Step02_organize_files.m

%Step02: Organize files
%Shao-Fang Wang 2016
%1. Split 4D file into individual 3D files
%2. Put the 4D file into another directory
%3. Put the first few volumes into another directory
%**Remember to edit initialize_vars

clear all;
clc

% get and set paths
scriptdir = pwd;
addpath('/Volumes/Macintosh HD/Users/Pamsfwang/Documents/MATLAB/spm12/')
addpath('/Users/Pamsfwang/Desktop/VR_nims/scripts/preprocessing/spm_preproc/'); % add any necessary paths (e.g., to initialize_vars)


subjects = {'vr15' 'vr23' 'vr29'};
mkdir_4D = '4D'; %folder for 4D file
mkdir_rmv = '5v'; %folder for removed volumes
n_rmv = 5; %number of volumes at the begining of a scan to be removed

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
errorlog = {};ctr = 1;

for i=1:length(subjects)
    fprintf('Processing subject %s \n',subjects{i})
    b = initialize_vars(subjects,i);
    
    for irun = 1:length(b.funcRuns)
        
        try
            fprintf('\t Processing %s \n',b.funcRuns{irun})
            cd([b.dataDir b.funcRuns{irun}])
            %making directory
            mkdir([b.dataDir b.funcRuns{irun}],mkdir_4D);
            mkdir([b.dataDir b.funcRuns{irun}],mkdir_rmv);
            
            %moving .mat and .nii file (4D) into the 4D folder
            fmat = dir('*.mat');
            fnii = dir('*.nii');
            movefile(fmat.name,[b.dataDir b.funcRuns{irun},'/',mkdir_4D]);
            movefile(fnii.name,[b.dataDir b.funcRuns{irun},'/',mkdir_4D]);
            
            %4D to 3D
            spm_file_split([b.dataDir b.funcRuns{irun},'/',mkdir_4D,'/',fnii.name],[b.dataDir b.funcRuns{irun}])
            nii_3D = dir('*.nii');
            
            for irmv = 1:n_rmv
                movefile(nii_3D(irmv).name,[b.dataDir b.funcRuns{irun},'/',mkdir_rmv,'/']);
            end
            
        catch err
            
            errorlog{ctr,1} = subjects{i};
            errorlog{ctr,2} = b.funcRuns{irun};
            errorlog{ctr,3} = err;
            ctr = ctr + 1;
            cd(scriptdir);
            
            continue;
        end %try
        
    end
    
end

if ~isempty(errorlog)
    disp(errorlog) % print error log at end
else
    disp('No errors detected.');
end