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Updated scripts
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@fzakirov
fzakirov committed Dec 9, 2024
1 parent 6bbb734 commit 1ab0863
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63 changes: 29 additions & 34 deletions code/preprocessing-eeg/create_mat.m
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,8 @@
% addpath(genpath([main_dir filesep 'MADE-EEG-preprocessing-pipeline']));% enter the path of the EEGLAB folder in this line
addpath(genpath('/home/data/NDClab/tools/lab-devOps/scripts/MADE_pipeline_standard/eeg_preprocessing'));% enter the path of the folder in this line

addpath(genpath('/home/data/NDClab/analyses/thrive-theta-ddm/code/matlab/'))

%Location of "EEG
% addpath(genpath([main_dir filesep 'eeglab13_4_4b']));% enter the path of the EEGLAB folder in this line
addpath(genpath('/home/data/NDClab/tools/lab-devOps/scripts/MADE_pipeline_standard/eeglab13_4_4b'));% enter the path of the EEGLAB folder in this line
Expand All @@ -30,7 +32,7 @@

%location of dataset folder
% dataset_dir = '/Users/fzaki001/thrive-theta-ddm';
dataset_dir = '/home/data/NDClab/datasets/thrive-dataset/derivatives/preprocessed/';
dataset_dir = '/home/data/NDClab/datasets/thrive-dataset';
% summary_csv_path = '/Users/fzaki001/thrive-theta-ddm/derivatives/behavior/summary.csv';
summary_csv_path = '/home/data/NDClab/analyses/thrive-theta-ddm/derivatives/behavior/summary.csv';

Expand Down Expand Up @@ -81,7 +83,10 @@
% outputHeader = {'id, s_resp_incon_error, s_resp_incon_corr, ns_resp_incon_error, ns_resp_incon_corr'};
% dlmwrite(strcat('thrive_trialCounts_respOnly', date, '.csv'), outputHeader, 'delimiter', '', '-append');

diary(sprintf('erp_log_%s.log', datestr(now, 'mm_dd_yyyy_HH_MM_SS')))

for subject=1:length(datafile_names)

EEG=[];

fprintf('\n\n\n*** Processing subject %d (%s) ***\n\n\n', subject, datafile_names{subject});
Expand Down Expand Up @@ -138,14 +143,14 @@

%count how many of each event type (combination of event types) of
%interest are present
s_resp_incon_error = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 0) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
s_resp_incon_corr = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
ns_resp_incon_error = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 0) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
ns_resp_incon_corr = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
s_stim_incon_corr = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "stim")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
s_stim_con_corr = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "stim")) & (strcmp({EEG.event.congruency}, "c")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
ns_stim_incon_corr = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "stim")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
ns_stim_con_corr = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "stim")) & (strcmp({EEG.event.congruency}, "c")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
s_resp_incon_error = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 0) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));
s_resp_incon_corr = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));
ns_resp_incon_error = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 0) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));
ns_resp_incon_corr = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));
s_stim_incon_corr = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "stim")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));
s_stim_con_corr = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "stim")) & (strcmp({EEG.event.congruency}, "c")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));
ns_stim_incon_corr = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "stim")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));
ns_stim_con_corr = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "stim")) & (strcmp({EEG.event.congruency}, "c")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));

%Create the trial counts table for trial counts
counts_table=table({datafile_names{subject}}, {s_resp_incon_error}, {s_resp_incon_corr}, {ns_resp_incon_error}, {ns_resp_incon_corr}, {s_stim_incon_corr}, {s_stim_con_corr}, {ns_stim_incon_corr}, {ns_stim_con_corr});
Expand All @@ -165,7 +170,7 @@

%specify min number of trials per condition (if file contains less than
%this number for ANY condition, then they will be skipped for ALL conditions
minTrials = 8;
minTrials = 6;

