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| '''Index''' | 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 (Lion and Mavericks). <<TableOfContents(3)>> === Get the Source Code === ''If you already have a working local copy of the CVS repository then you can skip this step.'' {{{ # Local CVS access: $> export CVSROOT=/space/repo/1/dev $> cvs checkout -P dev |
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| This page is targeted at those who wish to develop and build the freesurfer source code on their Mac OSX platform. These instructions have been tested for Mac 10.6 (Snow Leopard) and 10.7 (Lion). | # Or for remote access: $> export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/space/repo/1/dev $> cvs checkout -P dev }}} 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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| <<TableOfContents(3)>> | === Download and Install the Libraries === |
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| === Get the Source Code === ''If you already have a working local copy of the CVS repository then you can ignore this step.'' |
In order to build Freesurfer, the following prerequisite software will need to be downloaded and installed on your OSX system: |
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| Local CVS access: | * [[https://download.qt.io/archive/qt/4.7/qt-mac-opensource-4.7.4.dmg|Qt 4.7.4]] * ''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""'' * [[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) or [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] (OSX versions 10.10 and higher) Install Xcode Command Line Tools: |
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| export CVSROOT=/space/repo/1/dev cvs checkout -P dev |
$> xcode-select --install |
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| Remote CVS access: | Install gcc v4.4.7: |
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| export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/space/repo/1/dev cvs checkout -P dev |
$> sudo port install gcc44 $> cd /opt/local/bin $> sudo ln -s gcc-mp-4.4 gcc $> sudo ln -s g++-mp-4.4 g++ |
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| === Get the Libraries === ''If you are at the NMR Center and already have {{{/usr/pubsw/packages}}} mounted on your system then you can skip this step.'' |
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| Freesurfer builds against a set of open-sourced libraries. Special bundles of this open-source code are available on the [[http://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/|distribution site]]. Once you have downloaded the bundle, execute the following command to install them into the {{{/usr/pubsw/packages}}} directory: | Download and install the prebuilt package of open-source libraries: |
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| mkdir -p /usr/pubsw/packages tar -C /usr/pubsw/packages -xzvf DownLoadedFileName.tar.gz |
$> 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 $> sudo tar -C /usr/pubsw/packages -xzvf MacOSX_Lion_Packages.tar.gz |
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| '''''NOTE:''' You may install the open-sourced libraries into any directory you wish but it is best to install them into the {{{/usr/pubsw/packages}}} directory, as that is where Freesurfer setup script checks for its packages during its setup. If you choose to install in a different location than the onus will be on you to setup everything correctly during the '''configure''' phase. That is outside the scope of this document.'' | |
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| export PATH=/usr/pubsw/packages/autotools/bin:$PATH | $> export PATH=/usr/pubsw/packages/autotools/bin:$PATH |
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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/zkaufman/freesurfer}}}. Type the following commands in the top-level Freesurfer directory (the directory that contains configure.in and all the mri_* and mris_* directories.) If your on Mac OSX 10.6 (Snow Leopard): |
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.) |
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| ./setup_configure ./configure \ --prefix=/Users/zkaufman/freesurfer make -j4 make install }}} If your on Mac OSX 10.7 (Lion): {{{ ./setup_configure ./configure \ --prefix=/Users/zkaufman/freesurfer \ --disable-GUI-build \ --with-Mac32-GUIs make -j4 make install |
$> ./setup_configure $> ./configure --prefix=/User/USER/freesurfer $> make -j4 $> make install |
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Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu |
Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu |
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 (Lion and Mavericks).
Contents
1. Get the Source Code
If you already have a working local copy of the CVS repository then you can skip this step.
# 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
Or, you can get readonly CVS access to the source code by following the directions on this page:
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:
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""
MacPorts (for installing gcc)
XQuartz 2.7.5 (OSX versions 10.9 and lower) or XQuartz 2.7.6 (OSX versions 10.10 and higher)
Install Xcode Command Line Tools:
$> xcode-select --install
Install gcc v4.4.7:
$> sudo port install gcc44 $> cd /opt/local/bin $> sudo ln -s gcc-mp-4.4 gcc $> sudo ln -s g++-mp-4.4 g++
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