Getting started with BESA data

Please add information if you're using BESA data and want to share info with other FieldTrip users.

Background

BESA is a commercial software package for EEG and MEG data analysis (see www.besa.de). One of BESA’s strong points is source analysis, in particular concerning dipole modeling. By including prior anatomical or functional knowledge as constraints on the source model, it is possible to make robust estimations of relatively complex source configurations. This is further facilitated by the easy to use GUI. Computation can be done using a number of pre-defined head models that can be extended to individual head models (FEM) when using the extension package BESA MRI or adapting your FEM to BESA standards. BESA’s source analysis methods also include some beamformers.

Fieldtrip has very extensive support for advanced frequency and time-frequency analysis of EEG and MEG data. The main approach for source analysis that is currently implemented in FieldTrip uses various beamformer methods in the time, but especially in the frequency domain. In that respect, it differs a little bit from BESA. However, a large difference between BESA and Fieldtrip is that the latter also includes support for advanced statistical analysis of channel and source level data.

One might wish to combine BESA’s capacities and convenience in spatiotemporal dipole modeling with Fieldtrip’s strength on advanced frequency estimates and statistical analysis on the channel and source level. This tutorial describes how you can read in channel and source level data that has been analyzed in BESA, and how you can enhance your analysis of that data in Fieldtrip.

Reading in data files from BESA

BESA has its own file formats for storing various aspects of the data. Most of the files contain the data in plain ascii format and it is relatively easy to read in their contents into Matlab or any other program. You can use a normal text editing program like Microsoft Wordpad to have a look at the content and format of the files.

Fieldtrip directly supports the following BESA file formats:

  • .avr contains an averaged ERP/ERF
  • .mul contains an averaged ERP/ERF stored in a multiplexed format
  • .elp contains electrode labels
  • .sfp contains electrode labels and positions
  • .pdg contains the settings of an analysis paradigm
  • .tfc contains a time-frequency representation of power or coherence
    • .dat contains multiple source beamformer output on a regular 3D grid


It is possible to use the low-level functions in Fieldtrip to read in the BESA data into Matlab, but it is preferred to use the high-level besa2fieldtrip function. That function will read the data and format it into a structure that is compatible with fieldtrip. Depending of the content of the file, the data will be formatted to appear similar to the output of one of the fieldtrip functions:

  • .avr converted to ft_timelockanalysis
  • .mul converted to ft_timelockanalysis
  • .tfc converted to ft_freqanalysis


For example, you can read in event-related potential data using

timelock = besa2fieldtrip('filename.avr');

or a time-frequency estimate of power using

freq = besa2fieldtrip('filename.tfc');

BESA Matlab toolbox

For some of the file formats, there happen to be two low-level conversion functions importers. FieldTrip comes with the low-level functions of itself, but there is also a BESA toolbox written by Karsten Hochstatter. The preferred method for using BESA2FIELDTRIP is to download the BESA toolbox and to add it to your Matlab path. The conversion function will automatically detect and use it when available on your path.

The BESA toolbox is maintained by BESA (www.besa.de) and included in the FieldTrip release as fieldtrip/external/besa for your convenience.

Electrode information

BESA electrode files can also be read into Matlab, using the ft_read_sens function. They do not directly correspond to a core Fieldtrip data structure, but you can add the electrode information to any fieldtrip data structure according to this:

data = besa2fieldtrip(‘yourbesafile.avr’);
data.elec = ft_read_sens(‘yourelectrodes.sfp’);

Reading *.dat files with source reconstructions

Because BESA *.dat files do not include mask information, the resulting data structure will not have the .inside and .outside fields assigned correctly, which will lead to errors in subsequent analyses in fieldtrip. Consequently these fields much be set for each subject. The following code is an example of how to develop a reasonable mask and apply it to all subjects (it masks out only those coordinates with a value of 0 for all subjects):

files=dir(['yoursubjectdirectory' filesep '*.dat']);
inside=[];
for k=1:length(files)
    src(k)=besa2fieldtrip(files(k).name);
    in=find(src(k).avg.pow);
    inside(end+1:end+length(in))=in;
end
inside=unique(inside);
outside=1:length(src(1).pos);
outside(inside)=[];
for k=1:length(files)
    src(k).outside=outside;
    src(k).inside=inside;
end

Continuous data in the *.besa format

The *.besa format contains continuous (unprocessed) data, including header and event details.

FIXME: needs elaboration

Events can also be stored in a data channel appended to the brain data channels. For instance, a photodiode transducer attached to a stimulus presentation screen may convert screen light into current. This way, changes in light are captured as an analog signal in that data channel and can be used to synchronize timing of the experiment with the brain recording. When the name or the channel index of the event channel is known, it becomes feasible to use that channel for reading data segments or trials of interest into the Matlab work environment using FieldTrip. The most straightforward approach is to create a trial function (as invoked with cfg.trialfun) that reads in the event channel and performs some form of thresholding on the signal in that channel to determine the events of interest. We provide an example pipeline below.