%specify min accuracy per condition (if file contains less than
%this number for ANY condition, then they will be skipped for ALL conditions
Expand Down Expand Up @@ -208,32 +213,18 @@
EEG = pop_selectevent( EEG, 'latency','-.1 <= .1','deleteevents','on');
EEG = eeg_checkset( EEG );

% NOTE %
%the logic of checking conditions and then looping over conditions
%below is fairly hard-coded and could be be substantially improved to
%allow for easier reuse when number of conditions or number of
%variables per condition changes.
%
%before pulling trials of interest, for any conditions, check to make
%sure this file/participant has more than minTrials for EACH condition.
%If the file/participant is below minTrials for even one of the
%conditions that will be pulled, then the file/participant is skipped
%entirely and no condition data at all will be pulled for this specific
%file (but the participant can still have data pulled for another one
%of their files from another visit).
%
%count trials for each condition of interest and store in numTrials vector
numTrials(1) = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 0) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
numTrials(2) = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
numTrials(3) = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 0) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
numTrials(4) = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) ));
numTrials(1) = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 0) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));
numTrials(2) = length(find( (strcmp({EEG.event.observation}, "s")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));
numTrials(3) = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 0) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));
numTrials(4) = length(find( (strcmp({EEG.event.observation}, "ns")) & (strcmp({EEG.event.eventType}, "resp")) & (strcmp({EEG.event.congruency}, "i")) & ([EEG.event.accuracy] == 1) & ([EEG.event.responded] == 1) & ([EEG.event.validRt] == 1) & ([EEG.event.extraResponse] == 0) ));

%logical test if the number of trials for each condition (numTrials vector)
%are NOTE all >= minTrials. If statement is true, then participant/file
%is skipped and for loop over files continues to next file
% if ~(sum(numTrials >= minTrials) == length(numTrials))
% continue
% end
if ~(sum(numTrials >= minTrials) == length(numTrials))
continue
end

% loop through conditions of interest for this file (combo of event types)
%
Expand All @@ -251,32 +242,36 @@
accuracy = 0;
responded = 1;
validRt = 1;
extraResponse = 0;
elseif (c==2) % social correct
observation = 's';
eventType = 'resp';
congruency = 'i';
accuracy = 1;
responded = 1;
validRt = 1;
extraResponse = 0;
elseif (c==3) % nonsocial error
observation = 'ns';
eventType = 'resp';
congruency = 'i';
accuracy = 0;
responded = 1;
validRt = 1;
extraResponse = 0;
elseif (c==4) % nonsocial correct
observation = 'ns';
eventType = 'resp';
congruency = 'i';
accuracy = 1;
responded = 1;
validRt = 1;
extraResponse = 0;
end

%select combintion of event types of interest based on vars above
EEG1 = pop_selectevent( EEG, 'latency','-1<=1','observation',observation,'eventType',eventType,'congruency',congruency,'accuracy',accuracy,'responded',responded,'validRt',validRt,'deleteevents','on','deleteepochs','on','invertepochs','off');
EEG1 = eeg_checkset( EEG1 );
EEG1 = pop_selectevent( EEG, 'latency', '-1<=1', 'observation', observation, 'eventType', eventType, 'congruency', congruency, 'accuracy', accuracy, 'responded', responded, 'validRt', validRt, 'extraResponse', extraResponse, 'deleteevents', 'on', 'deleteepochs', 'on', 'invertepochs', 'off');
EEG1 = eeg_checkset(EEG1);

% Average across epoch dimension
% this all Channel ERP only needs to be computed once
Expand All @@ -300,4 +295,4 @@
end

%save the erps and subject list
save('thrive_Resp_erps_min_8t_60acc.mat','erpDat_data', 'erpDat_subIds')
save(sprintf('thrive_Resp_erps_min_6t_60acc_%s.mat', datestr(now, 'mm_dd_yyyy_HH_MM_SS')), 'erpDat_data', 'erpDat_subIds')
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