If you're going to be doing specialized custom operations at each window location, then you need to us nlfilter. You define a function and then do whatever you want in there. Attached is a demo. Of you could have some nested for loops, over rows and columns, then inside there call a function like AnalyzeWindow() which you write to do your operations and return your feature vector.
[rows, columns, numberOfColorChannels] = size(yourImage);
for col = 1 : columns-7
for row = 1 : rows-30
results = AnalyzeWindow(yourImage, row, column); % You write this function.
end
end
