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WIKIBrainStem: a new ex vivo anatomical atlas of the human brainstem from ultra-high field MRI (11.7 T)

The Ginkgo team (BAOBAB / NeuroSpin), in collaboration with the Inserm iBRAIN U1253 unit (Tours), published in NeuroImage the first anatomical atlas of the human brainstem at mesoscopic scale from ultra-high field MRI. Freely available as a wiki, this atlas will be used in particular by neuroanatomists and by neurosurgeons to guide their surgical procedures.

Published on 28 April 2021
The human brainstem, located at the base of the brain, as an extension of the spinal cord, is a brain’s region of great anatomical complexity. It is involved in many reptilian functions such as breathing and heart rate control, but also in the pain control, balance and motor skills (oculomotricity, paralysis of the body during REM sleep, fine motor control during movements ...) and in many cerebral pathologies, in particular motor disorders like Parkinson's disease. The brainstem is made up of several dozen nuclei[1] whose size, extremely variable, can sometimes be less than a millimeter. The finesse of its structures, its permanent movement punctuated by the pulsation of cerebrospinal fluid as well as its positioning near air-filled bones make the brainstem one of the most complex regions to map by MRI.
In order to meet this challenge, a collaboration between the Ginkgo team, led by Cyril Poupon (BAOBAB / NeuroSpin) and a team from the Inserm iBRAIN U1253 unit (neuroanatomy team led by Professor Christophe Destrieux, CHU Bretonneau, Faculty of Medicine of Tours), started building a new ex vivo high field MRI atlas of the brainstem. This collaborative work is part of the Human Brain Project (European FET flagship). Several brainstems were scanned ex vivo on the preclinical 11.7 T MRI of the NeuroSpin imaging platform by the Ginkgo team, using an imaging protocol allowing the acquisition of anatomical data at very high resolution (100 micrometers) and mesoscopic scale diffusion data (300 micrometers). The combination of anatomical maps (contrast between white and gray matter) and diffusion data (orientation of the fiber bundles) allowed the neuroanatomists of the project to carry out the segmentation[2] of all the structures and to create the first anatomical atlas of the human brainstem at the mesoscopic scale from ultra high field MRI. This atlas, published in the journal Neuroimage, is already available in the form of a wiki: WIKIBrainStem ( It will be used by both neuroanatomists for training and neurosurgeons for guiding their surgical procedures, whether in oncology or when implanting devices for the treatment of Parkinson's disease.
The future of the project will consist in completing the atlas by mesoscopic mapping of brain connections, reconstructed using diffusion MRI, and studying ten different brainstems to take into account individual variability.

 WikiBrainStem interface screenshot: Inner structures of the brainstem mapped using a combination of ultra-high field (11.7 T) anatomical and diffusion MRIs. Each color identifies an anatomical structure of the brainstem. © WikiBrainStem

[1] brainstem nuclei: clusters of neurons that relay information between the cerebral cortex and the cerebellar cortex.

[2] Segmentation: manual contouring of anatomical structures

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