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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 == | '''Index''' <<TableOfContents>> |
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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. | = 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 [[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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| 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:XQuartz_screencapture.png}} |
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| attachment:install-x.jpg | Download the freesurfer '''dmg''' installation package and double click on it to expand the package: |
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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-5mpkg.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. | ## Double click on the '''mpkg''' to launch the installation wizard. If you get this error: ## ## {{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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| After the package integrity has been verified, the introductory screen will appear. | After the package integrity has been verified, the introductory screen will appear. Click on '''Continue''': |
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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: | Next is the Read Me window. 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. | Next is the Software License Agreement window. Click on '''Continue''': |
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| ## attachment:install-7license.jpg | {{attachment:SLA.png}} |
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| Click on '''Continue''' and a window will appear with the option to agree or disagree to the license. | Next is the Destination Select window. Click '''Change Install Location...''' to change the default installation disk and folder (/Applications/freesurfer). Or click '''Install''' to go with default: |
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| ## attachment:install-8licenseclick.jpg | {{attachment:install-9selectdestination.jpg}} |
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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. | |
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| ## attachment:install-9selectdestination.jpg | You may need to enter you password. The installation process will begin to write files and will take a few minutes to complete. |
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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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| ## attachment:install-10destinationselected.jpg | {{attachment:success.png}} |
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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: 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. ## attachment:install-13procfsbins.jpg ## attachment:install-14procfssupport.jpg ## attachment:install-15procdata.jpg ## attachment:install-16procminc.jpg ## attachment:install-17procfullinst.jpg The installer may then optimize the hard drive for performance. ## attachment:install-18optimisinghd.jpg Once the optimization is finished, the installation process is successfully concluded: attachment:install-19success.jpg |
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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.]] |
Index
Contents
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.
Download the freesurfer dmg installation package and double click on it to expand the package:
After the package integrity has been verified, the introductory screen will appear. Click on Continue:
Next is the Read Me window. Click on Continue:
Next is the Software License Agreement window. Click on Continue:
Next is the Destination Select window. Click Change Install Location... to change the default installation disk and folder (/Applications/freesurfer). Or click Install to go with default:
You may need to enter you password. The installation process will begin to write files and will take a few minutes to complete.
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.