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FreeSurfer Mac OS X Installation and Setup
This page details how to install FreeSurfer on a Mac OS X machine, from download to set up. The full installation package provided by MGH includes support libraries and a sample data set.
Prerequisite: The Max OS X machine must have the X11 package installed before installing FreeSurfer. It will appear in the Finder under Applications -> Utilities -> X11.
attachment:install-x.jpg
If it is not present it can be downloaded from [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/X11User-Darwin.dmg ftp://surfer.nmr.mgh.harvard.edu/pub/dist/X11User-Darwin.dmg]. To launch a X terminal window, start X11 by double clicking on it in the Finder, and the Terminal application can be found under Applications menu item on the top left of the screen. A new terminal can also be opened by pressing Apple-N while X11 is the primary application. Be sure not to confuse the X11 Terminal application with Apple's Terminal application, which does not directly support X11 applications (such as FreeSurfer's tkmedit, tksurfer and tkregister).
The FreeSurfer software is distributed through the NMR ftp site. Look for the latest version at [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ ftp://surfer.nmr.mgh.harvard.edu/pub/dist/] and save freesurfer-Darwin-tiger-full.dmg to your local machine. It contains the FreeSurfer binaries, support software, and a sample data set, and may take a few minutes to download even on a fast connection.
Once the dmg has been downloaded, double click on it in the Finder to expand the package, which will result in the following:
attachment:install-4mpkg.jpg
Double click on the mpkg and the installation wizard will launch as a guide through the set up.
After the package integrity has been verified, the introductory screen will appear.
attachment:install-5intro.jpg
Click on Continue, and read the explanatory text on the Read Me screen, as it contains information useful during the next stage of the installation:
attachment:install-6readme.jpg
Click on Continue, and read the end user license agreement, scrolling down using the bar along the right side of the window.
Click on Continue and a window will appear with the option to agree or disagree to the license.
Click on Agree, and the next screen will appear. Select where to install the software. The directory /Users/Shared on the selected disk will be used.
Click on the hard drive on which to install the software; that icon will highlight (if it has not been already selected, which may occur if only one disk is installed).
Click on Continue to confirm the disk selection. From the next screen, the default is to click on Upgrade for a simple installation of all packages in the archive:
attachment:install-11easyinstall.jpg
To customize the installation, click on Customize and this screen will appear, allowing selection of packages to install:
attachment:install-12custominstall.jpg
If not all of the packages are selectable, check in the directory /Library/Receipts for directories matching the package names. The operating system will compare the new installation against any old installations, and will prevent upgrades if the version of the package being installed is older than the one currently installed. Remove the receipt directory to reinstall a new version of the desired software packages and restart the installer by double clicking on the mpkg.
Click on Install and packages will begin to be installed on the designated hard drive.
The installer may then optimize the hard drive for performance.
Once the optimization is finished, the installation process is successfully concluded:
attachment:install-19success.jpg
If you encounter errors during the installation, while still in the Installer, and Installer is still the primary application, click the Window -> Installer Log menu item to show the error log to see why installation failed.
Otherwise, click on Close to exit the installer.
[wiki:SetupConfiguration Setup and configuration of the environment is described next.]