2023_Kalantari_AIDAqc/code/MotionAddition_rsfmri.m

% Input folder path containing fMRI data
input_folder = "C:\Users\aswen\Desktop\TestingData\Aswendt_qc_data\proc_data";

% Get all rsfMRI files in the input folder
searchpath = fullfile(input_folder, '**', 'func', '*EPI.nii.gz');
rsfmri_files = dir(searchpath);
rsfmri_files = fullfile({rsfmri_files.folder}, {rsfmri_files.name});

% Parameters for motion addition
translation_amount_initial = 7; % Initial translation amount in pixels
translation_amount_growth = 1; % Amount by which translation increases at each time point
translation_amount_max = 30; % Maximum translation amount in pixels
timepoints = size(Im, 4); % Number of time points

% Loop through each rsfMRI file for motion addition
for i = 1:numel(rsfmri_files)
    % Read file
    file = rsfmri_files{i};
    
    % Load the 4D rsfMRI image and its info
    Im = niftiread(file);
    info = niftiinfo(file);

    % Initialize translation amount
    translation_amount = translation_amount_initial;
    
    % Add motion by shifting each volume in the time series
    for t = 1:timepoints
        % Apply translation to simulate motion
        Im(:,:,:,t) = imtranslate(Im(:,:,:,t), [translation_amount, 0, 0]);
        
        % Update translation amount for the next time point
        translation_amount = min(translation_amount + translation_amount_growth, translation_amount_max);
    end
    
    % Save the motion-added 4D rsfMRI image
    [filepath, filename, ext] = fileparts(file);
    output_filename = [filename '_motion_added' ext]; % Appending '_motion_added' to the filename
    output_path = fullfile(filepath, output_filename);
    niftiwrite(Im, output_path, info, 'Compressed', true);
end