The nucleus is the largest and one of the best studied members of the caudal/lower group of rafe nuclei. It lies in the midline of the transition between the medulla and the bridge/pons, in front (ventrally of) the 4th ventricle and contains the serotoninergic cell group B3.
The nucleus raphe magnus is considered to be one of the brain's pain-modifying systems. The nucleus receives signals from the PAG, hypothalamus and amygdala; All three areas, which with some parts also belong to the pain modifying system.