Use tck&fixel in template to AFD

Hi,MRtrix3 experts:
As the figures showing. I have gotten the fixel in template space and the tracks. I do know how to calculate the AFD in these ROIs of the tracks. I would be grateful if you could teach me how to use the command.

Hi @yichao,

Once you have a fixel mask corresponding to the pathway of interest, the mrstats command can be run directly on image afd.mif, providing that fixel mask via the -mask option, to calculate statistics such as the mean within only that set of fixels of interest.

For the derivation of that fixel mask, there’s an infinite number of ways in which such a mask could be derived. The simplest however is to, for each pathway of interest, calculate the streamline count per fixel (tck2fixel command), and then apply a threshold (mrthreshold) to produce a fixel mask for that pathway.