Tags: dataformat tmsi eeg

Getting started with TMSi data

Twente Medical Systems International or TMSi is a Dutch company with a focusses on EEG amplifiers. Some of the TMSi amplifiers are or have been used by other companies under their own brand names, notably the Refa system which was integrated by ANT Neuro and by BrainProducts in their own system. TMSi also has its own acquisition software for its amplifiers, Polybench, which is probably the software that you are using if you purchased your EEG hardware directly from TMSi. The remainder of this page deals with the EEG data recorded using Polybench.

The Polybench acquisition software writes the data to the .Poly5 file format. To read the data in the normal and recommended fashion, you would do

cfg = [];
cfg.dataset = 'Filename.Poly5';
data = ft_preprocessing(cfg);

Prior to calling ft_preprocessing you can use ft_definetrial to define segments of interest based on triggers in the data. That is explained in more detail in the preprocessing tutorials.

The way that stimulus presentation systems (such as NBS Presentation, E-Prime, PsychoPy, or Psychophysics Toolbox) are hooked up to the EEG acquisition setup appears to vary between labs and between different TMSi systems. Sometimes triggers are represented as 8-bit integer numbers, ranging from 1-255. In other cases, each of the trigger bits is controlled with a separate TTL signal, leading to 8 different event codes that can be used. If the default settings of ft_definetrial does not return the trigger codes that you were expecting, you can use the low-level reading functions to figure out the specific options that apply to your recordings.

You can read the header with ft_read_header, the data with ft_read_data and the events with ft_read_event. These functions do not return valid FieldTrip data structures to be used with other FieldTrip functions, but help in debugging.

hdr = ft_read_header('Filename.Poly5')  % do _not_ use a semicolon at the end of the line, so you can see the header details
dat = ft_read_data('Filename.Poly5');   % use a semicolon, since you do not want the complete data printed on screen
event = ft_read_event('Filename.Poly5')

% show the first 10 events  
for i=1:10

% show the event types, i.e. the name of the trigger channel

sample = [event.sample]
value = [event.value]
plot(sample/hdr.Fs, value, '.')
xlabel('time (s)')
ylabel('trigger value')

If this does not show the triggers at the moment you were expecting, or the trigger values are not as you would expect, you can try again with the detectflank option:

event_up       = ft_read_event('Filename.Poly5', 'detectflank', 'up')       % this is the default
event_updiff   = ft_read_event('Filename.Poly5', 'detectflank', 'updiff')
event_down     = ft_read_event('Filename.Poly5', 'detectflank', 'down')     % this is to be used with pull-down triggers
event_downdiff = ft_read_event('Filename.Poly5', 'detectflank', 'downdiff')
event_any      = ft_read_event('Filename.Poly5', 'detectflank', 'any')
event_biton    = ft_read_event('Filename.Poly5', 'detectflank', 'biton')    % this is when you use single TTL channels
event_bitoff   = ft_read_event('Filename.Poly5', 'detectflank', 'bitoff')   % this is when you use single TTL channels with pull-down triggers

If this still does not give the expected results, you should check whether the correct trigger channel is being used. For that you can look in the header (i.e. hdr.label), you can plot the data, and you can specify the trigger channels like this

event_up = ft_read_event('Filename.Poly5', 'detectflank', 'up', 'chanindx', 33)       % channel 33 contains the triggers
event_up = ft_read_event('Filename.Poly5', 'detectflank', 'biton', 'chanindx', 41:48) % channels 41:48 contains bit-wise triggers

Once you have figured out what the proper low-level settings are for your setup and recording, you can use them with the high-level FieldTrip functions as follows

cfg = [];
cfg.dataset               = 'Filename.Poly5';
cfg.trialfun              = 'ft_trialfun_general';
cfg.trialdef.eventtype    = ...
cfg.trialdef.eventvalue   = ...
cfg.trialdef.prestim      = 0.2; % in seconds
cfg.trialdef.poststim     = 0.8; % in seconds
cfg.trialdef.detectflank  = 'biton';
cfg.trialdef.chanindx     = 41:48;

% define the segments of interest
cfg = ft_definetrial(cfg);

% read the segments of interest
data = ft_preprocessing(cfg);

See also