Dot indexing is not supported for variable of this type.

Hi all,

I want to use EEGLAb function to remove the epochs with a value greater than +-150uV in the time interval of 0-0.8ms. I have epoched data (of 1s, at sampling frequency 1200hz).

The data is in order of number of channels x number of samples x number of epochs = 66 x 1200 x 200. I am entering this command:

[EEG Indexes] = pop_eegthresh( epochs,[1:6], -150, 150, 0.01, 0.8);

and it gives this error:

Dot indexing is not supported for variables of this type.
Error in pop_eegthresh (line 169)
if any(starttime < EEG.xmin)

Any idea in how to fix this.?

Here is the function:

% pop_eegthresh() - reject artifacts by detecting outlier values.  This has 
%                   long been a standard method for selecting data to reject.
%                   Applied either for electrode data or component activations.
% Usage:
%   >> pop_eegthresh( INEEG, typerej); % pop-up interactive window
%   >> [EEG Indexes] = pop_eegthresh( INEEG, typerej, elec_comp, lowthresh, ...
%                upthresh, starttime, endtime, superpose, reject);
%
% Graphic interface:
%   "Electrode|Component indices(s)" - [edit box] indices of the electrode(s) or 
%                 component(s) to take into consideration. Same as the 'elec_comp'
%                 parameter from the command line.
%   "Minimum rejection threshold(s)" - [edit box] lower threshold limit(s) 
%                 (in uV|std. dev.). Sets command line parameter 'lowthresh'.
%   "Maximum rejection threshold(s)" - [edit box] upper threshold limit(s) 
%                  (in uV|std. dev.). Sets command line parameter 'upthresh'.
%   "Start time limit(s)" - [edit box] starting time limit(s) (in seconds). 
%                 Sets command line parameter 'starttime'.
%   "End time limit(s)" - [edit box] ending time limit(s) (in seconds). 
%                 Sets command line parameter 'endtime'.
%   "Display previous rejection marks: " - [Checkbox]. Sets the command line
%                 input option 'eegplotplotallrej'.
%   "Reject marked trials: " - [Checkbox]  Sets the command line
%                 input option 'eegplotreject'.
%
% Inputs:
%   INEEG      - input EEG dataset
%   typerej    - type of rejection (0 = independent components; 1 = raw
%              data). Default is 1. For independent components, before
%              thresholding the activations are normalized (to have std. dev. 1).
%   elec_comp  - [e1 e2 ...] electrode|component numbers to take 
%              into consideration for rejection
%   lowthresh  - lower threshold limit (in uV|std. dev. For components, the 
%              threshold(s) are in std. dev.). Can be an array if more than one 
%              electrode|component number is given in elec_comp (above). 
%              If fewer values than the number of electrodes|components, the 
%              last value is used for the remaining electrodes|components. 
%   upthresh   - upper threshold limit (in uV|std dev) (see lowthresh above)
%   starttime  - rejection window start time(s) in seconds (see lowthresh above)
%   endtime    - rejection window end time(s) in seconds (see lowthresh)
%   superpose  - [0|1] 0=do not superpose rejection markings on previous
%              rejection marks stored in the dataset: 1=show both current and
%              previously marked rejections using different colors. {Default: 0}.
%   reject     - [1|0] 0=do not actually reject the marked trials (but store the 
%              marks: 1=immediately reject marked trials. {Default: 1}.
% Outputs:
%   Indexes    - index of rejected trials
%     When eegplot() is called, modifications are applied to the current 
%     dataset at the end of the call to eegplot() when the user presses 
%     the 'Reject' button.
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
%
% See also: eegthresh(), eeglab(), eegplot(), pop_rejepoch() 

% Copyright (C) 2001 Arnaud Delorme, Salk Institute, [e-mail]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% 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.  See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

% 01-25-02 reformated help & license -ad 
% 03-07-02 added srate argument to eegplot call -ad

function [EEG, Irej, com] = pop_eegthresh( EEG, icacomp, elecrange, negthresh, posthresh, ...
   						starttime, endtime, superpose, reject, topcommand);

