% folder location
subjfolder = '/Users/Desktop/XXX/CPU';
subjpattern = 'CPU*';
funcfolder = 'functional';
anatfolder = 'struct';

% settings (for spm5_preprojobs)
funcpattern = 'r*340';
anatpattern = '';
usestruct = true;
runjobs = true;
disdaqs = 5;
smoothmm = 6;
sliceorder = 'aio';
tr = 2;

% complete settings
if ~isempty(funcpattern)
    ffp = [funcfolder '/' funcpattern];
else
    ffp = funcfolder;
end
if ~isempty(anatpattern)
    anatpattern = [anatfolder '/' anatpattern];
else
    anatpattern = anatfolder;
end
ppopts = struct( ...
    'fun2str', usestruct, ...
    'jobrun', runjobs, ...
    'skip', disdaqs, ...
    'smk', smoothmm, ...
    'sto', sliceorder, ...
    'sttr', tr);

% find subjects
subjects = findfiles(subjfolder, subjpattern, 'depth=1', 'dirs=1');

% for each subject
for sc = 1:numel(subjects)

    % determine whether the subject needs processing
    rps = findfiles([subjects{sc} '/' funcfolder], 'rp*.txt');
    if ~isempty(rps)
        continue;
    end
    
    % get subject ID
    [basefld, subjid] = fileparts(subjects{sc});
    subjid(subjid == '_') = [];
    
    % run fMRI quality on all runs
    runs = findfiles([subjects{sc} '/' funcfolder], funcpattern, 'dirs=1', 'depth=1');
    for rc = 1:numel(runs)
        q = fmriquality(findfiles(runs{rc}, {'*.img', '*.nii'}));
        save(sprintf('%s/fmriquality.mat', runs{rc}), 'q');
        clear q;
    end
    
    % run preprocessing
    [j, jh, ppfiles] = spm5_preprojobs(subjects{sc}, ffp, anatpattern, ppopts);
    
    % for each run, create one VTC
    for rc = 1:numel(ppfiles)
        [basefld, runid] = fileparts(fileparts(ppfiles{rc}{1}));
        vtc = importvtcfromanalyze(ppfiles{rc});
        vtc.TR = round(1000 * tr);
        vtc.SaveAs(sprintf('%s/%s/%s_%s.vtc', subjects{sc}, funcfolder, subjid, runid);
        vtc.ClearObject;
    end
end