Hi, Zhihao-

Another thing that came up while we were discussing this briefly-- FreeSurfer actually distributes AFNI's 3dvolreg, and has for quite some time. It used to just be called "3dvolreg", but to avoid path/version confusion, they changed its name to "3dvolreg.afni". It is an older 3dvolreg---the compile date on that appears to be Aug 29, 2012, even in FS 6.0.0---but do you think it is possible that you might have a very old FreeSurfer on that node, before they renamed it? (This is an outside-the-box idea for hypothesizing how a different form of 3dvolreg might have come to be run on your data; it is very likely this is not the actual reason, but maybe something to check.)

As to what might have changed, it is hard to say without knowing the date of "that" 3dvolreg; there are a number of tweaks/changes from around/before 2017:
[github.com]

--pt