Yes I caught that study! It’s a fantastic foray into how existing brains which have already been influenced by social pressures interact in the real world. Unfortunately, however, it isn’t explanatory and there’s a lot of methodological considerations which still need to be explored. Of note, much of what I’m going to bring up below are also brought up by Cordelia Fine in the fantastic book I mentioned above as they are considerations often overlooked when designing studies to find differences between sex or gender.

It should be noted first and foremost that most brain imaging data is not a reflection of structure itself, it’s a reflection of activity in specific areas of brains. But even that is circumspect for a number of reasons, most notably that you can reliably detect brain activity in individuals which are not alive. Ignoring some of the technical issues with detection of activity itself, in the context of activation patterns, we should expect significant difference from individual to individual in how thoughts are processed, and we likely should see patterns amongst individuals which share commonalities such as social identities. We can, for example, see reliable patterns of activity amongst world class athletes as compared to those with no training. Patterns of activity in the motor cortex based on physical requirements of one individual isn’t quite comparable to a social identity, however, and for a closer analogy we could look to language or social status to see that patterns of activation are rather malleable and can denote all kinds of social roles.

Applying that to social roles, such as gender, it is not surprising in the least that we can detect gendered differences based on how society treats us and what roles it provides and gives us access to. For example, ignoring brain imaging studies for a moment, we can detect reliable differences between the sexes when we give them math tests. However, a deeper analysis on this difference reveals that this can be easily reversed and influenced merely by priming the individuals. In fact, when we go a step further and look at brain imaging and activation patterns, we also see that there are sex differences in how the math areas are activated. Unfortunately, however, I have yet to see a design which combines those two concepts together - how do brain activation patterns differ when an individual is primed with a narrative which runs counter to that which they have internalized from society?

To take this point even further, I think it’s important to note that the study you are linking includes exactly zero transgender individuals. It also doesn’t attempt to investigate nor discover differences in gender expression or conformity to social roles. The patterns that they have detected could very easily be a reflection of internalizing the values which society instills in us based on our gender roles - there is simply no way to separate the two with this existing literature. But to take that a step even further, even if we did find that there were reproducible sex-based differences which persisted even across a representative sample of gender diverse individuals, we would need to also conduct this kind of imaging at different points in these individuals lives (especially early on and through childhood where one’s concept of gender evolves) to understand just how much is biological and how much is an influence of nurture. Even then we would still only have at best an understanding of brain activation profiles which happen to meet statistical significance, a trait shared with brain activation profiles of completely dead individuals, which calls into question the statistical validity of the precision at which the imaging technology is calibrated - we would need to redo all of that research with more precisely tuned imaging to be sure it’s an accurate reflection of brain activation… and we still would not be able to make any definitive statements about structural differences because activation is a reflection of action potentials at a specific point in time (notably all action potentials, not just the ones used in the cognitive process of the task at hand, but also those involved in living and perceiving an environment and thinking about other things) and not a true understanding of the underlying architecture which supports these action potentials (two very different circuit boards can produce the same electrical current in the same spatiotemporal area).