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.

Contents

  1. Get the Source Code
  2. Get the Libraries
  3. Set Your Path
  4. 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. Get the Libraries

You will need to download and install prepackaged bundle of open-sourced libraries on your system.

To install the prepackaged bundle of open-source libraries, execute the following command after downloading it: 

mkdir -p /usr/pubsw/packages
tar -C /usr/pubsw/packages -xzvf centos6-x86_64-packages.tar.gz

3. Set Your Path

export PATH=/usr/pubsw/packages/autotools/bin:$PATH

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