I don't know the details of your study nor your analysis, so I can only make some general comment.
> 1. A lot of studies have demonstrated that the pre-processing steps used by the authors still might not fully take
> care of motion artifacts and we know that there are strong group-level differences in motion parameters.
One possibility is to control the motion effect at the group level by using those motion parameters as an explanatory variable (i.e., covariate).
> 2. My main comments to the paper are that the authors do not show how the results could be affected
> by artifacts and noise in the data that clearly affect global connectivity results.
To address that concern, you may perform another analysis without controlling for the effects of those artifacts and noise, and see how they differ.
Gang
