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== Internal FreeSurfer ==
People within the MGH/MIT/HMS Martinos Center should use the [[InternalFreeSurferDistributions|Internal FreeSurfer Distributions]] because !FreeSurfer is already installed on your system.
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Operating System: Linux, Mac OS X, Windows (via !VirtualBox)<<BR>> Operating System: Linux, macOS<<BR>>
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Size of installation package: 8.5GB<<BR>>
Typical size of a processed subject: 370MB<<BR>>
Tutorial dataset size: 18GB<<BR>>
Size of installation package: 10GB<<BR>>
Typical size of a processed subject: 300MB<<BR>>
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'''[[https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall6.0-beta| ANNOUNCING THE RELEASE OF FREESURFER v6-BETA. LOOKING FOR BETA TESTERS.]]''' '''!FreeSurfer 6.0''' ReleaseNotes
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'''Freesurfer 5.3''' ReleaseNotes ----
'''''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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'''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.

'''Important Note for Mac OS X users:''' Mac OS X platform requires the installation of XQuartz for freesurfer to work properly. OSX versions '''10.6 - 10.9''' require [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]]. OSX versions '''10.10''' and higher require [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]].
'''''Important Note for macOS users:''' macOS machines require the installation of XQuartz for !FreeSurfer to work properly.''
 * [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]] (macOS versions 10.6 - 10.9)
 * [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] (macOS versions 10.10 and higher)
----
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|| 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 ||
||<-6> *Virtualbox installation instructions [[http://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage#RunningtheVirtualBoxforthefirsttime|can be found here]]. The root password for the Virtualbox release is '''''freesurfer'''''||
|| Linux || CentOS 6 x86_64 (64b)|| stable v6.0.0 || 23 Jan 2016 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz|freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz]]||4.6G||
|| macOS || Lion OS X 10.7 (64b Intel) || stable v6.0.0 || 23 Jan 2016 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg|freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg]] || 4.4G ||
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$> tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz $> tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
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'''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]]. '''Mac:''' [[MacOsInstall|Step-by-step]] instructions, including notes on how to bypass the '''unidentified developer''' issue. The default !FreeSurfer installation location on macOS is in the {{{/Applications}}} directory.

FreeSurfer Download and Install

FreeSurfer System Requirements

Summary of Requirements:
Operating System: Linux, macOS
Processor Speed: 2GHz at least
RAM: 8GB recommended
Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers
Size of installation package: 10GB
Typical size of a processed subject: 300MB
Other requirements: Matlab (only needed to run FS-FAST, the fMRI analysis stream)

Download

FreeSurfer 6.0 ReleaseNotes


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).

Important Note for macOS users: macOS machines require the installation of XQuartz for FreeSurfer to work properly.


OS

Platform

Version

Release Date

Download

Size

Linux

CentOS 6 x86_64 (64b)

stable v6.0.0

23 Jan 2016

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz

4.6G

macOS

Lion OS X 10.7 (64b Intel)

stable v6.0.0

23 Jan 2016

freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg

4.4G

Development Version: Daily builds of FreeSurfer can be downloaded from here.

Previous Releases: Old releases of FreeSurfer can be downloaded from here.

Installation

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:

$> tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz

Mac: Step-by-step instructions, including notes on how to bypass the unidentified developer issue. The default FreeSurfer installation location on macOS is in the /Applications directory.

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

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.

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.

$> cp $FREESURFER_HOME/subjects/sample-001.mgz .
$> 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.

freeview_67.jpeg

Additional Resources

Try our tutorials

Sign up for a FreeSurfer course

Join the FreeSurfer mailing list, ask a question, or view the archives

DownloadAndInstall (last edited 2020-06-24 19:45:52 by DevaniCordero)