organizeconcatData.m

% Get subject numbers for everyone in LMB_Analysis folder 
root_dir = '/mnt/diskArray/projects/LMB_Analysis';
%sub_list = HCP_autoDir(root_dir);

%sub_list = {'NLR_110_HH','NLR_145_AC','NLR_150_MG','NLR_160_EK','NLR_161_AK'...
%    'NLR_162_EF','NLR_163_LF','NLR_164_SF','NLR_170_GM','NLR_174_HS'};

sub_list = {'NLR_IB357'};
% sub_list = {'NLR_GB310','NLR_GB355','NLR_GB387','NLR_GB267','NLR_JB420',...
%     'NLR_JB423','NLR_197_BK','NLR_KB218','NLR_HB275'};
    

    % For each subject (si = subject index)
for si = 1:length(sub_list)
    % Get the visit dates 
    visit_dir = strcat(root_dir,'/',sub_list{si});
    cd(visit_dir)
    mkdir('concatVistaAligned')
    concatDir = strcat(visit_dir,'/concatVistaAligned');
    visit_dates = HCP_autoDir(visit_dir);
    % For each visit (vi = visit index)
    for vi = 1:length(visit_dates)
        % Check to see if the vist date folder is actually a date
        a = visit_dates{vi};
        sizeA = size(a);
        sizeA = sizeA(2);
        if sizeA == 8
            raw_dir = strcat(root_dir, '/', sub_list{si}, '/',visit_dates{vi},'/raw');
            cd(raw_dir);
            EPI_names = dir('*EPI_106VOL*.PAR'); % check the raw directory for 70V functionals 
            nFunctionals = size(EPI_names);
            nFunctionals = nFunctionals(1);
            if ~isempty(EPI_names) %If there are functionals, make fmri directory and convert parrec files
            % Convert to nifti and sace into functional directory
                for fi = 1:nFunctionals
                    parrecCommand = strcat('parrec2nii -o', {' '},concatDir,{' '},'-c -b',{' '},EPI_names(fi).name);
                    parrecCommand = parrecCommand{1};
                    system(parrecCommand)           
                end
            
            end
        end 
    end 
end