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Is olfactory input processed by the thalamus? I know olfaction is the only sense that can bypass the thalamus, but are there cases where the input can project to the thalamus?

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Short answer
Third-order olfactory neurons project to the thalamus and mediate conscious perception of odors.

Background
The human olfactory system is schematically depicted in Fig. 1. The olfactory system is indeed interesting, as it is the only sensory system in which the primary receptor cells project directly to the brain. The olfactory cells in the nasal sensory epithelium project via small, unmyelinated axons via the first cranial nerve to the olfactory bulb in the brain.

In the olfactory bulb, so-called mitral cells project to the olfactory cortex via the olfactory tract. Medial fibers project to the anterior olfactory nucleus and septal areas. Some others cross over to the contralateral olfactory bulb. Lateral fibers contact the primary olfactory cortex.

Now it becomes interesting - third-order neurons in aforementioned regions send projections to the dorsomedial nucleus of the thalamus, the basal forebrain, and the limbic system.

The thalamic connections are thought to mediate conscious perception of odor perception. The amygdala and the entorhinal area are neural components of the limbic system and may be involved in the affective and aversive components of olfaction.

rhinal pathway
Fig. 1. Olfactory pathway. source: Medscape

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