For some time I have been trying to understand the relationship between the thalamus and the cortex in consciousness. I have been ignoring the basal ganglia. That is probably a mistake, for although the basal ganglia do not seem to be at the heart of consciousness (as the thalamus and cortex are), they are probably involved to some extent. They are certainly important to movement, decisions, and emotions at least.
I have taken some illustrations from Scholarpedia to show the complexity and the interconnectedness of the feedback loops through the basal ganglia. In all of these diagrams the neurotransmitters are coded: dopamine is green, GABA (inhibitory) is blue and glutamate (excitatory) is red. Output can roughly be thought of as the balance between direct striatonigral inhibitory connections that promote behaviour (the direct pathway), and the indirect pathway via relays in the external globus pallidus (GPe) and subthalamic nucleus (STN) which suppresses behaviour. The balance between these two projections was thought to be regulated by afferent dopaminergic signals from substantia nigra pars compacta (SNc) acting on differentially distributed D1 and D2 dopamine receptors.
Functional territories represented at the level of cerebral cortex are maintained thoughout the basal ganglia nuclei and the thalamic relays. Note, however, for each loop, the relay points in the cortex, basal ganglia, and thalamus, offer opportunities for activity inside the loop to be modified/modulated by signals from outside the loop.
These loops are in addition to the thalamocortical loops that are necessary for consciousness.
Peter Redgrave (2011). Basal Ganglia scholarpedia, 2 (6) DOI: 10.4249/scholarpedia.1825