You can find the unique prefixes in the filename, and then use it to generate the string of numbers to rename the file. Here is an example to generate the filenames as per your need.
filename={'S01_0_VJ_01', 'S01_0_VJ_02', 'S01_0_VJ_03', 'S01_0_SP_04', 'S01_0_SP_05', ...
'S01_0_SP_06','S01_4_VJ_07','S01_4_VJ_08','S01_4_VJ_09','S01_4_SP_10','S01_4_SP_11',...
'S01_4_SP_12','S01_8_VJ_13','S01_8_VJ_14','S01_8_VJ_15','S01_8_SP_16','S01_8_SP_17','S01_8_SP_18'};
unique_prefix=unique(cellfun(@(x) x(1:8), filename,'uni', 0),'stable')
for unique_pre_index=1:length(unique_prefix)
new_filename{unique_pre_index}=arrayfun(@(x) strcat(unique_prefix{unique_pre_index},{'_'},num2str([x],'%02d')), ...
1:length(find(contains(filename,unique_prefix{unique_pre_index}))));
end
new_filenames=cat(2,new_filename{:});
old_new_filenames=[filename; new_filenames]'
In order to read all the filenames from a folder, you can use dir command to read all the files, and use this output to extract the filenames. Here is an example for this (You can uncomment the below two lines when running in your terminal):
% F=dir('S01*')
% filenames={F().name}
