I have a number of scans for older subjects that I am attempting to skull strip but due to the high variability in atrophy rates and the increased ventricles I am getting back some output that is not up to the level I need it at. In attempts to find the best options within skull strip to run on my subjects I ran a number of different options simutaneously so that I could compare the outputs. I wanted to compare these back to the original anatomical datasets by overlaying the skull_stripped version over the regular structural scan but after skull_stripping a number of the scans seem to be off from the original orientation such that they do not overlay properly. Is there are way to compensate for this in the skull_stripping syntax or what would be the best way to then register these together to compensate?