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#pragma section-numbers on
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.
<<TableOfContents(3)>>
=== 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]]:
{{{
# 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
}}}

/* === 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}}} */


=== Install System Libraries ===

Depending on your specific linux distribution, the following system packages are required will be required:

'''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 \
            liblapack-devel.x86_64 \
            libXaw-devel.x86_64 \
            libpng-devel.x86_64
}}}

'''Ubuntu 14.04 LTS'''
{{{
$> sudo apt-get install build-essential
}}}

=== 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.

/* '''''On 64bit systems''''' */
{{{
$> 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
$> cd centos6-x86_64-packages
$> ./setup.sh
}}}

=== Setup, Configure, Make ===
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.)
{{{
$> ./setup_configure
$> ./configure --prefix=/home/username/fs_install --with-pkgs-dir=/home/username/centos6-x86_64-packages
$> make -j4
$> make install
}}}
Done!

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
}}}

Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu