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| == Internal FreeSurfer == People within the MGH/MIT/HMS Martinos Center should use the [[InternalFreeSurferDistributions|InternalFreeSurferDistributions]]. Freesurfer is already installed on your system. |
=== Latest Version 7 Release is 7.4.1 (June 2023) === |
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| <<TableOfContents>> | Public links to the Freesurfer v7 release downloads and installation instructions are on the release 7 downloads page [[rel7downloads|7.X_releases]]. Please note that Linux RPM/DEB and MacOS installer packages are available. |
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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: 8GB recommended<<BR>> Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers<<BR>> Size of installation package: 8.5GB<<BR>> Typical size of a processed subject: 370MB<<BR>> Tutorial dataset size: 18GB<<BR>> Other requirements: Matlab (only needed to run FS-FAST, the fMRI analysis stream) |
If you have not yet upgraded to Freesurfer version 7, you can read about and compare versions 7 and 6 in the ReleaseNotes. |
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| == Download == '''Freesurfer 5.3 stable release''' (ReleaseNotes) |
Martinos users should visit InternalFreeSurferDistributions for instructions on how to use pre-installed !FreeSurfer distributions. |
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| '''Important Note:''' 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. | Instructions are available [[https://drive.google.com/file/d/1uNwv29fCeuMHrmTyXw94ZSuroNsPOxu-/view?usp=sharing|here]] about how to setup the 7.4.1 release in a virtual machine (VM) guest OS (Ubuntu 22) hosted by the open source application [[https://www.virtualbox.org/|Virtual Box]] from Oracle systems. The Virtual Box application runs on most any Windows, Mac and Linux machine equipped with an Intel processor. As of this writing, Virtual box does not work on arn64 based machines such as the silicon macs with M1, M2, M3 processors. For a Windows only VM setup, see the instructions [[https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl_ubuntu|here]] about how to install and run Freesurfer on the Windows Subsystem for Linux. Please note WSL2 requires an additional install of a 3rd party X-server on the Windows host in order to view images in applications such as Freeview (not necessary when running Virtual Box).<<BR>> |
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| '''Important Note for Mac OS X users:''' Mac OS X platform requires the installation of XQuartz for freesurfer to work properly. Pre-Yosemite versions of OSX require [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]]. Post-Yosemite versions of OSX require [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] (or higher). | === Previous Version 6 Release (Jan 2017) === |
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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 || |
Freesurfer v6 release downloads and installation instructions are [[rel6downloads|here]]. |
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| '''Development Version:''' Daily builds of !FreeSurfer can be downloaded from [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev|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).'' |
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| '''Previous Releases:''' Old releases of !FreeSurfer can be downloaded from [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer|here]]. | === Other Versions === |
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| == Installation == | '''Development Version:''' Daily builds of the !FreeSurfer development branch can be downloaded from [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev|here]]. |
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| '''Linux:''' Installing !FreeSurfer on Linux systems involves simply extracting the contents of the .tar.gz file somewhere on your machine. Installing into the directory {{{/usr/local}}} is recommended. For example: | '''Older Releases:''' Previous releases of !FreeSurfer can be downloaded from [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer|here]]. |
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| {{{ $> tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz }}} '''Mac:''' Installing !FreeSurfer on Mac systems involves simply double clicking the .dmg file and clicking thru the steps. The default installation location is in the {{{/Applications}}} directory. For more detailed instructions, please see the following [[MacOsInstall#SetupandConfiguration|step-by-step]]. == Setup & Configuration == To begin using !FreeSurfer, you need to open a terminal window and define and environment variable called '''{{{FREESURFER_HOME}}}''' which is set to the location !FreeSurfer was installed, and then source the setup script. Sourcing !FreeSurfer needs to be done every time you open a new terminal window. Or, you can add the two lines below to your default setup file (.bashrc or .cshrc) and !FreeSurfer will be sourced automatically everytime you open a new window. '''Linux:''' {{{ ## bash $> export FREESURFER_HOME=/usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh ## tcsh $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.csh }}} '''Mac:''' {{{ $> export FREESURFER_HOME=/Applications/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh }}} If done correctly, 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 }}} |
'''Freeview:''' For instructions on how to update Freeview, !FreeSurfer's visualization app, visit the following page: [[UpdateFreeview|Updating Freeview]]. |
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== Test your FreeSurfer Installation == !FreeSurfer comes with two sample data files (sample-001.mgz and sample-002.mgz) as well as a fully recon-ed subject named bert. These data files can be used to test that your !FreeSurfer installation was done properly. To test your installation, please try the following examples: '''Example 1:''' Convert the sample-001.mgz to nifti format. {{{ $> cd $FREESURFER_HOME/subjects $> mri_convert sample-001.mgz sample-001.nii.gz ... reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... }}} '''Example 2:''' View the output volumes, surfaces and subcortical segmentation of fully recon-ed subject bert. {{{ $> cd $FREESURFER_HOME/subjects $> freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red }}} The freeview above command will open the freeview GUI and should look similar to the image below. {{attachment:freeview_67.jpeg}} |
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{{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
Latest Version 7 Release is 7.4.1 (June 2023)
Public links to the Freesurfer v7 release downloads and installation instructions are on the release 7 downloads page 7.X_releases. Please note that Linux RPM/DEB and MacOS installer packages are available.
If you have not yet upgraded to Freesurfer version 7, you can read about and compare versions 7 and 6 in the ReleaseNotes.
Martinos users should visit InternalFreeSurferDistributions for instructions on how to use pre-installed FreeSurfer distributions.
Instructions are available here about how to setup the 7.4.1 release in a virtual machine (VM) guest OS (Ubuntu 22) hosted by the open source application Virtual Box from Oracle systems. The Virtual Box application runs on most any Windows, Mac and Linux machine equipped with an Intel processor. As of this writing, Virtual box does not work on arn64 based machines such as the silicon macs with M1, M2, M3 processors. For a Windows only VM setup, see the instructions here about how to install and run Freesurfer on the Windows Subsystem for Linux. Please note WSL2 requires an additional install of a 3rd party X-server on the Windows host in order to view images in applications such as Freeview (not necessary when running Virtual Box).
Previous Version 6 Release (Jan 2017)
Freesurfer v6 release downloads and installation instructions are 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).
Other Versions
Development Version: Daily builds of the FreeSurfer development branch 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 visualization app, visit 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.