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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 and Ubuntu 12.04 i386 platforms.
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=== 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
}}}
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'''''On 64bit systems'''''
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=== Set Your Path ===
'''''On 32bit 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
mkdir -p /usr/pubsw/packages
tar -C /usr/pubsw/packages -xzvf centos6-x86_64-packages.tar.gz
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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 and Ubuntu 12.04 i386 platforms.

Contents

  1. Get the Source Code
  2. Get the build tools (Ubuntu plantforms only)
  3. Get the Libraries
  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 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