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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. | 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. |
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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. 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: export CVSROOT=/space/repo/1/dev cvs checkout -P dev |
# Local: $> export CVSROOT=/space/repo/1/dev $> cvs checkout -P dev |
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| # Or for remote access: export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/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]]: | |
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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: |
/* === 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}}} */ === Download and Install the Libraries === The following system packages are required on CentOS6 systems before building. Equivalent or similar packages will be required on other linux distributions. |
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| sudo apt-get install autoconf libtool gfortran cvs | $> 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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| Download and install the prepackaged bundle of open-source libraries required for building Freesurfer: | |
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| === 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''''' |
/* '''''On 64bit systems''''' */ |
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| 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 |
$> wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz $> sudo mkdir -p /usr/pubsw/packages $> sudo tar -C /usr/pubsw/packages -xzvf centos6-x86_64-packages.tar.gz |
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| '''''On 32bit systems''''' | Lastly, some system will complain about a missing jpeg library. If this happens, create the following symbolic link: |
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| 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 |
$> cd /usr/lib64 $> sudo ln -s libjpeg.so.62 libjpeg.so |
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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 }}} */ |
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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.) |
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| ./setup_configure ./configure \ --prefix=/Users/USER/freesurfer \ make -j4 make install |
$> ./setup_configure $> ./configure --prefix=/home/USER/freesurfer $> make -j4 $> make install |
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. Download and Install the Libraries
The following system packages are required on CentOS6 systems before building. Equivalent or similar packages will be required on other linux distributions.
$> 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_64Download and install the prepackaged bundle of open-source libraries required for building Freesurfer:
$> wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64/centos6-x86_64-packages.tar.gz $> sudo mkdir -p /usr/pubsw/packages $> sudo tar -C /usr/pubsw/packages -xzvf centos6-x86_64-packages.tar.gz
Lastly, some system will complain about a missing jpeg library. If this happens, create the following symbolic link:
$> cd /usr/lib64 $> sudo ln -s libjpeg.so.62 libjpeg.so
3. 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! Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu