FreeSurfer should already be setup on all CoreB machines. If you need to install FreeSurfer on a separate workstation (e.g., your own laptop/desktop), or you need to update FreeSurfer, follow the Download and Installation instructions from the FreeSurfer wiki (but see the following note).
N.B. The FreeSurfer instructions suggest adding some lines to your .profile file (for Mac users) so that FreeSurfer is automatically accessible when you open the Terminal. This is a good idea, but we have taken the approach of placing these same lines in the .cshrc file in the home directory (~/.cshrc on any Mac; /Users/imaginguser/.cshrc on CoreB machines more specifically). This is simply because we use the tcsh shell by default (as it is the preferred shell for AFNI scripts). You should add the following lines to your .cshrc file (ToDo add link: or see the example .cshrc file from a CoreB machine):
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR ~/MR_DATA/surfaces
source ${FREESURFER_HOME}/SetUpFreeSurfer.csh
After you save the .cshrc file, when you subsequently open a new Terminal, you will be able to call FreeSurfer commands directly. In addition, this will setup the shared surfaces directory, which is ~/MR_DATA/surfaces/ on CoreB machines. You can change this for your own setup if you'd like.
Finally, if you know what you are doing, you should certainly feel free to setup your environment variables using a different file (e.g., .bashrc if you use the bash shell).
After setting up FreeSurfer, you'll need to Convert the T1/T2 Images.