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| ''If you already have a working local copy of the CVS repository then you can skip this step.'' The steps below are only applicable if you have access within the Martinos Center firewall. Outside users can get readonly CVS access to the source code by following the directions [[https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS|on this page]]: | If you have access within the Martinos Center firewall, follow the steps below to download the source code from CVS. Non-Martinos users can get readonly CVS access to the source code by following the directions [[https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS|on this page]]: |
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| # Local CVS access: | # Local: |
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| # Or for remote access: $> export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/space/repo/1/dev |
# Remote: $> export CVSROOT=:ext:USERNAME@door.nmr.mgh.harvard.edu:/space/repo/1/dev |
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| === Download and Install the Libraries === | === Install System Libraries === |
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| The following system packages are required on CentOS6 systems before building. Equivalent or similar packages will be required on other linux distributions. | Depending on your specific linux distribution, the following system packages are required will be required: |
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| '''CentOS 6:''' | |
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| Download and install the prepackaged bundle of open-source libraries required for building Freesurfer: | '''Ubuntu 14.04 LTS:''' {{{ $> sudo apt-get install build-essential \ libtool \ automake \ gfortran \ libglu1-mesa-dev \ freetype* \ uuid-dev \ libxmu-dev \ libxmu-headers \ libxi-dev \ libx11-dev \ libxt-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. |
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| $> sudo mkdir -p /usr/pubsw/packages $> sudo tar -C /usr/pubsw/packages -xzvf 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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| Lastly, some system will complain about a missing jpeg library. If this happens, create the following symbolic link: | === 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.) {{{ $> ./setup_configure $> ./configure --prefix=/home/username/fs_install --with-pkgs-dir=/home/username/centos6-x86_64-packages $> 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: |
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| /* '''''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 }}} */ === 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.) {{{ $> ./setup_configure $> ./configure --prefix=/home/USER/freesurfer $> make -j4 $> make install }}} Done! |
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 desktop edition.
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. Non-Martinos users can get readonly CVS access to the source code by following the directions on this page:
# 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
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 \
freetype* \
uuid-dev \
libxmu-dev \
libxmu-headers \
libxi-dev \
libx11-dev \
libxt-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.
$> 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.)
$> ./setup_configure $> ./configure --prefix=/home/username/fs_install --with-pkgs-dir=/home/username/centos6-x86_64-packages $> 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