All high-level FieldTrip functions take a configuration input structure as first input argument. The FieldTrip functions in general work like this

dataout = functionname(cfg);               % e.g. ft_preprocessing
dataout = functionname(cfg, datain, ...);  % e.g. ft_freqanalysis
functionname(cfg, datain, ...);            % e.g. plotting functions 

Type 'help functionname' to see which input arguments (cfg.xxx) ought to be defined before calling the function. The datain and dataout arguments to all FieldTrip main functions can be categorized in a limited number of data types, all of which are structures with a characteristic set of fields. The different datatypes are described here.