Hey Sila,
Was really hoping that someone would take this one on while I was away on leave; alas… Although I’m working on developments with respect to stats and the GLM, I’m by no means an expert yet, so I’ll say what I can and we’ll see if anybody comes to my rescue.
For example, in FSL you can set up your GLM to handle repeated measures by either setting up a paired t-test to test a group difference (which I guess might be possible in CFE), …
Any experiment that you can express as a design matrix and contrast vector should be compatible with fixelcfestats. Having said that, we haven’t yet ourselves gotten to longitudinal analyses yet (as far as I know…), so I’d be curious to see how you progress with it.
… but for a group-difference over time the 4D input file is subtracted over time (e.g. ) to test a group difference over time.
If you need to / it is more convenient to pre-calculate individual difference-over-time images, this is absolutely possible; an advantage of the new fixel format is that each fixel is consistently represented using the same index across all fixel data files, and therefore commands such as mrcalc can in fact perform operations on fixel data files.
I imagine this might get tricky when dealing with different fibre directions over time…
The above is obviously only possible if you have fixel correspondence across all subjects and time points. So you’ll need a single fixel template for all data, not one for each time point.
Thinking about it on-the-fly, there’s a danger that if the results of FOD segmentation vary between time points for a particular subject (e.g. two lobes at timepoint 1 being segmented as a single lobe at timepoint 2), you could end up with massive false temporal changes that will significantly impact the GLM fit. So you will need to find a way of detecting when such mismatches occur, and probably set the temporal change to zero for that subject (I’ll have a better solution for this in the future…)
I think maybe the other option would be to generate whole-brain AFD maps…
… 
I reckon shoot for the FBA. This is something we need to support, so you might as well be the pioneer… 
Keep in touch if you need to.
Rob