Irej = [];
com = '';
if nargin < 1
   help pop_eegthresh;
   return;
end;  
if nargin < 2
   icacomp = 1;
end;  

if icacomp == 0
	if isempty( EEG.icasphere )
		disp('Error: you must run ICA first'); return;
	end;
end;
if exist('reject') ~= 1
    reject = 1;
end;

if nargin < 3
    
    % which set to save
    % -----------------
    promptstr = { fastif(icacomp,'Electrode (indices(s), Ex: 2 4 5):'   , 'Component (indices, Ex: 2 6:8 10):'), ...
                  fastif(icacomp,'Minimum rejection threshold(s) (uV, Ex:-20 -10 -15):', 'Minimum rejection threshold(s) (std. dev,  Ex: -3 -2.5 -2):'), ...
                  fastif(icacomp,'Maximum rejection threshold(s) (uV, Ex: 20 10 15):'  , 'Maximum rejection threshold(s) (std. dev, Ex: 2 2 2.5):'), ...
                  'Start time limit(s) (seconds, Ex -0.1 0.3):', ...
                  'End time limit(s) (seconds, Ex 0.2):', ...
                  'Display previous rejection marks', ...
                  'Reject marked trial(s)' };
    inistr = { fastif(icacomp, ['1:' int2str(EEG.nbchan)], '1:5'), ...
               fastif(icacomp, '-10', '-20'),  ...
               fastif(icacomp, '10', '20'), ...
               num2str(EEG.xmin), ...
               num2str(EEG.xmax), ...
               '0', ...
               '0' };
    
    g1 = [1 0.1 0.75];
    g2 = [1 0.22 0.85];
    geometry = {g1 g1 g1 g1 g1 1 g2 g2};
    uilist = {...
              { 'Style', 'text', 'string', promptstr{1}} {} { 'Style','edit'      ,'string' ,inistr{1}  'tag' 'cpnum'}...
              { 'Style', 'text', 'string', promptstr{2}} {} { 'Style','edit'      ,'string' ,inistr{2} 'tag' 'lowlim' }...
              { 'Style', 'text', 'string', promptstr{3}} {} { 'Style','edit'      ,'string' ,inistr{3}  'tag' 'highlim'}...
              { 'Style', 'text', 'string', promptstr{4}} {} { 'Style','edit'      ,'string' ,inistr{4}  'tag' 'starttime'}...
              { 'Style', 'text', 'string', promptstr{5}} {} { 'Style','edit'      ,'string' ,inistr{5}  'tag' 'endtime'}...
              {}...
              { 'Style', 'text', 'string', promptstr{6}} {} { 'Style','checkbox'  ,'string'  ,' ' 'value' str2double(inistr{6}) 'tag','rejmarks' }...
              { 'Style', 'text', 'string', promptstr{7}} {} { 'Style','checkbox'  ,'string'  ,' ' 'value' str2double(inistr{7}) 'tag' 'rejtrials'} ...
               };
    figname = fastif(icacomp == 0, 'Rejection abnormal comp. values -- pop_eegthresh()','Rejection abnormal elec. values -- pop_eegthresh()');
    result = inputgui( geometry,uilist,'pophelp(''pop_eegthresh'');', figname);
    
    size_result  = size( result );
    if size_result(1) == 0 return; end;
    elecrange    = result{1};
    negthresh    = result{2};
    posthresh    = result{3};
    starttime    = result{4};
    endtime      = result{5};
    superpose    = result{6};
    reject       = result{7};
end;

if isstr(elecrange) % convert arguments if they are in text format
    calldisp = 1;
    elecrange = eval( [ '[' elecrange ']' ]  );
    negthresh = eval( [ '[' negthresh ']' ]  );
    posthresh = eval( [ '[' posthresh ']' ]  );
    if isstr(starttime)
        starttime = eval( [ '[' starttime ']' ]  );
    end;
    if isstr(endtime)
        endtime   = eval( [ '[' endtime ']' ]  );
    end;
else
    calldisp = 0;
end;

if any(starttime < EEG.xmin) 
 fprintf('Warning : starttime inferior to minimum time, adjusted\n'); 
	starttime(find(starttime < EEG.xmin)) = EEG.xmin; 
end;
if any(endtime   > EEG.xmax) 
	fprintf('Warning : endtime superior to maximum time, adjusted\n'); 
	endtime(find(endtime > EEG.xmax)) = EEG.xmax;
end;

if icacomp == 1
	[Itmp Irej NS Erejtmp] = eegthresh( EEG.data, EEG.pnts, elecrange, negthresh, posthresh, [EEG.xmin EEG.xmax], starttime, endtime);
    tmpelecIout = zeros(EEG.nbchan, EEG.trials);
    tmpelecIout(elecrange,Irej) = Erejtmp;
else
    icaacttmp = eeg_getdatact(EEG, 'component', elecrange);
	[Itmp Irej NS Erejtmp] = eegthresh( icaacttmp, EEG.pnts, 1:length(elecrange), negthresh, posthresh, [EEG.xmin EEG.xmax], starttime, endtime);
    tmpelecIout = zeros(size(EEG.icaweights,1), EEG.trials);
    tmpelecIout(elecrange,Irej) = Erejtmp;
end;

