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 10.11 (El Capitan). See the linux build page for instructions on how to build on linux platform.
1. Get the Source Code
The Freesurfer source code can be cloned from the official Freesurfer github page:
git clone https://github.com/freesurfer/freesurfer.git
1.1. Get the Data Files (optional)
The Freesurfer repository contains a large number data files which are not included with a default git clone of the repo. Instead, these data files are distributed via the git-annex software. Users who only want the repository for the purposes of compiling binaries and/or inspecting source code, the git clone command from above is all you need to do. Users who want to run build time checks, or perform a full local installation, or just want all the contents of the repository, will need to add a special data store remote repository in order to retrieve these files.
To add the data store repository (this only needs to be done once):
cd freesurfer git remote add datasrc https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git git fetch datasrc
And to retrieve data files:
git annex get <filename>
The data files have been broken down into categories, those being required for build time checks, those required for a local installation, and everything else. Use one of the following commands depending on your needs:
## Get only the data files required for build time checks (1.9 GB) git annex get --metadata fstags=makecheck . ## Get only the data files required for local installation (4.3 GB) git annex get --metadata fstags=makeinstall . ## Just give me everything! Not Recommended (6.8 GB) 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 gcc48 ## Set gcc44 to be the default compiler $> sudo port select --set gcc mp-gcc48 $> gcc --version gcc (MacPorts gcc48 4.8.5_1) 4.8.5
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.
3. Library Dependencies
In order to compile freesurfer, you will need to download and install our prebuilt bundle of 3rd party dependencies. Download the package and extract its content. Remember the extraction location as you will need to pass that directory to the configure script.
$> mkdir ~/osx-lion-packages $> cd ~/osx-lion-packages $> 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 --disable-Werror --prefix=/Users/username/fs_install $> make -j4 $> make install
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