You probably want to work on the Diff-Spect images which is the direct comparison between the two images instead of the individual images as those are not normalized and cannot be compared directly easily. You probably want to do a "paired" analysis instead of averaging the individual data. I would "Save Images in Reference Space" for your results and then you can import them into Matlab/SPM etc. and do whatever other analysis you want. Other tools in BioImage Suite can also do some things like this. These aspects of the Data Tree are not the best tested (and have not been used much since it was originally written ~10 years ago so I would not try to do too much within this.)