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.sil...@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 <fis...@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 .shOn 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'> > > > > > >_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer