You can use a filedatastore with a reader function that loads the appropriate variables from the .mat files.
Or you can use dir with ** wildcard:
dinfo = dir('D:\ABIDEdataset\Outputs\dparsf\nofilt_noglobal\rois_aal\**\*.mat');
filenames = fullfile({dinfo.folder}, {dinfo.name});
numfiles = length(filenames);
for K = 1 : numfiles
thisfile = filenames{K};
do something with thisfile
end
