SRMR2_01_prepro_1_automatic_Rpeakdetection.m

% Author: Birgit Nierula
% nierula@cbs.mpg.de

%% SpinCCsep_01_prepro_1_automatic_Rpeakdetection

srmr_nr = 2;
ana_dir = '/data/pt_02151/';
cfg_path =  [ana_dir 'analysis/manuscript_sep/scripts/cfg_srmr2/']; % here is important info for the analysis
% Add paths
addpath('/data/pt_02068/toolboxes/eeglab14_1_2b/')
addpath(genpath('/data/pt_02068/analysis/manuscript_sep/scripts/functions/'))
% Start EEGLab
eeglab; 
close

n_subjects = 24;

for subject = 1:n_subjects
    
    % set path
    subject_id = sprintf('sub-%03i', subject);
    analysis_path = [ana_dir 'analysis/final/tmp_data/' subject_id '/'];
    
    % define different endings for each block
    for condition = 1:5 % 1 = rest, 2 = median digits, 3 = median mixed nerve, 4 = tibial digits, 5 = tibial mixed nerve
        [cond_info] = get_conditionInfo(condition, srmr_nr);
        cond_name = cond_info.cond_name;
        nblocks = cond_info.nblocks;
        
    
        
        for iblock = 1:nblocks
            
            
            %% ===== load data =============
            load([cfg_path 'cfg.mat'], 'srate_rpeak')
            fname = ['noStimart_sr' num2str(srate_rpeak) '_ecgChan_' cond_name '_' num2str(iblock) '.set'];            
            cnt = pop_loadset('filename', fname, 'filepath', analysis_path);
            
            
            %% ===== R-peak detection =============
            % run qrs detection plugin from fmrib toolbox
            ecg_channel = 1;
            cnt_qrs = pop_myfmrib_qrsdetect(cnt, ecg_channel, 'qrs', 'no');
            cnt = cnt_qrs; clear cnt_qrs
            
            
            %% ===== save =============
            fname_new = ['noStimart_sr' num2str(srate_rpeak) '_rpeak_autocorrect_ecgChan_' cond_name '_' num2str(iblock) '.set'];
            cnt = pop_saveset(cnt, 'filename', fname_new, 'filepath', analysis_path);
            
            % clear unnecessary variables
            clearvars -except subjects subject condition cond_name iblock
        end
    end
end