Hello @Benjamin_Deck ,
If you want to compare fixels across your participants, there needs to be fixel correspondence along the length of your tracts of interest. I’m not sure how you would ensure this if they were not mapped to a common template.
Perhaps worth reading this page to understand the intended use of tck2fixel and see if it is indeed what you need. Otherwise you could use tcksample to get FA values or similar from each point along the tract and then compare these values across participants - again as the spatial overlap of these points is not ensured, you will have to find a way to ensure you are comparing the same part of the tract (perhaps by comparing the connectivity at a percentage distance of the length of the tract).
Hope this helps,
Nick