2023_Kalantari_AIDAqc/code/MotionCorrection_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', '*nii.gz');
rsfmri_files = dir(searchpath);
rsfmri_files = fullfile({rsfmri_files.folder}, {rsfmri_files.name});

% Parameters for motion correction
transformType = 'translation'; % Type of transformation (e.g., translation)
[optimizer,metric] = imregconfig("multimodal")
% Loop through each rsfMRI file for motion correction
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);

    % Drop the first 10 volumes
    Im = Im(:,:,:,11:end);
    info.ImageSize(4) = size(Im, 4); % Adjust header info to the new size
    
    % Reference image for registration (using the first volume)
    fixed = Im(:,:,:,1);
    
    % Perform motion correction for each volume
    for t = 2:size(Im, 4)
        % Register the current volume to the reference volume
        moving = Im(:,:,:,t);
        moving_reg = imregister(moving, fixed, transformType, optimizer, metric);
        
        % Replace the original volume with the registered volume
        Im(:,:,:,t) = moving_reg;
    end
    
    % Save the motion-corrected 4D rsfMRI image
    [filepath, filename, ext] = fileparts(file);
    output_filename = [filename '_mc' ext]; % Appending '_mc' to the filename
    output_path = fullfile(filepath, output_filename);
    niftiwrite(Im, output_path, info, 'Compressed', true);
end