He registered in my mind. He was John Anderson.
(Meaning that I knew who the person was.)
Is this a common idiom? If not, what's the closest alternative?
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Not an idiom per se. But use it; why not? Some of the definitions for register supports such usage.
Plus, I'd rephrase it to: "It registered in my mind; he was John Anderson."
Using "in my mind" is actually unnecessary if you are already using "registered", but it's fine to have some redundancy.
Register -- ODO
(verb) 3.2 usually with negative Notice or become aware of.
‘he hadn't even registered her presence’
3.3 no object, usually with negative Make an impression on a person's mind.
‘My mind registers that there's a guy pulling me down.’