Getting started with Blackrock data
FIXME This getting started guide and the reading code are still under development, see http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2964. However, we very much welcome you to start using this functionality, and would be happy with any feedback provided.
The specifications of this data format can be found on the company’s website. Basically, the files come in 2 flavors. One type of file has as extension .nev, and contains information about extracellularly recorded spiking activity. The other file type has as extension .nsX, with X any number between 1 and 9. These files contain continuously sampled data (e.g. Local Field Potentials).
To read Blackrock data into FieldTrip, you will need the NPMK toolbox. The latest version of it can be cloned from github: https://github.com/BlackrockMicrosystems/NPMK. This is a MATLAB-toolbox provided by Blackrock microsystems. FieldTrip relies on the low-level reading functionality of this code. Make sure that the .m files in the NPMK toolbox are on the MATLAB path.
To get started, you should add the FieldTrip main directory to your path, and execute the ft_defaults function, which sets the defaults and configures up the minimal required path settings. See also this frequently asked question.
addpath `<full_path_to_fieldtrip>` ft_defaults
Reading header information
To read header information, use
filename = 'your_cyberkinetics_file.nev'; hdr = ft_read_header(filename, 'headerformat', 'neuroshare');
This calls the NPMK toolbox and gives back the header structure in FieldTrip format, which includes the original header information (included as hdr.orig) as retrieved with the neuroshare functions openNSx or openNEV.
Reading triggers and other events
To read events, use
filename = 'your_datafile'; event = ft_read_event(filename, 'eventformat', 'neuroshare');
TO BE DONE.
Reading LFP data
To read analog data, use
filename = 'your_datafile.ns1'; data = ft_read_data(filename);
This calls the NPMK toolbox (using the function openNSx) and gives back a data structure in FieldTrip format.
Optional input arguments should be specified in key-value pairs and may includ
% 'chanindx' = list with channel indices to read % 'begsample = first sample to read % 'endsample = last sample to read
TO BE DONE.
Reading spike data
To read spike data, use
filename = 'your_cyberkinetics_file.nev'; spike = ft_read_spike(filename, 'spikeformat', 'neuroshare');
TO BE DONE.
- http://www.blackrockmicro.com Blackrock Microsystems (formerly the Research Products Division of Cyberkinetics Inc.)