External Email - Use Caution        

Yes, as Viviana said, you need to specify the path to the Applications folder by using a leading slash “/“ character.

You can test that path /Applications/freesurfer/subjects is OK by opening the terminal application and then typing at the dollar sign prompt,

$ ls /Applications/freesurfer/subjects

.. which should not give you an error and show some files are there.

Unless someone changed the shell preferences for your account on the Mac, then the default shell at the $ prompt in the terminal window is bash shell for Mac OS 10.14.  There should be no need to type “bash” again (and start another shell).

So in the terminal window it should work for you to type the lines after the dollar sign prompt  (you could cut and paste the below), and then see if you get the same output.

$ ls -d /Applications/freesurfer
/Applications/freesurfer

$ export FREESURFER_HOME=/Applications/freesurfer
$ echo $FREESURFER_HOME
/Applications/freesurfer

$ ls $FREESURFER_HOME/SetUpFreeSurfer.sh
/Applications/freesurfer/SetUpFreeSurfer.sh

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

If the “source" command results in an error, then you can try to see what failed by running the shell script with “sh -x” instead of “source”.

$ sh -x $FREESURFER_HOME/SetUpFreeSurfer.sh

If running the script with “sh -X” does not end with a “return 0” statement displayed on the terminal, then you cost cut and paste the last several lines before the error and email it back to us.

- R.

On Aug 31, 2019, at 00:04, Viviana Siless <viviana.siless@gmail.com> wrote:

        External Email - Use Caution        


Hi, I think you are just mistyping it, if the subjects dir is in "/Applications/freesurfer/subjects/ " the command  should be:
export SUBJECTS_DIR=/Applications/freesurfer/subjects/ 

( instead of  export SUBJECTS_DIR=<Applications/freesurfer/subjects>)


Viv


On Fri, Aug 30, 2019 at 4:35 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
oh, the export command is failing? You mentioned you weren't running bash 
(which is the shell that knows what to do with an export command). Can you 
install bash? If not, you can use setenv instead of export and the .csh 
file instead of the .sh


On Fri, 
30 Aug 2019, michele rizzi wrote:

> 
>         External Email - Use Caution        
> 
> 
> I put 
> 
> 
> export SUBJECTS_DIR=<Applications/freesurfer/subjects>
> 
> 
> 
> but again I get 
> 
> 
> 
> -bash: syntax error near unexpected token `newline'
> 
> 
> 
> 
> 
> 
>_______________________________________________
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