Hi there,
I just installed freesurfer onto a mac os x. My computer seems to default to bash, so I created a .bashrc file in my home directory and added the lines:
export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
but just in case I also created a .cshrc and added the c shell version of that code. I also created the .license file as per the installation instructions. Then I opened up the terminal, in bash, and did the export and source thing again. I also updated the SetUpFreeSurfer file so that it has the correct path: /Applications/freesurfer. However, when I try to test the installation and type in recon-all -s bert -autorecon1 (i have to use sudo as well bc it keeps telling me i don't have write permission) I always get back FREESURFER_HOME: Undefined variable. I've seen several other people post this same problem to this forum in the past but no one has ever posted a response that I can see. I tried reinstalling, and typing in the command from different directories, and sourcing again, but I always get back the same response. The really frustrating thing is, when I type echo $FREESURFER_HOME I get back /Applications/freesurfer which is correct! Any thoughts on what I'm doing wrong here?
Thanks in advance.