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.
1. 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. Make sure you first check what is in those directories (e.g. docker and other packages could have files there). If you really want to start fresh, do:
sudo rm -Rf /usr/local/* sudo rm -Rf /opt/local
This has been safely done 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 already):
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
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 brew install git-annex
You should now be setup with the gnu tools to build freesurfer, so let's get the source and libraries.
2. 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
2.1. 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 .
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. Download 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
WORK IN PROGRESS
The packages directory in the freesurfer source tree contains scripts that pull the source for the various 3rd-party libs that freesurfer needs to build. The intent is to run these scripts to build a needed package, and configure will automatically find it.
4. Setup, Configure, Make
First, we setup the environment, and we'll run the configure, telling it where to find our compilers and allowing it to have warnings:
./setup_configure ./configure F77=/usr/local/bin/gfortran-4.9 CC=/usr/local/bin/gcc-4.9 CXX=/usr/local/bin/g++-4.9 --disable-Werror . . . 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 F77=/usr/local/bin/gfortran-4.9 CC=/usr/local/bin/gcc-4.9 CXX=/usr/local/bin/g++-4.9 \ --with-pkgs-dir="$HOME/osx-lion-packages" --disable-Werror . . . 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 F77=/usr/local/bin/gfortran-4.9 CC=/usr/local/bin/gcc-4.9 CXX=/usr/local/bin/g++-4.9 \ --with-pkgs-dir=$HOME/osx-lion-packages --disable-Werror --disable-GUI-build . . . FreeSurfer is now configured for x86_64-apple-darwin17.3.0 Source directory: . Build directory: /Users/nicks/dev/freesurfer Install directory: /Applications/freesurfer C compiler: gcc -g -O3 -msse2 -mfpmath=sse -Wall -Wno-unused-but-set-variable -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fopenmp -DHAVE_OPENMP -m64 -DDarwin -DANSI -DUSE_LOCAL_MINC C++ compiler: g++ -g -O3 -msse2 -mfpmath=sse -Wall -Wno-unused-but-set-variable -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fopenmp -DHAVE_OPENMP -m64 -DDarwin -DANSI -DUSE_LOCAL_MINC Fortran: gfortran -g -O3 -msse2 -mfpmath=sse -m64 Linker: /usr/bin/ld -fopenmp -dead_strip -L/Users/nicks/dev/pkgs/vxl/current/lib Libs: -lz -lm -ldl -lpthread -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib
Now we're ready to build.
Determine the location you want Freesurfer to be installed. For example, in this case we will assume the user wants Freesurfer to be installed in /home/USER/freesurfer. Type the following commands in the top-level Freesurfer directory (the directory that contains configure.in and all the mri_* and mris_* directories.):
./setup_configure ./configure F77=/usr/local/bin/gfortran-4.9 CC=/usr/local/bin/gcc-4.9 CXX=/usr/local/bin/g++-4.9 \ --with-pkgs-dir=$HOME/osx-lion-packages --disable-Werror --disable-GUI-build \ --prefix=$HOME/fsdev_install make -j 8 make install
Done! (Only make install if you downloaded the necessary binaries from git-annex above).
Note: you can spare yourself from some typing by including vars for F77, CC and CXX in your startup .cshrc (or similar):
setenv G49BIN /usr/local/bin if (-e $G49BIN/gcc-4.9) then setenv F77 $G49BIN/gfortran-4.9 setenv CC $G49BIN/gcc-4.9 setenv CXX $G49BIN/g++-4.9 endif
5. Contributing Changes
Users who wish 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:
Send your comments/questions/feedback to email@example.com