Description of SpectrogramBands

0001 function bands = SpectrogramBands(spectrogram,frequencies,varargin)
0002 
0003 %SpectrogramBands - Determine running power in physiological bands.
0004 %
0005 %  USAGE
0006 %
0007 %    bands = SpectrogramBands(spectrogram,frequencies,<options>)
0008 %
0009 %    spectrogram    spectrogram obtained using <a href="matlab:help MTSpectrogram">MTSpectrogram</a>
0010 %    frequencies    frequency bins for spectrogram
0011 %    <options>      optional list of property-value pairs (see table below)
0012 %
0013 %    =========================================================================
0014 %     Properties    Values
0015 %    -------------------------------------------------------------------------
0016 %     'smooth'      smoothing for ratio (0 = no smoothing) (default = 2)
0017 %     'delta'       set delta band (default = [0 4])
0018 %     'theta'       set theta band (default = [7 10])
0019 %     'spindles'    set spindle band (default = [10 20])
0020 %     'lowGamma'    set low gamma band (default = [30 80])
0021 %     'highGamma'   set high gamma band (default = [80 120])
0022 %     'ripples'     set ripple band (default = [100 250])
0023 %     'broadLow'    set broad low frequency band (default = [1 12])
0024 %     'amyGamma'    set amygdala gamma band (default = [45 65])
0025 %    =========================================================================
0026 %
0027 %  OUTPUT
0028 %
0029 %    bands.delta      delta power
0030 %    bands.theta      theta power
0031 %    bands.spindles   spindle power
0032 %    bands.lowGamma   low gamma power
0033 %    bands.highGamma  high gamma power
0034 %    bands.ripples    ripple power
0035 %    bands.broadLow   broad low frequency power
0036 %    bands.amyGamma   amygdala gamma power
0037 %
0038 %    bands.ratios.hippocampus      theta/delta ratio
0039 %    bands.ratios.cortex           [0.5 4.5]/[0.5 9] and [0.5 20]/[0.5 55]
0040 %    bands.ratios.amygdala         gamma/broad low ratio
0041 %
0042 %    Heuristic ratios for cortex are from Gervasoni et al. (2004).
0043 %
0044 %  SEE
0045 %
0046 %    See also MTSpectrogram.
0047 
0048 % Copyright (C) 2004-2014 by Michaël Zugaro, Gabrielle Girardeau
0049 %
0050 % This program is free software; you can redistribute it and/or modify
0051 % it under the terms of the GNU General Public License as published by
0052 % the Free Software Foundation; either version 3 of the License, or
0053 % (at your option) any later version.
0054 
0055 % Defaults
0056 smooth = 2;
0057 delta = [0 4];
0058 theta = [7 10];
0059 spindles = [10 20];
0060 lowGamma = [30 80];
0061 highGamma = [80 120];
0062 ripples = [100 250];
0063 broadLow = [1 12];
0064 amyGamma = [45 65];
0065 
0066 % Check number of parameters
0067 if nargin < 2,
0068   error('Incorrect number of parameters (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0069 end
0070 
0071 % Check parameter sizes
0072 if ~isdmatrix(spectrogram),
0073     error('Parameter ''spectrogram'' is not a matrix (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0074 end
0075 if ~isdvector(frequencies) | length(frequencies) ~= size(spectrogram,1),
0076     error('Parameter ''frequencies'' is not a vector or does not match spectrogram size (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0077 end
0078 
0079 % Parse options
0080 for i = 1:2:length(varargin),
0081     if ~ischar(varargin{i}),
0082         error(['Parameter ' num2str(i) ' is not a property (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).']);
0083     end
0084     switch(lower(varargin{i})),
0085         case 'smooth',
0086             smooth = varargin{i+1};
0087             if ~isdscalar(smooth,'>=0'),
0088                 error('Incorrect value for property ''smooth'' (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0089             end
0090         case 'delta',
0091             delta = varargin{i+1};
0092             if ~isdvector(delta,'>=0','<','#2'),
0093                 error('Incorrect value for property ''delta'' (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0094             end
0095         case 'theta',
0096             theta = varargin{i+1};
0097             if ~isdvector(theta,'>=0','<','#2'),
0098                 error('Incorrect value for property ''theta'' (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0099             end
