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This page is targeted at those who wish to develop and build the freesurfer source code on their Linux platform. These instructions have been tested for CentOS6 x86_64 desktop edition. This page is targeted at those who wish to build and develop the !FreeSurfer source code on their Linux platform. These instructions have been tested for CentOS6, CentOS7, Ubuntu 14.04 LTS, Ubuntu 16.04 LTS, and Debian 8. See the [[freesurfer_mac_developers_page|Mac OSX build page]] for instructions on how to build on Mac OS X platform.
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=== Get the Source Code ===
If you have access within the Martinos Center firewall, follow the steps below to download the source code from CVS. Non-Martinos users can get readonly CVS access to the source code by following the directions [[https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS|on this page]]:		 === 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 [[https://github.com/freesurfer/freesurfer|Freesurfer github page]]:
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# Local:
$> export CVSROOT=/space/repo/1/dev
$> cvs checkout -P dev

# Remote:
$> export CVSROOT=:ext:USERNAME@door.nmr.mgh.harvard.edu:/space/repo/1/dev
$> cvs checkout -P dev		 git clone https://github.com/freesurfer/freesurfer.git
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/* === Get the build tools (Ubuntu plantforms only) === If you are on an Ubuntu machine you will have to install the following packages:{{{sudo apt-get install autoconf libtool gfortran cvs}}} */ Note: have a look at the [[Freesurfer_github]] local wiki page too.

==== 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 [[https://git-annex.branchable.com/|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 https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git
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 .
}}}
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The following system packages are required on CentOS6 systems before building. Equivalent or similar packages will be required on other linux distributions. 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:
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'''CentOS 6:'''
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            liblapack-devel.x86_64 \
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'''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 \
            blas-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 \
            liblapack-dev
}}}

'''Ubuntu 16.04 LTS:'''
<<BR>>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

}}}
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In order to compile freesurfer, you will need to download and install our prebuilt bundled of 3rd party dependancies. Download the package and remember the location as you will need to pass the directory containing the 3rd party libraries to the {{{configure}}} script. 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.
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$> cd ~
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$> cd centos6-x86_64-packages
$> ./setup.sh		 $> ./centos6-x86_64-packages/setup.sh
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Determine the location you want Freesurfer to be installed. For example, in case case we will assume the user wants freesurfer to be installed in {{{/home/USER/freesurfer}}}. Type the following commands in the top-level Freesurfer directory (the directory that contains configure.in and all the mri_* and mris_* directories.) Determine the location you want Freesurfer to be installed. For example, in the case below we will assume the user wants freesurfer to be installed in {{{/home/USER/freesurfer}}}. Type the following commands in the top-level Freesurfer directory (the directory that contains configure.in and all the mri_* and mris_* directories.):
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$> cd ~/freesurfer
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$> ./configure --prefix=/home/username/fs_install --with=pkgs-dir=/home/username/centos6-x86_64-packages
## 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
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## Run build time checks. Requires data files. (See "Data Files" from above)
$> make check

## Install locally. Requires data files. (See "Data Files" from above)
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Its possible some systems (Ubuntu) will complain about a missing jpeg library after the {{{configure}}} script is run, or during runtime. If this happens, create the following symbolic link:
{{{
$> cd /usr/lib64
$> sudo ln -s libjpeg.so.62 libjpeg.so
}}}		 === Contributing Changes ===
Users who wish to make contributions to the Freesurfer code base should see the following pages
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  https://surfer.nmr.mgh.harvard.edu/fswiki/Freesurfer_github - how to fork the Freesurfer repository and submit pull requests
  
  https://surfer.nmr.mgh.harvard.edu/fswiki/Freesurfer_design - insights into the design of the freesurfer code


----

This page is targeted at those who wish to build and develop the FreeSurfer source code on their Linux platform. These instructions 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.

Contents

  1. Getting the Source Code
  2. Install System Libraries
  3. Library Dependencies
  4. Setup, Configure, Make
  5. Contributing Changes

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 https://github.com/freesurfer/freesurfer.git

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  https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git
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 \
            libpng-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 \
            blas-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 \
            liblapack-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 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz
$> tar -xzvf centos6-x86_64-packages.tar.gz
$> ./centos6-x86_64-packages/setup.sh

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 configure.in 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

Done!

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 zkaufman@nmr.mgh.harvard.edu