Hi Milo,

Thanks for using SLOMOCO. It should be performed on the raw data, before any other correction or preprocessing has been done. The blur command inside the script is to assist the volumetric registration to work on single slice data hidden inside a volume of fixed data. The registration I'm using was never intended to work in this manner, but with these methods it does work. Any other processing you wish to do should follow SLOMOCO.

You mentioned despiking, does your data have gradient/RF spike artifact in it?

Erik