FreeSurfer Dev Guide

Visit the BuildGuide for instructions on building and installing freesurfer manually.
Visit the GitHub page for an introduction to the github workflow.
Visit the GitAnnex page for detailed instructions on using git annex.

Adding a New C Program

If you'd like to add a new program to the tree, you should create a new subdirectory with the title of your tool. As an example, let's create a new c++ program called mri_process. First, we'll create a top-level subdirectory that contains our new c++ file and an empty CMakeLists.txt file:

freesurfer/
    mri_process/
        CMakeLists.txt
        mri_process.cpp

In order to configure our new code, we should add the following to the empty CMakeLists.txt file.

project(mri_process)

include_directories(${FS_INCLUDE_DIRS})

add_executable(mri_process mri_process.cpp)
target_link_libraries(mri_process utils)

install(TARGETS mri_process DESTINATION bin)

This will compile mri_process.cpp, link it against the utils freesurfer library, and copy the executable to the $FREESURFER_HOME/bin directory during install. To include this subdirectory in the main freesurfer build, make sure to modify the top-level CMakeLists.txt by adding mri_process to the long list of included directories at the bottom of the file. Now, after reconfiguring your build, you can run make in the mri_process directory of your build tree to successfully compile the new program. If you're having trouble configuring and building freesurfer, be sure to visit the BuildGuide for step-by-step instructions.