MCFLIRT question: Granted that we use the -refvol default of the middle
volume as the reference, and call that volume N. The MCFLIRT web page
explains how volume N+1 is registered to N via a search for the best
fit. We're not able to determine something about how N+2 (or any N+x) is
A simple alternative is that the search for each of the N=? volumes is
relative to N. Downsides of that are that (1) it won't handle a gradual
motion that may be small from volume to volume but accrues too large
more distant in time from N and (2) that accrual problem will be worse
for longer recording sessions.
The MCFLIRT web page says that the N+1 adjustment is used as an estimate
for adjusting N+2. Our question is: what is meant by "estimate"? Read
literally, the web page could be understood to mean that the N+1
adjustment is applied to N+2 (i.e., no further search or optimization is
done for N+2). That would mean that the only motion that can be
corrected is that which occurs from N to N+1 or from N to N-1 (surely
not the case). Or, "search" could mean "starting point" for an
optimization for N+2.
A second alternative is that each N+x+1 volume is registered by
comparison to the N+x volume, with the final registration applied to
N+x+1 being the cumulative or net registration of all volumes N+1 to
A concrete implication of this choice is: if one sets a 2 mm criterion
for maximum allowed motion, in the first alternative that 2 mm is the
difference allowed between the N+x volume and the N (middle) volume,
whereas in the second alternative the 2 mm is the difference allowed
between adjacent volumes (thus, the change from N to N+x could be almost
as large as 2*x mm).
Thanks in advance.