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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 (Apr 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 || |
Freesurfer 7 release downloads and setup: [[https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads|here]]. ''Downloads not yet available'' |
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| == Installation == Please select the instructions for the type you downloaded: * [[LinuxInstall|Linux Installation]] |
=== Previous Version 6 Release (Jan 2017) === |
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| * [[MacOsInstall|Mac OS X Installation]] | Freesurfer 6 release downloads and setup: [[https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads|here]]. |
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| * [[Installation/FreeSurferVirtualImage|FreeSurfer Virtual Image Installation using VirtualBox]] | '''''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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| == 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 }}} |
'''Ubuntu 18.04 VM disk image (.vdi) with 6.0.0 Release and Development 7.0.0 beta 1 Release:''' A [[https://www.virtualbox.org/wiki/Downloads|VirtualBox]] Ubuntu image to run on Windows, the Mac and/or other Linux OS flavors [[https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67|VM_setup]]. Can be used to run the freesurfer tutorial commands. |
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| 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). | '''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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| {{{ setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh }}} |
'''Older Releases:''' Previous releases of !FreeSurfer can be downloaded from [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer|here]]. |
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| **Where <freesurfer_installation_directory> is replaced with the location you installed !FreeSurfer (e.g., /Applications/freesurfer). To save your changes in pico, hit Ctrl+x to exit and then type 'y' and press enter to save the changes. 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 }}} If you see the above, it means the !SetUpFreeSurfer.csh script was sourced successfully. 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. |
'''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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| '''Note: '''Registering for the license key does not enable one to post messages to the Freesurfer mailing list. To post to the list, you must subscribe to the list [[http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|by following this link]] | [[https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials|Try our tutorials]] |
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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/CourseDescription|Sign up for a FreeSurfer course]] |
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| Copy and paste this command into the terminal window: {{{ freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz \ $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/FreeSurferSupport|Join the FreeSurfer mailing list, ask a question, or view the archives]] {{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 (Apr 2020)
Freesurfer 7 release downloads and setup: here. Downloads not yet available
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).
Ubuntu 18.04 VM disk image (.vdi) with 6.0.0 Release and Development 7.0.0 beta 1 Release: A VirtualBox Ubuntu image to run on Windows, the Mac and/or other Linux OS flavors VM_setup. Can be used to run the freesurfer tutorial commands.
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.