Documentation: Functions for reading and writing data files

IN CONSTRUCTION

Location of Data Files

The data that we record (using the BrainVision Recorder) is stored in raw format in a subdirectory of EEG_RAW_DIR (global variable). The naming scheme for the subdirectories is Subject_yy_mm_dd, e.g., Gabriel_02_11_24. One data set in BrainVision generic data format consists for three files: (1) a binary data file, extension .eeg, (2) a header file holding information on the settings of the recording as sampling rate, used channels, etc., extension .vhdr, and (3) a marker file, extension .vmrk. Data we receive in other formats from other labs are stored in a subdirectory of EEG_IMPORT_DIR.

Preprocessed data is stored in matlab format in a subdirectory of EEG_MAT_DIR. The name of this subdirectory should be the same as that of the raw data. Typically the data is stored in a version which is just downsampled and in a version which is filtered and downsampled for display purpose. The former fi le is called like the original data, and the latter has the appendix _display. Each matlab file should include the variables cnt, mrk and mnt, see Section 2.1.

Loading Data which is in the Original Generic Data Format

For the EEG experiments, that we record at our lab, we store data in "preprocessed" formats see Sec. 2.2. One version is just downsampled, which can also be done when reading the original data (using readGenericEEG). But loading the preprocessed data (using eegfile_loadMatlab) has the advantage that the markers are already brought to a nice format. If you want to load data in this convenient way, see Sec. 2.4. Otherwise read on in this section.

   1 cnt = readGenericEEG(file, [clab, fs, from, maxlen]);

This function can be used to load data which is in BrainVision's generic data format. So far it is quite constrained to take only specific variants of the general generic data format. Data must be multiplexed and in the binary format INT16. (To read data in binary format float there is the function readGenericEEG_float: should be integrated in one function?) To determine the available channels or the length of the data use the function readGenericHeader.

file	is taken relative to EEG_RAW_DIR, unless it starts with the character '/'. (Under Windows the condition for an absolute pathname is that the second character is a ':'.)
clab	labels of the channels to be loaded.
fs	sampling rate to which the original data are to be downsampled. The default value is 100. This works only when fs is a divisor of the original sampling rate. To read data in the original sampling rate use 'raw'.
from	is the start in msec from which data is to be read.
maxlen	is the maximum length of data in msec to be read.

Output:

cnt	struct of continous EEG data, as described in Section 2.1.

See also: eegfile_loadMatlab, readGenericHeader, readGenericMarkers.

   1 [clab, scale, fs, endian, len] = readGenericHeader(file);

This function is used by readGenericEEG. It can also be called directly to determine the original sampling rate, the length of the signals and the recorded channels.

file	is the name of the header file (without the extension .vhdr). The same applies as for read readGenericEEG.

Output:

clab	cell array of electrode labels.
scale	vector specifying the scaling factor for each channel by which each sample value (in INT16 format) has to be multiplied to obtain the µV value.
fs	sampling rate in which the signals are stored.
endian	big ('b') or little ('l') endian byte order.
len	length of the EEG signals in seconds.

   1 Mrk = readGenerikMarkers(file, [outputStructArray]);

This function reads all markers of BrainVision's generic data format. If you are only interested in 'Stimulus' and 'Response' markers, readMarkerTable is your friend. Note: this function returns the markers in the original sampling rate. In contrast, readMarkerTable returns markers by default resampled to 100 Hz.

file	is the name of the header file (without the extension .vmrk). The same applies as for readGenericEEG.
outputStructArray	specifies the output format, default 1. If false the output is a struct of arrays, not a struct array.

Output:

Mrk	struct array of markers with fields type, desc, pos, length, chan, time which are defined in the BrainVision generic data format, see the comment lines in any *.vmrk marker file.
fs	sampling rate, as read from the corresponding header file.

See also: readMarkerTable, readGenericHeader.

   1 mrk = readMarkerTable(file, [fs=100, markerTypes, flag]);

This function reads all 'Stimulus' and 'Response' markers from the header file. For reading markers of other types you can use readAlternativeMarker. See also readMarkerTableArtifacts for reading the marker file of an artifact measurement (with annotated artifacts), and readSegmentBorders. A general function that reads all marker information of the BrainVision generic data format is readGenericMarkers.

file	is the name of the header file (without the extension .vmrk). The same applies as for readGenericEEG.
fs	sampling rate for the returned marker structure. The default value is 100.
markerTypes	read only markers of this type, default {'Stimulus','Response'}.
flag	a vector of the same length as markerTypes which defines the sign of the marker values (in the type-of-event field toe of the returned marker structure). The default is [1 -1], i.e., stimulus markers give positive marker numbers and response markers give negative marker numbers.

