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| [wiki:Self:FreeSurferWiki top] | [wiki:Self:Installation previous] | [wiki:Self:SetupConfiguration next] | [[DownloadAndInstall|top]] | [[Installation|previous]] | [[SetupConfiguration|next]] |
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| == FreeSurfer Mac OS X Installation and Setup == | = FreeSurfer Mac OS X Installation and Setup = '''Before proceeding:''' The Max OS X machine must have [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]] installed before you can run !FreeSurfer (new versions of XQuartz break some of the GUIs). To check if you already have [[http://xquartz.macosforge.org/landing|XQuartz]], open a Finder window and look for it under '''Applications -> Utilities -> XQuartz'''. If it is not there, please download and install [[http://xquartz.macosforge.org/landing|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 [[http://xquartz.macosforge.org/landing|XQuartz]]. |
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| 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. | {{attachment:XQuartz_screencapture.png}} |
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| 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'''. | Once the '''dmg''' installation file has been downloaded, double click on it to expand the package: |
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| attachment:install-x.jpg | {{attachment:install-4mpkg.jpg}} |
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| 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 Terminal can be found under Applications. A new terminal can also be opened by pressing Apple-N while X11 is the primary application. | Double click on the '''mpkg''' to launch the installation wizard. If you get this error: |
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| 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. | {{attachment:install_error.png}} |
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| ## attachment:install-2filelisting.jpg | 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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| 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. |
{{attachment:allow_anywhere.png}} |
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| attachment:install-5intro.jpg | {{attachment:install-5intro.jpg}} |
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| 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: | Click on '''Continue''': |
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| attachment:install-6readme.jpg | {{attachment:install-6readme.jpg}} |
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| Click on '''Continue''', and read the end user license agreement, scrolling down using the bar along the right side of the window. | 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. <<BR>> Click '''Continue'''. |
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Click on '''Continue''' and a window will appear with the option to agree or disagree to the license. |
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| 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. | 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. |
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| ## attachment:install-9selectdestination.jpg | {{attachment:install-9selectdestination.jpg}} |
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| 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). | |
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| 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: | Click '''Continue'''. |
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| attachment:install-11easyinstall.jpg | {{attachment:install-11easyinstall.jpg}} |
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| To customize the installation, click on '''Customize''' and this screen will appear, allowing selection of packages to install: | ## To customize the installation, click on '''Customize''' and this screen will appear, allowing selection of packages to install: |
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| attachment:install-12custominstall.jpg | ## attachment:install-12custominstall.jpg |
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| 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. | ## 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. |
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| Click on '''Install''' and packages will begin to be installed on the designated hard drive. | 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. |
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| The installer may then optimize the hard drive for performance. |
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| Once the optimization is finished, the installation process is successfully concluded: | Once the optimization is finished, the installation process should be successful: |
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| attachment:install-19success.jpg | {{attachment:install-19success.jpg}} |
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| Otherwise, click on '''Close''' to exit the installer and begin setting up the environment. | Otherwise, click on '''Close''' to exit the installer. |
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| [wiki:Self:SetupConfiguration Setup and configuration of the environment is described next.] | 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'''. {{attachment:no_sleep.png}} If you came from the Quick Install page, return to that [[QuickInstall|here]].<<BR>> Otherwise, setup and configuration of the environment is described [[SetupConfiguration_Mac|next.]] |
FreeSurfer Mac OS X Installation and Setup
Before proceeding: The Max OS X machine must have XQuartz 2.7.5 installed before you can run FreeSurfer (new versions of XQuartz break some of the GUIs). 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.
Once the dmg installation file has been downloaded, double click on it to expand the package:
Double click on the mpkg to launch the installation wizard. If you get this error:
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.
After the package integrity has been verified, the introductory screen will appear.
Click on Continue:
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.
Click Continue.
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:
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.
If you came from the Quick Install page, return to that here.
Otherwise, setup and configuration of the environment is described next.