Hi Paras, The tcsh warning is ok, but see this link for more info and a fix: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg28980.html

The unrecognized flag error is because you have a space between the dash and subjid, just delete that space. -Louis

On Thu, 3 Jul 2014, Paras Patel wrote:

Dear Sir/Madam,

I am a masters student at Newcastle University using Freesurfer to extract data from MRI scans.

When trying to use the command lines in terminal, I seem to be getting an error message which I was wondering if you could help me with.

The command line I am using is : recon-all -autorecon-all - subjid sam01

The error message displayed is:

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

ERROR: Flag - unrecognized. -autorecon-all -subjid try01 Linux xubuntu-VirtualBox 3.2.4-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC

recon-all -s exited with ERRORs at Mon Jun 23 06:47:34 EDT 2014

I have tried the help guide which suggest to update the VM and I have tried to uninstall and re-install Freesurfer but I still get the same error message. I also get the same error message when trying with a different subjid .

Please can you give me further guidance on how to fix this error so that I can continue working with Freesurfer.

Thank You, Kind Regards, Paras Patel Newcastle University

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