Reading is slow, can I write my raw data to a more efficient file format?

Usually the ft_preprocessing function will read small segments of data from your original data file, corresponding to the trials in your experiment. Some file formats are inefficient to read in, and if you read many small segments from such a file, you may notice that it is very slow. One method to speed it up is by converting your original raw data into a more efficient format. Another method is to first preprocess all data as a single long continuous segment. Subsequently the data can be cut into smaller pieces, corresponding with the trials as indicated by the trigger events.

Preprocessing all continuous data at once, cut out the trials later

If the file format is continuous, you can simply call ft_preprocessing without defining any trials:

cfg = [];
cfg.dataset = 'yourfile.ext';
% other options ...
data_all = ft_preprocessing(cfg);

Subsequently you can use ft_definetrial and/or your own trial function to define segments of interest. These segments or “trials” are specified in a Nx3 matrix with the begin sample, end sample and offset of each trial. The ft_redefinetrial function can be used to cut the selected trials out of the preprocessed continuous data.

Converting to another format

A very simple and efficient file format supported by fieldtrip is labeled 'fcdc_matbin'. It is not an official file format, but was invented here at the FCDC. It consists of two files: a *.mat matlab file that contains the header (and optionally the events) and a *.bin binary file that contains the data.

The mat file is just a standard matlab file and it contains the header (and optionally events) just like they are returned by the ft_read_header and ft_read_event functions. So you don't lose any information in the mat file.

The bin file contains the data samples as double precision floating point values, precisely the same as it is returned by the ft_read_data function. The bin file is channel-multiplexed and little-endian. Reading from the data file is fast because the reading function can jump immediately to the desired location in the file with fseek and read the data, without any processing, conversion or calibration.

Below is an example how you can convert an arbitrary file (here a BCI2000 file) to the fcdc_matbin format.

hdr = ft_read_header('eeg1_2.dat');
dat = ft_read_data('eeg1_2.dat', 'header', hdr);

>> whos dat hdr
  Name       Size                  Bytes  Class     Attributes
  dat       64x19696            10084352  double              
  hdr        1x1                  128768  struct   

ft_write_data('test.bin', dat, 'header', hdr, 'dataformat', 'fcdc_matbin');

>> ls test.*
test.bin	test.mat

You can read the fcdc_matbin file just like any other file format in FieldTrip, i.e. by using the ft_read_header and ft_read_data function. For ft_preprocessing you can specify the name of the dataset like this

cfg = []
cfg.dataset = 'test.bin'

and the ft_preprocessing function (or any other function that needs to read from the file) will automatically figure out that the data is contained in the bin/mat pair.

With the code above the events (e.g. trigger codes) are not stored in the output. Since the sample indexing remains exactly the same, you can simply do

event = ft_read_event('eeg1_2.dat')
save event.mat event

i.e. and simply save the events to a MATLAB file for later reuse.

faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format.txt · Last modified: 2015/06/12 23:46 by

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