remove_artifact_ics() - Removes the independent components (ICs) of an
EEGLAB "EEG" variable that have been labeled as an
artifact in EEG.ic_labels or EEG.reject.gcompreject.
The artifacts are removed from EEG.data and
EEG.data is optionally baselined. Artifact
status of labels in EEG.ic_labels is based on
is_art.m. Note that EEG.ic_labels is a field
unique to Kutaslab data.
Usage:
>> art_ics=remove_artifact_ics(bsln_wind,verblevel);
Required Global Variable:
EEG - EEGLAB EEG variable. EEG.data field will be modified by this
function.
Optional Inputs:
bsln_wind - [start_time stop_time or NaN] Two element vector specifying
baseline window in milliseconds or NaN. If NaN, data are
not baselined. Otherwise, the mean EEG at each channel and
epoch in this window will be removed from each epoch.
verblevel - an integer specifiying the amount of information you want
functions to provide about what they are doing during runtime.
Options are:
0 - quiet, only show errors, warnings, and EEGLAB reports
1 - stuff anyone should probably know
2 - stuff you should know the first time you start working
with a data set {default value if not already globally
specified}
3 - stuff that might help you debug (show all
reports)
Outputs:
art_ics - [integer vector] Indices of ICs labeled as artifacts
Author:
David Groppe
Kutaslab, 9/20100001 % remove_artifact_ics() - Removes the independent components (ICs) of an 0002 % EEGLAB "EEG" variable that have been labeled as an 0003 % artifact in EEG.ic_labels or EEG.reject.gcompreject. 0004 % The artifacts are removed from EEG.data and 0005 % EEG.data is optionally baselined. Artifact 0006 % status of labels in EEG.ic_labels is based on 0007 % is_art.m. Note that EEG.ic_labels is a field 0008 % unique to Kutaslab data. 0009 % 0010 % 0011 % Usage: 0012 % >> art_ics=remove_artifact_ics(bsln_wind,verblevel); 0013 % 0014 % Required Global Variable: 0015 % EEG - EEGLAB EEG variable. EEG.data field will be modified by this 0016 % function. 0017 % 0018 % Optional Inputs: 0019 % bsln_wind - [start_time stop_time or NaN] Two element vector specifying 0020 % baseline window in milliseconds or NaN. If NaN, data are 0021 % not baselined. Otherwise, the mean EEG at each channel and 0022 % epoch in this window will be removed from each epoch. 0023 % verblevel - an integer specifiying the amount of information you want 0024 % functions to provide about what they are doing during runtime. 0025 % Options are: 0026 % 0 - quiet, only show errors, warnings, and EEGLAB reports 0027 % 1 - stuff anyone should probably know 0028 % 2 - stuff you should know the first time you start working 0029 % with a data set {default value if not already globally 0030 % specified} 0031 % 3 - stuff that might help you debug (show all 0032 % reports) 0033 % 0034 % Outputs: 0035 % art_ics - [integer vector] Indices of ICs labeled as artifacts 0036 % 0037 % 0038 % Author: 0039 % David Groppe 0040 % Kutaslab, 9/2010 0041 0042 % Changes 0043 % 8/23/2012 - NaN now a possible value for bsln_wind to avoid any 0044 % baselining 0045 0046 function art_ics=remove_artifact_ics(bsln_wind,verblevel) 0047 0048 global EEG; 0049 global VERBLEVEL; 0050 0051 if isempty(EEG.icawinv), 0052 %ICA hasn't been applied to these data 0053 art_ics=[]; 0054 return 0055 else 0056 0057 if nargin<1 0058 bsln_wind=[]; 0059 end 0060 0061 if nargin<2, 0062 if ~isnan(bsln_wind) 0063 fprintf('NOT baselining data.