This has not worked for me nor did the solutions posted previously. So I appreciate that this is probably not the correct method or indeed good practice but here is my solution.
1.Assuming Piwik is installed and setup add your Limesurvey root URL as a website to track e.g.
www.somewebsite.com/limesurvey (in piwik 1.9.2 this is done by going Settings > Websites > Add new website)
2.This will generate the custom Piwik Javascript tracking code, it will look almost identical to the above posted by Denis.
3.Create a new blank html document, with nothing in it, place the Javascript code just before the </body> tag.
4.Upload the documents to your template folder.
5.Open your welcome.pstpl in the last section after (WELCOME) but before any closing </td></tr></table> tags (this will depend on your template) add a link to your blank page using an iframe.
You then need to style the iframe (not the embedded page) using CSS to make it invisible, you can either add this to your template CSS or do it inline. Below is an example:
<iframe name='iframe1' id="iframe1" src="/templates/mytemplate/blank.html" frameborder="0" border="0" cellspacing="0" style="border-style: none;width: 100%; height: 0px;"></iframe>
If you keep this in templates you will not need to worry when you run a LS update. If you use more than one template just replicate it there as well.
…there must be a better way but I have not found it.