The human brainstem, located at the base of the brain and in line with the spinal cord, is a cerebral region of great anatomical complexity. It is involved in many "reptilian" functions such as the control of breathing and heart rate, but also in the control of pain, balance and motor function (oculomotion, sleep paralysis during REM sleep, fine motor control during movements, etc.) and in many brain pathologies, especially motor disorders such as Parkinson's disease.

The brainstem is composed of several dozen brainstem nuclei of extremely variable size, and are sometimes less than a millimeter in size. The fineness of its structures, its constant movement set by the pulsation of the cerebrospinal fluid, and its position near the air-filled petrous bones make the brainstem one of the most complex regions to map with MRI.

In order to take on this challenge and finely map its structures, NeuroSpin researchers (BAOBAB/Ginkgo, CNRS, University Paris-Saclay, CEA) have launched the construction of a new ultra-high field ex vivo MRI atlas of the brainstem, in close collaboration with an Inserm team from Tours (iBrain U1253, Faculté de Médecine de Tours, CHU Bretonneau) , in the frame of  the European flagship program Human Brain Project to be soon made available through the eBRAINS portal.

For this, the BAOBAB/Ginkgo team scanned several ex vivo brainstems provided by the INSERM iBrain team using the preclinical 11.7 Tesla MRI system of the NeuroSpin imaging platform.  A specific imaging protocol taking several days to scan a single brainstem specimen was designed to allow the acquisition of ultra high resolution anatomical data (100 micrometers) as well as mesoscopic diffusion-weighted data (300 micrometers). The combination of anatomical (contrast between white and grey matter) and diffusion (orientation of fiber bundles) mappings allowed the project's neuroanatomists to segment all of the structures and to create the first anatomical atlas of the human brainstem at the mesoscopic scale using extreme field MRI.

This atlas, entitled WIKIBrainStem, is now available online as a wiki.

It will be used both as a teaching tool for neuroanatomists and as a guide for neurosurgeons, whether in oncology or when implanting devices to treat Parkinson's disease.

The next step of the project is to complete the atlas with a joint mesoscopic atlas of the brainstem connections inferred from diffusion MRI, and to study the variability of these connections and of the brainstem nuclei they connect across specimens