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| <<TableOfContents>> | ## page was renamed from QuickInstall |
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| == FreeSurfer System Requirements == '''Summary of Requirements:'''<<BR>> Operating System: Linux, Mac OS X, Windows (via !VirtualBox)<<BR>> Processor Speed: 2GHz at least<<BR>> RAM: 4GB at least (8GB recommended)<<BR>> Graphics card: 3D with its own graphics memory & accelerated OpenGL drivers<<BR>> Install's Disk space usage: 8.5GB<<BR>> Typical subject size: 370MB<<BR>> Tutorial dataset size: 18GB<<BR>> Other requirements: Matlab (only needed to run FS-FAST, the fMRI analysis stream) |
= FreeSurfer Download and Install = |
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| == Download == '''Important:''' It is essential to process all your subjects with the same version of !FreeSurfer, on the same OS platform and vendor, and to be completely safe, even the same version of the OS. |
You can read and compare the version 7 and 6 release notes [[https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes|here]]. |
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| == Freesurfer 5.3 stable release == Please refer to the ReleaseNotes page for per-release information. |
=== Latest Version 7 Release (May 2020) === |
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| ||'''OS''' || '''Platform''' || '''Version''' || '''Release Date''' || '''Download''' || '''Size''' || || Linux || CentOS 6 x86_64 (64b)|| stable v5.3.0 ||15 May 2013 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz|freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz]]||4.2G|| || Linux || CentOS 4 x86_64 (64b)|| stable v5.3.0 ||15 May 2013 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz|freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz]]||4.0G|| || Linux || CentOS 4 (32b)|| stable v5.3.0 ||15 May 2013|| [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz|freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz]]|| 3.8G || || Mac || Lion OX X 10.7 (64b Intel) || stable v5.3.0 || 15 May 2013 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg|freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg]] || 3.5G || || Mac || !SnowLeopard OS X 10.6 (32b Intel) || stable v5.3.0 || 15 May 2013 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg|freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg]] || 3.2G || || Virtualbox || Xubuntu 12.04 || stable v5.3.0 || 15 Aug 2013 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz|freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz]] || 9.0G || |
Please note Linux rpm and debian package installers are available as well a MacOS installer package. We also provide documentation and a download for a VM (virtual machine) with the Freesurfer release pre-installed that can run on any Windows, Linux or Mac operating system supported by Oracle's [[https://www.virtualbox.org/wiki/Downloads|VirtualBox]] application. Instructions are available to install and run Freesurfer on linux inside the Windows Subsystem for Linux ([[https://docs.microsoft.com/en-us/windows/wsl/about|WSL]]) including setup for the WSL environment.<<BR>> |
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| == Installation == Please select the instructions for the type you downloaded: * [[LinuxInstall|Linux Installation]] * [[MacOsInstall|Mac OS X Installation]] * [[Installation/FreeSurferVirtualImage|FreeSurfer Virtual Image Installation using VirtualBox]] == Set Up & Configuration == Set the default shell to be permanently switched to tcsh by typing the following in a terminal window and then pressing enter: {{{ chsh -s /bin/tcsh }}} Set up your shell's configuration file ('''.tcshrc''') so that !FreeSurfer is sourced every time you open a new terminal window. You can do this by adding the two commands in the box below to any part of the .tcshrc file. Use pico or any other text editor to create a .tcshrc file or to open the .tcshrc file and make this change (i.e. type "pico .tcshrc" on the command-line). |
Freesurfer 7.X.X release downloads and installation instructions are: [[https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads|here]].<<BR>> |
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| setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh |
Step-by-step Installation Demo for Macs can be found in the link below: |
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| * '''[[attachment:installFS_demo.mp4]]''' <<BR>> |
|
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| **Where <freesurfer_installation_directory> is replaced with the location you installed !FreeSurfer (e.g., /Applications/freesurfer). | === Previous Version 6 Release (Jan 2017) === |
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| To save your changes in pico, hit Ctrl+x to exit and then type 'y' and press enter to save the changes. | Freesurfer 6 release downloads and setup: [[https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads|here]]. |
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| To check that you have done everything correctly, open a new terminal window. You should see output similar to this: {{{ Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni }}} |
'''''Important Note:''' When processing a group of subjects for your study, it is essential to process all your subjects with the same version of !FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions).'' |
