There is a follow-up software available at https://www.nitrc.org/projects/visualign/, it allows users to make in-plane nonlinear refinements on top of QuickNII results.
Two remarks:
 - VisuAlign needs the JSON variant of QuickNII output, so if it does not list anything when you try to open a series, open it in QuickNII and save as JSON first
 - VisuAlign is available for Windows at the moment. If you need it for Mac, please let me know, I think I can make such version in a finite timeframe.