How to fix choppy/lagging video from Canon t3i?
There's a number of things that can be the issue, and a number of ways to try to work around them. 

The first is that depending on the specs of your computer, it might not be able to decode the video files quickly enough, which could cause a stutter. Similar to how people used to have issues trying to watch 1080p videos on Netbooks that didn't have much horsepower. What kind of PC are you using?

What video editing software are you using? Different editing softwares prefer different file formats. What kind of footage and for what purpose? Family footage or more professional presentation work? Are you planning on uploading it to youtube or the net or preserving it on a large hard drive somewhere? With those questions answered, I can recommend some codecs for editing, and codecs that you'll want to export to when you're all edited and finished. 

There are a number of free tools for converting video files. FFMPEG is a great one, but it has a little bit of a learning curve if you're not familiar with command line applications. If you'd like to take a stab at it, link below:

http://ffmpeg.zeranoe.com/builds/

If not, there are some GUI front-ends that you can use along with FFMPEG, that basically make it more user friendly by giving it buttons and sliders like applications you're used to. One of which is below:

http://avanti.arrozcru.com/