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bjh_00_main_BIDS.m
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%% bjh_00_main_BIDS
% author: Bjoern Holtze
% date: 12.05.2020
% adapted from: bjh_main_01.m
%% General Info %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
MAINPATH = fullfile(pwd, '..', filesep);
% add EEGLAB path
addpath(fullfile('C:\Users\bjh\Desktop\bjh_name\software\eeglab13_6_5b\'));
eeglab;
close 'EEGLAB v13.6.5b';
% add name of folder to which BIDS data was downloaded
BIDS_dataset_name = 'bjh_name';
SOURCEDATAPATH = [MAINPATH,BIDS_dataset_name,filesep,'sourcedata',filesep];
STIMPATH = [MAINPATH,BIDS_dataset_name,filesep,'stimuli',filesep];
DATAPATH = [MAINPATH,'analysis',filesep];
mkdir(DATAPATH);
% included participants
incl_subj = {'001','002','003','005','006','008','009','011','012','013','014',...
'015','017','018','019','020','021','022','023','024','025'};
% attended channel
attended_ch = [1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2,1];
% condition order
con_order = {'OBOB','BOBO','OBOB','BOBO','OBOB','BOBO','OBOB','BOBO',...
'OBOB','BOBO','OBOB','BOBO','OBOB','BOBO','OBOB','BOBO',...
'OBOB','BOBO','OBOB','BOBO','OBOB','BOBO','OBOB','BOBO','OBOB'};
%% Independent Component Analysis (ICA) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
prob = 2; % local threshold for pop_jointprob
kurt = 2; % global threshold for pop_jointprob
ext_ica = ['_prob_', num2str(prob), '_kurt_', num2str(kurt)];
run_mode = 'reproduce'; % either 'new' if ICA should newly run and badcomps should be newly identified
% or 'reproduce' if previous ICA results and identified badcomps should be used
if strcmp(run_mode,'new')
for s = 1:size(incl_subj,2)
PATHIN_ICA = [MAINPATH,BIDS_dataset_name,filesep,'sub-',incl_subj{s},...
filesep,'eeg',filesep];
PATHOUT_ICA = DATAPATH;
load_name_ica = ['sub-',incl_subj{s},'_task-AttendedSpeakerParadigmOwnName_eeg'];
save_name_ica = ['sub-', incl_subj{s}, '_ica_tmp', ext_ica];
bjh_02_ica(PATHIN_ICA,PATHOUT_ICA,load_name_ica,save_name_ica,prob,kurt);
end
elseif strcmp(run_mode,'reproduce')
files_fdt = dir([SOURCEDATAPATH,'*.fdt']);
files_set = dir([SOURCEDATAPATH,'*.set']);
files_mat = dir([SOURCEDATAPATH,'*.mat']);
for s = 1:size(incl_subj,2)
copyfile([SOURCEDATAPATH, files_fdt(s).name], [DATAPATH, files_fdt(s).name]);
copyfile([SOURCEDATAPATH, files_set(s).name], [DATAPATH, files_set(s).name]);
copyfile([SOURCEDATAPATH, files_mat(s).name], [DATAPATH, files_mat(s).name]);
end
end
%% Visually Inspect ICs and Reject Artefactual Components %%%%%%%%%%%%%%%%%
PATHIN_ICLABEL = DATAPATH;
PATHOUT_ICLABEL = DATAPATH;
for s = 1:size(incl_subj,2)
load_name_iclabel = ['sub-', incl_subj{s}, '_ica_tmp', ext_ica];
load_name_imported = [MAINPATH,BIDS_dataset_name,filesep,'sub-',incl_subj{s},...
filesep,'eeg',filesep,'sub-',incl_subj{s},...
