To cite package ‘freesurfer’ in publications use:

  Fischl B (2012). “FreeSurfer.” _Neuroimage_, *62*(2), 774-781.

A BibTeX entry for LaTeX users is

  @Article{fischl2012freesurfer,
    title = {FreeSurfer},
    author = {Bruce Fischl},
    journal = {Neuroimage},
    volume = {62},
    number = {2},
    pages = {774--781},
    year = {2012},
    publisher = {Elsevier},
  }