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Set up FreeSurfer

Before using any FreeSurfer command, including freeview (or tksurfer etc), FreeSurfer has to be set properly (in the terminal). The steps in bash are:

  • export FREESURFER_HOME=/Applications/freesurfer
  • source $FREESURFER_HOME/SetUpFreeSurfer.sh
  • export SUBJECTS_DIR=/full/path/to/subject/dir
  • cd to/the/functional/data/folder

Note: for FreeSurfer 7.1 or later, you may need to update bash if you are still using the default bash in Mac. You may follow the instruction here.