The FreeSurfer tools, and brain image processing tools in general, are best understood in the context of a work-flow used to accomplish a certain task necessitated by a research program. Outside of this context, understanding the tools and commands can be difficult.
The core utility of the FreeSurfer tools is to reconstruct a 3D volume of the brain from MRI image slices, and from that reconstruction, create a cortical surface, and to segment and label the subcortical structures. Upon the cortical surface structure, fMRI data can be overlayed. It is possible to gather cortical thickness data from the surface structure as well. Volumetric data on the subcortical structures can also be gathered. There are many other examples of research data which may be gathered using the FreeSurfer tools in specialized workflows. The most commonly encountered workflows are described in these pages: