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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?

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closed as primarily opinion-based by L.Dutch, TCAT117, Trish, JBH, Aify Jun 17 '18 at 18:38

Many good questions generate some degree of opinion based on expert experience, but answers to this question will tend to be almost entirely based on opinions, rather than facts, references, or specific expertise. If this question can be reworded to fit the rules in the help center, please edit the question.

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    $\begingroup$ As you state, an alien would be different from us, and its biology too. Therefore I see no way that any answer to answer this question is a way that is objective. $\endgroup$ – L.Dutch Jun 17 '18 at 16:20
  • $\begingroup$ @L.Dutch An alien would be different, but there are definite bounds on what the plausible options are for any given biological function. In this case a large part of the question is whether or not there even are any other options for synaptic neurochemistry that are dramatically different from ours, and the request for an example would already be implicit on an affirmative. $\endgroup$ – AJMansfield Jun 17 '18 at 16:42
  • $\begingroup$ You say "many of the same solutions". Do you mean by this, that they are the same in setup or not? Are they 'green space babes' and 'funny forehead sculpts' or are they as distinct as Yautja/Hish-Qu-Ten? Or shall we let everything loose we know about mankind and creae Xenomorphs, Zergs and Tyranids by extrapolating insects? TELL us about your species, how they developed and we might come to an answer why a design made for human brains would have troubles. $\endgroup$ – Trish Jun 17 '18 at 17:18
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    $\begingroup$ This is impossible to answer. "what plausible alternative neurochemical makeups..." I doubt a PhD could answer that. We have no evidence of alien life, so what basis could be used to even invent it? It doesn't matter how much description you provide. It's questions like these that brought about the technobabble in Star Trek. You're asking us to invent life "not as we know it." AKA too broad. Too, too, too, too broad. The answer we might be able to answer is "given this specific neurochemical makeup (which I provided), could it be imaged by an FMRI scanner?" Even that would be tough. $\endgroup$ – JBH Jun 17 '18 at 18:10
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    $\begingroup$ MRI (and in extension, fMRI) do not work on electrical currents - you might be thinking of EEG? - they work on magnetic properties of different molecules - fMRI can image the oxygen uptake (via the differing magnetic properties of oygenated vs disoxygenated blood). Your alien would need a CNS that also drew oxygen in relation to the activity within, with no parallel processes that would mask the magnetic property-change. Note that with enough time and some subjects, it may be possible to program a MRI to look for other changes denoting activity in alien CNS, a afMRI, so to speak. $\endgroup$ – bukwyrm Oct 11 '18 at 8:11
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As you say a similar mechanism will have a similar signature; as such using an FMRI to get a picture should be easy, but I would suggest that it will require some extensive re-calibration to differentiate nerve impulses based on a different chemical interactions. This is an issue of both recognising the impulse for what it is and of measuring it's relative intensity for the creature.

Getting useful information out of the imaging process is going to be much harder. FMRIs supply us with useful information largely because we know what most of the various structures within the human brain do, or we think we do. An alien physiology will throw up many issues even once the machine is properly calibrated. It's going to take a long time to get a good image and then understand what you're seeing, like years.

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