Hi Anupa

you need to specify each input volume with -i if there are more than one. In your example you would need an inner loop of the form

set inputs = () foreach vol (SZ*.nii) set input = ($inputs -i $vol) end recon-all $inputs ...

cheers Bruce

On Wed, 17 Apr 2013, Anupa AV wrote:

Dear All,

I want to run recon-all for multiple subjects. I named my sbjects as SZ01.nii, SZ02.nii etc.

After setting the cd and environmanet variable, I ran using following for loop:

...

for x in * do recon-all -i SZ*.nii -s $x -all done

I got the following error: WHAT MIGHT BE THE REASON FOR THE ERROR???

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ01.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux

recon-all -s  exited with ERRORS at Fri Apr 19 11:43:24 IST 2013

For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ02.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux

recon-all -s  exited with ERRORS at Fri Apr 19 11:43:24 IST 2013

For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ03.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux

recon-all -s  exited with ERRORS at Fri Apr 19 11:43:24 IST 2013

For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ04.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux

recon-all -s  exited with ERRORS at Fri Apr 19 11:43:24 IST 2013

For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting