This page is targeted at those who wish to build and develop the FreeSurfer source code on their Linux platform. The instructions below have been tested for CentOS6, CentOS7, Ubuntu 14.04 LTS, Ubuntu 16.04 LTS, and Debian 8. See the Mac OSX build page for instructions on how to build on Mac OS X platform.

Please note that the build instructions below reference building Freesurfer with the automake tools. As of mid-2018 it is now possible to build the freesurfer source using cmake to generate the makefiles instead of using automake. There is a brief page describing the cmake build here, Freesurfer development is ongoing using the cmake build, e.g., we will be using the cmake build on newer versions of linux and Mac OS. Hence we suggest you try and use the cmake build as we cannot guarantee the automake build will be kept as up to date.

1. Getting the Source Code

The first thing users at the Martinos Center need to do is prepend the directory /usr/pubsw/packages/git-annex/current/bin to their PATH. Once that is done, the Freesurfer source code can be cloned from the official Freesurfer github page:

git clone

Note: have a look at the Freesurfer_github local wiki page too.

1.1. Get the Data Files (Optional)

The Freesurfer repository contains a large number data files which are not included with a default git clone of the repo. Instead, these data files are distributed via the git-annex software. Users who only want the repository for the purposes of compiling binaries and/or inspecting source code, the git clone command from above is all you need to do. Users who want to run build time checks, or perform a full local installation, or just want all the contents of the repository, will need to add a special data store remote repository in order to retrieve these files.

To add the data store repository (this only needs to be done once):

cd freesurfer
git remote add datasrc
git fetch datasrc

And to retrieve data files:

git annex get <filename>

The data files have been broken down into categories, those being required for build time checks, those required for a local installation, and everything else. Use one of the following commands depending on your needs:

## Get only the data files required for build time checks (1.9 GB)
git annex get --metadata fstags=makecheck .

## Get only the data files required for local installation (4.3 GB)
git annex get --metadata fstags=makeinstall .

## Just give me everything! Not Recommended (6.8 GB)
git annex get .

2. Install System Libraries

Building freesurfer requires various system specific libraries be installed on your machine. Depending on your specific linux distribution, the required system packages are listed below:

CentOS 6:

$> yum groupinstall "Development Tools"
$> yum install mesa-libGLU-devel \
            freetype-devel.x86_64 \
            libuuid-devel.x86_64 \
            uuid-c++-devel.x86_64 \
            libXmu-devel.x86_64 \
            libXi-devel.x86_64 \
            lapack-devel.x86_64 \
            libXaw-devel.x86_64 \

CentOS 7:

$> yum groupinstall "Development Tools"
$> yum install mesa-libGLU-devel \
            freetype-devel.x86_64 \
            libuuid-devel.x86_64 \
            uuid-c++-devel.x86_64 \
            libXmu-devel.x86_64 \
            libXi-devel.x86_64 \
            libXaw-devel.x86_64 \
            libpng-devel.x86_64 \
            lapack-static.x86_64 \

Ubuntu 14.04 LTS / Debian 8:

$> sudo apt-get update
$> sudo apt-get install build-essential \
            tcsh \
            libtool-bin \
            libtool \
            automake \
            gfortran \
            libglu1-mesa-dev \
            libfreetype6-dev \
            uuid-dev \
            libxmu-dev \
            libxmu-headers \
            libxi-dev \
            libx11-dev \
            libxml2-utils \
            libxt-dev \
            libjpeg62-dev \
            libxaw7-dev \

Ubuntu 16.04 LTS:
Ubuntu 16 requires all the same packages required by Ubuntu 14 (listed above), along with the additional requirement of installing gcc v4.8 (this is due to errors generated by the default version of gcc included with Ubuntu 16). Update to pip 18, because a bug in pip 8 causes the ./python subdirectory install to fail with "distutils.errors.DistutilsOptionError: can't combine user with prefix, exec_prefix/home, or install_(plat)base".

## Install as above then ...

## Install gcc/g++/gfortran version 4.8
$> sudo apt-get install gcc-4.8 g++-4.8 libgfortran-4.8-dev

## Set gcc/g++ 4.8 to be the default compiler
$> sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 50
$> sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 50

$> sudo /usr/bin/python3.5 -m pip install --upgrade pip

3. Library Dependencies

In order to compile freesurfer, you will need to download and install our prebuilt bundle of 3rd party dependancies. Download the package and extract its content. Remember the extraction location as you will need to pass that directory to the configure script.

$> cd ~
$> wget
$> tar -xzvf centos6-x86_64-packages.tar.gz
$> ./centos6-x86_64-packages/

4. Setup, Configure, Make

Determine the location you want Freesurfer to be installed. For example, in the case below we will assume the user wants freesurfer to be installed in /home/USER/freesurfer. Type the following commands in the top-level Freesurfer directory (the directory that contains and all the mri_* and mris_* directories.):

$> cd ~/freesurfer
$> ./setup_configure

## Centos/Debian
$> ./configure --disable-Werror --with-pkgs-dir=/home/username/centos6-x86_64-packages

## Ubuntu
$> ./configure --disable-Werror --with-pkgs-dir=/home/username/centos6-x86_64-packages --disable-xawplus-apps --disable-tcltk-apps

$> make -j4

## Run build time checks. Requires data files. (See "Data Files" from above)
$> make check

## Install locally. Requires data files. (See "Data Files" from above)
$> make install


5. Contributing Changes

Users who wish to make contributions to the Freesurfer code base should see the following pages

Send your comments/questions/feedback to

freesurfer_linux_developers_page (last edited 2018-11-19 00:16:18 by buildqa)