Hi Rujing,
AFNI has used the Euclidean norm, sqrt(sum squares), since long before FD was suggested, and it still does. RMS is slightly different, too, which is scaled down by (sqrt of) the number of terms.
Note that FD does not make so much sense to use as a distance measure in any case. For example, the distance between points at (0,0,0) and (1,1,1) should be sqrt(3)~=1.73, not 3.
- rick