fmrwhy_settings_validate.m

function options = fmrwhy_settings_validate(options)
    % fmrwhy_settings_validate: Validate and derive settings for the fmrwhy_workflow_qc pipeline

    % BIDS structure values
    options.bids_dataset = bids.layout(options.bids_dir);
    options.subjects = bids.query(options.bids_dataset, 'subjects');
    options.sessions = bids.query(options.bids_dataset, 'sessions');
    options.runs = bids.query(options.bids_dataset, 'runs');
    options.tasks = bids.query(options.bids_dataset, 'tasks');
    options.types = bids.query(options.bids_dataset, 'types');
    options.modalities = bids.query(options.bids_dataset, 'modalities');

    % set list of subjects for which to generate QC output
    % If options.subjects_output is set to 'all' (default), read the list from the bids.query output, otherwise leave as is
    if strcmp(options.subjects_output, 'all')
        options.subjects_output = options.subjects;
    end

    % Set template for functional realignment purposes (if not needed, set to [])
    options.template_sub = options.subjects{1};

    % Dataset parameters
    options.Nsessions = numel(options.sessions);
    options.Ntasks = numel(options.tasks);
    options.Nruns = numel(options.runs);

    % Derive template flags from BIDS structure
    options.has_sessions = ~isempty(options.sessions);
    options.has_runs = ~isempty(options.runs);
    if options.has_sessions
        if options.has_runs
            filenames = bids.query(options.bids_dataset, 'data', 'sub', options.template_sub, 'task', options.template_task, 'sess', options.template_session, 'run', options.template_run, 'type', 'bold');
        else
            filenames = bids.query(options.bids_dataset, 'data', 'sub', options.template_sub, 'task', options.template_task, 'sess', options.template_session, 'type', 'bold');
        end
    else
        if options.has_runs
            filenames = bids.query(options.bids_dataset, 'data', 'sub', options.template_sub, 'task', options.template_task, 'run', options.template_run, 'type', 'bold');
        else
            filenames = bids.query(options.bids_dataset, 'data', 'sub', options.template_sub, 'task', options.template_task, 'type', 'bold');
        end
    end
    options.N_echoes = numel(filenames);
    options.is_multiecho = false;
    if options.N_echoes > 1
        options.is_multiecho = true;
    end

    % Sequence parameters
    options.Ne = numel(options.TE);

    if options.is_multiecho
        if options.N_echoes ~= options.Ne
            disp('ERROR: number of echoes derived from BIDS dataset (using bids-matlab) do not match the number of echo times specified in settings file. FIX!');
        end
    end