I’m trying to register two head and neck ct volumes with BRAINS , yet I’m not having a good result, any suggestions?
I would recommend to remove the u-shaped head holder (e.g., using Mask volume effect in Segment Editor) before registration.
You may also need to tune registration parameters, because BRAINS often does not work well with the default settings. Alternatively, you can use SlicerElastix or SlicerANTs extension, because they typically provide good registration results with default settings.