baseline_TFR() - Baselines the spectrograms in a TFR variable.
Usage:
>> TFR=baseline_TFR(TFR,units,bsln_wind,bsln_type,bin);
Required Inputs:
TFR - A MATLABmk TFR variable. These are produced by the
MATLABmk function set2tfr.m. It contains spectrograms from
one or more participants, their grand averages, and
associated information.
units - ['raw' or 'dB' or empty set] 'raw' is raw spectral power
(which is in units of (uV^2)/Hz). 'dB' is decibels (units
of 10*log10((uV^2)/Hz)). Provide the empty set (i.e., [])
to keep units the same as they currently are.
bsln_wind - [start_time end_time] Temporal boundaries of baseline
window (in units of ms). Provide the empty set (i.e., [])
to keep baseline window the same as it currently is.
bsln_type - ['absolute', 'relative', or empty] Type of baseline
normalization. If 'absolute', the mean power in the
baseline window is subtracted from the rest of the time
points. If 'relative', the mean power in the baseline
window is divided from the rest of the time points. Provide
the empty set (i.e., []) to keep baseline type the same as
it currently is.
Optional Inputs:
bin - [integer or vector of integers] The bin or bins you would
like to transform. If not specified, all bins will be
transformed.
Notes:
-If you transform a subset of bins in the TFR variable, the baseline
fields of the TFR variable will be set to 'may vary across bins'.
Examples:
Using a relative baseline with a baseline window of -500 to 0 ms and raw
spectral power. All bins will be affected.
>> TFR=baseline_TFR(TFR,'raw',[-500 0],'relative');
Using a relative baseline with a baseline window of -500 to 0 ms and raw
spectral power. Only Bin 1 will be affected.
>> TFR=baseline_TFR(TFR,'raw',[-500 0],'relative',1);
Just converting to dB (no change of baseline). All bins will be affected.
>> TFR=baseline_TFR(TFR,'dB',[],[]);
Author:
David Groppe
Kutaslab, 4/20110001 % baseline_TFR() - Baselines the spectrograms in a TFR variable. 0002 % 0003 % Usage: 0004 % >> TFR=baseline_TFR(TFR,units,bsln_wind,bsln_type,bin); 0005 % 0006 % Required Inputs: 0007 % TFR - A MATLABmk TFR variable. These are produced by the 0008 % MATLABmk function set2tfr.m. It contains spectrograms from 0009 % one or more participants, their grand averages, and 0010 % associated information. 0011 % units - ['raw' or 'dB' or empty set] 'raw' is raw spectral power 0012 % (which is in units of (uV^2)/Hz). 'dB' is decibels (units 0013 % of 10*log10((uV^2)/Hz)). Provide the empty set (i.e., []) 0014 % to keep units the same as they currently are. 0015 % bsln_wind - [start_time end_time] Temporal boundaries of baseline 0016 % window (in units of ms). Provide the empty set (i.e., []) 0017 % to keep baseline window the same as it currently is. 0018 % bsln_type - ['absolute', 'relative', or empty] Type of baseline 0019 % normalization. If 'absolute', the mean power in the 0020 % baseline window is subtracted from the rest of the time 0021 % points. If 'relative', the mean power in the baseline 0022 % window is divided from the rest of the time points. Provide 0023 % the empty set (i.e., []) to keep baseline type the same as 0024 % it currently is. 0025 % 0026 % Optional Inputs: 0027 % bin - [integer or vector of integers] The bin or bins you would 0028 % like to transform. If not specified, all bins will be 0029 % transformed. 0030 % 0031 % Notes: 0032 % -If you transform a subset of bins in the TFR variable, the baseline 0033 % fields of the TFR variable will be set to 'may vary across bins'. 0034 % 0035 % 0036 % Examples: 0037 % Using a relative baseline with a baseline window of -500 to 0 ms and raw 0038 % spectral power. All bins will be affected. 0039 % >> TFR=baseline_TFR(TFR,'raw',[-500 0],'relative'); 0040 % 0041 % Using a relative baseline with a baseline window of -500 to 0 ms and raw 0042 % spectral power. Only Bin 1 will be affected. 0043 % >> TFR=baseline_TFR(TFR,'raw',[-500 0],'relative',1); 0044 % 0045 % Just converting to dB (no change of baseline). All bins will be affected. 