Currently, the Terminologia Anatomica term refers exclusively to this separate cell mass in the caudal and dorsal aspect of the dorsal thalamus (the epithalamus), embedded in the posterior end of the medullary stria from which it receives most of its afferent fibers. By way of the retroflex fasciculus (habenulointerpeduncular tract) it projects to the interpeduncular nucleus and other paramedian cell groups of the midbrain tegmentum.
The habenula was traditionally divided into lateral (limbic) and medial (motor) parts. Detailed examination of the region in the rat, however, suggested that the lateral part should be further divided into ten distinct subnuclei and the medial into five distinct subnuclei.
The primary input regions to the lateral habenula are the lateral preoptic area (bringing input from the hippocampus and lateral steptum), the ventral pallidum (bringing input from the nucleus accumbens and mediodorsal nucleus of the thalamus), the lateral hypothalamus, and the internal segment of the globus pallidus (bringing input from other basal ganglia structures)..
The outputs of the lateral habenula target dopaminergic regions (substantia nigra pars compacta and the ventral tegmental area), serotinergic regions (median raphe and dorsal raphe nuclei), and a cholinergic region (the laterodorsal tegmental nucleus).
Input to the medial hebanula comes from a variety of regions and carries a number of different chemicals. Input regions include septal nuclei (the fimbrialis septi and triangularis septi nuclei), dopaminergic inputs from the interfascicular nucleus of the ventral tegmental area, noradrenergic inputs from the locus ceruleus, and GABAergic inputs from the diagonal band of Broca.
The medial habenula sends outputs of substance P and acetylcholine to the interpeduncular nucleus as well as to the pineal gland.
The habenular nuclei have been shown to be involved in many functions, including pain processing, reproductive behavior, nutrition, sleep-wake cycles, stress responses, and learning. Recent demonstrations using fMRI and single unit electrophysiology have closely linked the function of the lateral habenula with reward processing, in particular with regard to encoding negative feedback or negative rewards. For instance, Matsumoto and Hikosaka showed in 2007 that the firing of lateral habenula neurons in rhesus monkeys was complementary to the firing of dopaminergic neurons in the substantia nigra pars compacta: dopaminergic neurons increase in firing rate in response to a stimulus that predicts reward, whereas lateral habenular neurons increase in firing rate in response to a stimulus that predicts a lack of reward.