0100         case 'spindles',
0101             spindles = varargin{i+1};
0102             if ~isdvector(spindles,'>=0','<','#2'),
0103                 error('Incorrect value for property ''spindles'' (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0104             end
0105         case 'lowgamma',
0106             lowGamma = varargin{i+1};
0107             if ~isdvector(lowGamma,'>=0','<','#2'),
0108                 error('Incorrect value for property ''lowGamma'' (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0109             end
0110         case 'highgamma',
0111             highGamma = varargin{i+1};
0112             if ~isdvector(highGamma,'>=0','<','#2'),
0113                 error('Incorrect value for property ''highGamma'' (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0114             end
0115         case 'ripples',
0116             ripples = varargin{i+1};
0117             if ~isdvector(ripples,'>=0','<','#2'),
0118                 error('Incorrect value for property ''ripples'' (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0119             end
0120         case 'broadlow',
0121             broadLow = varargin{i+1};
0122             if ~isdvector(broadLow,'>=0','<','#2'),
0123                 error('Incorrect value for property ''broadLow'' (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0124             end
0125         case 'amygamma',
0126             amyGamma = varargin{i+1};
0127             if ~isdvector(amyGamma,'>=0','<','#2'),
0128                 error('Incorrect value for property ''amyGamma'' (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).');
0129             end
0130         otherwise,
0131             error(['Unknown property ''' num2str(varargin{i}) ''' (type ''help <a href="matlab:help SpectrogramBands">SpectrogramBands</a>'' for details).']);
0132     end
0133 end
0134 
0135 n = size(spectrogram,1);
0136 
0137 % Select relevant frequency bins
0138 thetaBins = frequencies >= theta(1) & frequencies <= theta(2);
0139 deltaBins = frequencies >= delta(1) & frequencies <= delta(2);
0140 spindleBins = frequencies >= spindles(1) & frequencies <= spindles(2);
0141 lowGammaBins = frequencies >= lowGamma(1) & frequencies <= lowGamma(2);
0142 highGammaBins = frequencies >= highGamma(1) & frequencies <= highGamma(2);
0143 rippleBins = frequencies >= ripples(1) & frequencies <= ripples(2);
0144 broadLowBins = frequencies >= broadLow(1) & frequencies <= broadLow(2);
0145 amyGammaBins = frequencies >= amyGamma(1) & frequencies <= amyGamma(2);
0146 
0147 % Compute physiological bands
0148 bands.theta = mean(spectrogram(thetaBins,:))';
0149 bands.delta = mean(spectrogram(deltaBins,:))';
0150 bands.spindles = mean(spectrogram(spindleBins,:))';
0151 bands.lowGamma = mean(spectrogram(lowGammaBins,:))';
0152 bands.highGamma = mean(spectrogram(highGammaBins,:))';
0153 bands.ripples = mean(spectrogram(rippleBins,:))';
0154 bands.broadLow = mean(spectrogram(broadLowBins,:))';
0155 bands.amyGamma = mean(spectrogram(amyGammaBins,:))';
0156 
0157 % Theta/delta ratio
0158 bands.ratios.hippocampus = Smooth(bands.theta./(bands.delta+eps),smooth);
0159 bands.ratio = bands.ratios.hippocampus;
0160 
0161 % Heuristic ratios from Gervasoni et al. (2004)
0162 range1 = [0.5 4.5];
0163 bins1 = frequencies >= range1(1) & frequencies <= range1(2);
0164 band1 =  mean(spectrogram(bins1,:))';
0165 range2 = [0.5 9];
0166 bins2 = frequencies >= range2(1) & frequencies <= range2(2);
0167 band2 =  mean(spectrogram(bins2,:))';
0168 bands.ratios.cortex(:,1) = Smooth(band1./(band2+eps),smooth);
0169 bands.ratio1 = bands.ratios.cortex;
0170 
0171 range1 = [0.5 20];
0172 bins1 = frequencies >= range1(1) & frequencies <= range1(2);
0173 band1 =  mean(spectrogram(bins1,:))';
0174 range2 = [0.5 55];
0175 bins2 = frequencies >= range2(1) & frequencies <= range2(2);
0176 band2 =  mean(spectrogram(bins2,:))';
0177 bands.ratios.cortex(:,2) = Smooth(band1./(band2+eps),smooth);
0178 bands.ratio2 = bands.ratios.cortex(:,2);
0179 
0180 % Amygdala ratio
0181 bands.ratios.amygdala = Smooth(bands.amyGamma./(bands.broadLow+eps),smooth);
0182 bands.ratio3 = bands.ratios.amygdala;
SpectrogramBands

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SOURCE CODE
