Hi Ana,

Do you mean that the glass-brain MIP and the "overlays -> sections" views are displayed differently (e.g. with the axial image on its side with anatomical left at the top) compared to using the Display or Check Reg buttons on the processed images (where e.g. axial is upright, with anatomical left on screen left)?

These are actually just display conventions; the image orientation itself, in terms of the mapping from voxel indices to mm coordinates, should be consistent. E.g. if you use Check Reg to compare one of the images from the SPM results directory (e.g. the mask image) to one of the processed images that go into the statistical model, you should find they are aligned.

As to why the MIP/overlays convention differs from the Display/CheckReg one, that is a good question... It's possible that SPM12 will offer the user a choice of either of these conventions (perhaps others too) and then use the chosen one consistently, but I can't promise this...

Best wishes,
Ged