There's 2 problems:
1) Do not include the "$>". That is just a symbol representing the beginning of the command line.
2) <source_freesurfer> is meant to be a generic term for the process of defining your FREESURFER_HOME environment variable and sourcing the setup script. On your macOS system this would be the following two steps:
$> export FREESURFER_HOME=/Applications/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh
This only needs to be done once when opening the terminal window.
On 01/17/2017 11:50 AM, Shapiro, Allison L wrote:
Dear FreeSurfer support,
I am a new user of the Freesurfer program and attempted to install everything this morning on my Mac OSx 10.11.6 (El Capitan). To preface everything, I updated my XQuartz program before installing, and I do not have Matlab on this computer and understand that I can’t use the fMRI functionality without this, but this is not my goal.
The installation appeared to go as planned, but when I went to test the installation with the commands:
$> <source_freesurfer>
$> freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
I received the following error:
-bash: $: command not found
I was not able to decipher this error with The Google, so I am hoping that you can help.
Thank you so much for your time!
Best Wishes,
Allie
Allison L B Shapiro, MPH, PhD
Postdoctoral Research Fellow
LEAD Center | Colorado School of Public Health
Office 303.724.7708
“Those who dare to fail miserably can achieve greatly” - JFK
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