr.mgh.harvard.edu>
Sent: Saturday, September 7, 2013 7:10 PM
Subject: Re: [Freesurfer] recon-all for multiple subjects
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-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anupa AV
> [av.an...@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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