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| This page is targeted at those who wish to develop and build the freesurfer source code on their OSX platform. These instructions have been tested for OSX 10.9 (Mavericks). | This page is targeted at those who wish to develop and build the freesurfer source code on their OSX platform. These instructions have been tested for OS X 10.7, 10.9, 10.11 (Lion, Mavericks, El Capitan). 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.'' | Users can download Freesurfer source code via the read-only git repo. A simple clone of the repo (187 Megs) 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 (6.6 Gigs). |
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| # Local CVS access: $> export CVSROOT=/space/repo/1/dev $> cvs checkout -P dev |
## Get the source code $> git clone http://freesurfer.net/anonftp/pub/dist/freesurfer/repo/freesurfer.git |
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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 |
## Get data files (only required for full installation) $> cd freesurfer $> git annex get . |
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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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| * ''After you install Qt, you must delete line 320 from the file'' {{{/Library/Frameworks/QtCore.framework/Headers/qglobal.h}}}'', the line that says "#warning "This version of Mac OS X is unsupported""'' | |
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| * [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]] (OSX versions 10.9 and lower) or [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] (OSX versions 10.10 and higher) | * [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]] (OSX versions 10.9 and lower) * [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] (OSX versions 10.10 and higher) |
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| Install Xcode Command Line Tools: | ''IMPORTANT: After you install Qt, you must delete line 320 from the file'' {{{/Library/Frameworks/QtCore.framework/Headers/qglobal.h}}}'', the line that says "#warning "This version of Mac OS X is unsupported""''. Next, install Xcode Command Line Tools my typing the following on the command line: |
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| Install gcc v4.4.7: | After Xcode has been installed, we need to install gcc v4.4.7 using MacPorts: |
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| $> cd /opt/local/bin $> sudo ln -s gcc-mp-4.4 gcc $> sudo ln -s g++-mp-4.4 g++ |
$> sudo port select --set gcc mp-gcc44 $> gcc --version gcc (MacPorts gcc44 4.4.7_10) 4.4.7 |
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| $> curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/mountain_lion/MacOSX_Lion_Packages.tar.gz | $> curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/lion/MacOSX_Lion_Packages.tar.gz |
This page is targeted at those who wish to develop and build the freesurfer source code on their OSX platform. These instructions have been tested for OS X 10.7, 10.9, 10.11 (Lion, Mavericks, El Capitan).
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.
Contents
1. Get the Source Code
Users can download Freesurfer source code via the read-only git repo. A simple clone of the repo (187 Megs) 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 (6.6 Gigs).
## Get the source code $> git clone http://freesurfer.net/anonftp/pub/dist/freesurfer/repo/freesurfer.git ## Get data files (only required for full installation) $> cd freesurfer $> git annex get .
2. Download and Install the Libraries
In order to build Freesurfer, the following prerequisite software will need to be downloaded and installed on your OSX system:
MacPorts (for installing gcc)
XQuartz 2.7.5 (OSX versions 10.9 and lower)
XQuartz 2.7.6 (OSX versions 10.10 and higher)
IMPORTANT: After you install Qt, you must delete line 320 from the file /Library/Frameworks/QtCore.framework/Headers/qglobal.h, the line that says "#warning "This version of Mac OS X is unsupported"". Next, install Xcode Command Line Tools my typing the following on the command line:
$> xcode-select --install
After Xcode has been installed, we need to install gcc v4.4.7 using MacPorts:
$> sudo port install gcc44 $> sudo port select --set gcc mp-gcc44 $> gcc --version gcc (MacPorts gcc44 4.4.7_10) 4.4.7
Download and install the prebuilt package of open-source libraries:
$> curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/lion/MacOSX_Lion_Packages.tar.gz $> sudo mkdir -p /usr/pubsw/packages $> sudo tar -C /usr/pubsw/packages -xzvf MacOSX_Lion_Packages.tar.gz
3. Set Your Path
$> export PATH=/usr/pubsw/packages/autotools/bin:$PATH
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 /User/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=/User/USER/freesurfer $> make -j4 $> make install
Done! Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu