If it's not spirit, what is it? You haven't touched the rock, nor heard or seen it. So there should be something at work that lets you accurately predict that the low ceiling is there that's not the 'primary 5 senses'.
For a start, you can hear it. Your senses are made to keep you from hurting yourself, so you can react without thinking 'hey, this will probably hurt me if I bump my head into it, so maybe I shouldn't do that.' If you're moving, there's subtle vibrations that echo from nearby objects, more audible the closer you are. So when your ears pick that up, your brain is adapted to make you not bump your head into whatever it is.

That's just one of the many ways you can not bash your head into low ceilings without there being a ghost inside whatever you're walking under.
EDIT:
And well... Your body could be listening to the echo or feel the cold from the rocks.
Didn't even think about the temperature difference you feel when close to things! That one you CAN consciously focus on!