It's one of the most popular software packages within the brain MR community. There are many alternatives, but FreeSurfer is one of the first and most robust packages that allows researchers to segment (divide the imaged tissue into classes: white matter, gray matter, cerebral spinal fluid), parcellate (add labels to different brain regions), and generate cortical surface models that can be used to quantify cortical thickness across the human brain.

FreeSurfer is also very influential because it offers a bunch of utility tools for doing analysis/stats on brain images and cortical surfaces, and these tools can be easily combined with other popular neuroimaging software packages.