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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 platforms. 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.
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=== Get the Libraries ===
Use the following commands to download and install the prepackaged bundle of open-source libraries required for building Freesurfer:
/* === 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}}} */


=== Download and Install the Libraries ===

The following packages are required before building.

{{{
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 \
            liblapack-devel.x86_64 \
            libpng-devel.x86_64
}}}

Download and install the prepackaged bundle of open-source libraries required for building Freesurfer:

/* '''''On 64bit systems''''' */
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mkdir -p /usr/pubsw/packages
tar -C /usr/pubsw/packages -xzvf centos6-x86_64-packages.tar.gz		 sudo mkdir -p /usr/pubsw/packages
sudo tar -C /usr/pubsw/packages -xzvf centos6-x86_64-packages.tar.gz
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=== Set Your Path ===
Lastly, establish a symbolic link to the jpeg library:
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export PATH=/usr/pubsw/packages/autotools/bin:$PATH cd /usr/lib64
sudo ln -s libjpeg.so.62 libjpeg.so
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/* '''''On 32bit systems'''''{{{wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz mkdir -p /usr/pubsw/packages tar -C /usr/pubsw/packages -xzvf centos6-x86_64-packages.tar.gz }}} */
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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 {{{/Users/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 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.)
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      --prefix=/Users/USER/freesurfer \       --prefix=/home/USER/freesurfer

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.

Contents

  1. Get the Source Code
  2. Download and Install the Libraries
  3. Setup, Configure, Make

1. Get the Source Code

If you already have a working local copy of the CVS repository then you can skip this step. 

# Local CVS access:
export CVSROOT=/space/repo/1/dev
cvs checkout -P dev

# Or for remote access:
export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/space/repo/1/dev
cvs checkout -P dev

Or, you can get readonly CVS access to the source code by following the directions on this page:

2. Download and Install the Libraries

The following packages are required before building. 

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 \
            liblapack-devel.x86_64 \
            libpng-devel.x86_64

Download and install the prepackaged bundle of open-source libraries required for building Freesurfer: 

wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz
sudo mkdir -p /usr/pubsw/packages
sudo tar -C /usr/pubsw/packages -xzvf centos6-x86_64-packages.tar.gz

Lastly, establish a symbolic link to the jpeg library: 

cd /usr/lib64
sudo ln -s libjpeg.so.62 libjpeg.so

3. 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/USER/freesurfer
make -j4
make install

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