eeg_load_scan3avg

(Toolbox/eeg_load_scan3avg.m in BrainStorm 2.0 (Alpha))

Function Synopsis

[avg] = eeg_load_scan3avg(FILENAME)

Help Text

EEG_LOAD_SCAN3AVG - Read a NeuroScan 3.x AVG File
 function [avg] = eeg_load_scan3avg(FILENAME)

 USEAGE:  [avg] = eeg_load_scan3avg(FILENAME)

   FILENAME     input Neuroscan .avg file (version 3.x)
   avg          output data structure, with fields:
   
   avg.signal      - ERP signal (uV, Npnts x Mchan)
   avg.variance    - variance of the signal (Npnts x Mchan)
   avg.chan_names  - electrode labels
   avg.pnts        - number of points in ERP waveform
   avg.rate        - sample rate (Hz)
   avg.xmin        - prestimulus epoch start (e.g., -100 msec)
   avg.xmax        - poststimulus epoch end (e.g., 900 msec)
   avg.nsweeps     - number of accepted trials/sweeps in avg
   
   e.g.
   avg = eeg_load_scan3avg( 'test.avg' );
   plot( avg.signal );

Cross-Reference Information

eeg2bs                             C:\BrainStorm_2001\Toolbox\eeg2bs.m

Listing of function C:\BrainStorm_2001\Toolbox\eeg_load_scan3avg.m

function [avg] = eeg_load_scan3avg(FILENAME)
%EEG_LOAD_SCAN3AVG - Read a NeuroScan 3.x AVG File
% function [avg] = eeg_load_scan3avg(FILENAME)
%
% USEAGE:  [avg] = eeg_load_scan3avg(FILENAME)
%
%   FILENAME     input Neuroscan .avg file (version 3.x)
%   avg          output data structure, with fields:
%   
%   avg.signal      - ERP signal (uV, Npnts x Mchan)
%   avg.variance    - variance of the signal (Npnts x Mchan)
%   avg.chan_names  - electrode labels
%   avg.pnts        - number of points in ERP waveform
%   avg.rate        - sample rate (Hz)
%   avg.xmin        - prestimulus epoch start (e.g., -100 msec)
%   avg.xmax        - poststimulus epoch end (e.g., 900 msec)
%   avg.nsweeps     - number of accepted trials/sweeps in avg
%   
%   e.g.
%   avg = eeg_load_scan3avg( 'test.avg' );
%   plot( avg.signal );
%

%<autobegin> ---------------------- 12-Oct-2004 01:11:13 -----------------------
% --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
%
% CATEGORY: Database Management
%
% At Check-in: $Author: Mosher $  $Revision: 4 $  $Date: 10/11/04 11:32p $
%
% This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 23-Sep-2004
% 
% Principal Investigators and Developers:
% ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
%    University of Southern California, Los Angeles, CA
% ** John C. Mosher, PhD, Biophysics Group,
%    Los Alamos National Laboratory, Los Alamos, NM
% ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
%    CNRS, Hopital de la Salpetriere, Paris, France
% 
% See BrainStorm website at http://neuroimage.usc.edu for further information.
% 
% Copyright (c) 2004 BrainStorm by the University of Southern California
% This software distributed  under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPL
% license can be found at http://www.gnu.org/copyleft/gpl.html .
% 
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%<autoend> ------------------------ 12-Oct-2004 01:11:13 -----------------------



% $Revision: 4 $ $Date: 10/11/04 11:32p $


% This program is distributed under the GNU GPL; you can redistribute 
% it and/or modify it. This program is distributed in the hope that it 
% will be useful, but WITHOUT ANY WARRANTY; without even the implied 
% warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

% Version 1.1, arno_delorme@salk.edu
% Version 1.2, Darren.Weber@flinders.edu.au
%
% Average data is stored as 4-byte floats in vectored format for each
% channel. Each channel has a 5-byte header that is no longer used. Thus,
% after the main file header, there is an unused 5-byte header followed by
% erp.pnts of 4-byte floating point numbers for the first channel; then a
% 5-byte header for channel two followed by erp.pnts*sizeof(float) bytes,
% etc. Therefore, the total number of bytes after the main header is:
% erp.nchannels * (5 + erp.pnts*sizeof(float)). To scale a data point to
% microvolts, multiply by the channel-specific calibration factor (i.e., for
% electrode j: channel[j]->calib) and divide by the number of sweeps in the
% average (i.e., channel[j]->n).

