Hi Jeff,

Yes, you will find plenty of references indicating that 6 minutes scanning sessions result in moderate to strong reliability for resting-state functional connectivity measures. For example you may point to Shehzad et al. 2009. "The Resting Brain: Unconstrained yet Reliable" (this is also the reference for the NYU test-retest dataset, in our own Whitfield-Gabrieli & Nieto-Castanon, 2012 manuscript we used this same dataset to show strong group-level reliability of connectivity measures using CONN). Another very good manuscript in this regard is Van Dijk et al. 2010. "Intrinsic Functional Connectivity As a Tool For Human Connectomics: Theory, Properties, and Optimization"

The reviewer is perhaps thinking along the lines of Birn et al. 2013. "The effect of scan length on the reliability of resting-state fMRI connectivity estimates", which recommends longer (12minutes or above) scanning sessions and show how that consistently increases the reliability of subject-level connectivity measures. If that is the case, perhaps you can simply point out that increases in within- and between-session reliability are only expected to increase your analysis power, but not change their validity (i.e. any significant results you are showing are still expected to be replicated in a higher-power experiment). There are, of course, many other factors which affect and limit the power of your analyses or your design choices. As you suggest practical concerns such as the ability to keep your subjects with minimal motion and compliant is one important consideration when determining the scan length. Also it is important to keep in mind that the between-subjects variability in connectivity measures is typically very large, and this very strongly limits the impact of improvements in the reliability of your single-subject measures on your second-level analysis sensitivity/power (e.g. doubling the number of subjects will typically have a much larger impact on your analyses power than doubling the scanning length). 

Hope this helps
Alfonso
Originally posted by Jeff Browndyke: