baseline_tfrGND() - Baselines the spectrograms in a tfrGND variable.
Usage:
>> tfrGND=baseline_tfrGND(tfrGND,units,bsln_wind,bsln_type);
Required Inputs:
tfrGND - A MATLABmk tfrGND variable. These are produced by the
MATLABmk function tfrs2tfrGND.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.
>> tfrGND=baseline_tfrGND(tfrGND,'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.
>> tfrGND=baseline_tfrGND(tfrGND,'raw',[-500 0],'relative',1);
Just converting to dB (no change of baseline). All bins will be
affected.
>> tfrGND=baseline_tfrGND(tfrGND,'dB',[],[]);
Author:
David Groppe
Kutaslab, 4/20110001 % baseline_tfrGND() - Baselines the spectrograms in a tfrGND variable. 0002 % 0003 % Usage: 0004 % >> tfrGND=baseline_tfrGND(tfrGND,units,bsln_wind,bsln_type); 0005 % 0006 % Required Inputs: 0007 % tfrGND - A MATLABmk tfrGND variable. These are produced by the 0008 % MATLABmk function tfrs2tfrGND.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 % 0032 % Notes: 0033 % -If you transform a subset of bins in the TFR variable, the baseline 0034 % fields of the TFR variable will be set to 'may vary across bins'. 0035 % 0036 % 0037 % Examples: 0038 % Using a relative baseline with a baseline window of -500 to 0 ms and raw 0039 % spectral power. All bins will be affected. 0040 % >> tfrGND=baseline_tfrGND(tfrGND,'raw',[-500 0],'relative'); 0041 % 0042 % Using a relative baseline with a baseline window of -500 to 0 ms and raw 0043 % spectral power. Only Bin 1 will be affected. 0044 % >> tfrGND=baseline_tfrGND(tfrGND,'raw',[-500 0],'relative',1); 0045 % 0046 % Just converting to dB (no change of baseline). All bins will be 0047 % affected. 0048 % >> tfrGND=baseline_tfrGND(tfrGND,'dB',[],[]); 0049 % 0050 % 0051 % Author: 0052 % David Groppe 0053 % Kutaslab, 4/2011 0054 0055 0056 % Notes: 0057 % How baseling could be done with the Fieldtrip function ft_freqbaseline 0058 % 1. Set up configuration parameters 0059 % cfg.baseline=[-.5 0]; 0060 % cfg.baselinetype='absolute'; 0061 % 0062 % 2. Extract data for this subject, sub, and bin, b. 0063 % data.powspctrm=squeeze(tfrGND.indiv{b}(sub,:,:,:)); 0064 % 0065 % 3. Baseline data 0066 % data=ft_freqbaseline(cfg,data); 0067 % 0068 % 4. Replace old data with baselined data 0069 % tfrGND.indiv{b}(sub,:,:,:)=data.powspctrm; 0070 0071 function tfrGND=baseline_tfrGND(tfrGND,units,bsln_wind,bsln_type,bin) 0072 0073 n_sub=size(tfrGND.indiv{1},1); 0074 n_bin=length(tfrGND.indiv); 0075 n_tpt=length(tfrGND.ftrip.time); 0076 changed=0; 0077 0078 %Error check bin argument 0079 if nargin<5, 0080 %if bin argument not specified, use all bins 0081 use_bins=1:n_bin; 0082 else 0083 if min(bin)<1, 0084 error('All elements of argument bin must be greater than 0.'); 0085 elseif max(bin)>n_bin, 0086 error('You can''t baseline Bin %d. This TFR variable only has % bins.',max(bin),n_bin); 0087 elseif ~isequal(bin,round(bin)), 0088 error('All elements of argument bin need to be integers.'); 0089 end 0090 use_bins=bin; 0091 end 0092 0093 %Make sure user isn't trying to unbaseline data 0094 if strcmpi(bsln_type,'none') && ~strcmpi(tfrGND.bsln_type,'none'), 0095 error('You can''t unbaseline data that have already been baselined.'); 0096 end 0097 0098 %If not specified as input arguments, using current values in tfrGND variable 0099 if isempty(units), 0100 units=tfrGND.units; 0101 end 0102 if isempty(bsln_wind), 0103 bsln_wind=tfrGND.bsln_wind; 0104 end 0105 if isempty(bsln_type), 0106 bsln_type=tfrGND.bsln_type; 0107 end 0108 0109 % First adjust units if necessary 0110 if ~strcmpi(units,tfrGND.units) 0111 changed=1; 0112 if strcmpi(tfrGND.units,'dB'), 0113 fprintf('Temporarily transforming tfrGND data from dB to raw power.\n'); 0114 if ~strcmpi(tfrGND.bsln_type,'none'), 0115 watchit(sprintf(['Since the data in this tfrGND variable were originally baselined, \n', ... 0116 'converting them to raw power from dB will produce somewhat different values than if you had initially created the tfrGND variable in units of raw power'])); 0117 end 0118 for b=use_bins, 0119 for sub=1:n_sub, 0120 tfrGND.indiv{b}(sub,:,:,:)=10.^(tfrGND.indiv{b}(sub,:,:,:)/10); 0121 end 0122 end 0123 tfrGND.units='raw'; 0124 else 0125 fprintf('Temporarily transforming tfrGND data from raw to dB power.\n'); 0126 if ~strcmpi(tfrGND.bsln_type,'none'), 0127 watchit(sprintf(['Since the data in this tfrGND variable were originally baselined, \n', ... 0128 'converting them to dB will produce somewhat different values than if you had converted the data to dB before baselining.'])); 0129 end 0130 for b=use_bins, 0131 for sub=1:n_sub, 0132 tfrGND.indiv{b}(sub,:,:,:)=10*log10(tfrGND.indiv{b}(sub,:,:,:)); 0133 end 0134 end 0135 tfrGND.units='dB'; 0136 end 0137 end 0138 0139 0140 % Next adjust baseline if necessary 0141 if ~isequal(bsln_wind,tfrGND.bsln_wind) || ~strcmpi(bsln_type,tfrGND.bsln_type) 0142 changed=1; 0143 0144 %error checking 0145 if strcmpi(bsln_type,'none'), 0146 error('You cannot un-baseline spectrograms once they''ve been baselined.'); 0147 end 0148 if isempty(bsln_wind), 0149 error('You cannot specify a baseline type without a baseline time window.'); 0150 end 0151 if bsln_wind(2)<bsln_wind(1), 0152 error('The start of your baseline time window, %g, is after the end of your baseline time window, %g\n', ... 0153 bsln_wind(1),bsln_wind(2)); 0154 end 0155 0156 %find time points to use for baselining 0157 start_tpt=find(tfrGND.ftrip.time<(bsln_wind(1)/1000)); %converting from ms to sec 0158 end_tpt=find(tfrGND.ftrip.time<=(bsln_wind(2)/1000)); %converting from ms to sec 0159 if isempty(start_tpt) 0160 if ~isempty(end_tpt), 0161 start_tpt=0; 0162 else 0163 error('The starting point of your baseline time window is earlier than the earliest time point in this tfrGND variable, %g.\n', ... 0164 tfrGND.ftrip.time(1)*1000); 0165 end 0166 end 0167 start_tpt=start_tpt(end)+1; 0168 end_tpt=end_tpt(end); 0169 0170 bsln_tpts=start_tpt:end_tpt; 0171 if isempty(bsln_tpts), 0172 error('The basline time window you specified does not include any time points in this tfrGND variable.'); 0173 end 0174 fprintf('Baseline time window is from %g to %g ms\n',tfrGND.ftrip.time(start_tpt)*1000, ... 0175 tfrGND.ftrip.time(end_tpt)*1000); %converting from sec to ms 0176 0177 for b=use_bins, 0178 for sub=1:n_sub, 0179 fprintf('Baselining data for Bin %d, Participant %d\n',b,sub); 0180 mn_in_wind=mean(tfrGND.indiv{b}(sub,:,:,start_tpt:end_tpt),4); 0181 if strcmpi(bsln_type,'absolute') 0182 tfrGND.indiv{b}(sub,:,:,:)=tfrGND.indiv{b}(sub,:,:,:)-repmat(mn_in_wind,[1 1 1 n_tpt]); 0183 else 0184 %relative baseline 0185 tfrGND.indiv{b}(sub,:,:,:)=tfrGND.indiv{b}(sub,:,:,:)./repmat(mn_in_wind,[1 1 1 n_tpt]); 0186 end 0187 end 0188 end 0189 tfrGND.bsln_wind=bsln_wind; 0190 tfrGND.bsln_type=bsln_type; 0191 end 0192 0193 0194 %reaverage grands 0195 for b=use_bins, 0196 fprintf('Recomputing grand averages for bin %d.\n',b); 0197 tfrGND.grands{b}=squeeze(mean(tfrGND.indiv{b},1)); 0198 end 0199 0200 %Indicate tfrGND variable hasn't been saved since last change 0201 if changed, 0202 tfrGND.saved='no'; 0203 end 0204 0205 %If only a subset of bins transformed, indicate this 0206 if ~isequal(use_bins,1:n_bin), 0207 tfrGND.bsln_type='may vary across bins'; 0208 tfrGND.bsln_wind='may vary across bins'; 0209 tfrGND.units='may vary across bins'; 0210 end