Anatomy of the encephalon (MRI) in axial slices


Antoine Micheau , Denis Hoa

Published on

Tuesday 12 November 2019


Head and Neck

Anatomical parts

Anatomy of the encephalon (MRI) in axial slices

We have created a brain atlas that is an interactive tool for studying the conventional anatomy of the normal brain based on a magnetic resonance imaging exam of the axial brain. Anatomical structures and particular areas are visible as interactive labeled images.



Cross sectional anatomy: MRI of the brain


  • An MRI was performed on a healthy subject, with several acquisitions with different weightings: spin-echo T1, T2 and FLAIR, T2 gradient-echo, diffusion, and T1 after gadolinium injection. We obtained 24 axial slices of the normal brain.
  • Data and DICOM images archived on our PACS (Picture Archiving and Communicating System) were processed and exported as JPEG images. Adobe Flash and Adobe Photoshop allowed us to develop an atlas-based application with suitable functionality and user interface for exploration of the neuroanatomy.
  • Anatomical structures were labelled according to the actual Terminologia Anatomica.


Cross sectional anatomy of the brain : a module based on MRI

Cross sectional anatomy of the brain : a module based on MRI

Anatomy of the brain: how to visualize anatomic labels


  • This module is a comprehensive and affordable learning tool for medical students and residents and especially for neuro-radiologists and radiation oncologists.
    It provides access to an atlas and to images in the axial planes, allowing the user to learn and review neuroanatomy interactively. Images are labelled, providing an invaluable teaching resource. The test mode allows the comprehensive evaluation of user progress.
  • The horizontal menu gives access to several groups of anatomical structures: encephalic sulci and gyri, limbic system, white matter, ventricle and cisterns architecture, basal nuclei and related structures, optic tract, cerebellum with its lobes according to numbered nomenclature, spinal cord. Vascularisation of the brain can be afforded with the arteries and venous sinuses sections. Pituitary and pineal glands are regrouped as “gland”.
  • As the cursor is moved over a particular anatomic area, that area is highlighted and labelled: this tool has been chosen to show encephalic lobes: frontal, occipital, parietal, temporal, insula, cerebellum (anterior, posterior and flocculonodular lobes).
  • The MRI is a particularly powerful exam for studying structures such as diencephalon, mesencephalon (mid brain), pons, myelencephalon (medulla oblongata, bulb) and spinal cord. 
  • The vertical left menu provides coronal and sagittal images of the brain, with anatomical schemas based on a three dimensional (3D) model.


Anatomy of the brain : axial slice T1 weighted

Anatomy of the brain : axial slice T1 weighted

Download e-Anatomy

Mobile and tablet users, you can download e-Anatomy on Appstore or GooglePlay.

e-Anatomy on Appstore e-Anatomy on Googleplay

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