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 ( 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.