|
Size: 4611
Comment:
|
Size: 5272
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| [wiki:Self:FreeSurferWiki top] | [wiki:Self:Installation previous] | [wiki:Self:SetupConfiguration next] | [[DownloadAndInstall|top]] | [[Installation|previous]] | [[SetupConfiguration|next]] |
| Line 3: | Line 3: |
| == FreeSurfer Mac OS X Installation and Setup == | '''Index''' <<TableOfContents>> |
| Line 5: | Line 5: |
| 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. |
| Line 7: | Line 13: |
| 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}} |
| Line 9: | Line 15: |
| attachment:install-x.jpg | Download the freesurfer '''dmg''' installation package and double click on it to expand the package: {{attachment:install-5mpkg.png}} |
| Line 11: | Line 18: |
| 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: ## ## {{attachment:install_error.png}} |
| Line 13: | Line 22: |
| 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'''. |
| Line 15: | Line 26: |
| ## attachment:install-2filelisting.jpg 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}} |
| Line 27: | Line 32: |
| 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''': {{attachment:install-5intro.jpg}} |
| Line 29: | Line 35: |
| attachment:install-5intro.jpg | Next is the README window. Click on '''Continue''': {{attachment:install-6readme.jpg}} |
| Line 31: | Line 38: |
| 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: | ## 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: |
| Line 33: | Line 40: |
| attachment:install-6readme.jpg | ## {{{ ## export FREESURFER_HOME=/Applications/freesurfer ## source $FREESURFER_HOME/SetUpFreeSurfer.sh ## }}} |
| Line 35: | Line 45: |
| Click on '''Continue''', and read the end user license agreement, scrolling down using the bar along the right side of the window. | 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'''. |
| Line 38: | Line 58: |
Click on '''Continue''' and a window will appear with the option to agree or disagree to the license. |
|
| Line 43: | Line 60: |
| 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. |
| Line 45: | Line 62: |
| ## attachment:install-9selectdestination.jpg | {{attachment:install-9selectdestination.jpg}} |
| Line 47: | Line 64: |
| 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). | |
| Line 51: | Line 67: |
| 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'''. |
| Line 53: | Line 69: |
| attachment:install-11easyinstall.jpg | {{attachment:install-11easyinstall.jpg}} |
| Line 55: | Line 71: |
| 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: |
| Line 57: | Line 73: |
| attachment:install-12custominstall.jpg | ## attachment:install-12custominstall.jpg |
| Line 59: | Line 75: |
| 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. |
| Line 61: | Line 77: |
| 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. |
| Line 69: | Line 85: |
| The installer may then optimize the hard drive for performance. |
|
| Line 73: | Line 87: |
| Once the optimization is finished, the installation process is successfully concluded: | Once the optimization is finished, the installation process should be successful: |
| Line 75: | Line 89: |
| attachment:install-19success.jpg | {{attachment:install-19success.jpg}} |
| Line 81: | Line 95: |
| [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 README window. Click on Continue: 
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.