How to do manual alignment

I currently have a mask that isn’t in standard space and is too small in volume, making it impossible for algorithms to automatically align it with the structural image. I’m looking for a tool to manually align it with the structural image in standard space.

Thank you!

Hi @SophieLKim - FSLeyes has a rudimentary feature called Nudge, which is available under the Tools menu, and which allows you to manually align two images, and save a FLIRT transformation matrix. Another option I can think of is ITK Snap, which has some registration capabilities, although I’ve never personally used it.