Hi @Joe,
If you already have a fixel mask of the “fixel region” you’re after, you’re very close to what you want to get. The key thing to realise is that many MRtrix commands designed to work on “voxel images” can work on fixel data files just as well… as long as those data files come with (a copy of) the same index.mif file. That would be the case already for your fixel mask as well as the data files (FD, FC, FDC), as they also share that requirement of a common index.mif for the fixel stats (and those you’ve been able to run successfully).
Your fixel mask, for instance, would be a binary “fixel data file” sitting in one of your fixel folders. Lets say it’s called “fixelmask.mif”. You’d also have fixel folder with all your FD fixel data files, if you’ve been running FBA analysis. Let’s say a subject’s data file in your FD fixel folder is named “subject001.mif” or something. You can then simply run mrstats (name doesn’t suggest being able to act on fixels, but it works nonetheless!) on subject001.mif and add the -mask option, while providing the latter with fixelmask.mif. The output would give you your mean FD within that fixel mask, for that subject (and a range of other stats as well, like the median, or min/max, etc… even the fixel count in your mask).
To already answer another potential question that might be coming up in this context: if you’re going to be averaging stuff within a (fixel) region, and wondering whether to use FC or log(FC), the answer is log(FC). 
Cheers,
Thijs