Introduction

Many cutting edge applications of advanced imaging, such as resting state connectivity and HARDI connectivity, necessarily require identification of seed and target ROIs. While larger brain structures, such as the sensorimotor cortex can be reliably identified in most humans using MRI, smaller structures such as dopaminergic and serotonergic nuclei are more difficult to identify, both due to their small size, and signal characteristics that are similar to adjacent brain tissue. Another alternative is using nuclear medicine tracers to identify these small foci, but the drawback is relatively poorer spatial resolution of PET systems, and the subsequent need to co-register the two modalities. Therefore, there is great utility is providing well-defined “recipes” on how to locate these small nuclei in conventional MRI. We present here two such methods for identification of the ventral tegmental area (VTA) and dorsal raphe nucleus (DRN) of the brainstem.

Methods

A gold standard for locating the VTA and DRN was based on three anatomic atlases: Olszewski and Baxter's Cytoartchitecture of the Human Brainstem 2014, Paxinos and Huang's Atlas of the Human Brainstem 1995, and Duvernoy's Atlas of the Human Brain Stem and Cerebellum 2009. Both nuclei were drawn for each atlas. Using a grid of 1mmx1mm for each available slice, the nuclei were filled in if at least half of the grid block was full. Then the 3 atlases were merged together to form the DRN and VTA. This merged version was then 'smoothed' such that the nuclei as a whole would have a cohesive shape and removing any extraneous pieces not in a cluster.
For both nuclei, the brain volume is oriented in the plane that runs through the middle of the mammillary body and the superior colliculus. If the head is rotated left or right, this should also be corrected.
For the DRN, all parts, ie ventral, dorsal, and intrafasicular parts were included. The DRN is 8mm thick. The inferior most level is at the isthmus, where the cerebral aqueduct forms into the 4th ventricle. The DRN lies at the midline of the brainstem and should follow along the cerebral aqueduct with the cerebral aqueduct being its posterior border. See Figure 1 for diagram.
For the VTA, the paranigral, interfasicaular, central linear, parabrachial pigmented, and rostral linear nuclei were included. These nuclei were included based on their projections to the limbic area, thalamus, and forebrain as well as the midline nuclei. The VTA is 6mm thick and extends inferiorly 2mm below the inferior red nucleus, but does not cross the decussation. The superior extent is approximately aligned with the inferior mammillary body. The VTA also lies at the midline of the brainstem with the interpeduncular fossa as its anterior border. See Figure 2 for diagram.
A validation of the above recipe to localize the DRN and VTA was performed with positron emission tomography studies that were made available from a previous nuclear medicine study. [¹⁸F]-MPPF scans were used to localize DRN in MRI scans co-localized to the PET imaging data. [¹¹C]-FeCIT scans, used to measure dopamine transporter activity, were used to localize VTA in MRI scan similarly co-localized. ROI’s for each VTA and DRN were determined using the above described methods using the co-localized MRI scans and compared for spatial overlap.

Results

Figures 1 and 2 show the anatomical delineation of the ROI’s using the prescribed method. Figures 3 and 4 show a clear overlap of DRN and VTA ROI’s defined using the landmark method described here and those determined using the relevant PET ligand studies.

Discussion

We have described a straightforward, anatomic landmark based methodology to produce ROI’s in the VTA and DRN of the brainstem. The method requires only a high resolution T1 weighted scan to produce the ROI’s. The landmarks employed are all conspicuous objects readily identifiable on MRI and the method is simply described to enable even researchers that are relatively naïve to cross sectional anatomy to produce robust, reproducible ROI’s.

Conclusion

Based on multiple brainstem atlases, we provide “recipes” to locate the DRN and VTA on MRI anatomical imaging. These steps are useful for connectivity analysis that require these small nuclei as endpoints.

Acknowledgements

This work was supported by Siemens Healthineers, Inc. The authors gratefully acknowledge the help of Tobias Kober of Siemens Healthineers for use of WIP944 (MP2RAGE).