We would like to thank the reviewers for their insightful comments. The major points that have been addressed are as follows:
It was not our intention to give the impression that one needs to scan human calibration phantoms at each site to properly power a multisite study with nonstandardized parameters, which is very costly. The statistical model which takes MRI bias into account has been emphasized instead. The bias that was measured and validated via calibration served to corroborate the scaling assumption of the statistical model. For other researchers planning multisite studies, the statistical model we proposed with the biases we reported should help plan and power a study.
Our measurements have been compared with other harmonization efforts, specifically \cite{cannon2014, jovicich2013brain} and \cite{Schnack_2004}.
The scanning parameters of our consortium have been better specified.
The independence assumption between the unobserved effect and the scaling factor for a particular site have been addressed. Specifically, we emphasized that this assumption could hold for MS patients based on our experiment. The need to validate this assumption for other situations by scanning human phantoms was recommended, and the equation of variance without the independence assumption has been provided for the readers.