42013-03-07 21:23:04localhostconverted to 1.6 markup32011-01-27 17:51:36JonathanPeelle22011-01-26 17:57:52JonathanPeelle12011-01-26 17:37:24JonathanPeelle

A much more thorough and complete guide can be found at . This is intended to give people who haven't used FieldTrip at all an overall feel for how data is structured and analyses are conducted.

Like SPM, FieldTrip is written in Matlab. Unlike SPM, there is no graphical interface for conducting analyses; everything is done through scripts. This provides a great deal of flexibility, and the ability to always be able to see exactly what analyses were run. However, it does take a bit of knowledge of Matlab (but not too much). (SPM now includes a distribution of FieldTrip, so many of the "behind the scenes" analyses are identical.) Because FieldTrip functions are written in Matlab, to get help on any function you can type "help <function>" in Matlab, or "edit <function>" to view the source (and help). It's a good habit to get into to look at the help for every function you use.

Most FieldTrip functions take as one of their arguments a configuration (cfg) structure. A structure is a Matlab variable that contains one or more fields, and each field can then in turn contain a type of information. An empty structure can be created using struct([]): > c = struct([]) ]]>> isstruct(c) ]]>> ]]>By convention, FieldTrip example scripts usually start by creating an empty matrix using [], and then assign some values to turn it into a structure: > c = [] ]]>> isstruct(c) ]]>> c.myfield = [1 2 3] ]]>> isstruct(c) ]]>> ]]>Now that we have a structure called c, we can add some fields to it using a dot notation (i.e., <structure>.<field>): > c.field1 = 1; >> c.field2 = 3.4; >> c.you_can_name_them_whatever_you_want = 'structures are fun'; >> c ]]>> ]]>Note that fields can take any kind of information: vectors, matrices, integers, strings...even other structures. From the perspective of FieldTrip, this makes it easy to pass a lot of information to a function using only a single variable.

To get started in FieldTrip, you just need to make sure that all of FieldTrip's functions are in your Matlab path. To do so, make sure the main FieldTrip distribution is in your path: > addpath /imaging/local/software/fieldtrip/fieldtrip-current]]>and then run the defaults function: > ft_defaults]]>Now you're ready to go!

For most things you do in FieldTrip, it's probably worth saving the scripts so that you can easily change options and see what you've done. In this case, note that the cfg structure is updated by ft_definetrial, and then for ft_preprocessing we are using this new cfg structure. You may end up with multiple data files (e.g., one per condition), which you can then go on to compare. == An example script == Here is a slightly longer example toy script that includes basic artifact rejection, time-locked averaging, and topographic plotting. FieldTrip also includes extensive options for doing statistics using permutation testing, which are worth looking into.