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@@ -1,249 +0,0 @@
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-function a6_automatic_artifact_correction(id, rootpath)
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-
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-if ismac % run if function is not pre-compiled
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- id = '1'; % test for example subject
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- currentFile = mfilename('fullpath');
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- [pathstr,~,~] = fileparts(currentFile);
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- cd(fullfile(pathstr,'..', '..'))
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- rootpath = pwd;
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-end
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-
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-% inputs
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-pn.eeg_BIDS = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'eeg_BIDS');
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-pn.channel_locations = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'channel_locations');
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-pn.events = fullfile(rootpath, 'data', 'inputs', 'rawdata', 'events');
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-pn.tools = fullfile(rootpath, 'tools');
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-% outputs
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-pn.eeg_ft = fullfile(rootpath, 'data', 'outputs', 'eeg');
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-pn.history = fullfile(rootpath, 'data', 'outputs', 'history');
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-
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-if ismac % run if function is not pre-compiled
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- addpath(fullfile(pn.tools, 'fieldtrip')); ft_defaults;
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- addpath(fullfile(pn.tools, 'helpers'));
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-end
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-
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-% N = 33
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-IDs = tdfread(fullfile(pn.eeg_BIDS, 'participants.tsv'));
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-IDs = cellstr(IDs.participant_id);
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-
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-id = str2num(id);
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-
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-display(['processing ID ' num2str(IDs{id})]);
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-
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-%% load data
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-
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-load(fullfile(pn.eeg_ft, [IDs{id}, '_task-xxxx_eeg_seg.mat']),'data_eeg', 'events');
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-
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-% remove M2 (collinear with M1 due to avg. mastoid REF: mean(M1,M2)=0)
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-cfg_preproc = [];
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-cfg_preproc.channel = {'all', '-M2'};
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-data_eeg = ft_preprocessing(cfg_preproc, data_eeg);
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-
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-data_ica = load(fullfile(pn.eeg_ft, [IDs{id}, '_task-xxxx_eeg_ica.mat']),'data');
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-
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-data = data_eeg; clear data_eeg;
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-data.elec = data_ica.data.elec;
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-data.chanlocs = data_ica.data.chanlocs; clear data_ica;
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-
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-%% ------------------ ARTIFACT DETECTION - PREPARATION ----------------- %%
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-
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-% load config
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-
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-load(fullfile(pn.history, [IDs{id}, '_task-xxxx_config.mat']),'config');
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-
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-config.elec = data.elec;
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-
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-%% ICA (from weights)
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-
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-% ica config
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-cfg.method = 'runica';
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-cfg.channel = {'all'}; % additional channels should be excluded already...
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-cfg.trials = 'all';
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-cfg.numcomponent = 'all';
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-cfg.demean = 'yes';
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-cfg.runica.extended = 1;
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-
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-% ICA solution
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-cfg.unmixing = config.ica1.unmixing;
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-cfg.topolabel = config.ica1.topolabel;
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-
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-% components
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-comp = ft_componentanalysis(cfg,data);
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-
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-% clear cfg
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-clear cfg data
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-
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-%% remove components
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-
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-% get IC labels
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-iclabels = config.ica1.iclabels.manual;
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-
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-% cfg for rejecting components (reject: blinks, eye movements,
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-% ecg, ref); JQK: added artifacts and emg
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-cfg.component = sortrows([iclabels.bli(:); iclabels.mov(:); iclabels.hrt(:); iclabels.ref(:); iclabels.art(:); iclabels.emg(:)])';
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-cfg.demean = 'yes';
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-
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-% reject components
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-data = ft_rejectcomponent(cfg,comp);
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-
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-% clear cfg
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-clear cfg comp
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-
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-%% remove eye & reference channels
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-
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-cfg.channel = {'all','-IO1','-IO2','-M1','-VEOG','-HEOG'};
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-cfg.demean = 'yes';
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-
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-% remove channels
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-tmpdat = ft_preprocessing(cfg,data);
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-
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-% clear cfg & data variable
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-clear cfg data
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-
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-%% ------------------------- ARTIFACT DETECTION ------------------------ %%
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-
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-% open log file
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-fid = fopen(fullfile(pn.history, [IDs{id}, '_task-xxxx_ArtCorr.txt']),'a');
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-
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-fprintf(fid,['********************* BLOCK *********************\n']);
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-fprintf(fid,['function: a6_automatic_artifact_correction.m \n\n']);
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-fprintf(fid,['eeg file = ' config.data_file '\n\n']);
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-
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-n_trl = length(tmpdat.trial);
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-
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-%% get artifact contaminated channels by kurtosis, low & high frequency artifacts
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-
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-cfg.criterion = 3;
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-cfg.recursive = 'no';
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-
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-[index0 parm0 zval0] = cm_MWB_channel_x_epoch_artifacts_20170922(cfg,tmpdat);
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-
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-% write log
