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| #pragma section-numbers on 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]]. <<TableOfContents(3)>> === 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 [[https://git-annex.branchable.com/ | 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 . }}} === 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: * [[https://download.qt.io/archive/qt/4.7/qt-mac-opensource-4.7.4.dmg|Qt 4.7.4]] * [[http://gcc.gnu.org/wiki/GFortranBinaries#MacOS|gfortran 4.8.2]] * [[https://www.macports.org/install.php|MacPorts]] (for installing gcc) * [[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) ''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 }}} === Set Your Path === {{{ $> export PATH=/usr/pubsw/packages/autotools/bin:$PATH }}} === 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 |
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