'_task-AttendedSpeakerParadigmOwnName_eeg'];
save_name_iclabel = ['sub-', incl_subj{s}, '_badcomps_removed', ext_ica];
bjh_03_iclabel(PATHIN_ICLABEL,PATHOUT_ICLABEL,load_name_iclabel,load_name_imported,...
save_name_iclabel,incl_subj{s},run_mode);
end
%% Filter (and Rereference) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
low_edge_erp = 0.1;
high_edge_erp = 10;
ext_filt_erp = ['_lp_',num2str(high_edge_erp),'_hp_',num2str(low_edge_erp)];
low_edge_xcorr = 1;
high_edge_xcorr = 15;
ext_filt_xcorr = ['_reref_lp_',num2str(high_edge_xcorr),'_hp_',num2str(low_edge_xcorr)];
PATHIN_FILT = DATAPATH;
PATHOUT_FILT = DATAPATH;
for s = 1:size(incl_subj,2)
load_name_filt = ['sub-', incl_subj{s}, '_badcomps_removed', ext_ica];
save_name_filt_erp = ['sub-', incl_subj{s}, '_filtered', ext_ica, ext_filt_erp];
save_name_filt_xcorr = ['sub-', incl_subj{s}, '_filtered', ext_ica, ext_filt_xcorr];
bjh_04_filter_lp_hp(PATHIN_FILT,PATHOUT_FILT,load_name_filt,save_name_filt_erp,low_edge_erp,high_edge_erp);
bjh_04_reref_and_filter_lp_hp(PATHIN_FILT,PATHOUT_FILT,load_name_filt,save_name_filt_xcorr,low_edge_xcorr,high_edge_xcorr);
end
%% NAME - ERP %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Add Control Events %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
PATHIN_CONTROL = DATAPATH;
PATHOUT_CONTROL = DATAPATH;
for s = 1:size(incl_subj,2)
load_name_control = ['sub-', incl_subj{s}, '_filtered', ext_ica, ext_filt_erp];
save_name_control = ['sub-', incl_subj{s}, '_control_words_added', ext_ica, ext_filt_erp];
bjh_05_add_control_events(PATHIN_CONTROL,PATHOUT_CONTROL,STIMPATH,...
load_name_control,save_name_control,attended_ch(str2double(incl_subj{s})),...
con_order{str2double(incl_subj{s})});
end
%% Epoch and Reject Artefactual Epochs %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
ep_start = -0.5;
ep_end = 1.5;
ext_ep = ['_eps_', num2str(ep_start), '_epe_', num2str(ep_end)];
PATHIN_EP_NAME_ERP = DATAPATH;
PATHOUT_EP_NAME_ERP = DATAPATH;
for s = 1:size(incl_subj,2)
load_name_ep_name_erp = ['sub-', incl_subj{s}, '_control_words_added', ext_ica, ext_filt_erp];
save_name_ep_name_erp = ['sub-', incl_subj{s}, '_epoch_rejected', ext_ica, ext_filt_erp, ext_ep];
bjh_05_tbt(PATHIN_EP_NAME_ERP,PATHOUT_EP_NAME_ERP,...
load_name_ep_name_erp,save_name_ep_name_erp,ep_start,ep_end);
end
%% Create Data Struct - Name %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
PATHIN_STRUCT_NAME_ERP = DATAPATH;
PATHOUT_STRUCT_NAME_ERP = DATAPATH;
load_name_struct_name_erp = ['_epoch_rejected',ext_ica,ext_filt_erp,ext_ep];
save_name_struct_name_erp = ['name_erp_struct',ext_ica,ext_filt_erp,ext_ep];
bjh_06_create_struct_name_erp(PATHIN_STRUCT_NAME_ERP,PATHOUT_STRUCT_NAME_ERP,...
