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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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''If you already have a working local copy of the CVS repository then you can skip this step.'' 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]]:
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# 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		 # 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
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Or, you can get readonly CVS access to the source code by following the directions [[https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS|on this page]]:
=== Get the Libraries ===
You will need to download and install prepackaged bundle of open-sourced libraries on your system.
 *[[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz|centos6-x86_64-packages.tar.gz]]
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To install the prepackaged bundle of open-source libraries, execute the following command after downloading it: /* === 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 ===

The following system packages are required on CentOS6 systems before building. Equivalent or similar packages will be required on other linux distributions.
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mkdir -p /usr/pubsw/packages
tar -C /usr/pubsw/packages -xzvf centos6-x86_64-packages.tar.gz		 $> 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
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=== Set Your Path ===
=== 3rd Party Depandancies ===


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

/* '''''On 64bit systems''''' */
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export PATH=/usr/pubsw/packages/autotools/bin:$PATH $> 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
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It is theoretically possible to install the bundle in any location on your system, but that would require manually passing the location for each library when running the {{{configure}}} script. By installing in {{{/usr/pubsw/packages}}} the {{{configure}}} script will automatically find them.

## Lastly, some system will complain about a missing jpeg library. If this happens, create the following symbolic link:
## {{{
## $> cd /usr/lib64
## $> sudo ln -s libjpeg.so.62 libjpeg.so
## }}}

/* '''''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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./setup_configure
./configure \
      --prefix=/Users/USER/freesurfer \
make -j4
make install		 $> ./setup_configure
$> ./configure --prefix=/home/USER/freesurfer
$> make -j4
$> make install

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. Install System Libraries
  3. 3rd Party Depandancies
  4. Setup, Configure, Make

1. 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 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

2. Install System Libraries

The following system packages are required on CentOS6 systems before building. Equivalent or similar packages will be required on other linux distributions. 

$> 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

3. 3rd Party Depandancies

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

It is theoretically possible to install the bundle in any location on your system, but that would require manually passing the location for each library when running the configure script. By installing in /usr/pubsw/packages the configure script will automatically find them.

4. 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