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@@ -1,7 +1,6 @@
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-%% B_visual_inspection_for_ica_170913
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+%% 02_visual_inspection
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-% 170913 | JQK adapted from MD script
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-% 180207 | adapted for STSWD OAs
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+% manually label bad segments
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%% initialize
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@@ -10,108 +9,99 @@ clear all; close all; pack; clc;
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%% pathdef
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-pn.study = '/Volumes/LNDG/Projects/StateSwitch/';
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-pn.eeg_root = [pn.study, 'dynamic/data/eeg/task/A_preproc/SA_preproc_study/'];
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-%pn.eeg_root = '/Users/kosciessa/Desktop/mountpoint_tardis_LNDG/LNDG/StateSwitch/WIP_eeg/SA_preproc_study/';
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-pn.dynamic_In = [pn.eeg_root, 'B_data/B_EEG_ET_ByRun/'];
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-pn.eyePlots = [pn.eeg_root, 'C_figures/B_EyeChannels/']; mkdir(pn.eyePlots);
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-pn.EEG = [pn.eeg_root, 'B_data/C_EEG_FT/']; mkdir(pn.EEG);
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-pn.History = [pn.eeg_root, 'B_data/D_History/']; mkdir(pn.History);
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+currentFile = mfilename('fullpath');
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+[pathstr,~,~] = fileparts( currentFile );
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+cd(pathstr)
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-%% add ConMemEEG tools
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+% inputs
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+pn.eeg_BIDS = fullfile('..', 'data', 'inputs', 'rawdata', 'eeg_BIDS');
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+pn.channel_locations = fullfile('..', 'data', 'inputs', 'rawdata', 'channel_locations');
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+pn.events = fullfile('..', 'data', 'inputs', 'rawdata', 'events');
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+% outputs
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+pn.eeg_ft = fullfile('..', 'data', 'outputs', 'eeg'); if ~exist(pn.eeg_ft); mkdir(pn.eeg_ft); end
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+pn.history = fullfile('..', 'data', 'outputs', 'history'); if ~exist(pn.history); mkdir(pn.history); end
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-pn.MWBtools = [pn.eeg_root, 'T_tools/fnct_MWB']; addpath(genpath(pn.MWBtools));
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-pn.THGtools = [pn.eeg_root, 'T_tools/fnct_THG']; addpath(genpath(pn.THGtools));
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-pn.commontools = [pn.eeg_root, 'T_tools/fnct_common']; addpath(genpath(pn.commontools));
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-pn.fnct_JQK = [pn.eeg_root, 'T_tools/fnct_JQK/']; addpath(genpath(pn.fnct_JQK));
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-pn.FT = [pn.eeg_root, 'T_tools/fieldtrip-20170904/']; addpath(pn.FT); ft_defaults;
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-
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-%% define Condition & IDs for preprocessing
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-
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-condEEG = 'dynamic';
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+% add fieldtrip toolbox
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+addpath(fullfile('..', 'tools', 'fieldtrip')); ft_defaults;
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%% define IDs for visual screening
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-% N = 48;
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-IDs = {'1117';'1118';'1120';'1124';'1126';'1131';'1132';'1135';'1136';'1138';'1144';'1151';'1158';'1160';'1163';'1164';'1167';'1169';'1172';'1173';'1178';'1182';'1213';'1215';'1216';'1219';'1221';'1223';'1227';'1228';'1233';'1234';'1237';'1239';'1240';'1243';'1245';'1247';'1250';'1252';'1257';'1261';'1265';'1266';'1268';'1270';'1276';'1281'};
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-
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-% N = 53 OAs;
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-IDs = {'2104';'2107';'2108';'2112';'2118';'2120';'2121';'2123';'2125';'2129';'2130';'2131';'2132';'2133';'2134';'2135';'2139';'2140';'2145';'2147';'2149';'2157';'2160';'2201';'2202';'2203';'2205';'2206';'2209';'2210';'2211';'2213';'2214';'2215';'2216';'2217';'2219';'2222';'2224';'2226';'2227';'2236';'2237';'2238';'2241';'2244';'2246';'2248';'2250';'2251';'2252';'2258';'2261'};
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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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%% loop IDs
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-for id = 4:length(IDs)
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- for indRun = 1:4
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- %% load data, start screening
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- clc;
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- ID = str2num(IDs{id}); disp(['Processing ',IDs{id}, ' Run ', num2str(indRun)]);
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- % load config
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- load([pn.History, num2str(ID), '_r',num2str(indRun), '_', condEEG, '_config.mat'],'config')
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- % load data
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- load([pn.EEG, num2str(ID), '_r',num2str(indRun), '_', condEEG, '_EEG_Raw_Rlm_Flh_Res.mat'],'data_EEG')
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- % data browser
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- if ~isfield(config,'visual_inspection')
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- cfg = [];
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- cfg.continuous = 'yes';
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- cfg.preproc.demean = 'yes'; % Baselinekorrektur
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- cfg.blocksize = 125;
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- cfg.ylim = [-50 50];
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- cfg.viewmode = 'vertical';
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- cfg.plotlabels = 'yes';
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- % cfg.channelcolormap = [];
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- else
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- cfg = config.visual_inspection;
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- end
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-
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- cfg.channel = {'all','-ECG', '-A1', '-REF'};
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-
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- % inspect data
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- cfg = ft_databrowser(cfg,data_EEG);
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-
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- % check if ICA conducted on this dataset; if so new artifacts not saved
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- if ~isfield(config,'ica1')
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-
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- % marked segments
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- reject = cfg.artfctdef.visual.artifact;
