FreeSurfer CMake Port
This page is mostly for documenting the process of converting the automake framework to cmake. General documentation for using cmake with freesurfer can be found here.
Configuring a Simple Build
CMake replaces the setup_configure and configure build steps. A build can be initialized in the working directory by running cmake </path/to/repo>. So, assuming you have a freesurfer repository stored in ~/dev/freesurfer, you could set up a simple in-source build with
cd ~/dev/freesurfer cmake .
or an out-of-source build with
cd ~/dev/fsbuild cmake ~/dev/freesurfer
Alternatively, ccmake can be used instead of cmake to configure/edit cached variables in a terminal GUI.
Configuration Options
CMake variables are set on the command line with the -D flag. For example, the standard way to configure a build with an install path is
cmake . -DCMAKE_INSTALL_PREFIX="/path/to/install/destination"
You can define any variable on the command line this way, even if the variable is never used in the CMakeLists.txt scripts. Boolean variables added with the option() function can be turned on/off on the command line as well. For example, freesurfer GUI builds can be disabled by running
cmake . -DBUILD_GUIS=OFF
Aside from this initial configuration step (which really only needs to be run once) and fact that make check is now make test, the rest of the build process is pretty much the same.
note: the make output is more condensed now, but make VERBOSE=1 will output everything.
Overview of the CMake Framework
The top-level CMakeLists.txt file is the main cmake configuration script (which replaces setup_configure, configure.in, and Makefile.am), and all subdirectories are added from here with the add_subdirectory() function. This main script is split into three parts: locating third-party packages, configuring compilation settings, and configuring freesurfer libs and programs.
Third-Party Packages
Most of the packages required by freesurfer are located via custom "find-modules" stored in the cmake subdirectory. These find-modules expect each package to be installed under a common path defined by FS_PACKAGES_DIR. On Martinos machines, this variable automatically defaults to /usr/pubsw/packages, but external developers must provide this path manually:
cmake . -DFS_PACKAGES_DIR="/path/to/packages"
If a package is not found under FS_PACKAGES_DIR, cmake will continue to look through the default search paths. Alternative paths to package installs can also be specified with the <PACKAGE>_DIR variables. For example, to use a non-default ITK version:
cmake . -DITK_DIR="/usr/pubsw/packages/itk/4.9.1"
Find Modules
In CMakeLists.txt, packages are located by using the find_package() function. Some larger, modern projects, like Qt, VTK, and ITK, distribute cmake config files within their installations, so locating the package's include directory and libraries is a fairly straightfoward process:
find_package(ITK HINTS ${ITK_DIR} REQUIRED)In this example, if ITK is found by cmake, then ITK_FOUND is set to true, and ITK_INCLUDE_DIR and ITK_LIBRARIES are set accordingly. This syntax and variables generated by find_package() all follow the same pattern.
However, most freesurfer dependencies don't ship with cmake configuration files, so we have to create our own find-modules. Fortunately, this isn't too difficult,
External Developers
In general, the goal is to distance ourselves from distributing the pre-built package tarballs since they are difficult to maintain across multiple platforms. The packages/build_packages.py script is a potential alternative to the pre-built archives - it's a utility script to help external developers build freesurfer dependencies on their own.
The packages configured within build_packages.py are built using the tarballs and buildscripts stored in the packages/source dir and will get installed to a destination directory specified on the command-line:
build_packages.py "/path/to/install/destination"
This script loops through each package in the pkgs list variable, extracts the associated tarball to destination/package-name/version/src, and runs the package build script. The individual build scripts (like [this ITK one](??)) always expect a single input argument that points to the desired install directory. After each successful package build, the checksum of the tarball is saved to the src dir - this way, the package is only rebuilt when the source code has been modified. Once the dependencies are compiled and installed, developers can then point FS_PACKAGES_DIR to their local install directory.
For now, we should still offer the prebuilt packages since it's just easier for most developers and we need them for the travis builds anyway.
Removing packages From Source
The non-FS libraries (like jpeg, glut, xml2, expat, minc, netcdf, etc...) that used to be built within freesurfer no longer get built by cmake. These packages are now expected in FS_PACKAGES_DIR. The main advantage of this