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 10.13 (High Sierra). See the linux 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.

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 Build Tools

In order to build Freesurfer, the following prerequisite software will need to be downloaded and installed on your OSX system. Homebrew is preferred over MacPorts. Homebrew needs to be installed first. However, if your Mac is polluted with various stuff in /usr/local and /opt/local, and you think you can live without whatever is there, a recommendation is to delete those directories entirely, so that debugging strange build issues is not confounded by overlap with old tools in those directories. To do so:

sudo rm -Rf /usr/local/*
sudo rm -Rf /opt/local

This has been safely done (once) on Mac High Sierra. Reboot once this is done, then to install Homebrew, open a Terminal, then type 'bash' (if that is not your default):

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Test it:

brew install wget
brew postinstall wget
wget --help

You should get wget help instructions, which means Homebrew is working. The brew install may output some error-looking stuff, but if wget --help works, then your set. Now use it to install autoconf, automake, libtool, and gcc v4.9:

brew install libtool
brew install automake
brew postinstall automake
brew install gcc49
brew postinstall gcc49

There may be gcc tools installed in /usr/bin, so you will want to make sure that the gcc 4.9 installed by Homebrew is used, so first run this in bash:

VER=4.9
LN_APPS="c++-$VER cpp-$VER g++-$VER gcc-$VER gcc-ar-$VER gcc-nm-$VER gcc-ranlib-$VER gcov-$VER gfortran-$VER"

cd /usr/local/bin
for app in $LN_APPS
do
        LN_NAME=$(echo $app | sed 's/\(.*\)-4.9/\1/')
        echo "ln -s $app $LN_NAME"
        sudo ln -s $app $LN_NAME
done

sudo ln -s glibtool libtool
sudo ln -s glibtoolize libtoolize

sudo mkdir -p /opt/local/bin
cd /opt/local/bin
sudo ln -s /usr/local/bin/libtool
sudo ln -s /usr/local/bin/libtoolize
sudo ln -s /usr/local/bin/glibtool
sudo ln -s /usr/local/bin/glibtoolize

Note that gcc-ar, gcc-nm and gcc-ranlib exist in the Homebrew gcc 4.9 install, but it seems that linking these to ar, nm and ranlib creates build problems, so those three tools will use the system default in /usr/bin. The linking of libtool in /opt/local/bin is because it seems that automake (when configure is run) looks for libtool there, and if it's not found, then later at link time of a freesurfer binary, it complains about mismatched libtool versions.

Then make sure that /usr/local/bin is first in your default path. Put this (for tsch) in your .cshrc:

setenv USR_LOCAL  /usr/local
if (-e $USR_LOCAL) then
  setenv PATH      "$USR_LOCAL/bin":"$PATH"
endif

You should now be setup with the gnu tools to build freesurfer.

3. Library Dependencies

In order to compile freesurfer, you will need to install the 3rd party lib dependencies. There are two options: use a prebuilt bundle (which may not be guaranteed to work with newer versions of gcc and Mac OS versions), or you can build each library independently.

3.1. Prebuilts

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

3.2. Build from source

TBD

4. Setup, Configure, Make

First, we setup the environment, and we'll run the default configure:

./setup_configure
./configure

.
.
.
checking for main in -lvnl... no
configure: error: FATAL: vnl lib not found. Set LDFLAGS or --with-vxl-dir.

This indicates it could not find the first dependency, the VXL libs. Let's point configure at the pre-built package dir:

./configure --with-pkgs-dir="$HOME/osx-lion-packages"

.
.
.

checking for main in -lKWWidgets... no
configure: error: FATAL: KWWidgets lib not found.   Set LDFLAGS or --with-KWWidgets-dir.

Oops! Looks like KWWidgets is not in the packages directory. It turns out that building the GUI apps in freesurfer (freeview, tk*, qdec) is a great big hassle due to the many 3rd-party libs. So for now, lets just not build those:

./configure --with-pkgs-dir=$PKGS --disable-GUI-build

.
.
.
FreeSurfer is now configured for x86_64-apple-darwin17.3.0

  Source directory:  .
  Build directory:   /Users/nicks/dev/freesurfer
  Install directory: /Applications/freesurfer

  C compiler:   gcc -g -O3 -msse2 -mfpmath=sse -Wall  -Wno-unused-but-set-variable -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fopenmp -DHAVE_OPENMP -m64 -DDarwin -DANSI  -DUSE_LOCAL_MINC
  C++ compiler: g++ -g -O3 -msse2 -mfpmath=sse -Wall  -Wno-unused-but-set-variable -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fopenmp -DHAVE_OPENMP -m64 -DDarwin -DANSI  -DUSE_LOCAL_MINC
  Fortran:      gfortran -g -O3 -msse2 -mfpmath=sse -m64
  Linker:       /usr/bin/ld  -fopenmp -dead_strip    -L/Users/nicks/dev/pkgs/vxl/current/lib
  Libs:            -lz -lm  -ldl -lpthread      -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib

Now we're ready to build.

Determine the location you want Freesurfer to be installed. For example, in this 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.):

./setup_configure
./configure --with-pkgs-dir=/Users/USERNAME/osx-lion-packages --disable-GUI-build --prefix=/Users/username/fs_install
make -j4
make install

Done!

5. Contributing Changes

Users who with to make contributions to the Freesurfer code base should see the following page which describes how to fork the Freesurfer repository and submit pull requests:

• https://surfer.nmr.mgh.harvard.edu/fswiki/Freesurfer_github

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