CONN_demo.m

clear all;
base_dir='D:\Reading_FC';

% get subject IDs

sub_ids = {dir([base_dir '/sub-047EPKL*']).name};

global CONN_gui; CONN_gui.usehighres=true;
clear batch;
% initiate batch
NSUBJECTS=length(sub_ids);
batch.filename=fullfile(base_dir,'conn_demo.mat');
batch.Setup.isnew=1;
%batch.parallel.N=height(sub_df);
% batch.parallel.N=5;
% batch.parallel.profile='Slurm computer cluster';

batch.Setup.nsubjects=NSUBJECTS;
batch.Setup.RT=2.34;
batch.Setup.functionals=repmat({{}},[NSUBJECTS,1]);


for nsub = 1:length(sub_ids)

    sub_id=sub_ids{nsub};
    anat_file=[base_dir '/' sub_id '/ses-1/anat/' sub_id '_ses-1_T1w.nii.gz'];
    func_files=dir([base_dir '/' sub_id '/ses-2/func/' sub_id '_ses-2_task-read_run-*.nii.gz']);
    timing_files=dir([base_dir '/' sub_id '/ses-2/func/' sub_id '_ses-2_task-read_run-*_events.tsv']);
    conditions={'W','PH'};
    for nses=1:length(func_files)
        batch.Setup.functionals{nsub}{nses}{1}=[func_files(nses).folder '/' func_files(nses).name];
        timing_file=[timing_files(nses).folder '/' timing_files(nses).name];

        % read timing file in array
        timing = readtable(timing_file,"FileType","text",'Delimiter', '\t');
        % set up timing files for each run
        for ncond=1:length(conditions)
            batch.Setup.conditions.names{ncond}=conditions{ncond};
            batch.Setup.conditions.onsets{ncond}{nsub}{nses}=table2array(timing(strcmp(timing.trial_type, conditions{ncond}),'onset'));
            batch.Setup.conditions.durations{ncond}{nsub}{nses}=table2array(timing(strcmp(timing.trial_type,conditions{ncond}),'duration'));
        end
    end
    batch.Setup.structurals{nsub}=anat_file;
end

% setting up group level covariates
batch.Setup.subjects.effect_names{1}='dysexia';
batch.Setup.subjects.effect_names{2}='spd';
batch.Setup.subjects.effect_names{3}='td';

batch.Setup.subjects.effects{1}=[ones(1,20) zeros(1,38)];
batch.Setup.subjects.effects{2}=[zeros(1,20) ones(1,16) zeros(1,22)];
batch.Setup.subjects.effects{3}=[zeros(1,36) ones(1,22)];


batch.Setup.overwrite=0; % not overwrite
batch.Setup.done=0; % not run Setup


conn_batch(batch)