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## page was renamed from freesurfer_mac_developers page
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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 OS X 10.7, 10.9, 10.11 (Lion, Mavericks, El Capitan). See the [[freesurfer_linux_developers_page|Mac OSX build page]] for instructions on how to build on Linux platform.
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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) and 10.8 (Mountain 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)>>

=== Get the Source Code ===
''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 https://surfer.nmr.mgh.harvard.edu/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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=== Get the Libraries === === Install System Libraries ===
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If you are at the NMR Center and already have {{{/usr/pubsw/packages}}} mounted on your system then you can skip this step. Otherwise, you are going to need to download and install a bundle of open-sourced libraries from the [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt|distribution site]]. Once you have downloaded the bundle, execute the following command to install them into the {{{/usr/pubsw/packages}}} directory on your machine: In order to build Freesurfer, the following prerequisite software will need to be downloaded and installed on your OSX system:
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You will need to download and install gfortran, qt4.7.4 and a prepackaged bundle of open-sourced libraries on your system.
 *[[http://gcc.gnu.org/wiki/GFortranBinaries#MacOS|gfortran]]
 *[[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/lion/qt-mac-opensource-4.7.4.dmg|qt-mac-opensource-4.7.4.dmg]].
 *[[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt|open-source libraries]]		  * [[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)
 * [[http://gcc.gnu.org/wiki/GFortranBinaries#MacOS|gfortran 4.8.2]]
 * [[https://www.macports.org/install.php|MacPorts]]
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The download and install of gfortran is straight forward, just click the .dmg file. To instal the prepackaged bundle of open-source libraries, execute the following command after downloading it: Once !MacPorts is installed, use it to install autoconf, automake, libtool, and gcc44:
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mkdir -p /usr/pubsw/packages
tar -C /usr/pubsw/packages -xzvf DownLoadedFileName.tar.gz		 $> sudo port install autoconf
$> sudo port install automake
$> sudo port install libtool
$> sudo port install gcc44

## Set gcc44 to be the default compiler
$> sudo port select --set gcc mp-gcc44
$> gcc --version
gcc (MacPorts gcc44 4.4.7_10) 4.4.7
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'''IMPORTANT:''' Do to a Qt bug, after you install Qt you must delete line 320 from the file '/Library/Frameworks/QtCore.framework/Headers/qglobal.h' (Removing the line that says '#warning "This version of Mac OS X is unsupported"') As of the writing of this document (June 2016) freeview is unable to build on OSX 10.11 platforms (El Capitan). This is due to an incompatibility between qt4.7 and OSX 10.11. If you are building on a pre-OSX 10.11 platform, and want to build freeeview, you will need to download and install [[https://download.qt.io/archive/qt/4.7/qt-mac-opensource-4.7.4.dmg|Qt 4.7.4]].''IMPORTANT: After you install Qt, you must delete line 320 from the file'' {{{/Library/Frameworks/QtCore.framework/Headers/qglobal.h}}}'', the line that says "#warning "This version of Mac OS X is unsupported""''. Next, install Xcode Command Line Tools my typing the following on the command line:
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=== Set Your Path ===
{{{
export PATH=/usr/pubsw/packages/autotools/bin:$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 {{{/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.)		 === Library Dependencies ===
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If your on Mac OSX 10.6 (Snow Leopard): In order to compile freesurfer, you will need to download and install our prebuilt bundle of 3rd party dependancies. Download the package and extract its content. Remember the extraction location as you will need to pass that directory to the {{{configure}}} script.
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./setup_configure
./configure \
      --prefix=/Users/USER/freesurfer \
      --with-vtk-cocoa-dir=/usr/pubsw/packages/vtk/5.6.1_cocoa
make -j4
make install		 $> cd ~
$> curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/OSX/osx-lion-packages.tar.gz
$> tar -xzvf osx-lion-packages.tar.gz
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If your on Mac OSX 10.7 or 10.8 (Lion or Mountain Lion): === 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.):
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./setup_configure
./configure \
      --prefix=/Users/USER/freesurfer \
      --with-vtk-cocoa-dir=/usr/pubsw/packages/vtk/5.6.1_cocoa \
      --disable-tcltk-apps \
      --with-qt=/usr/bin \
      --with-Mac32-GUIs		 $> cd ~/freesurfer
$> ./setup_configure
$> ./configure --with-pkgs-dir=/Users/username/osx-lion-packages --prefix=/Users/username/fs_install
$> make -j4
$> make install
}}}
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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). See the Mac OSX build page for instructions on how to build on Linux platform.

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
  2. Install System Libraries
  3. Library Dependencies
  4. Setup, Configure, Make

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 https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/freesurfer.git

## Get data files (only required for full installation)
$> cd freesurfer
$> git annex get .

2. Install System Libraries

In order to build Freesurfer, the following prerequisite software will need to be downloaded and installed on your OSX system:

Once MacPorts is installed, use it to install autoconf, automake, libtool, and gcc44: 

$> sudo port install autoconf
$> sudo port install automake
$> sudo port install libtool
$> sudo port install gcc44

## Set gcc44 to be the default compiler
$> sudo port select --set gcc mp-gcc44
$> gcc --version
gcc (MacPorts gcc44 4.4.7_10) 4.4.7

As of the writing of this document (June 2016) freeview is unable to build on OSX 10.11 platforms (El Capitan). This is due to an incompatibility between qt4.7 and OSX 10.11. If you are building on a pre-OSX 10.11 platform, and want to build freeeview, you will need to download and install Qt 4.7.4.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:

3. Library Dependencies

In order to compile freesurfer, you will need to download and install our prebuilt bundle of 3rd party dependancies. Download the package and extract its content. Remember the extraction location as you will need to pass that directory to the configure script. 

$> cd ~
$> curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/OSX/osx-lion-packages.tar.gz
$> tar -xzvf osx-lion-packages.tar.gz

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 /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.): 

$> cd ~/freesurfer
$> ./setup_configure
$> ./configure --with-pkgs-dir=/Users/username/osx-lion-packages --prefix=/Users/username/fs_install
$> make -j4
$> make install

Done!

Send your comments/questions/feedback to zkaufman@nmr.mgh.harvard.edu