FMRI machines are commonly used to allow direct observation of brain activity, and can be used for non-human animals. However in the case of an alien from a different planet, it's unclear how difficult it would be to adapt an FMRI machine to be able to pick up on alien brain activity.
As I understand it, FMRI mainly picks up on the small electrical currents through synapse ion channels, and assuming the alien in question uses similar ion channels for it's neurological activity there would be little trouble picking up that as well.
While of course their hormonal systems and the regulatory chemical pathways would be dramatically different, it's unclear what or even if there are any reasonable alternatives that could serve the role that ion channels serve in humans.
The alien species in question evolved independently from earth life, but ultimately arrived at many of the same solutions to most basic biological problems: phospholipid cell membranes; first polysaccharide then polypeptide macromolecules; oxy-saccharide cell respiration; DNA genetic material, albeit with a different transcription mechanism; Krebs cycle lipid energy storage (with different but analogous enzymes); central nervous system; endoskeletons; humanoid kinematics; similar social behaviors to humans; etc.
Given all this, what plausible alternative neurochemical makeups might exist, and how difficult would they be to image with an FMRI scanner designed for humans?