So you problem is that you cannot figure out how to save a file to a new same-name file in another directory?
If so something like this should be the pattern:
Dicomfiles = dir('*.dcm');
New_dir = 'Dir4newsmallimages';
mkdir(New_dir);
for iFile = 1:numel()
X = dicomread(Dicomfiles(iFile).name);
INFO = dicominfo(Dicomfiles(iFile).name);
% and whatever you need from the file
Xout = improcessing(X); % or whatever you need to do with the image
INFO = metadatafixing(INFO); % You might have to modify the meta-data to match Xout
outname = fullfile(New_dir,Dicomfiles(iFile).name)
dicomwrite(Xout, outname, INFO);
end
HTH