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'''Before proceeding:''' You need to install XQuartz. Pre-Yosemite versions of OS X require [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]], Yosemite requires [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] or higher. ----
'''Before proceeding:''' Mac OSX requires the installation of XQuartz for freesurfer to function properly.
 * OSX versions 10.6, 10.7, 10.8, and 10.9 require [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]] (or earlier).
 * OSX versions 10.10 and later requires [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] (or higher).
----
Check '''Application -> Utilities''' to see if XQuartz is already installed. If not use the links above to download the proper version and install. You may need to logout and log back in after XQuartz is installed.
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Once the '''dmg''' installation file has been downloaded, double click on it to expand the package: Download the freesurfer '''dmg''' installation package and double click on it to expand the package:

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Index

Contents

  1. Installation

Installation


Before proceeding: Mac OSX requires the installation of XQuartz for freesurfer to function properly.

  • OSX versions 10.6, 10.7, 10.8, and 10.9 require XQuartz 2.7.5 (or earlier).

  • OSX versions 10.10 and later requires XQuartz 2.7.6 (or higher).


Check Application -> Utilities to see if XQuartz is already installed. If not use the links above to download the proper version and install. You may need to logout and log back in after XQuartz is installed.

XQuartz_screencapture.png

Download the freesurfer dmg installation package and double click on it to expand the package:

install-4mpkg.jpg

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

install_error.png

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.

allow_anywhere.png

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

install-5intro.jpg

Click on Continue:

install-6readme.jpg

If you're not sure how to follow the instructions in the Read Me window, don't worry - we'll come back to them. To set up your computer to automatically load FreeSurfer when a terminal window is opened, add the following lines to the .profile file in your home directory:

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

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:

pico .profile

Copy and paste the two lines from the previous box into the blank screen that appears. After that, type Ctrl+x to exit. Then type 'y' and then hit enter to save your changes.

On the installation wizard, click on Continue and read the end user license agreement, scrolling down using the bar along the right side of the window.
Click Continue.

After you agree to the license agreement, you can select where to install the software. Highlight the hard drive where you want to install it (if not already highlighted). To change the directory where it is installed (Applications is the default location), hit the Choose button.

install-9selectdestination.jpg

Click Continue.

install-11easyinstall.jpg

Click on Install and the package will begin to be installed at the location you chose. The installer may then optimize the hard drive for performance.

Once the optimization is finished, the installation process should be successful:

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.

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.

no_sleep.png

If you came from the Quick Install page, return to that here.
Otherwise, setup and configuration of the environment is described next.

MacOsInstall (last edited 2020-03-04 14:59:29 by LeahMorgan)