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## page was renamed from QuickInstall

= FreeSurfer Download and Install =
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Operating System: Linux, Mac OS X, Windows (via !VirtualBox)<<BR>> Operating System: Linux, macOS<<BR>>
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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 (to run FS-FAST)		 RAM: 8GB recommended<<BR>>
Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers<<BR>>
Size of installation package: 10GB<<BR>>
Typical size of a processed subject: 300MB<<BR>>
Other requirements: Matlab (only needed to run FS-FAST, the fMRI analysis stream)
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'''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.
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== Freesurfer 5.3 stable release ==
Please refer to the ReleaseNotes page for per-release information.		 '''!FreeSurfer 6.0''' ReleaseNotes
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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 ||		 ----
'''''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:''
 * [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]]
----

||'''OS''' || '''Build Platform''' || '''Version''' || '''Release Date''' || '''Download''' || '''Size''' ||
|| Linux || CentOS 6 x86_64 (64b)|| stable v6.0.0 || 23 Jan 2017 || [[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 2017 || [[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 ||

'''Development Version:''' Daily builds of !FreeSurfer can be downloaded from [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev|here]].

'''Previous Releases:''' Old releases of !FreeSurfer can be downloaded from [[ftp://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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Please select the instructions for the type you downloaded (and be sure to come back to this page afterwards):
 * [[LinuxInstall|Linux Installation]]
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 * [[MacOsInstall|Mac OS X 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:
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 * [[Installation/FreeSurferVirtualImage|FreeSurfer Virtual Image Installation using VirtualBox]] {{{
$> tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
}}}

'''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/freesurfer}}} 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.

[[https://surfer.nmr.mgh.harvard.edu/registration.html|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.

{{attachment:freeview_67.jpeg}}

== Additional Resources ==

[[https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials|Try our tutorials]]

[[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription|Sign up for a FreeSurfer course]]

[[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport|Join the FreeSurfer mailing list, ask a question, or view the archives]]

FreeSurfer Download and Install

Contents

  1. FreeSurfer Download and Install
    1. FreeSurfer System Requirements
    2. Download
    3. Installation
    4. Setup & Configuration
    5. License
    6. Test your FreeSurfer Installation
    7. Additional Resources

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

Build Platform

Version

Release Date

Download

Size

Linux

CentOS 6 x86_64 (64b)

stable v6.0.0

23 Jan 2017

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 2017

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.

Freeview: For instructions on how to update Freeview - FreeSurfer's mri viewing application - go to the following page: Updating Freeview

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/freesurfer 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 2025-08-21 10:57:32 by JacksonNolan)