ica_cleaning.m

% Spatial smoothing the motion-corrected images with a Gaussian kernel 
% with FWHM = FWHM_ica; Run ICA on smoothed images with #IC=50 
% (feed 'inputs_ica.m' to the GIFT toolbox).

%%%%%%%%%%%%%% set parameters %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
data_dir='/path/to/data';
FWHM_ica=0.7; %FWHM=0.7mm
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Author: Yikang Liu
% Last modified data: 05/24/2020

rat_list = dir(fullfile(data_dir, 'rat*'));
for i=1:length(rat_list)
    cd(fullfile(data_dir, rat_list(i).name, 'rfmri_intermediate'));
    scan_list = dir('*warped.nii.gz'); 
    
    for j = 1:length(scan_list)
        scan_name = scan_list(j).name(1:2);
        
        % make a folder for ICA results
        folder = fullfile(pwd, [scan_name, '.gift_ica']);
        mkdir(folder);
        delete([folder, '/*']);
        
        % load a motion corrected image
        nii = load_nii([scan_name, '_warped.nii.gz']);
        img = nii.img;
        
        % spatial smoothing
        if FWHM_ica > 0
            img = rsfmri_smooth(img,FWHM_ica,nii.hdr.dime.pixdim(2));
            img(isnan(img)) = 0;
            nii.img = img;
            tmp = fullfile(pwd, [scan_name, '_despiked_registered_aligned_sm_ica.nii']);
            save_nii(nii, tmp);
        else
            tmp = fullfile(pwd, [scan_name, '_despiked_registered_aligned_sm_ica.nii']);
            save_nii(nii, tmp);
        end
        
        % write a script for GIFT ICA
        script_dir = strrep(mfilename('fullpath'), mfilename, '');
        fi = fopen(fullfile(script_dir, 'inputs_ica.m'),'r'); % open a script template
        fileo = fullfile(script_dir, ['inputs_ica',...
            rat_list(i).name,'_',scan_list(j).name(3:4),'.m']); 
        fo = fopen(fileo,'w'); % the file to write into
        
        % replace strings in the template to generate script for the scan
        while ~feof(fi)
            l = fgetl(fi);
            if strfind(l,'outputDir') == 1
                l = ['outputDir = ''',...
                    folder, ''';'];
            end
            if strfind(l,'input_data_file_patterns =') == 1
                l = ['input_data_file_patterns = {''',...
                    tmp, '''};'];
            end
            fprintf(fo,'%s\n',l);
        end
        fclose(fi);
        fclose(fo);
        
        cd(folder);
        icatb_batch_file_run(fileo); % run the script with GIFT ICA
        close all;
        
        % delete spatially-smoothed image after ICA
        cd(fullfile(data_dir, rat_list(i).name, 'rfmri_intermediate'));
        delete(tmp);

        % save .json file
        fid = fopen([scan_name, '_warped.json'], 'r');
        s = fread(fid);
        a = jsondecode(char(s)');
        a.Steps.Order = [a.Steps.Order, '; IC Noise Cleaning'];
        a.Steps.ICA.software = 'GIFT ICA';
        a.Steps.ICA.spatial_smoothing_fwhm = [num2str(FWHM_ica), ' mm'];
        a.Steps.ICA.IC_number = 50;
        
        s = jsonencode(a);
        json = [scan_name, '_cleaned.json'];
        fid = fopen(json, 'w');
        fwrite(fid, s, 'char');
        fclose(fid);
        a = loadjson(json); savejson('', a, json); % reformat
    end
end