Output:

mrk	struct of EEG marker, as described in Section 2.1

Saving and Loading EEG Data in Matlab Format

   1 [dat, mrk, mnt] = eegfile_loadMatlab(file, [opt]);
   2 [var1, var2, ...] = eegfile_loadMatlab(file, opt);

This function loads EEG data, that was stored using eegfile_saveMatlab. It can also concat a series of such files.

file	name of data file, or cell array of file names. In the latter case all files are concatenated. Each file name is taken relative to opt.path (see below), unless it starts with the character '/'. (Under Windows the condition for an absolute pathname is that the second character is a ':').

The options struct or property/value list (see Section A.2) can have the following properties:

.clab	Channel labels (cell array of strings) for loading a subset of all channels. Default 'ALL' means all available channels. See function chanind for valid formats. In case opt.clab is not 'ALL' the electrode montage mnt is adapted automatically.
.vars	Variables (cell array of strings) which are to be loaded, default 'dat','mrk','mnt'. The names 'dat', 'cnt' and 'epo' are treated equally and all match the data structure.
.path	In case file does not include an absolute path, opt.path is prepended to file. Default EEG_MAT_DIR (global variable).

Output:

dat	structure of continuous or epoched signals
mrk	marker structure
mnt	electrode montage structure
varx	variables as requested by opt.vars.

Example:

   1 >> file= 'Gabriel_03_05_21/selfpaced2sGabriel';
   2 >> [cnt,mrk,mnt]= eegfile_loadMatlab(file);
   3 >> %% or just to load variables 'mrk' and 'mnt':
   4 >> [mrk,mnt]= eegfile_loadMatlab(file, {'mrk','mnt'});
   5 >> %% or to load only some central channels
   6 >> [cnt, mnt]= eegfile_loadMatlab(file, 'clab','C5-6', 'vars',{'cnt','mnt'});

   1 eegfile_saveMatlab(file, dat, mrk, mnt, [opt]);

This functions saves (potentially preprocessed) EEG data along with structures defining markers and a display montage. Optionally additional variable can also be stored.

|| file|| is the name of the file. The same applies as for eegfile_loadMatlab.||

dat	structure of EEG data, may be continuous or epoched.
mrk	marker structure
mnt	electrode montage structure

The options struct or property/value list (see Section A.2) can have the following properties:

.path	In case file does not include an absolute path, opt.path is prepended to file. Default EEG_MAT_DIR (global variable).
.channelwise	If true, signals are saved channelwise. This is an advantage for big files, because it allows to load selected channels.
.format	'double', 'float', 'int16', or 'auto' (default). In 'auto' mode, the function tries to find a lossless conversion of the signals to INT16 (see property .resolution_list). If this is possible .format is set to 'INT16', otherwise it is set to 'DOUBLE'.
.resolution	Resolution of signals, when saving in format INT16. (Signals are divided by this factor before saving.) The resolution may be selected for each channel individually, or globally for all channels. In the 'auto' mode, the function tries to find for each channel a lossless conversion to INT16 (see property .resolution_list). For all other channels the resolution producing least information loss is chosen (under the resolutions that avoid clipping). Possible values: (1) 'auto' (default), (2) numerical scalar, or (3) numerical vector of length 'number of channels' (i.e., length(dat.clab)).
.resolution_list	Vector of numerical values. These values are tested as resolutions to see whether lossless conversion to INT16 is possible. Default [1 0.5 0.1].
vars	Additional variables that should be stored. opt.vars must be a cell array with a variable name / variable value structure, e.g., {'Mrk',Mrk, 'blah',blah} when Mrk and blah are the variables to be stored.

Exporting Data to the Generic Data Format

   1 writeGenericData(dat, [mrk, scale]);

dat	structure of continuous or epoched EEG data.
mrk	struct of EEG marker, as described in Section 2.1.
scale	scaling factor used in the generic data format to bring data from the INT16 range -32768 to 32767 to µV values. This is implemented as a division by the scaling factor before saving the signals. Individual scaling factors may be specified for each channel in a vector, or a global scaling as scalar, default is 0.1 (i.e., signal range is -3276.8 to 3276.7 µV). Use scale= max(abs(cnt.x))'/32768 to achive best resolution (least information loss in INT16 conversion) without clipping.

IDA Wiki: IDA/BerlinBCI/ToolBox/ToolboxFileio (last edited 2011-05-30 14:41:30 by BenjaminBlankertz)