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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, 10.11 (Lion, Mavericks, El Capitan). |
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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). | 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 === |
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| <<TableOfContents(3)>> | 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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| === Get the Source Code === ''If you already have a working local copy of the CVS repository then you can ignore this step.'' Local CVS access: |
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| 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 ## Get data files (only required for full installation) $> cd freesurfer $> git annex get . |
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| Remote CVS access: | === 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: |
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| export CVSROOT=:ext:USER@door.nmr.mgh.harvard.edu:/space/repo/1/dev cvs checkout -P dev |
$> xcode-select --install |
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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: | After Xcode has been installed, we need to install gcc v4.4.7 using MacPorts: |
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| mkdir -p /usr/pubsw/packages tar -C /usr/pubsw/packages -xzvf DownLoadedFileName.tar.gz |
$> sudo port install gcc44 $> sudo port select --set gcc mp-gcc44 $> gcc --version gcc (MacPorts gcc44 4.4.7_10) 4.4.7 |
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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.'' | 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 $> sudo tar -C /usr/pubsw/packages -xzvf MacOSX_Lion_Packages.tar.gz }}} |
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| export PATH=/usr/pubsw/packages/autotools/bin:$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, 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