clear, clc
% voxel size of EPI images
vars.vox_size = [2 2 2];
% smoothing vector
vars.smooth_vec = [6 6 6];
% bounding box
vars.b_box = [-90 -126 -72; 90 90 108];
% assign appropriate vector for the phase encoding direction
vars.wrapping_dir = 'z';

% slice timinig parameters
slice_timing.nslices = 34;      % # of slices
slice_timing.TR = 2;            % TR in secs
slice_timing.sliceOrder = [1:2:slice_timing.nslices 2:2:slice_timing.nslices]; % order of slices
slice_timing.refSlice = 17;     % reference slice, should be set to middle slice

%% Full path of experiment folder
data_path = '/media/System/Glad/Matlab_Kurs';

%% Field Map Directory name (not full path)
fieldMapDir = '01_gre_field_34_2x_betrag';

%% Subjects and sessions folders (not full path)
subjects = {
            'subject1',...
            'subject2'
            };
%  Sequence folders
sessions = {
            'wasser',...
            'jaw'
            };
        
%% Initialise SPM defaults
spm('Defaults','fMRI');
spm_jobman('initcfg');

preprocessing_job(data_path,fieldMapDir,subjects,sessions,vars,slice_timing);
