We’re working on better mechanisms to do this sort of thing, but for now you can definitely get it done with existing tools.
Since you’re only interested in the 3D spatial location of effects, and not orientation, you don’t actually need to worry about preserving orientation information for this particular purpose. I would just reduce the fixel-wise thresholded result in your study-specific template space to a voxel mask using the
fixel2voxel command, and transform the resulting binary mask to MNI space (based on having registered your population template to the MNI template). If you have multiple significant pathways, you could break them up using
maskfilter connect, followed by
mrcalc -eq to get a 3D binary mask corresponding to each connected component.
I do have an MRtrix3 command sitting here for calculating the centre-of-mass of an image, which would take such 3D binary masks and give you a single 3D location for each. Trouble is, I can’t decide what to call it