WikiBS: a public wiki for segmenting high resolution brainstem images

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Poster No:


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Abstract Submission 


François Lechanoine1, Timothée Jacqueson2, Barthélemy Serres3, Mohammad Mohammadi4, Justine Beaujoin5, Frédéric Andersson4, Fabrice Poupon5, Cyril Poupon5, Christophe Destrieux4


1Service de Neurochirurgie, CHU de Grenoble, Grenoble, France, 2Multidisciplinary Skull Base Unit, Department of Neurosurgery, Wertheimer Neurological hospital, Lyon, France, 3ILIAD3, Université de Tours, Tours, France, 4UMR 1253, iBrain, Université de Tours, Inserm, Tours, France, 5CEA - NeuroSpin, Gif-sur-Yvette, Ile de France

First Author:

François Lechanoine, MD  
Service de Neurochirurgie, CHU de Grenoble
Grenoble, France


Timothée Jacqueson  
Multidisciplinary Skull Base Unit, Department of Neurosurgery, Wertheimer Neurological hospital
Lyon, France
Barthélemy Serres  
ILIAD3, Université de Tours
Tours, France
Mohammad Mohammadi, MSc  
UMR 1253, iBrain, Université de Tours, Inserm
Tours, France
Justine Beaujoin  
CEA - NeuroSpin
Gif-sur-Yvette, Ile de France
Frédéric Andersson, PhD  
UMR 1253, iBrain, Université de Tours, Inserm
Tours, France
Fabrice Poupon  
CEA - NeuroSpin
Gif-sur-Yvette, Ile de France
Cyril Poupon  
CEA - NeuroSpin
Gif-sur-Yvette, Ile de France
Christophe Destrieux  
UMR 1253, iBrain, Université de Tours, Inserm
Tours, France


Brainstem contains a large number of white and gray structures involved in almost all central nervous system functions, some of them being additionally potential targets for deep electrical stimulation in various motor and psychiatric diseases. Its fine anatomical study was for long limited to histological methods but recently became accessible to ultrahigh field (UHF) MRI performed ex vivo at a resolution as high as 50 microns (Makris et al. 2019). Reproducible segmentation of such datasets requires a high degree of anatomical knowledge and a precise definition of segmentation rules. The purpose of this work was to propose a practical tool, WikiBS, helping the user to manually delineate major gray matter structures within the human brainstem.


Specimen: a human brainstem obtained from body donation was extracted less than 24 hours after death and fixed in 10% formalin for 3 months. It was soaked in a phosphate-buffered saline solution for rehydration during 3 weeks before the acquisitions.

UHF-MRI protocol: acquisitions were performed on a 11.7T MRI Bruker preclinical scanner with strong gradients (780mT/m). A dedicated MRI protocol was tuned including 1) anatomical scans using spin-echo sequences : isotropic 185μm/100μm resolution, TE=26.5/20ms, TR=13000/500 ms; 2) diffusion-weighted (DW) scans using Pulsed Gradient Spin Echo (PGSE) sequences: isotropic 300μm resolution, b=1000/3000/4500 /7500/10000s/mm, 30/30/400/30/30 directions, TE=21.3/23.3/24.6/40.3/55.3ms, TR=5500 /6000/9000/9500/11000ms, δ=4.3ms, Δ=11/13/14.4/30/45ms. Directional tensor RGB maps were obtained from these diffusion data.

Definition of anatomical classes: anatomical literature (Mai and Paxinos 2012; Nieuwenhuys, Voogd, and Huijzen 2008; Naidich and Duvernoy 2009) was reviewed to select a set of gray matter structures which appear segmentable on the obtained datasets. For each structure, a manual segmentation was performed and precise rules of segmentation were defined by one operator (FL) and reviewed by two additional experts (CD and TJ).

Visualization interface: 3D models of the smoothed anatomical classes was superimposed on a semitransparent representation of the brainstem surface which can be interactively rotated and zoomed. It was possible to selectively display a group of structures (proper, cranial nerves or reticular nuclei) or a single structure (fig 1).

Wiki pages: on the visualization interface, hyperlinks were pointing to wiki pages created for each of the segmented structures.
Supporting Image: wikiATLAS_fig1_1000px_wi.jpg
   ·Figure1. Visualization interface. 1: 3D model of the brainstem and segmented structures; 2: menu for selecting structures to display; 3: hyperlinks pointing to the corresponding wiki pages.


124 anatomical classes of gray matter were segmented: 52 proper nuclei/subnuclei, 34 cranial nerves nuclei/subnuclei, 38 reticular nuclei/subnuclei. For each of these anatomical classes, a wiki page described the information obtained from the literature review (anatomy, function, connectivity) and segmentation rules (fig 2). The latter included: (1) a list of datasets used for segmentation (T2 185μm, T2100μm, RGB, FA, combination of several of these layers); (2) a first rough localization of the structure of interest; (3) a second fine segmentation with the help of anatomical landmarks in conventional directions; and (4) a list of difficulties in delineating this structure. For each structure, several figures illustrated the main segmentation rules to help reproducibility. A fully web accessible version of this atlas will soon be available.
Supporting Image: wikiATLAS_fig2.jpg
   ·Figure2. Wiki page for the red nucleus. (1) 3D model, (2) anatomy, (3) function, (4) main connectivity and (5) proposed segmentation rules for this structure.


WikiBS is a database including anatomical information and segmentation rules for 124 of the main gray matter structures of the human brainstem. This free online tool will be a major help in reproducible segmentation of human brainstem datasets. Using the acquired diffusion data, it will also permit to further study the inner connectivity of the brainstem.

Modeling and Analysis Methods:

Segmentation and Parcellation 1

Neuroanatomy, Physiology, Metabolism and Neurotransmission:

Neuroanatomy Other 2



1|2Indicates the priority used for review

My abstract is being submitted as a Software Demonstration.


Please indicate below if your study was a "resting state" or "task-activation” study.


Healthy subjects only or patients (note that patient studies may also involve healthy subjects):

Healthy subjects

Was any human subjects research approved by the relevant Institutional Review Board or ethics panel? NOTE: Any human subjects studies without IRB approval will be automatically rejected.


Was any animal research approved by the relevant IACUC or other animal research panel? NOTE: Any animal studies without IACUC approval will be automatically rejected.

Not applicable

Please indicate which methods were used in your research:

Structural MRI
Diffusion MRI
Postmortem anatomy

For human MRI, what field strength scanner do you use?

If Other, please list  -   11.7

Which processing packages did you use for your study?

Free Surfer
Other, Please list  -   Connectomist

Provide references using author date format

Mai, J.K. (2012). 'The Human Nervous System'. Elsevier.
Makris, N. (2019). '3D Exploration of the Brainstem in 50-Micron Resolution MRI.' Preprint. Neuroscience.
Naidich, T.P (2009). 'Duvernoy’s Atlas of the Human Brain Stem and Cerebellum: High-Field MRI: Surface Anatomy, Internal Structure, Vascularization and 3D Sectional Anatomy'. Wien ; New York: Springer.
Nieuwenhuys, R, (2008). 'The Human Central Nervous System'. Berlin; New York: Springer.