\n') 0064 elseif (length(bsln_wind)~=2) || ~isnumeric(bsln_wind), 0065 if ~isempty(bsln_wind) 0066 error('Baseline window needs to be a two element vector composed of start and stop times (in ms).'); 0067 end 0068 end 0069 0070 if isempty(VERBLEVEL) 0071 VERBLEVEL=2; 0072 end 0073 else 0074 VERBLEVEL=verblevel; 0075 end 0076 0077 if nargin>2, 0078 error('remove_artifact_ics.m accepts only two arguments.'); 0079 end 0080 0081 0082 [n_chans, n_pts, n_epochs]=size(EEG.data); 0083 0084 if ~isempty(bsln_wind), 0085 bsln_pts(1)=find_tpt(bsln_wind(1),EEG.times); 0086 bsln_pts(2)=find_tpt(bsln_wind(2),EEG.times); 0087 end 0088 0089 fldnames=fieldnames(EEG); 0090 iclabels_used=0; 0091 for fn=1:length(fldnames), 0092 if strcmpi(fldnames{fn},'iclabels') 0093 iclabels_used=1; 0094 end 0095 end 0096 0097 n_ics=size(EEG.icawinv,2); 0098 if iclabels_used, 0099 n=length(EEG.iclabels); 0100 else 0101 n=0; 0102 end 0103 art_ics=[]; 0104 if VERBLEVEL>=2, 0105 fprintf('Removing artifact ICs from EEG set file: %s\n',EEG.setname); 0106 if n 0107 %n is only non-zero if there are IC labels 0108 disp('Artifact ICs:'); 0109 end 0110 end 0111 for dg=1:n, 0112 if is_art(EEG.iclabels{dg}), 0113 art_ics=[art_ics dg]; 0114 if VERBLEVEL>=2, 0115 fprintf('IC %d: %s\n',dg,EEG.iclabels{dg}); 0116 end 0117 end 0118 end 0119 0120 %Check EEG.iclabels artifact ICs against EEG.reject 0121 eeglab_rej=find(EEG.reject.gcompreject==1); 0122 if iclabels_used, 0123 dif1=setdiff(eeglab_rej,art_ics); 0124 dif2=setdiff(art_ics,eeglab_rej); 0125 if ~isempty(dif1) || ~isempty(dif2) 0126 if isempty(eeglab_rej), 0127 rej_ic_str='None'; 0128 else 0129 rej_ic_str=int2str(eeglab_rej); 0130 end 0131 msg=['The ICs marked for rejection by EEGLAB in EEG.reject.gcompreject differ from those labeled as artifacts in EEG.iclabels.' ...); 0132 10 'Only the artifact labels in EEG.iclabels will be used.' 10 ... 0133 'The ICs labeled by artifacts by EEG.reject.gcompreject are: ' rej_ic_str]; 0134 watchit(msg); 0135 end 0136 else 0137 art_ics=eeglab_rej; 0138 end 0139 0140 if VERBLEVEL>=2, 0141 fprintf('%d total artifact ICs will be removed.\n',length(art_ics)); 0142 end 0143 0144 nonart_ics=setdiff(1:n_ics,art_ics); 0145 if ~isempty(nonart_ics), 0146 %zero IC artifact ICS 0147 unmix=EEG.icaweights*EEG.icasphere; 0148 fltr=EEG.icawinv(:,nonart_ics)*unmix(nonart_ics,:); 0149 EEG.data=fltr*reshape(EEG.data,n_chans,n_pts*n_epochs); 0150 0151 if isempty(bsln_wind) || sum(isnan(bsln_wind)), 0152 EEG.data=reshape(EEG.data,n_chans,n_pts,n_epochs); 0153 else 0154 %baseline data 0155 if VERBLEVEL>=2, 0156 fprintf('Baselining data by removing mean EEG between %d and %d ms (time points %d and %d).\n', ... 0157 bsln_wind(1),bsln_wind(2),bsln_pts(1),bsln_pts(2)); 0158 end 0159 0160 EEG.data=rmbase(EEG.data,n_pts,bsln_pts(1):bsln_pts(2)); 0161 EEG.data=reshape(EEG.data,n_chans,n_pts,n_epochs); 0162 end 0163 else 0164 error('All ICs have been labeled as artifacts.'); 0165 end 0166 0167 end