fprintf('%d channel selected\n', size(elecrange(:), 1));
fprintf('%d/%d trials marked for rejection\n', length(Irej), EEG.trials);
tmprejectelec = zeros( 1, EEG.trials);
tmprejectelec(Irej) = 1;

rej  = tmprejectelec;
rejE = tmpelecIout;
if calldisp
    if icacomp == 1 macrorej  = 'EEG.reject.rejthresh';
        			macrorejE = 'EEG.reject.rejthreshE';
    else			macrorej  = 'EEG.reject.icarejthresh';
        			macrorejE = 'EEG.reject.icarejthreshE';
    end;
	
	colrej = EEG.reject.rejthreshcol;
	eeg_rejmacro; % script macro for generating command and old rejection arrays
	     
    if icacomp == 1
        eegplot( EEG.data(elecrange,:,:), 'srate', EEG.srate, 'limits', [EEG.xmin EEG.xmax]*1000 , 'command', command, eegplotoptions{:}); 
    else
        eegplot( icaacttmp, 'srate', EEG.srate, 'limits', [EEG.xmin EEG.xmax]*1000 , 'command', command, eegplotoptions{:}); 
    end;
else 
    if reject == 1
        EEG = pop_rejepoch(EEG, rej, 0);
    end;
end;
if ~isempty(rej)
    if icacomp	== 1
        EEG.reject.rejthresh  = rej;
        EEG.reject.rejthreshE = rejE;
    else
        EEG.reject.icarejthresh  = rej;
        EEG.reject.icarejthreshE = rejE;
    end;
end;

%com = sprintf('Indexes = pop_eegthresh( %s, %d, [%s], [%s], [%s], [%s], [%s], %d, %d);', ...
%   inputname(1), icacomp, num2str(elecrange),  num2str(negthresh), ...
%   num2str(posthresh), num2str(starttime ) , num2str(endtime), superpose, reject ); 
com = [ com sprintf('%s = pop_eegthresh(%s,%s);', inputname(1), ...
		inputname(1), vararg2str({icacomp,elecrange,negthresh,posthresh,starttime,endtime,superpose,reject})) ]; 
if nargin < 3
	Irej = com;
end;

return;

% reject artifacts in a sequential fashion to save memory (ICA ONLY)
% -------------------------------------------------------
function [Irej, Erej] = thresh( data, elecrange, timerange, negthresh, posthresh, starttime, endtime);
    Irej    = [];
    Erej    = zeros(size(data,1), size(data,2));
    for index = 1:length(elecrange)
       tmpica = data(index,:,:);
       tmpica = reshape(tmpica, 1, size(data,2)*size(data,3));
       
       % perform the rejection
       % ---------------------	
	   tmpica = (tmpica-mean(tmpica,2)*ones(1,size(tmpica,2)))./ (std(tmpica,0,2)*ones(1,size(tmpica,2)));
	   [I1 Itmprej NS Etmprej] = eegthresh( tmpica, size(data,2), 1, negthresh, posthresh, ...
						timerange, starttime, endtime);
 	   Irej = union_bc(Irej, Itmprej);
 	   Erej(elecrange(index),Itmprej) = Etmprej;
	end;

Answer 1

[Guillaume]

Any idea in how to fix this.?

Not being snarky, but reading the documentation of the function would be the way to fix it.

%   >> [EEG Indexes] = pop_eegthresh( INEEG, typerej, elec_comp, lowthresh, ...
%                upthresh, starttime, endtime, superpose, reject);
% Inputs:
%   INEEG      - input EEG dataset
%   typerej    - type of rejection (0 = independent components; 1 = raw
%              data). Default is 1. For independent components, before
%              thresholding the activations are normalized (to have std. dev. 1).
% ...

So, the first input should be an EEG dataset. The documentation doesn't give any detail of what that actually mean, but from the code in the function, an EEG dataset is a structure (or class) with several fields (icasphere, xmin, xmax, etc.). Clearly that's not what you're passing to the function.

Similarly, the 2nd input, the type of rejection, should be 0 or 1, so 1:6 as a 2nd input is not going to cut it.

Unfortunately for you, the code is not very well written so it doesn't do any check on the inputs it receives to confirm that they are what is expected, so expect lots of obscure messages when it attempt to use your incorrect inputs.

Answer 2

[Image Analyst]

You're passing in epochs, which that function calls EEG internally. Why do you think your epochs object has an xmin property? Evidently it does not. Make sure you pass in the right thing, which is not epochs.