I don't know how far you have gotten with this; but here are two pretty common ways to get it done. 
I have heard that this first (and easier) one doesn't always work; but it has proven great for some.
sudo add-apt-repository ppa:zedtux/naturalscrolling
sudo apt-get update
sudo apt-get install naturalscrolling
Otherwise:
- In terminal:
gksu gedit
- Paste the following to the text file.
pointer = 1 2 3 5 4 6 7 8 9 10 11 12
(notice that #4 and #5 are switched. This represents the switch in the vertical scrolling direction... if you want the horizontal scrolling to switch as well, just switch the 6 and 7)
Save the file with the name .Xmodmap (with the dot in front) in the Home folder.
Close the file as well as terminal.
Log in & out and the mouse scrolling direction should change now.
To revert the setting, just remove the .Xmodmap file from you system.