% define trials
cfg            = [];
cfg.dataset    = 'dataset.besa';
cfg.trialfun   = 'trialfun_besa';
cfg            = ft_definetrial(cfg);

where 'trialfun_besa' is a self-specified Matlab function for conditional selection of data segments or trials of interest. See below and this wiki page for examples.

% read and preprocess the data
cfg.continuous = 'yes';
cfg.channel    = 'all';
data           = ft_preprocessing(cfg);

Note that filtering, re-referencing, etcetera can be performed at the preprocessing stage. Type 'help ft_preprocessing' to get an overview of the possibilities. Now that the raw data is in the matlab environment it becomes possible, as shown below, to use ft_databrowser to browse through the raw segmented data. See also this wiki page for a number of strategies on how to inspect and clean up the data from artifacts.

% visually inspect the data
cfg            = [];
cfg.viewmode   = 'vertical';
ft_databrowser(cfg, data);

Trial functions

Hereunder are two examples of a trial function. See also this wiki page for more examples. Ensure that your trial function is available on the matlab path for it to be found by Matlab and invoked by the call to ft_define_trial (see above). The below examples assume that the experiment events are stored in a data channel whose name or index (referred to as chanindx in the code) is known to the user.

The example scripts also assume that the event is marked by an 'up flank' in the recorded signal (e.g., by virtue of an increase in light on the photodiode transducer). Down flanks can also be detected by specifying cfg.detectflank = 'down'. The trigger threshold can be a hard threshold, i.e. numeric, or flexibly defined by an executable string (e.g., to calculate the 'median' of the analog signal). In the first example, we define a 'segment' as one second preceding this trigger until 2 seconds thereafter:

function [trl, event] = trialfun_besa(cfg)

% read the header information
hdr           = ft_read_header(cfg.dataset);

% read the events from the data
chanindx      = 1;
detectflank   = 'up';
threshold     = '(3/2)*nanmedian'; % or, e.g., 1/2 times the median for down flanks
event         = ft_read_event(cfg.dataset, 'chanindx', chanindx, 'detectflank', detectflank, 'threshold', threshold);

% define trials around the events
trl           = [];
pretrig       = 1 * hdr.Fs; % e.g., 1 sec before trigger
posttrig      = 2 * hdr.Fs; % e.g., 2 sec after trigger
for i = 1:numel(event)
    offset    = -hdr.nSamplesPre;  % number of samples prior to the trigger
    trlbegin  = event(i).sample - pretrig;
    trlend    = event(i).sample + posttrig;
    newtrl    = [trlbegin trlend offset];
    trl       = [trl; newtrl]; % store in the trl matrix
end

In this second example, we define a data segment as the time the trigger was 'on', i.e. during the 'up flank', until it was 'off':

function [trl, event] = trialfun_besa(cfg)

% read the header information
hdr           = ft_read_header(cfg.dataset);
  
% read the events from the data
chanindx      = 1;
detectflank   = 'both'; % detect up and down flanks
threshold     = '(3/2)*nanmedian';
event         = ft_read_event(cfg.dataset, 'chanindx', chanindx, 'detectflank', detectflank, 'threshold', threshold);

% look for up events that are followed by down events (peaks in the analog signal)
trl           = [];
waitfordown   = 0;
for i = 1:numel(event)
  if ~isempty(strfind(event(i).type, 'up')) % up event
    uptrl     = i;
    waitfordown = 1;
  elseif ~isempty(strfind(event(i).type, 'down')) && waitfordown % down event
    offset    = -hdr.nSamplesPre;  % number of samples prior to the trigger
    trlbegin  = event(uptrl).sample;
    trlend    = event(i).sample;
    newtrl    = [trlbegin trlend offset];
    trl       = [trl; newtrl]; % store in the trl matrix
    waitfordown = 0;
  end
end

Alternatively, when the event channel index is unknown, but its name, or a part thereof (e.g., 'DC01'), is, one may use:

chanindx      = find(ismember(hdr.label, ft_channelselection('*DC01*', hdr.label)));
getting_started/besa.txt · Last modified: 2016/01/22 20:52 by robert

You are here: startgetting_startedbesa
CC Attribution-Share Alike 3.0 Unported
www.chimeric.de Valid CSS Driven by DokuWiki do yourself a favour and use a real browser - get firefox!! Recent changes RSS feed Valid XHTML 1.0
This DokuWiki features an Anymorphic Webdesign theme, customised by Eelke Spaak and Stephen Whitmarsh.
Mobile Analytics Website Security Test