Hi Clelia,
That mv command is failing presumably because SetUpFreeSurfer.txt does not exist in that directory.  What are you trying to do with the mv command?

It does look like freesurfer was sourced successfully.  Are the FreeSurfer related commands still not found?

Don't forget to cc the freesurfer mailing list.

-Louis

On Fri, 24 May 2013, clelia pellicano wrote:

Hi Louise,
I'm now using tcsh. Here what I did

      [dyn1097-8:~] cpellica% setenv FREESURFER_HOME /Applications/freesurfer
[dyn1097-8:~] cpellica% source /Applications/freesurfer/SetUpFreesurfer.csh
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME       /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/subjects
MNI_DIR           /Applications/freesurfer/mni
FSL_DIR           /usr/local/fsl
[dyn1097-8:~] cpellica% mv  SetUpFreeSurfer.txt SetUpFreeSurfer.csh 
mv: rename SetUpFreeSurfer.txt to SetUpFreeSurfer.csh: No such file or directory

Do you have any advice?

Thanks

Clelia





On Fri, May 24, 2013 at 3:04 PM, Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu> wrote:
      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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