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

  FT_COMPILE_MEX can be used for compiling most of the FieldTrip MEX files Note that
  this function does not put the MEX files in the correct location in the private
  folders, this is managed by a Bash script. In case you are not working with Git and
  you want to recompile the mex files for your platform, you can find all mex files
  for your platform and move them to a backup directory that is not on your MATLAB
  path. Subsequently you can rtun this function to recompile it on your platform with
  your compiler settings
  The standards procedure for compiling mex files is detailled on
  Please note that this script does NOT set up your MEX environment for you, so in
  case you haven't selected the C compiler on Windows yet, you need to type 'mex
  -setup' first to choose either the LCC, Borland or Microsoft compiler. If you want
  to use MinGW, you also need to install Gnumex (,
  which comes with its own procedure for setting up the MEX environment.
  The logic in this script is to first build a list of files that actually need
  compilation for the particular platform that MATLAB is running on, and then to go
  through that list. Functions are added to the list by giving their destination
  directory and (relative to that) the name of the source file (without the .c).
  Optionally, you can specify a list of platform this file needs to be compiled on
  only, and a list of platforms where you don't compile it on. Finally, you can give
  extra arguments to the MEX command, e.g., for including other c-sources or giving
  compiler flags.
  See also MEX