Basic system level diagram of the brain

You ask some huge questions not easily answered.

You are asking about the fundamental operations of the most complicated structure known to mankind. The detailed answers could easily fill volumes of textbooks. I will try to hit the highlights here but but I am warning you ahead of time - while this is a very long post I am leaving very much unsaid and unexplained. Let’s start with your first bulleted item.

The thalamus is broadly interconnected with the cortex at all points. Some have described this as the seventh layer of the cortex but that is much too simple. The connections to the body pass through the thalamus to the cortex. There are connection paths between the cortex and the thalamus. Numenta is starting to work in this area. See this thread for more details.

The thalamus also drives a basic heartbeat function that binds activity patterns together. This post addresses part of your question about layers and the thalamus:

Possibly the best description that I have read on the interactions between the thalamus and the cortex is in this paper. It’s a demanding read but well worth the effort. It addresses more of the question about layers and the thalamus - it describes the predictive mechanism in the feedback direction. This is distinctly different from HTM which describes prediction in the feedforward direction.:

So on your question regarding information vs modulation - all of the above.

I have been addressing various details of how all these bits work together in the forum for a long time. You can take this collection of posts together as loose documentation of how I see these parts working together. These papers start to address your prediction question; since it describes the basic operations and interactions of the parts it is possible to describe what will happen if you interrupt those functions:

This describes the action of the Layer 2/3 in coordinating various cortical areas and recognizing and communicating spatial and temporal pattern recognition. This is where the lateral and inter-area binding occur. This binding can be described as temporal and spatial pooling.

Everything up to this point has been the answer to the thalamus & cortex part of your question

A major sub-cortical structure is the cerebellum
While it is often thought of as connecting movements together to convert the parallel motor commands from the cortex into smooth sequential commands down the spine, it also feeds back into the brain to make our thought coordinated.

How about those other sub-cortical structures?
I refer you to this post. You will have to click-through this to see the nested links.

What are those subcortical structures?

What do they do?

And what are the subcortical connections to the body and its sensors?

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