These instructions have moved to: HowTo Install AFNI



  * Note that 10.8 does not come with X11 (or XQuartz) installed.  When afni
    is started for the first time, you should be directed (by the operating
    system) to a link to install XQuartz.


1. account setup
    Assuming a user account exists, these steps are all optional

    1a. Create a user account with su (Administrator) privileges
        (via "System Preferences", under "Accounts").

        Note: Admin privleges are needed for fink.

    1b. (optional) Set the shell to /bin/tcsh.  This no longer works using
        the chsh command.

        Under System Preferences : System : Accounts menu, right-click on the
        user to get the Advanced Options menu and change the Login shell to
        /bin/tcsh.

    1c. (optional) Under System Preferences : Sharing : Services, enable
        Remote Login to allow ssh access.

    1d. Set the policy where "focus follows mouse", so that it is not
        necessary to first click on a new window (to select it) before
        subsequent clicks are applied to that window.  There are 3 applications
        that this might apply to, so we make sure...

        From a terminal window, enter:

           defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
           defaults write org.x.X11 wm_ffm -bool true
           defaults write com.apple.Terminal FocusFollowsMouse -string YES

2. Xcode installation
    Xcode is needed for the gcc compiler and related tools  It is best to start
    with the most recent version from the apple website. 

        o  go to http://developer.apple.com
             - a login account is necessary to download, sign up the first time
             - sign up via "Register as an Apple Developer", it is free
        o  get your current Command Line Tools package (part of Developer Tools) and install
             - current version is 4.6.2
             - installation defaults are good, to complete installation

3. HomeBrew installation
At this point, we will install Homebrew.  The Homebrew installation takes less time than the Fink installation.

    3a. Install HomeBrew and Python
 

        o  Type this command to run the Homebrew installation script:

           bash syntax:

              ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
                    
           tcsh syntax:

              curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install | ruby


    3b. Make sure Homebrew installation succeeded with no errors by typing this command:

          brew doctor

    3c. Install PyQt4 for use of the uber_*.py programs.

          brew install pyqt
    

4. AFNI installation 
    4a. Download and unpack the current binaries into your home directory,
        changing the directory name to 'abin'.

          cd
          curl -O http://afni.nimh.nih.gov/pub/dist/tgz/macosx_10.7_Intel_64.tgz
          tar -xzf macosx_10.7_Intel_64.tgz
          mv macosx_10.7_Intel_64 abin
          rm macosx_10.7_Intel_64.tgz

    4b. Update the path and library path.

        tcsh users:

          echo 'set path = (/usr/local/bin $path $HOME/abin )' >> .cshrc
          echo 'setenv DYLD_FALLBACK_LIBRARY_PATH $HOME/abin' >> .cshrc
          echo 'setenv PYTHONPATH /usr/local/lib/python2.7/site-packages' >> .cshrc
          source .cshrc
          rehash

        bash users:

          echo 'export PATH=/usr/local/bin:$PATH:$HOME/abin' >> .profile
          echo 'export DYLD_FALLBACK_LIBRARY_PATH=$HOME/abin' >> .profile
          echo 'export PYTHONPATH=/usr/local/lib/python2.7/site-packages' >> .profile
          . .profile

    4c. Try it out!  If these start, you should be in good shape.  Note that
        10.8 users may need to follow the link to install XQuartz.

          afni
          suma

    4d. 10.8 - install XQuartz

        When prompted, install XQuartz.

    4e. (optional, but helpful)  Update help files for tab-completion.
        Run this command, and then follow the brief instructions.

          apsearch -update_all_afni_help

    4f. Get sample data and review AFNI handouts.

          Class Data and Handouts