Using cd makes code slow and harder to debug: instead of using cd simply use faster and more reliable relative/absolute filenames. Try doing something like this:
D = 'MainFolder';
Ss = dir(fullfile(D,'Subject_*'));
Ss = natsortfiles(Ss([Ss.isdir])); % alphanumeric sort by folder name
for ks = 1:numel(Ss)
tmp = [Ss(Ks).name,'_*.txt'];
Sf = dir(fullfile(D,Ss(Ks).name,tmp));
Sf = natsortfiles(Sf); % alphanumeric sort by filename
for kf = 1:numel(Sf)
tmp = fullfile(D,Ss(ks).name,Sf(kf).name);
table = readtable(tmp);
...
end
end
To get the filenames in the correct order I used my FEX submission natsortfiles, which provides an alphanumeric sort of filenames. To use it you will need to download it, unzip it, and place it on the MATLAB Search Path (e.g. in the current directory):
