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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 Centos 6 desktop edition and Ubuntu 14.04. 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 [[https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide#Addinganewbinarytothetree|Developers Guide]]. |
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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: |
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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: | Non-Martinos users can access a read-only git repo which mirrors the CVS repo (requires git annex): |
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| mkdir -p /usr/pubsw/packages tar -C /usr/pubsw/packages -xzvf centos6-x86_64-packages.tar.gz |
$> git clone http://freesurfer.net/anonftp/pub/dist/freesurfer/repo/freesurfer.git $> cd freesurfer $> git annex get . |
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| === Set Your Path === | /* === Get the build tools (Ubuntu plantforms only) === If you are on an Ubuntu machine you will have to install the following packages:{{{sudo apt-get install autoconf libtool gfortran cvs}}} */ === Install System Libraries === Depending on your specific linux distribution, the following system packages are required will be required: '''CentOS 6:''' |
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| export PATH=/usr/pubsw/packages/autotools/bin:$PATH | $> 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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'''Ubuntu 14.04 LTS:''' {{{ $> sudo apt-get install build-essential \ libtool \ automake \ gfortran \ libglu1-mesa-dev \ libfreetype6-dev \ uuid-dev \ libxmu-dev \ libxmu-headers \ libxi-dev \ libx11-dev \ libxt-dev \ libxaw7-dev \ liblapack-dev }}} === 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. /* '''''On 64bit systems''''' */ {{{ $> 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 $> cd centos6-x86_64-packages $> ./setup.sh }}} |
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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.): '''CentOS 6:''' |
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| ./setup_configure ./configure \ --prefix=/Users/USER/freesurfer \ make -j4 make install |
$> cd ~/freesurfer $> ./setup_configure $> ./configure --disable-Werror --with-pkgs-dir=/home/username/centos6-x86_64-packages --prefix=/home/username/fs_install $> make -j4 $> make install |
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'''Ubuntu 14.04 LTS:''' {{{ $> ./setup_configure $> ./configure --disable-GUI-build --disable-Werror --with-pkgs-dir=/home/username/centos6-x86_64-packages --prefix=/home/username/fs_install $> make -j4 $> make install }}} |
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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 }}} |
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 and Ubuntu 14.04.
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
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 # Remote: $> export CVSROOT=:ext:USERNAME@door.nmr.mgh.harvard.edu:/space/repo/1/dev $> cvs checkout -P dev
Non-Martinos users can access a read-only git repo which mirrors the CVS repo (requires git annex):
$> git clone http://freesurfer.net/anonftp/pub/dist/freesurfer/repo/freesurfer.git $> 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:
$> sudo apt-get install build-essential \
libtool \
automake \
gfortran \
libglu1-mesa-dev \
libfreetype6-dev \
uuid-dev \
libxmu-dev \
libxmu-headers \
libxi-dev \
libx11-dev \
libxt-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 $> cd 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.):
CentOS 6:
$> cd ~/freesurfer $> ./setup_configure $> ./configure --disable-Werror --with-pkgs-dir=/home/username/centos6-x86_64-packages --prefix=/home/username/fs_install $> make -j4 $> make install
Ubuntu 14.04 LTS:
$> ./setup_configure $> ./configure --disable-GUI-build --disable-Werror --with-pkgs-dir=/home/username/centos6-x86_64-packages --prefix=/home/username/fs_install $> 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