Tags: example raw preprocessing trialfun trialdef

Making your own trialfun for conditional trial definition

The ft_definetrial function allows you to specify your own MATLAB function for conditional selection of data segments or trials of interest. That is done using the cfg.trialfun option. Using a trial-function you can use an arbitrary complex conditional sequence of events to select data, e.g. only correct responses, or only responses that happened between 300 and 750 ms after the presentation of the stimulus. You can also use your own reading function to obtain the events, or you can read the data from an EMG channel to detect the onset of muscle activity.

This trial-function should be a MATLAB function with the following function definition

function [trl, event] = your_trialfun_name(cfg);

The configuration structure will contain the fields cfg.dataset, cfg.headerfile and cfg.datafile. If you want to pass additional information (e.g. trigger value), then you should do that in the sub-structure cfg.trialdef.xxx. The second output argument of the trialfun is optional, it will be added to the configuration if present (i.e. for later reference).

In the fieldtrip/trialfun directory you can find a number of example trial functions.

An example

function [trl, event] = your_trialfun_name(cfg);

% read the header information and the events from the data
hdr   = ft_read_header(cfg.dataset);
event = ft_read_event(cfg.dataset);

% search for "trigger" events
value  = [event(find(strcmp('trigger', {event.type}))).value]';
sample = [event(find(strcmp('trigger', {event.type}))).sample]';

% determine the number of samples before and after the trigger
pretrig  = -round(cfg.trialdef.pre  * hdr.Fs);
posttrig =  round(cfg.trialdef.post * hdr.Fs);

% look for the combination of a trigger "7" followed by a trigger "64"
% for each trigger except the last one
trl = [];
for j = 1:(length(value)-1)
trg1 = value(j);
trg2 = value(j+1);
if trg1==7 && trg2==64
  trlbegin = sample(j) + pretrig;       
  trlend   = sample(j) + posttrig;       
  offset   = pretrig;
  newtrl   = [trlbegin trlend offset];
  trl      = [trl; newtrl];
end
end

When calling ft_definetrial, you would specify

cfg = ...
cfg.trialfun = 'your_trialfun_name';
cfg.trialdef.pre  = 0.5;
cfg.trialdef.post = 1.0;

and you would call

cfg = ft_definetrial(cfg);

followed by

data = ft_preprocessing(cfg);

You could of course also make the trigger value (which are hard-coded here) configurable by passing them in the cfg structure.

Another example

Let’s say that your EEG acquisition system has separate inputs for the stimulus and the response and that ft_read_event represents them as a “stimulus” and as a “response”, then the following trialfun could be used to select trials time-locked to the stimulus but conditional to the response.

function [trl, event] = another_trialfun_example(cfg);

% read the header information and the events from the data
hdr   = ft_read_header(cfg.dataset);
event = ft_read_event(cfg.dataset);

% determine the number of samples before and after the trigger
pretrig  = -round(cfg.trialdef.pre  * hdr.Fs);
posttrig =  round(cfg.trialdef.post * hdr.Fs);

% search for "stimulus" events
stimulus_value  = [event(find(strcmp('stimulus', {event.type}))).value]';
stimulus_sample = [event(find(strcmp('stimulus', {event.type}))).sample]';

% search for "response" events
response_value  = [event(find(strcmp('response', {event.type}))).value]';
response_sample = [event(find(strcmp('response', {event.type}))).sample]';

if length(stimulus_sample)~=length(response_sample)
error('the number of stimuli and responses is different');
end

if any((response_sample-stimulus_sample)<=0)
error('there is a response prior to a stimulus');
end

reaction_time = (response_sample-stimulus_sample)/hdr.Fs;

% define the trials
trl(:,1) = stimulus_sample + pretrig;  % start of segment
trl(:,2) = stimulus_sample + posttrig; % end of segment
trl(:,3) = pretrig;                    % how many samples prestimulus

% add the other information
% these columns will be represented after ft_preprocessing in "data.trialinfo"
% the last column in this example contains a "correct" boolean flag for each trial
trl(:,4) = stimulus_value;
trl(:,5) = response_value;
trl(:,6) = reaction_time;
trl(:,7) = (stimulus_value==3 & response_value==103) | (stimulus_value==4 & response_value==104);

When calling ft_definetrial, you would specify

cfg = ...
cfg.trialfun = 'another_trialfun_example';
cfg.trialdef.pre  = 0.5;
cfg.trialdef.post = 1.0;

and you would call

cfg = ft_definetrial(cfg);

followed by

data = ft_preprocessing(cfg);

Finding out which trigger codes are used

You can use a small piece of code like this to see which trigger codes are used in your recording.

event = ft_read_event(filename);
plot([event.sample], [event.value], '.')

In case the triggers are of different types, e.g. like here

disp(unique({event.type}))
'CM_in_range'    'Epoch'    'STATUS'

you can use this to select only the events of a particular type

% select only the trigger codes, not the CM_in_range and Epoch events
sel = find(strcmp({event.type}, 'STATUS'));
event = event(sel);