First, install Apple's X11 environment. This allows you to run X11 (XWindows, or graphical Unix) programs on your Mac. This is currently available at:

http://www.apple.com/macosx/features/x11/

Folow the instructions to install this package. It is free.

Next, you need to install some software that will allow you to easily install other libraries from source code. We recommend using Fink, an open source front-end to the apt tools.

http://fink.sourceforge.net/

Follow the instructions on this page for completing a new Fink installation.

We also recommend using a graphical front-end to Fink called FinkCommander:

http://finkcommander.sourceforge.net/

This is not strictly necessary but makes the next few steps much easier.

Run FinkCommander. The first thing you should do is enable the unstable tree to allow access to a package that is not considered stable by the Fink crew, but is necessary to use some FreeSurfer applications. In the FinkCommander menu, open the Preferences dialog. Click the Fink tab at the top, then check the "Use unstable packages" dialog box. Click the OK button. You may need to enter your admin password and wait for Fink to chug around a bit.

Now install some libraries. We'll start with jpeg. In the search field at the top right of the main Fink window, type 'jpeg' and press return. Look at the results; you should see libjpeg, libjpeg-bin, and libjpeg-shlib, among others. Click on the libjpeg entry, and click on the button in the toolbar that looks like a plus sign over a document with a .h on it, second from the left. This will download the sources for libjpeg, build them, and install them.

If you get an error about cc or a compiler not being present, Try clicking the button that looks like a plus sign over a document with the Application icon on it (a stylized A) to install the packages as binaries.

Follow this procedure for libtiff, glut, tcltk, tix, and blt.

You will also need to install the MNI software. Information on their OS X distribution is here:

http://www.bic.mni.mcgill.ca/software/distribution/osx.html

You should now have all the prerequisites installed. After installing FreeSurfer and creating your SetUpFreeSurfer.csh file, launch the X11 application. This will give you a terminal from which you can run FreeSurfer programs. Note that you must use the terminal within the X11 application to run FreeSurfer graphics tools; they will not work if you are running them from the regular OS X terminal.
2005-Feb-16 3:19pm kteich