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-
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- trl = [];
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-
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- % generate "trial" (i.e. segment) structure for ICA
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- if exist('reject','var')
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- if min(size(reject)) ~= 0 % JQK fix: 170915
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- for j = 1:size(reject,1)+1
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- if j == 1
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- trl(j,:) = [1 reject(j,1)-1 0];
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- elseif j <= size(reject,1)
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- trl(j,:) = [reject(j-1,2)+1 reject(j,1)-1 0];
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- else
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- trl(j,:) = [reject(j-1,2)+1 size(data_EEG.trial{1},2) 0];
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- end
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- end; clear j
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- else
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- trl = [1 size(data_EEG.trial{1},2) 0];
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- end
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+for id = 28:length(IDs)
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+ %% load data, start screening
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+ clc;
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+ ID = str2num(IDs{id}); disp(['Processing ',IDs{id}]);
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+ % load config
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+ load(fullfile(pn.history, [IDs{id}, '_task-xxxx_config.mat']),'config');
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+ % load data
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+ load(fullfile(pn.eeg_ft, [IDs{id}, '_task-xxxx_eeg_raw.mat']),'data_eeg');
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+ % data browser
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+ if ~isfield(config,'visual_inspection')
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+ cfg = [];
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+ cfg.continuous = 'yes';
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+ cfg.preproc.demean = 'yes';
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+ cfg.blocksize = 400;
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+ cfg.ylim = [-50 50];
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+ cfg.viewmode = 'vertical';
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+ cfg.plotlabels = 'yes';
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+ cfg.linecolor = [.2 .2 .2];
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+ else
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+ cfg = config.visual_inspection;
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+ end
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+
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+ cfg.channel = {'all','-ECG', '-A1', '-REF'};
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+
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+ % inspect data
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+ cfg = ft_databrowser(cfg,data_eeg);
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+
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+ % check if ICA conducted on this dataset; if so new artifacts not saved
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+ if ~isfield(config,'ica1')
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+
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+ % marked segments
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+ reject = cfg.artfctdef.visual.artifact;
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+
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+ trl = [];
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+
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+ % generate "trial" (i.e. segment) structure for ICA
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+ if exist('reject','var')
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+ if min(size(reject)) ~= 0 % JQK fix: 170915
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+ for j = 1:size(reject,1)+1
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+ if j == 1
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+ trl(j,:) = [1 reject(j,1)-1 0];
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+ elseif j <= size(reject,1)
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+ trl(j,:) = [reject(j-1,2)+1 reject(j,1)-1 0];
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+ else
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+ trl(j,:) = [reject(j-1,2)+1 size(data_eeg.trial{1},2) 0];
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+ end
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+ end; clear j
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+ else
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+ trl = [1 size(data_eeg.trial{1},2) 0];
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end
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+ end
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- % eliminate trials without data points
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- ex = find((trl(:,1)-trl(:,2))==0);
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- trl(ex,:) = []; clear ex
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+ % eliminate trials without data points
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+ ex = find((trl(:,1)-trl(:,2))==0);
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+ trl(ex,:) = []; clear ex
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- % eliminate trials shorter than 3 sec (! srate = 250 Hz)
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- ex = find((trl(:,2)-trl(:,1))<750);
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- trl(ex,:) = []; clear ex
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+ % eliminate trials shorter than 3 sec (! srate = 250 Hz)
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+ ex = find((trl(:,2)-trl(:,1))<750);
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+ trl(ex,:) = []; clear ex
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- % add to config structure
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- config.visual_inspection = cfg;
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- config.trl_ica1 = trl;
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+ % add to config structure
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+ config.visual_inspection = cfg;
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+ config.trl_ica1 = trl;
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- % save config
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- save([pn.History, num2str(ID), '_r',num2str(indRun), '_', condEEG, '_config.mat'],'config')
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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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- else
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+ else
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- warning('ICA already conducted. Changes not saved.')
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+ warning('ICA already conducted. Changes not saved.')
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- end
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- end % run loop
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+ end
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end % id loop
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kosciessa