Well it would be at 16.5 pixels, but you don't need that at all. If the centers, wherever they may be, are 3 pixels apart, then so are the left sides, right sides, top edges, and bottom edges, so your left edges would be at 1,4,7,10,13, etc.
for col = 1:3:128
for row = 1:3:128
subMatrix = fullMatrix(row:row+31, col:col+31);
end
end
