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If you have access within the Martinos Center firewall, follow the steps below to download the source code from CVS: {{{ # Local: $> export CVSROOT=/space/repo/1/dev $> cvs checkout -P dev |
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# Remote: $> export CVSROOT=:ext:USERNAME@door.nmr.mgh.harvard.edu:/space/repo/1/dev $> cvs checkout -P dev }}} |
Users can download Freesurfer source code via the read-only git repo. A simple clone of the repo is enough to perform a build of all freesurfer binaries. However, if a user wishes to perform full Freesurfer installation locally, he/she will need [[https://git-annex.branchable.com/ | git-annex]] in order to download all the data files required for a full installation. |
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| Non-Martinos users can access a read-only git repo which mirrors the CVS repo (requires git annex): | |
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## get data files if installing locally |
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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 Centos 6 Desktop Edition, Ubuntu 14.04 LTS, and Debian 8.
Those who wish to add a binary to the freesurfer software suite should consult the 'Adding a new binary to the tree' section of the Developers Guide.
1. Get the Source Code
Users can download Freesurfer source code via the read-only git repo. A simple clone of the repo is enough to perform a build of all freesurfer binaries. However, if a user wishes to perform full Freesurfer installation locally, he/she will need git-annex in order to download all the data files required for a full installation.
$> git clone http://freesurfer.net/anonftp/pub/dist/freesurfer/repo/freesurfer.git ## get data files if installing locally $> cd freesurfer $> git annex get .
2. Install System Libraries
Depending on your specific linux distribution, the following system packages are required will be required:
CentOS 6:
$> 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_64Ubuntu 14.04 LTS / Debian 8:
$> sudo apt-get install build-essential \
tcsh \
libtool-bin \
libtool \
automake \
gfortran \
libglu1-mesa-dev \
libfreetype6-dev \
uuid-dev \
libxmu-dev \
libxmu-headers \
libxi-dev \
libx11-dev \
libxt-dev \
libjpeg62-dev \
libxaw7-dev \
liblapack-dev
3. Library Dependencies
In order to compile freesurfer, you will need to download and install our prebuilt bundle of 3rd party dependancies. Download the package and extract its content. Remember the extraction location as you will need to pass that directory to the configure script.
$> cd ~ $> wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz $> tar -xzvf centos6-x86_64-packages.tar.gz $> ./centos6-x86_64-packages/setup.sh
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.):
$> cd ~/freesurfer $> ./setup_configure # Centos $> ./configure --disable-Werror --with-pkgs-dir=/home/username/centos6-x86_64-packages --prefix=/home/username/fs_install # Ubuntu $> ./configure --disable-Werror --with-pkgs-dir=/home/username/centos6-x86_64-packages --prefix=/home/username/fs_install --disable-xawplus-apps --disable-tcltk-apps $> make -j4 $> make install
Done!
Its possible some systems (Ubuntu) will complain about a missing jpeg library after the configure script is run, or during runtime. If this happens, create the following symbolic link:
$> cd /usr/lib64 $> sudo ln -s libjpeg.so.62 libjpeg.so
Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu