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
CautionHi, I think you are just
mistyping it, if the subjects dir is in "/Applications/freesurfer/subjects/ "
the commandshould be:export
SUBJECTS_DIR=/Applications/freesurfer/subjects/( instead
ofexport 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 youinstall bash? If not, you can use setenv instead of export and the
.cshfile 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