0046 % >> TFR=baseline_TFR(TFR,'dB',[],[]); 0047 % 0048 % 0049 % Author: 0050 % David Groppe 0051 % Kutaslab, 4/2011 0052 0053 0054 % Notes: 0055 % How baseling could be done with the FieldTrip function ft_freqbaseline 0056 % 1. Set up configuration parameters 0057 % cfg.baseline=[-.5 0]; 0058 % cfg.baselinetype='absolute'; 0059 % 0060 % 2. Baseline data in Bin 1 0061 % TFR.bins{1}=ft_freqbaseline(cfg,TFR.bins{1}); 0062 % 0063 0064 function TFR=baseline_TFR(TFR,units,bsln_wind,bsln_type,bin) 0065 0066 n_bin=length(TFR.bins); 0067 n_tpt=length(TFR.bins{1}.time); 0068 changed=0; 0069 0070 %Error check bin argument 0071 if nargin<5, 0072 %if bin argument not specified, use all bins 0073 use_bins=1:n_bin; 0074 else 0075 if min(bin)<1, 0076 error('All elements of argument bin must be greater than 0.'); 0077 elseif max(bin)>n_bin, 0078 error('You can''t baseline Bin %d. This TFR variable only has % bins.',max(bin),n_bin); 0079 elseif ~isequal(bin,round(bin)), 0080 error('All elements of argument bin need to be integers.'); 0081 end 0082 use_bins=bin; 0083 end 0084 0085 %Make sure user isn't trying to unbaseline data 0086 if strcmpi(bsln_type,'none') && ~strcmpi(TFR.bsln_type,'none'), 0087 error('You can''t unbaseline data that have already been baselined.'); 0088 end 0089 0090 %If not specified as input arguments, using current values in TFR variable 0091 if isempty(units), 0092 units=TFR.units; 0093 end 0094 if isempty(bsln_wind), 0095 bsln_wind=TFR.bsln_wind; 0096 end 0097 if isempty(bsln_type), 0098 bsln_type=TFR.bsln_type; 0099 end 0100 0101 % First adjust units if necessary 0102 if ~strcmpi(units,TFR.units) 0103 changed=1; 0104 if strcmpi(TFR.units,'dB'), 0105 fprintf('Temporarily transforming TFR data from dB to raw power.\n'); 0106 if ~strcmpi(TFR.bsln_type,'none'), 0107 watchit(sprintf(['Since the data in this TFR variable were originally baselined, \n', ... 0108 'converting them to raw power from dB will produce somewhat different values than if you had initially created the TFR variable in units of raw power'])); 0109 end 0110 for b=use_bins, 0111 TFR.bins{b}.powspctrm=10.^(TFR.bins{b}.powspctrm/10); 0112 end 0113 TFR.units='raw'; 0114 else 0115 fprintf('Temporarily transforming TFR data from raw to dB power.\n'); 0116 if ~strcmpi(TFR.bsln_type,'none'), 0117 watchit(sprintf(['Since the data in this TFR variable were originally baselined, \n', ... 0118 'converting them to dB will produce somewhat different values than if you had converted the data to dB before baselining.'])); 0119 end 0120 for b=use_bins, 0121 TFR.bins{b}.powspctrm=10*log10(TFR.bins{b}.powspctrm); 0122 end 0123 TFR.units='dB'; 0124 end 0125 end 0126 0127 0128 % Next adjust baseline if necessary 0129 if ~isequal(bsln_wind,TFR.bsln_wind) || ~strcmpi(bsln_type,TFR.bsln_type) 0130 changed=1; 0131 0132 %error checking 0133 if strcmpi(bsln_type,'none'), 0134 error('You cannot un-baseline spectrograms once they''ve been baselined.'); 0135 end 0136 if isempty(bsln_wind), 0137 error('You cannot specify a baseline type without a baseline time window.'); 0138 end 0139 if bsln_wind(2)<bsln_wind(1), 0140 error('The start of your baseline time window, %g, is after the end of your baseline time window, %g\n', ... 0141 bsln_wind(1),bsln_wind(2)); 0142 end 0143 0144 %find time points to use for baselining 0145 start_tpt=find(TFR.bins{1}.time<(bsln_wind(1)/1000)); %converting from ms to sec 0146 end_tpt=find(TFR.bins{1}.time<=(bsln_wind(2)/1000)); %converting from ms to sec 0147 if isempty(start_tpt) 0148 if ~isempty(end_tpt), 0149 start_tpt=0; 0150 else 0151 error('The starting point of your baseline time window is earlier than the earliest time point in this TFR variable, %g.\n', ... 0152 TFR.bins{1}.time(1)*1000); 0153 end 0154 end 0155 start_tpt=start_tpt(end)+1; 0156 end_tpt=end_tpt(end); 0157 0158 bsln_tpts=start_tpt:end_tpt; 0159 if isempty(bsln_tpts), 0160 error('The basline time window you specified does not include any time points in this TFR variable.'); 0161 end 0162 fprintf('Baseline time window is from %g to %g ms\n',TFR.bins{1}.time(start_tpt)*1000, ... 0163 TFR.bins{1}.time(end_tpt)*1000); %converting from sec to ms 0164 0165 for b=use_bins, 0166 fprintf('Baselining data for Bin %d\n',b); 0167 mn_in_wind=mean(TFR.bins{b}.powspctrm(:,:,start_tpt:end_tpt),3); 0168 if strcmpi(bsln_type,'absolute') 0169 TFR.bins{b}.powspctrm=TFR.bins{b}.powspctrm-repmat(mn_in_wind,[1 1 n_tpt]); 0170 else 0171 %relative baseline 0172 TFR.bins{b}.powspctrm=TFR.bins{b}.powspctrm./repmat(mn_in_wind,[1 1 n_tpt]); 0173 end 0174 end 0175 TFR.bsln_wind=bsln_wind; 0176 TFR.bsln_type=bsln_type; 0177 end 0178 0179 0180 %Indicate TFR variable hasn't been saved since last change 0181 if changed, 0182 TFR.saved='no'; 0183 end 0184 0185 %If only a subset of bins transformed, indicate this 0186 if ~isequal(use_bins,1:n_bin), 0187 TFR.bsln_type='may vary across bins'; 0188 TFR.bsln_wind='may vary across bins'; 0189 TFR.units='may vary across bins'; 0190 end