STIMPATH,load_name_struct_name_erp,save_name_struct_name_erp,...
incl_subj,con_order);
%% Exctract P3 Amplitudes and Latencies %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
p3_min = 500; % minimum of P3 time window
p3_max = 1200; % maximum of P3 time window
smoothwin = 100; % in ms
ampwin = 100; % in ms
PATHIN_P3_AMP_LAT = DATAPATH;
PATHOUT_P3_AMP_LAT = DATAPATH;
ext_p3 = ['_ampwin_', num2str(ampwin)];
load_name_p3_amp_lat = save_name_struct_name_erp;
save_name_p3_amp_lat = ['p3_amp_lat', ext_ica,ext_filt_erp,ext_ep,ext_p3];
bjh_08_get_p3_amp_lat(PATHIN_P3_AMP_LAT,PATHOUT_P3_AMP_LAT,load_name_p3_amp_lat,...
save_name_p3_amp_lat,p3_min,p3_max,smoothwin,ampwin);
%% Plotting ERP - Name %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
PATHIN_PLOT_NAME_ERP = DATAPATH;
PATHOUT_PLOT_NAME_ERP = DATAPATH;
load_name_plot_name_erp = save_name_struct_name_erp;
save_name_plot_name_erp = ['name_erp',ext_ica,ext_filt_erp,ext_ep];
load_name_plot_p3_amp_lat = save_name_p3_amp_lat;
save_name_plot_p3_amp_lat = ['p3_amp_lat',ext_ica,ext_filt_erp,ext_ep];
%%% ERPs %%%
%%% Conditions Separate %%%
% Figure 7 (inset) %
bjh_09_plot_name_erp_cond_sep(PATHIN_PLOT_NAME_ERP,PATHOUT_PLOT_NAME_ERP,...
load_name_plot_name_erp,save_name_plot_name_erp,smoothwin);
%%% Conditions Pooled and Detected Names ~ P3 Amplitude%%%
% Grand Average %
% Figure 3 %
bjh_09_plot_name_erp_cond_pool(PATHIN_PLOT_NAME_ERP,PATHOUT_PLOT_NAME_ERP,...
load_name_plot_name_erp,load_name_plot_p3_amp_lat,...
save_name_plot_name_erp,p3_min,p3_max,smoothwin);
%%% P3 Amplitude and Latency %%%
%%% Conditions Separate %%%
% Single Subject %
% Figure 7 %
bjh_09_plot_p3_amp_p3_lat_det_name_cond_sep(PATHIN_P3_AMP_LAT,...
PATHOUT_P3_AMP_LAT,load_name_plot_p3_amp_lat,...
save_name_plot_p3_amp_lat);
%% NAME - CROSS - CORRELATION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Create segments relative to name onsets %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
segsize = 5; % in sec (30 needs to be devisible by that number without rest)
namecut = 0.6; % data from name onset to namecut (in s) is cut out
PATHIN_SEG_XCORR_NAME = DATAPATH;
PATHOUT_SEG_XCORR_NAME = DATAPATH;
ext_seg_name = ['_segsize_', num2str(segsize),'_cut_end_',num2str(namecut)];
load_name_seg_xcorr_name = ['_filtered', ext_ica, ext_filt_xcorr];
save_name_seg_xcorr_name = ['xcorr_name_seg_struct',ext_ica,ext_filt_xcorr,ext_seg_name];
bjh_06_create_struct_seg_xcorr_name(PATHIN_SEG_XCORR_NAME,PATHOUT_SEG_XCORR_NAME,...
STIMPATH,load_name_seg_xcorr_name,...
save_name_seg_xcorr_name,incl_subj,attended_ch,segsize,namecut);
%% Cross-correlate segments relative to name onset %%%%%%%%%%%%%%%%%%%%%%%%
max_lag = 500; % in samples
PATHIN_XCORR_NAME = DATAPATH;
PATHOUT_XCORR_NAME = DATAPATH;
load_name_xcorr_name = save_name_seg_xcorr_name;
save_name_xcorr_name = ['xcorr_name_struct',ext_ica,ext_filt_xcorr,ext_seg_name];
bjh_07_create_struct_xcorr_name(PATHIN_XCORR_NAME,PATHOUT_XCORR_NAME,load_name_xcorr_name,...
