Hello QuickNII community, 

My name is Penny Young and I am a MSc candidate at the University of Victoria. I was wondering if anyone has figured out a way to perform free-form registration with the QuickNII tool or if the makers have shared that they are working on this? I find QuickNII is a wonderful tool to circumnavigate slice angle irregularities, but without being able to warp the atlas I can't use most of my serial sections. Does anyone have any suggestions? I have also looked into aMAP, but I find it is not as user friendly. 

Thank you for your time and input.

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.

Hello Gergely, thank you very much this is very helpful. I do work on a Macbook Air at home, but it only has 4GB RAM. If VisuAlign requires more I may just need to upgrade computers, possibly to a Windows. How long does it take to make VisuAlign for Mac, and what sort of fee would it cost my lab?

Thank you for your time.

Hi Penelope, VisuAlign for Mac is available for download at https://www.nitrc.org/frs/?group_id=1426
It has not much documentation, but "Quick reference" in the Help menu lists the controls at least.

Thank you very much Gergely!