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Slepi/Code/Utilities/spm12/spm_eeg_artefact_threshchan.m
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spm_eeg_artefact_threshchan.m
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function res = spm_eeg_artefact_threshchan(S)
% Plugin for spm_eeg_artefact doing artefact detection by chanel thresholding.
% S - input structure
% fields of S:
% S.D - M/EEG object
% S.chanind - vector of indices of channels that this plugin will look at.
%
% Additional parameters can be defined specific for each plugin
% Output:
% res -
% If no input is provided the plugin returns a cfg branch for itself
%
% If input is provided the plugin returns a matrix of size D.nchannels x D.ntrials
% with zeros for clean channel/trials and ones for artefacts.
%______________________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Vladimir Litvak
% $Id: spm_eeg_artefact_threshchan.m 6060 2014-06-19 13:31:19Z vladimir $
%-This part if for creating a config branch that plugs into spm_cfg_eeg_artefact
% Any parameters can be specified and they are then passed to the plugin
% when it's called.
%--------------------------------------------------------------------------
if nargin == 0
threshold = cfg_entry;
threshold.tag = 'threshold';
threshold.name = 'Threshold';
threshold.strtype = 'r';
threshold.num = [1 1];
threshold.help = {'Threshold value to apply to all channels'};
excwin = cfg_entry;
excwin.tag = 'excwin';
excwin.name = 'Excision window';
excwin.strtype = 'r';
excwin.num = [1 1];
excwin.val = {1000};
excwin.help = {'Window (in ms) to mark as bad around each jump (for mark mode only), 0 - do not mark data as bad'};
threshchan = cfg_branch;
threshchan.tag = 'threshchan';
threshchan.name = 'Threshold channels';
threshchan.val = {threshold, excwin};
res = threshchan;
return
end
SVNrev = '$Rev: 6060 $';
%-Startup
%--------------------------------------------------------------------------
spm('sFnBanner', mfilename, SVNrev);
spm('FigName','M/EEG threshold channels');
D = spm_eeg_load(S.D);
chanind = S.chanind;
threshold = S.threshold;
res = zeros(D.nchannels, D.ntrials);
if isequal(S.mode, 'reject')
%-Artefact detection
%--------------------------------------------------------------------------
spm_progress_bar('Init', D.ntrials, 'Trials checked');
if D.ntrials > 100, Ibar = floor(linspace(1, D.ntrials,100));
else Ibar = [1:D.ntrials]; end
for i = 1:D.ntrials
res(chanind, i) = squeeze(max(abs(D(chanind, :, i)), [], 2))>threshold;
if ismember(i, Ibar), spm_progress_bar('Set', i); end
end
spm_progress_bar('Clear');
elseif isequal(S.mode, 'mark')
multitrial = D.ntrials>1;
if multitrial
spm_progress_bar('Init', D.ntrials, 'Trials checked');
if D.ntrials > 100, Ibar = floor(linspace(1, D.ntrials,100));
else Ibar = [1:D.ntrials]; end
end
for i = 1:D.ntrials
bad = abs(squeeze(D(chanind, :, i)))>threshold;
if ~any(bad(:))
if multitrial && ismember(i, Ibar), spm_progress_bar('Set', i); end
continue;
end
if S.excwin>0
excwin = ones(1, round(5e-4*S.excwin*D.fsample));
end
if ~multitrial
spm_progress_bar('Init', D.nchannels, 'Channels checked');
if D.nchannels > 100, Ibar = floor(linspace(1, D.nchannels,100));
else Ibar = [1:D.nchannels]; end
end
res = [];
for j = 1:length(chanind)
bad(j, :) = ~~conv(double(bad(j, :)), excwin, 'same');
if (bad(j, :)/size(bad,2))>S.badchanthresh
onsets = 1;
offsets = size(bad,2)+1;
else
onsets = find(bad(j, :));
offsets = find(~bad(j, :));
onsets(find(diff(onsets)<2)+1) = [];
if bad(j, end)
offsets(end+1) = length(bad)+1;
end
end
for k = 1:length(onsets)
res(end+1).type = 'artefact_threshold';
res(end).value = char(D.chanlabels(chanind(j)));
res(end).time = D.time(onsets(k)+1) - D.time(1) + D.trialonset(i);
res(end).duration = (min(offsets(offsets>onsets(k)))-onsets(k))./D.fsample;
end
if ~multitrial && ismember(j, Ibar), spm_progress_bar('Set', j); end
end
if ~multitrial, spm_progress_bar('Clear'); end
if ~isempty(res)
ev = D.events(i);
if iscell(ev)
ev = ev{1};
end
if ~S.append
ev(strmatch('artefact_threshold', {ev.type})) = [];
end
D = events(D, i, spm_cat_struct(ev, res));
end
if multitrial && ismember(i, Ibar), spm_progress_bar('Set', i); end
end
if multitrial, spm_progress_bar('Clear'); end
res = D;
end
spm('FigName', 'M/EEG threshold channels: done');
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