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| [wiki:Self:FreeSurferWiki top] | [wiki:Self:Installation previous] | [[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/landing|XQuartz]] installed before you can run !FreeSurfer. 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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| === 1.0 Downloading software === | Once the '''dmg''' installation file has been downloaded, double click on it to expand the package: |
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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'''. | {{attachment:install-4mpkg.jpg}} |
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| attachment:install-x.jpg | Double click on the '''mpkg''' to launch the installation wizard. If you get this error: |
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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. | {{attachment:install_error.png}} |
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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. | 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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| ## attachment:install-2filelisting.jpg === 2.0 Installing software === 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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| === 3.0 Setting up environment === | 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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| The read-me screen of the installer provides directions on setting up the environment to allow running FreeSurfer, and this is reviewed next. | {{attachment:no_sleep.png}} |
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| ## attachment:install-6readme.jpg Usage of C shell (csh) or enhanced C shell (tcsh) is recommended. The shell type on your system can be checked by typing '''ps''' at the command line in an X terminal window. If csh or tcsh does not appear as one of the processes in the right hand column of output, the default shell must be changed to csh or tcsh. Otherwise, explicitly launch csh or tcsh before attempting to go further. To explicitly launch csh or tcsh (tcsh is recommended), simply enter the following command in an X terminal window: {{{ tcsh }}} The prompt may change, and some login files may not be run in the new shell environment. See the man pages for tcsh for details. If you do not have a preference for a particular shell, the default shell under Mac OS X can be permanently switched from bash to tcsh by typing the following: {{{ chsh -s /bin/tcsh }}} The file freesurfer/SetUpFreeSurfer.csh is a csh (C-shell) script that will configure the environment so that FreeSurfer can be used. It sets a few environment variables, sources other csh scripts to set up support libraries, and performs some checks that need to be passed before FreeSurfer can start. This file needs to be sourced before running any FreeSurfer binaries. This can be done manually via typing the following command in an X terminal window: {{{ source /Users/Shared/freesurfer/SetUpFreeSurfer.csh }}} Alternately, the resource file for the shell can be configured to source the file automatically each time the shell is started. In the home directory of the user who will be running FreeSurfer binaries, edit the file '''.cshrc''' if C-shell will be used, or '''.tcshrc''' for enhanced C-shell, to include the line: {{{ source /Users/Shared/freesurfer/SetUpFreeSurfer.csh }}} A sample subject directory is provided with the full installation, in /Users/Shared/freesurfer/subjects. If custom subject directories are created using mksubjectdirs or a different sample data set is used, let FreeSurfer know where to look by inserting the following line before the source command above: {{{ setenv SUBJECTS_DIR [path to subject directory] }}} Make sure to use C shell (csh) or enhanced C shell (tcsh). This can be checked by typing '''ps''' at the command line in an X terminal window. If csh or tcsh does not appear as one of the processes in the right hand column of output, the default shell must be changed to csh or tcsh. Otherwise, explicitly launch csh or tcsh before attempting to go further. To explicitly launch csh or tcsh (tcsh is recommended), simply enter the following command in an X terminal window: {{{ tcsh }}} The prompt may change, and some login files may not be run in the new shell environment. See the man pages for tcsh for details. As the shell starts up, messages are printed out showing the environment variables that have been set by the configuration scripts. The following example shows a case where the SUBJECTS_DIR has been set to something other than the default: {{{ Setting up environment for FreeSurfer/FS-FAST FREESURFER_HOME /Users/Shared/freesurfer FSFAST_HOME /Users/Shared/freesurfer/fsfast SUBJECTS_DIR /Users/Shared/freesurfer/subjects FUNCTIONALS_DIR /Users/Shared/freesurfer/sessions MINC_BIN_DIR /Users/Shared/freesurfer/lib/mni/bin MINC_LIB_DIR /Users/Shared/freesurfer/lib/mni/lib QTDIR /Users/Shared/freesurfer/lib/qt LIBS_DIR /Users/Shared/freesurfer/lib/misc }}} If any warnings appear, it's usually safe to ignore them, but make sure that they are not stating that a file or directory that should exist cannot be found. If any error messages appear, check that the installation process was successfully completed. === 4.0 Practice data === A public distribution data set is available to run the tutorials. It contains 40 subjects, and occupies about 21G of disk-space. The file is available from the [ftp://surfer.nmr.mgh.harvard.edu/pub/dist distribution site], and is called [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_public_distribution.tar.gz buckner_public_distribution.tar.gz]. Once the file is downloaded, move the file to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following command: {{{ tar zxvf buckner_public_distribution.tar.gz }}} The downloaded file can then be deleted. To setup the environment variables SUBJECTS_DIR and SUBJECTS to point to this data, type the following command or include in your .cshrc or .tcshrc file: {{{ source $FREESURFER_HOME/subjects/buckner_public_distribution/sample_group_study/scripts/subjects.csh }}} |
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 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.
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.