• freesurfer_linux_developers_page

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 and Ubuntu 12.04 i386 platforms.

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. 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

3. Get the Libraries

Use the following commands to download and install the prepackaged bundle of open-source libraries required for building Freesurfer:

On 64bit 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

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

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 /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.)

./setup_configure
./configure \
      --prefix=/Users/USER/freesurfer \
make -j4
make install

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