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| If you see the above, it means the !SetUpFreeSurfer.csh script was sourced successfully. | '''Development Version:''' Daily builds of !FreeSurfer can be downloaded from [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev|here]]. |
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| 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. | '''Older Releases:''' Previous releases of !FreeSurfer can be downloaded from [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer|here]]. '''Freeview:''' For instructions on how to update Freeview - !FreeSurfer's mri viewing application - go to the following page: [[UpdateFreeview|Updating Freeview]] |
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| You must register to obtain a license key [[https://surfer.nmr.mgh.harvard.edu/registration.html|here]]. The license is free but your !FreeSurfer installation will not work without it. | A license key must be obtained to make the !FreeSurfer tools operational. Obtaining a license is free and comes in the form of a license.txt file. Once you obtain the license.txt key file, copy it to your !FreeSurfer installation directory. This is also the location defined by the '''{{{FREESURFER_HOME}}}''' environment variable. |
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| Once you register, you will be emailed the license key. This license key needs to be saved in a text file in the location where you installed !FreeSurfer. To do this, open a new terminal window and type each line of command below (hit enter after each line): {{{ cd $FREESURFER_HOME pico .license }}} |
[[https://surfer.nmr.mgh.harvard.edu/registration.html|Follow this link to obtain a license key.]] |
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| Copy and paste the text between the "CUT HERE" lines in the license email onto the blank screen (which is the text file called .license). To save your changes in pico, hit Ctrl+x to exit and then type 'y' and press enter to save the changes. | == Additional Resources == |
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| == Test your FreeSurfer Installation == Close any terminal windows you have open and then open a new one. |
[[https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials|Try our tutorials]] |
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| Copy and paste this command into the terminal window: {{{ freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz \ -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow \ -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow \ -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red \ -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red }}} |
[[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription|Sign up for a FreeSurfer course]] |
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| The above command will open the freeview GUI and the subject named 'bert' which comes with your !FreeSurfer installation and can be used as an example for what !FreeSurfer output should look like. | [[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport|Join the FreeSurfer mailing list, ask a question, or view the archives]] |
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| == Sign up for the Mailing List == If you encounter problems with your installation or have any questions about !FreeSurfer, you can post those questions to the listserv after you sign up [[http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|here]]. |
{{attachment:openneuro_badge.svg}} A free and open platform that can be used to run !FreeSurfer. For more information, [[https://surfer.nmr.mgh.harvard.edu/fswiki/OpenNeuro|click here]]. |
FreeSurfer Download and Install
You can read and compare the version 7 and 6 release notes here.
Latest Version 7 Release (May 2020)
Please note Linux rpm and debian package installers are available as well a MacOS installer package. We also provide documentation and a download for a VM (virtual machine) with the Freesurfer release pre-installed that can run on any Windows, Linux or Mac operating system supported by Oracle's VirtualBox application. Instructions are available to install and run Freesurfer on linux inside the Windows Subsystem for Linux (WSL) including setup for the WSL environment.
Freesurfer 7.X.X release downloads and installation instructions are: here.
Step-by-step Installation Demo for Macs can be found in the link below:
Previous Version 6 Release (Jan 2017)
Freesurfer 6 release downloads and setup: here.
Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions).
Development Version: Daily builds of FreeSurfer can be downloaded from here.
Older Releases: Previous releases of FreeSurfer can be downloaded from here.
Freeview: For instructions on how to update Freeview - FreeSurfer's mri viewing application - go to the following page: Updating Freeview
License
A license key must be obtained to make the FreeSurfer tools operational. Obtaining a license is free and comes in the form of a license.txt file. Once you obtain the license.txt key file, copy it to your FreeSurfer installation directory. This is also the location defined by the FREESURFER_HOME environment variable.
Follow this link to obtain a license key.
Additional Resources
Sign up for a FreeSurfer course
Join the FreeSurfer mailing list, ask a question, or view the archives
A free and open platform that can be used to run FreeSurfer. For more information, click here.