The brainstem is the structure anterior to the cerebellum and inferior to the thalamus. It consists of the medulla oblongata, midbrain, and pons. In the sagittal view, the brainstem appears as two separate structures laterally but then fuse to form a single structures medially. (Fig. 1, Fig. 2, Fig. 3)
Start in the sagittal view at the most lateral slice. Begin masking the brainstem when the lateral geniculate body appears and inferior to that as an anterior protrusion appears from the cerebellum. Trace the lateral geniculate body’s inferior boundary and connect the superior ends of the inferior boundary by cutting straight across the ends. Mask everything within. Trace the anterior boundary of the anterior protrusion in the cerebellum then also connect the posterior ends by cutting across the ends. Mask everything within (Fig. 4). The two separate regions should begin to approach each other as the view becomes more medial (Fig. 5)
As the two regions fuse, trace the outline of the brainstem into the deepest points allowed in the cerebellum and connect the two ends (Fig. 6, Fig. 7). Continue this until the brainstem’s posterior boundary near the cerebellum can be defined as a straight line (Fig. 8). At this point, trace the boundary of the brainstem in its entirety. Note the brainstem is anterior to the fourth ventricle (Fig. 9, Fig. 10).
As the brain stem extends inferiorly to the bottom of the image, begin to monitor the superior part of the brainstem for the superior colliculus. (Fig. 11)
Soon after the superior colliculus can be identified, take note of the separation between the main body of the brainstem and the superior colliculus and trace this distinction. Also, take note of the protrusion anterior to the superior colliculus, the mamillary body, and mask this area (Fig. 12).
Follow steps 1-5 in reverse order for the left hemisphere (medial to lateral) until the lateral geniculate body and the anterior protrusion from the cerebellum cannot be distinguished as protrusions.