Note that this reference documentation is identical to the help that is displayed in Matlab when you type “help ft_prepare_atlas”.

  FT_PREPARE_ATLAS reads in a specified atlas with coordinates and
  anatomical labels. It either uses the AFNI brik file that is available
  from http://afni.nimh.nih.gov/afni/doc/misc/ttatlas_tlrc, or it
  uses one of the WFU atlasses available from http://fmri.wfubmc.edu.
 
  This function is called by other FieldTrip functions that make
  use of an atlas, for example for plotting or for selection of an
  anatomical region of interest.
 
  Use as
    [atlas] = ft_prepare_atlas(cfg)
 
  where the configuration should contain
    cfg.atlas      string, filename of the atlas to use
 
  See also FT_VOLUMELOOKUP, FT_SOURCEPLOT, FT_SOURCESTATISTICS