How to Diagnose and Fix Freezing For A few Seconds Every Few Minutes

When your desktop freezes, write down the exact time.

Either wait for the desktop to unfreeze or ssh into the machine, and then view /var/log/syslog for the time that you wrote down it freezing.

In the my case the logs had NOUVEAU lines around the time of the freeze, I replaced the Nouveau display driver with the NVIDIA binary driver, and that resolved the intermittent freezes.

For me there was nothing showing in /var/log/syslog, however I noticed it happened every time I copied to the clipboard. Turned out to be a clipboard manager called copyq. Ran apt purge copyq && apt install copyq and the problem went away. This probably isn't helpful to know my solution, but it may be helpful to know the problem isn't always output to the syslog.