2023_Blaschke_Stroke_tDCS_rsfMRI/scripts/addendum/transform_data2BIDS.m

parent_path = "E:\Projects\CBIrep_Imaging\Raw";
cd (parent_path)
addpath("..\scripts\toolbox\DVARS-master\")
addpath("..\scripts\toolbox\DVARS-master\Nifti_Util\")
addpath("..\scripts")
addpath("..\scripts\toolbox\spm12")
addpath("..\scripts\toolbox\fMRI-Quality-Checker-master")
addpath("..\scripts\toolbox\spm12\matlabbatch")
addpath("..\scripts\toolbox\nifti_utils-master\")

%% Preps
BIDS_path = "E:\Projects\CBIrep_Imaging\subjects";

% physio_files = "F:\Projects\StrokePT_tDCS_rsfmri\physio";
    % cd (physio_files)
    % phx = dir("SB*");

timeX = {'tpA','tpB','tpC','tpD','tpE','tpF','tpG'};

%% level1: subjects
cd (parent_path)
gx = dir("sub*"); 

for g = 18:length(gx)
    subject = gx(g).name;
    cd (fullfile(gx(g).folder,gx(g).name,"MRI/"))

%% level2: timepoints
    tx = dir('tp*');
    for t = 1:length(tx)
        time = tx(t).name;
        cd (fullfile(tx(t).folder,tx(t).name))
        session = strcat('ses-',num2str(find(strcmp(time,timeX))));

%% level3: scans
% copy data to BIDS
            folder_from = pwd;
            folder_to = fullfile(BIDS_path,subject,session);
              
                if ~exist(folder_to,"dir")
                    mkdir(folder_to)
                end
% copy MRI data
                copyfile(folder_from,folder_to)
                
% % % % %                 copy physio data
% % % %             if exist("physiofolder","var")
% % % %                 physio_to = fullfile(folder_to,"physio",phx(physioID).name);
% % % %                 if ~exist(physio_to,"dir")
% % % %                     mkdir(physio_to)
% % % %                 end
% % % %                 copyfile(physiofolder,physio_to);
% % % %             end

%%
cd (folder_to)
if exist("fMRI","dir")==7
movefile("fMRI","func")
end
if exist("T2w\","dir")==7
movefile("T2w","anat")
end


    end
end