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 fischl@nmr.mgh.harvard.edu To: "Watson, Christopher" Christopher.Watson@childrens.harvard.edu Cc: Anupa AV av.anupa@yahoo.com; KOOL P.C.M.P.Koolschijn@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-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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