You can read in the data from the original data format using ft_preprocessing and subsequently use the ft_write_data function to write the data to another format that you can specify.

The ft_write_data function requires that you construct a header structure that describes the data (i.e. channel names, sampling frequency) similar to what is returned by ft_read_header. If your data is represented as a FieldTrip raw data structure, i.e. consistent with the documentation in ft_datatype_raw, you can use ft_fetch_header to construct a header on the fly, e.g.

hdr = ft_fetch_header(data);

If your data is continuous and hence the data structure contains only a single (very long) trial do:

dat = data.trial{1};
ft_write_data('yourfile.ext', dat, 'header', hdr, ...)

If you want to write multiple trials, you have to concatenate them and like this:

dat = cat(2,data.trial{:})
ft_write_data('yourfile.ext', dat, 'header', hdr, ...)

Note that in the additional options to ft_write_data you should specify the file format. The ft_write_data function can export data to the following file formats

• edf
• gdf
• brainvision_eeg
• neuralynx_ncs
• neuralynx_sdma
• plexon_nex
• riff_wave
• fcdc_matbin
• fcdc_mysql
• fcdc_buffer
• matlab