save_name_xcorr_name,max_lag);
%% Plot cross-correlation relative to name onset %%%%%%%%%%%%%%%%%%%%%%%%%%
xlim_ms = [-150,500]; % limits of displayed cross-correlation functions
PATHIN_PLOT_XCORR_NAME = DATAPATH;
PATHOUT_PLOT_XCORR_NAME = DATAPATH;
load_name_plot_xcorr_name = save_name_xcorr_name;
save_name_plot_xcorr_name = ['xcorr_name',ext_ica,ext_filt_xcorr,ext_seg_name];
% CC Magnitude (values averaged over time lags) relative to name onset (time course and boxplot)
% Figure 5
bjh_09_plot_xcorr_name_cond_pool(PATHIN_PLOT_XCORR_NAME,PATHOUT_PLOT_XCORR_NAME,...
load_name_plot_xcorr_name,save_name_plot_xcorr_name);
% P3 Amp ~ CC Magnitude Diff (Att) ~ CC Magnitude Diff (Unatt)
% Figure 6 (3D)
bjh_09_plot_xcorr_name_att_diff_unatt_diff_p3_amp_cond_pool_3d(PATHIN_PLOT_XCORR_NAME,...
PATHOUT_PLOT_XCORR_NAME,load_name_plot_xcorr_name,save_name_p3_amp_lat,...
save_name_plot_xcorr_name);
% GFP 500 Diff (Omni and Beam separately)
% Supplementary Figure 2
bjh_09_plot_xcorr_name_att_diff_unatt_diff_cond_sep(PATHIN_PLOT_XCORR_NAME,...
PATHOUT_PLOT_XCORR_NAME,load_name_plot_xcorr_name,...
save_name_plot_xcorr_name,con_order);
%% CROSS - CORRELATION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Create Segments Struct (Speech Envelope and EEG) %%%%%%%%%%%%%%%%%%%%%%%
% Segments unrelated to name onsets %
PATHIN_SEG_XCORR = DATAPATH;
PATHOUT_SEG_XCORR = DATAPATH;
ext_seg = ['_segsize_', num2str(segsize)];
load_name_seg_xcorr = ['_filtered', ext_ica, ext_filt_xcorr];
save_name_seg_xcorr = ['xcorr_seg_struct',ext_ica,ext_filt_xcorr,ext_seg];
bjh_06_create_struct_seg_xcorr(PATHIN_SEG_XCORR,PATHOUT_SEG_XCORR,STIMPATH,...
load_name_seg_xcorr,save_name_seg_xcorr,incl_subj,attended_ch,segsize);
%% Perform Cross-Correlation (save results as struct) %%%%%%%%%%%%%%%%%%%%%
% Segments unrelated to name onsets %
PATHIN_XCORR = DATAPATH;
PATHOUT_XCORR = DATAPATH;
load_name_xcorr = save_name_seg_xcorr;
save_name_xcorr = ['xcorr_struct',ext_ica,ext_filt_xcorr,ext_seg];
bjh_07_create_struct_xcorr(PATHIN_XCORR,PATHOUT_XCORR,STIMPATH,...
load_name_xcorr,save_name_xcorr,max_lag);
%% Plotting (Cross-Correlation) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Segments unrelated to name onsets %
PATHIN_PLOT_XCORR = DATAPATH;
PATHOUT_PLOT_XCORR = DATAPATH;
load_name_plot_xcorr = save_name_xcorr;
save_name_plot_xcorr = ['xcorr',ext_ica,ext_filt_xcorr,ext_seg];
% CC magnitude (attend, unattend, control)
% Figure 4
bjh_09_plot_xcorr_cond_pool(PATHIN_PLOT_XCORR,PATHOUT_PLOT_XCORR,...
load_name_plot_xcorr,save_name_plot_xcorr,xlim_ms);