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# 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

This function is called by

    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;

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