Hi,
I think you should be able to do that regardless of the template yes, as the pipeline does not rely on the template at this stage, that only has to do with how you processed the fixel data.
I have not tried myself but I don’t think all participants need to be included for fixelcfestats to work (the number of rows in the design matrix should match your inputted files.txt list though). You could try to make a design matrix with an intercept column made of 1s, no group column this time, and only your patient rows. The model should then test the effect of the IV you want to test across the participants in the rows.
Maybe this thread can help:
https://community.mrtrix.org/t/cfe-multiple-partial-correlation/
Charly