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Nlx2MatSpike.m
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Nlx2MatSpike.m
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% NLX2MATSPIKE Imports data from Neuralynx NSE, NST and NTT files to Matlab variables.
%
% [Timestamps, ScNumbers, CellNumbers, Features, Samples, Header] =
% Nlx2MatSpike( Filename, FieldSelectionFlags,
% HeaderExtractionFlag, ExtractMode, ExtractionModeVector);
%
% Version 6.0.0
%
% Requires MATLAB R2012b (8.0) or newer
%
%
% INPUT ARGUMENTS:
% FileName: String containing either the complete ('C:\CheetahData\
% SE1.nse') or relative ('SE1.nse') path of the file you wish
% to import.
% FieldSelectionFlags: Vector with each item being either a zero (excludes
% data) or a one (includes data) that determines which
% data will be returned for each record. The order of
% the items in the vector correspond to the following:
% FieldSelectionFlags(1): Timestamps
% FieldSelectionFlags(2): Spike Channel Numbers
% FieldSelectionFlags(3): Cell Numbers
% FieldSelectionFlags(4): Spike Features
% FieldSelectionFlags(5): Samples
% EXAMPLE: [1 0 0 0 1] imports timestamp and samples
% data from each record and excludes all other data.
% HeaderExtractionFlag: Either a zero if you do not want to import the header
% or a one if header import is desired..
% ExtractionMode: A number indicating how records will be processed during
% import. The numbers and their effect are described below:
% 1 (Extract All): Extracts data from every record in
% the file.
% 2 (Extract Record Index Range): Extracts every record
% whose index is within a range.
% 3 (Extract Record Index List): Extracts a specific list
% of records based on record index.
% 4 (Extract Timestamp Range): Extracts every record whose
% timestamp is within a range of timestamps.
% 5 (Extract Timestamp List): Extracts a specific list of
% records based on their timestamp.
% ExtractionModeVector: The contents of this vector varies based on the
% ExtractionMode. Each extraction mode is listed with
% a description of the ExtractionModeVector contents.
% 1 (Extract All): The vector value is ignored.
% 2 (Extract Record Index Range): A vector of two indices,
% in increasing order, indicating a range of records to
% extract. A record index is the number of the record in
% the file in temporal order (i.e. first record is index
% 1, second is 2, etc.). This range is inclusive of the
% beginning and end indices. If the last record in the
% range is larger than the number of records in the
% file, all records until the end of the file will be
% extracted.
% EXAMPLE: [10 50] imports the 10th record through the
% 50th record (total of 41 records) of the file.
% 3 (Extract Record Index List): A vector of indices
% indicating individual records to extract. A record
% index is the number of the record in the file in
% temporal order (i.e. first record is index
% 1, second is 2, etc.). Data will be extracted in the
% order specified by this vector. If an index in the
% vector is less than 1 or greater than the number of
% records in the file, the index will be skipped.
% EXAMPLE: [7 10 1] imports record 7 then 10 then 1,
% it is not sorted temporally
% 4 (Extract Timestamp Range): A vector of two timestamps,
% in increasing order, indicating a range of time to use
% when extracting records. If either of the timestamps
% in the vector are not contained within the timeframe
% of the file, the range will be set to the closest
% valid timestamp (e.g. first or last). The range is
% inclusive of the beginning and end timestamps. If a
% specified timestamp occurs within a record, the entire
% record will be extracted. This means that the first
% record extracted may have a timestamp that occurs
% before the specified start time.
% EXAMPLE: [12500 25012] extracts all records that
% contain data that occurred between the timestamps
% 12500 and 25012, inclusive of data at those times.
% 5 (Extract Timestamp List): A vector of timestamps
% indicating individual records to extract. If a
% specified timestamp occurs within a record, the entire
% record will be extracted. This means that the a record
% extracted may have a timestamp that occurs before the
% specified timestamp. If there is no data available for
% a specified timestamp, the timestamp will be ignored.
% Data will be retrieved in the order specified by this
% vector.
% EXAMPLE: [45032 10125 75000] imports records that
% contain data that occurred at timestamp 45035 then
% 10125 then 75000, it is not sorted temporally.
%
% Notes on output data:
% 1. Each output variable's Nth element corresponds to the Nth element in
% all the other output variables with the exception of the header output
% variable.
% 2. The value of N in the output descriptions below is the total number of
% records extracted.
% 3. For more information on Neuralynx records see:
% http://neuralynx.com/software/NeuralynxDataFileFormats.pdf
% 4. Output data will always be assigned in the order indicated in the
% FieldSelectionFlags. If data is not imported via a FieldSelectionFlags
% index being 0, simply omit the output variable from the command.
% EXAMPLE: FieldSelectionFlags = [1 0 0 0 1];
% [Timestamps,Samples] = Nlx2MatSpike('test.ntt',FieldSelectionFlags,0,1,[]);
%
% OUTPUT VARIABLES:
% Timestamps: A 1xN integer vector of timestamps.
% ScNumbers: A 1xN integer vector of spike channel numbers. This is the order that
% the spike AEs were created and have nothing to do with the
% AD channel number.
% CellNumbers: A 1xN integer vector of classified cell numbers. If no cell was
% classified for this spike, this value will be zero.
% Features: A 8xN integer vector of the features (e.g. Peak, Valley, etc.) calculated
% by Cheetah.
% Samples: A 32xMxN integer matrix of the data points. Where M is the number of
% subchannels in the spike file (NTT M = 4, NST M = 2, NSE M = 1).
% These values are in AD counts.
% Header: A Mx1 string vector of all the text from the Neuralynx file header, where
% M is the number of lines of text in the header.
%
%
% EXAMPLE: [Timestamps, ScNumbers, CellNumbers, Features, Samples, Header] =
% Nlx2MatSpike('test.nst', [1 1 1 1 1], 1, 1, [] );
% Uses extraction mode 1 to return all of the data from all of the records
% in the file test.nst.
%
% EXAMPLE: [Timestamps, Samples, Header] = Nlx2MatSpike('test.ntt',
% [1 0 0 0 1], 1, 2, [14 30]);
% Uses extraction mode 2 to return the Timestamps and Samples at between
% record index 14 and 30 as well as the complete file header.
%