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FreeSurfer Mac OS X Installation and Setup

Before proceeding: The Max OS X machine must have XQuartz installed before you can run FreeSurfer. To check if you already have XQuartz, open a Finder window and look for it under Applications -> Utilities -> XQuartz. If it is not there, please download and install XQuartz before proceeding with the FreeSurfer installation. *NOTE:* Major upgrades to you Mac system (e.g. from Mountain Lion to Mavericks) will require a reinstallation of XQuartz.

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Once the dmg installation file has been downloaded, double click on it to expand the package:

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Double click on the mpkg to launch the installation wizard. If you get this error:

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Then you need to adjust your security settings to allow applications from 3rd party developers to be installed. To do this go to System Preferences -> Security & Privacy -> General. Click the lock on the bottom left to make changes and under Allow applications downloaded from: select Anywhere.

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After the package integrity has been verified, the introductory screen will appear.

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Click on Continue:

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If you're not sure how to follow these instructions, don't worry - we'll come back to them. To set up your computer to automatically load FreeSurfer whenever a terminal window is opened add the following lines to the .profile file in your home directory (If you don't already have a .profile file in your home directory, you can go ahead and create one using pico or some other text editor): 

export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

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 /Applications on the selected disk will be used. If you wish to install to a different directory, click on Choose and select an alternate installation location.

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If it is not already highlighted, click on the hard drive on which to install the software.

Click on Continue to confirm the disk selection.

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Click on Install and the package 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:

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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.

Lastly, if you intend to run recon-all (the processing script which can run for 24 hours) on your mac, we recommend setting your Power Adapter Energy Settings to 'Never' sleep, otherwise recon-all will only run when you are logged-in. This is done under System Preferences -> Energy Saver.

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Setup and configuration of the environment is described next.