afni.nimh.nih.gov

Yep, that's normal. See, for example, from pg 32 onward here describing more about the *.grid files:
[afni.nimh.nih.gov]
But, all the targets in a network are not necessarily connected directly to all other targets (that is the case biologically, and also for tracking, possible for related or different reasons); in general (and esp. for larger networks), that is not the case, and the "zeros" in the NT matrix (and also appearing in others) show where tracts were not found.

--pt