Let me break it down so you see the point I was making - in case the bold wasn't enough:

Using high-resolution scanners, researchers at the Universities of Cambridge and Oxford have shown microscopic, structural abnormalities in the brainstems of those recovering from COVID-19. Signs of brain inflammation were present up to 18 months after first contracting the SARS-CoV-2 virus.

Here, they refer to people recovering from COVID-19, thus clearly indicate that patients are alive.

[…] In living brains of those with long COVID, however, conventional MRI studies have shown no structural abnormalities in the brainstem.

This paragraph immediately follows one that talks about autopsy(!) results, and here, they start a sentence with "in living brains [..], however", setting the sentence up as a contradiction to the previous one, with an emphasis on the word living in the article itself.

Here's an example how the sentence should be written to not seemingly cause a contradiction / misdirect the reader:

However, previous studies conducted with conventional MRI had shown no structural abnormalities in the brainstem in living brains.

They put emphasis on the change in observation from autopsy to living brains, linking this paragraph more strongly to the preceeding one, when they should have put emphasis on the conventional studies, building the context for the subsequent paragraph.