|
Size: 9631
Comment:
|
Size: 3962
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| This page takes you through all the steps necessary for downloading & installing !FreeSurfer but lacks the detail & options presented on the DownloadAndInstall wiki. | ## page was renamed from QuickInstall |
| Line 3: | Line 3: |
| <<TableOfContents>> | = FreeSurfer Download and Install = |
| Line 5: | Line 5: |
| == 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) |
=== Latest Version 7 Release is 7.4.1 (June 2023) === |
| Line 16: | Line 7: |
| == 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. |
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. We also provide a [[attachment:installFS_demo.mp4|step-by-step installation demo video]] for MacOS. |
| Line 19: | Line 9: |
| '''Freesurfer 5.3 stable release''' <<BR>>Please refer to the ReleaseNotes page for per-release information. |
If you have not yet upgraded to Freesurfer version 7, you can read about and compare versions 7 and 6 in the ReleaseNotes. |
| Line 22: | Line 11: |
| ||'''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 || |
Martinos users should visit InternalFreeSurferDistributions for instructions on how to use pre-installed !FreeSurfer distributions. |
| Line 30: | Line 13: |
| == Installation == Please select the instructions for the type you downloaded: * [[LinuxInstall|Linux Installation]] |
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>> |
| Line 34: | Line 15: |
| * [[MacOsInstall|Mac OS X Installation]] | === Previous Version 6 Release (Jan 2017) === |
| Line 36: | Line 17: |
| * [[Installation/FreeSurferVirtualImage|FreeSurfer Virtual Image Installation using VirtualBox]] | Freesurfer v6 release downloads and installation instructions are [[rel6downloads|here]]. |
| Line 38: | Line 19: |
| == 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 }}} |
'''''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).'' |
| Line 44: | Line 21: |
| 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). | === Other Versions === |
| Line 46: | Line 23: |
| {{{ setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh }}} |
'''Development Version:''' Daily builds of the !FreeSurfer development branch can be downloaded from [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev|here]]. |
| Line 51: | Line 25: |
| **''Where <freesurfer_installation_directory> is replaced with the location you installed !FreeSurfer (e.g., /Applications/freesurfer).'' | '''Older Releases:''' Previous releases of !FreeSurfer can be downloaded from [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer|here]]. |
| Line 53: | Line 27: |
| 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 visualization app, visit the following page: [[UpdateFreeview|Updating Freeview]]. |
| Line 71: | Line 30: |
| 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. |
| Line 73: | Line 32: |
| 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.]] |
| Line 79: | Line 34: |
| 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 == |
| Line 81: | Line 36: |
| == 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]] |
| Line 84: | Line 38: |
| 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]] |
| Line 94: | Line 40: |
| 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]] |
| Line 96: | Line 42: |
| == 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]]. == Get Started! == === Practice data & commands === We highly recommend downloading the [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data|tutorial dataset]] and learning !FreeSurfer with our guided tutorials. You can find the list of tutorials on our course wiki, under the [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial#CourseSchedule|Course Schedule section]]. Here, you will also find slides from our most recent lecture series with videos of the lectures [[http://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA|here]]. === Preparing to work with FreeSurfer === Whenever you want to work with !FreeSurfer, you must make sure three things have happened: 1. The variable {{{FREESURFER_HOME}}} is set (so your computer knows where !FreeSurfer is installed): {{{setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer}}} 1. The !FreeSurfer set up script must be sourced (so !FreeSurfer knows the location of everything it needs): {{{source $FREESURFER_HOME/SetUpFreeSurfer.csh}}} 1. !FreeSurfer has been pointed to a directory of subjects to work on: {{{setenv SUBJECTS_DIR /location/of/subjects}}} If you followed all the Quick Install instructions on this page, you have set it up so all 3 of these things happen automatically when you open a terminal window. However, when working on the tutorial data or on your own data, keep in mind that you may need to redo #3 in order to specify a different set of subjects for !FreeSurfer to work with. You can change the location the {{{SUBJECTS_DIR}}} variable is set to in the {{{$FREESURFER_HOME/SetUpFreeSurfer.csh}}} file or you can run the command listed in step #3 every time you open a new terminal window. === Processing your first subject === If you have data you would like to process with !FreeSurfer, you can do so using the command {{{recon-all}}}. An example of how to run this command is below: {{{ recon-all \ -all \ -i <one slice in the anatomical dicom series> \ -s <subject id that you make up> \ }}} Things to note: * -all will run all the steps in the !FreeSurfer processing stream. Alternatively, you can run different parts of the stream. * -i stands for input. Here, you would specify one dicom file/slice in the MPRAGE scan series you collected (!FreeSurfer will find the rest of the slices automatically). You could also specify nifti files as input. If you have more than one MPRAGE or input for a given subject, use another -i flag for each one. * -s specifies the name of the subject and will create a directory with that name for all the subject's !FreeSurfer output. The process is complete when the last line printed to the screen (and in the recon-all.log found in the subject's scripts directory) says "recon-all exited without errors". If you run into errors, search the [[http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/|mailing list]] for help or follow the steps in BugReporting. === Resources === You may find these wiki pages helpful as you get started: *The [[UserContributions/FAQ|FAQ]] *A list of helpful [[FsTutorial/Scripts|scripts]] to make working with !FreeSurfer easier *The complete list of [[https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials|tutorials]] we offer |
{{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. We also provide a step-by-step installation demo video for MacOS.
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.