Hi Clelia, What do you run to source FS and do you get any output in your terminal after doing so? What operating system are you running? You might try using c-shell instead of bash. -Louis

On Fri, 24 May 2013, clelia pellicano wrote:

Hi Louis, thank you for your answer.  I sourced freesurfer again, but I still  get 'command not found'. What can I try? Thank you,

Clelia

On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote: Hi Clelia, If this is in a new terminal then you'll have to source freesurfer again. See here for details: https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -Louis

  On Wed, 22 May 2013, clelia pellicano wrote:

        Hi,
        I have run recon-all -s bert -all to try my installation and it worked.
        Now, when I try to use other command (and also again recon-all -s bert -all) I always get this:

        dyn1097-8:subjects cpellica$ tkmedit bert orig.mgz
        -bash: tkmedit: command not found
        dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz
        -bash: tkmedit: command not found
        dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial
        -bash: tksurfer: command not found
        dyn1097-8:subjects cpellica$ qdec
        -bash: qdec: command not found
        dyn1097-8:subjects cpellica$ recon-all help
        -bash: recon-all: command not found
        dyn1097-8:subjects cpellica$ recon-all -s bert -all
        -bash: recon-all: command not found


        I don't know how to do. Please, could you help me?

        Thanks

        Clelia

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