% UPDATE    version remark
% 1062001   0.1     primitive version based on a C program 
% 1092001   1.0     fully working version based on loadegg.m that I programmed 
% 1102001   1.1     adding channel names loading
% 03/2002   1.2     Darren.Weber@flinders.edu.au
%                   - S_nsweeps_offset from 362 to 364;
%                     so that it finds ACCEPTED not TOTAL SWEEPS, which
%                     has a great impact on conversion to uV.
%                   - modified xmin/xmax to msec from sec.
%                   - modified output to structure with fields
%                   - Changed the name of the function (from loadavg).
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% ------------------------ BrainStorm Script History ---------------------------
% JCM 11-Oct-2004 commenting header
% ------------------------ BrainStorm Script History ---------------------------


if nargin<1,
help eeg_load_scan3avg; return;
end;

fid = fopen(FILENAME,'r','ieee-le');

if fid<0,
    msg = sprintf('EEG_LOAD_SCAN3AVG: Cannot find:\n... %s\n', FILENAME);
    error(msg);
end;

BOOL='int16';
ULONG='int32'; 
FLOAT='float32';

% read # of channels, # of samples, variance flag, and time bounds
% ----------------------------------------------------------------
S_nsweeps_offset    = 364; % Darren Weber modified this from 362
S_pnts_offset       = 368;
S_nchans_offset     = 370;
S_variance_offset   = 375;
S_rate_offset       = 376;
S_xmin_offset       = 505;
S_xmax_offset       = 509;
packed_sizeof_SETUP = 900;

fseek(fid, S_nsweeps_offset, 'bof');    avg.nsweeps = fread(fid, 1, 'ushort');
fseek(fid, S_pnts_offset, 'bof');       avg.pnts = fread(fid, 1, 'ushort');
fseek(fid, S_nchans_offset, 'bof');     chan = fread(fid, 1, 'ushort');
fseek(fid, S_variance_offset, 'bof');   variance_flag = fread(fid, 1, 'uchar');
fseek(fid, S_rate_offset, 'bof');       avg.rate = fread(fid, 1, 'ushort');
fseek(fid, S_xmin_offset, 'bof');       avg.xmin = fread(fid, 1, 'float32') * 1000;
fseek(fid, S_xmax_offset, 'bof');       avg.xmax = fread(fid, 1, 'float32') * 1000;
fseek(fid, packed_sizeof_SETUP, 'bof');

fprintf('number of channels : %d\n', chan);
fprintf('number of points   : %d\n', avg.pnts);
fprintf('sampling rate (Hz) : %f\n', avg.rate);
fprintf('xmin (msec)        : %f\n', avg.xmin);
fprintf('xmax (msec)        : %f\n', avg.xmax);
fprintf('Accepted sweeps    : %d\n', avg.nsweeps);

% read electrode configuration
% ----------------------------
fprintf('Electrode configuration\n');
for elec = 1:chan,
    channel_label_tmp = fread(fid, 10, 'uchar');
    avg.chan_names(elec,:) = channel_label_tmp';
    for index = 2:9,
        if avg.chan_names(elec,index) == 0,
            avg.chan_names(elec,index) = ' ';
        end;
    end;
    erp = fread(fid, 47-10, 'uchar');
    baseline(elec) = fread(fid, 1, 'ushort');
    erp = fread(fid, 10, 'uchar');
    sensitivity(elec) = fread(fid, 1, 'float32');
    erp = fread(fid, 8, 'uchar');
    calib(elec) = fread(fid, 1, 'float32');
    fprintf('%s: baseline: %d\tsensitivity: %f\tcalibration: %f\n', avg.chan_names(elec,1:4), baseline(elec), sensitivity(elec), calib(elec));
    factor(elec) = calib(elec) * sensitivity(elec) / 204.8;
end;

% Read signal data (amplifier units)
signal = zeros(avg.pnts, chan);
for elec = 1:chan,
    fseek(fid, 5, 'cof'); % skip sweeps header
    signal(:, elec) = fread(fid, avg.pnts, 'float32');
end;

if variance_flag,
    variance = zeros(avg.pnts, chan);
    for elec = 1:chan,
        variance(:, elec) = fread(fid, avg.pnts, 'float32');
    end;
    avg.variance = variance';
else
    avg.variance = [];
end;

% Convert signal to microvolts
baseline = repmat(baseline,avg.pnts,1);
calib    = repmat(calib,   avg.pnts,1);

if avg.nsweeps,
    signal = (signal - baseline) .* calib ./ avg.nsweeps;
else
    signal = (signal - baseline) .* calib;
end

avg.signal = signal';

fclose(fid);
return;