my software revision is 02.00.0003
As I said in my post of 6/21, you need to have the newest SW, or pretty close to it. The current version is 3.50.something. It is available here:
http://www.agilent.com/find/scope-apps-sw Once you have done that, you will be able to follow Kevin's instructions to get the decode. The update will take an hour or two, since you are so far behind. You will have to run a user calibration on it after doing the update.
First, before you load the latest firmware, you should connect it to the internet, and run Microsoft Update as many times as necessary, if you haven't done that in a while. Make sure you get all of the latest .NET patches. Remember, besides being a scope, it's a PC. If you don't have antivirus SW, you should install some. I recommend Microsoft Security Essentials (MSE). It's free and relatively low-load.
Now I just have 1 channel serial decode. 2 wire SPI works fine, but 4 wire doesn't.
You don't have a "true" 4-wire SPI, so as I said earlier, using the 4 wire decode doesn't and won't work. You need to treat it like 2 2-wire SPI links, that happen to share a clock. to do that, you need the newest SW, and you'll use 2 probes on the clock.
Also I plan to read oscilloscope data via MATLAB. Does the software and firmware revision influence the result of my MATLAB script?
In some cases, yes. While you are installing the newest SW, read the "ReadMe" document, that talks about the changes that have been added since you last updated. Then, look in the "Script and Programs" section for some pointers, including examples. If you post there, others will get the benefit of seeing the answers.
Al