Clelia,

Please type the following commands in the terminal window and provide us
any error message you may receive.

 >> setenv FREESURFER_HOME /Applications/freesurfer
 >> source $FREESURFER_HOME/SetUpFreesurfer.csh
 >> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz

If a window with an image pops open than freesurfer is installed and
ready to go. If not than please provide whatever error message you may
receive.

-Zeke

On 05/24/2013 12:15 PM, clelia pellicano wrote:
> Hi Louise,

> yes, teh FreeSurfer related commands are still not found. The other
> thing is that I had problem with license file. I have created a file in
> Applications/Freesurfer named .license and tried to copy inside le
> license key but I'm not sure that it worked beacuse if I write cd
> .license I get 'it is not a file not a directory'.
> Thanks
> Clelia
>
> On Fri, May 24, 2013 at 5:09 PM, Louis Nicholas Vinke

> <vinke@nmr.mgh.harvard.edu <mailto:vinke@nmr.mgh.harvard.edu>> wrote:
>
>     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 <mailto: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

>         <mailto: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

>         <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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