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-tmp_log = '';
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-for j = 1:length(index0.c)
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- tmp_log = [tmp_log num2str(index0.c(j)) ' '];
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-end; clear j
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-tmp_log = [tmp_log(1:end-1) '\n'];
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-fprintf(fid,'(1) automatic bad channel detection:\n');
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-fprintf(fid,['MWB: channel(s) ' tmp_log]);
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-
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-% clear cfg
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-clear cfg tmp_log
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-
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-%% get artifact contaminated channels by FASTER
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-
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-cfg.criterion = 3;
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-cfg.recursive = 'no';
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-
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-[index1 parm1 zval1] = THG_FASTER_1_channel_artifacts_20140302(cfg,tmpdat);
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-
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-% write log
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-tmp_log = '';
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-for j = 1:length(index1)
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- tmp_log = [tmp_log num2str(index1(j)) ' '];
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-end; clear j
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-tmp_log = [tmp_log(1:end-1) '\n'];
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-fprintf(fid,['FASTER: channel(s) ' tmp_log]);
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-
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-% clear cfg
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-clear cfg tmp_log
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-
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-%% interpolate artifact contaminated channels
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-
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-% collect bad channels
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-badchan = unique([index0.c; index1]);
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-
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-fprintf(fid,['--> ' num2str(length(badchan)) ' channels interpolated\n\n']);
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-
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-cfg.method = 'spline';
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-cfg.badchannel = tmpdat.label(badchan);
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-cfg.trials = 'all';
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-cfg.lambda = 1e-5;
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-cfg.order = 4;
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-cfg.elec = config.elec;
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-
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-% interpolate
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-tmpdat = ft_channelrepair(cfg,tmpdat);
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-
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-% clear cfg
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-clear cfg
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-
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-%% equalize duration of trials to the trial with fewest samples
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-
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-for indTrial = 1:numel(tmpdat.trial)
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- TrialLength(indTrial) = size(tmpdat.trial{indTrial},2);
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-end
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-[val, idx] = min(TrialLength);
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-for indTrial = 1:numel(tmpdat.trial)
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- tmpdat.trial{indTrial} = tmpdat.trial{indTrial}(:,1:val);
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- tmpdat.time{indTrial} = tmpdat.time{idx};
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-end
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-
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-%% get artifact contaminated epochs & exclude epochs
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-% includes: - THG_MWB_channel_x_epoch_artifacts_20140311
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-% - THG_FASTER_2_epoch_artifacts_20140302
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-% recursive epoch exclusion!
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-
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-[tmpdat index] = THG_automatic_artifact_correction_trials_20170922(tmpdat);
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-
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-% write log
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-fprintf(fid,'(2) automatic recursive bad epoch detection:\n');
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-fprintf(fid,['MWB & FASTER: ' num2str(n_trl-length(index)) ' bad epoch(s) detected\n\n']);
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-
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-%% get channel x epoch artifacts
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-
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-% cfg
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-cfg.criterion = 3;
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-cfg.recursive = 'yes';
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-
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-[index3 parm3 zval3] = THG_FASTER_4_channel_x_epoch_artifacts_20140302(cfg,tmpdat);
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-
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-% write log
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-fprintf(fid,'(3) automatic single epoch/channel detection:\n');
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-fprintf(fid,['FASTER: ' num2str(sum(sum(index3))) ' channel(s) x trial(s) detected\n\n']);
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-
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-% clear cfg
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-clear cfg
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-
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-%% collect and save detected artifacts & artifact correction infos
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-
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-% include ArtDect.parameters
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-
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-% bad channels
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-ArtDect.channels = badchan;
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-
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-% bad trials
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-tmp = zeros(n_trl,1); tmp(index,1) = 1;
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-badtrl = find(tmp==0);
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-ArtDect.trials = badtrl;
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-clear tmp
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-
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-% bad single epoch(s)/channel(s) - after exclusion of bad epochs
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-ArtDect.channels_x_trials = index3;
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-
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-% overview
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-ind = [1:n_trl];
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-ind(badtrl) = [];
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-tmp = ones(length(tmpdat.label),n_trl);
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-tmp(:,ind) = index3;
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-tmp(badchan,:) = 1;
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-ArtDect.channels_x_trials_all = tmp;
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-clear tmp
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-
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-% save version
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-ArtDect.version = 'JQK 20180123';
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-
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-% add to config
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-config.ArtDect = ArtDect;
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-
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-% save config
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-save(fullfile(pn.history, [IDs{id}, '_task-xxxx_config.mat']),'config');
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-
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-%% finalize log
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-
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-% log
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-fprintf(fid,'Artifact detection completed.\n');
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-fprintf(fid,['Information saved to: ' IDs{id} '_config.mat\n\n']);
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-fclose(fid);
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-
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-end
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