Anatomy of the brain (MRI) - cross-sectional atlas of human anatomy


Antoine Micheau, MD , Denis Hoa, MD

Published on

Monday 09 December 2019


Head and Neck



Anatomical parts

Anatomy of the brain (MRI) - cross-sectional atlas of human anatomy

The module on the anatomy of the brain based on MRI with axial slices was redesigned, having received multiple requests from users for coronal and sagittal slices. The elaboration of this new module, its labeling of more than 524 structures on 353 MRI images in three different views and on 26 anatomical diagrams, took more than 6 months.  
This module is intended for all physicians and non-physicians with an interest in neuroanatomy and medical imaging, particularly for general practitioners and specialists in neurology, neurosurgery, anatomy and neurosciences, as well as speech pathologists and psychomotor therapists.


Anatomy of the encephalon in MRI (axial, coronal and sagittal slices)

Anatomy of the encephalon in MRI (axial, coronal and sagittal slices)


Cerebral images used for this module on human anatomy

An MRI was performed in thin slices (0.6 mm) on a healthy individual, with volumetric 3D imaging using T1 weighting without injection of gadolinium in the three normally used views, with a matrix of 320/320 pixels, using an MRI machine of 1.5 Tesla.

Brain - Coronal section:Basal nuclei and related structures, Corpus callosum, Septum pellucidum

Brain : Coronal section


A time-of-flight MR angiogram of the circle of Willis was performed and a venous MR angiogram by phase contrast was also performed on the same subject at a different time.
The slice images were resized and cropped using Adobe Photoshop, and then integrated into a module. To facilitate data download, the images were compressed in jpeg format, but the “HQ” function allows the user to download the images in optimal quality (note: the starting matrix is still 320/320 pixels).

3D image reconstructions for the brain, the ventricles, the brainstem, the cerebellum, the cerebral arteries and the venous sinuses were created from images in slices by means of a DICOM reconstruction console.


Cerebral sulci - Longitudinal cerebral fissure

Cerebral sulci


Please note that the reconstructions were based on images of the same patient that allows the user to compare imaging in slices with 3D imaging of the human brain. In addition, some of the reconstructions were minimally retouched using Adobe Photoshop in order to improve their didactic value and to remove certain artifacts, but no structure of any kind was added artificially (thus, for example, the cranial nerves are only visible on the brainstem images). For more complete diagrams, we would recommend the module on brain anatomy in illustrations.


Profiling cerebral anatomic zones

Several types of profiles were created for both the slices and the 3D images:

  • Cerebral lobes: frontal lobe, parietal lobe, temporal lobe, occipital lobe, insula, limbic system (note that the limbic system is a functional unit that links parts of other lobes, and thus, zones are superposed).
Cerebral lobes

Cerebral lobes


  • Cerebellar lobes: Anterior lobe of the cerebellum, posterior lobe of the cerebellum, and the flocculonodular lobe
  • Brainstem: Mesencephalon, pons and medulla oblongata (bulb, myelencephalon)
  • Levels of the central nervous system: telencephalon, diencephalon (divided into the thalamus, hypothalamus, metathalamus, epithalamus and subthalamus), rhombencephalon, and the spinal cord.
  • Association fibers of the telencephalon: Uncinate fasciculus, Superior (arched) and inferior longitudinal fasciculus, caudal and lingual fibers, Note: this outline was created using data which have been continuously updated since accession of the images using tensor diffusion imaging, and as a result, these representations could be improved.


Brain - White matter : Association fibres of telencephalon, Superior longitudinal fasciculus; Arcuate fasciculus

Brain : White matter


  • Arterial vascular territories: This part is difficult to summarize, since it applies to anatomic territories as well as to clinical syndromes (ischemic cerebrovascular accidents), therefore we only included the main territories: superficial and deep territories of the middle and anterior cerebral arteries, territory of the posterior cerebral artery, junctional cortical territories and deep anterior choroidal artery territory, territory of the posterior communicating artery, territory of the superior (SCA), anterior (AICA), and posterior (PICA) cerebellar arteries, territory of branches of the basilar artery, territory of branches of the vertebral artery and the anterior spinal artery.



Vasculary territories - Brain

Vasculary territories :Brain


Anatomical structures labelled:

In order to facilitate the reading of the module, the structures of the human brain have been classified into groups and subgroups that can be displayed by categories:

  • Cerebral lobes and regions of the brain, brain stem and cerebellum
  • Cerebrum with the various lobes, the cerebral commissural fibres (corpus callosum, fornix, tapetum, forceps), association fibres of the cerebrum, basal nuclei and related structures (basal ganglia, pallidum, lenticular nucleus, putamen, internal and external capsules...), basal forebrain (with olfactory striae, the amygdalo-claustrum region, the amygdaloid body, the anterior perforated substance), and finally the Brodmann area (note that the classification has over a century and is often questioned, moreover, the numerical nomenclature is permanent but the literal designation of Brodmann areas is subject to multiple variations).


Cerebral cortex: Brodmann areas

Brodmann areas


  • Diencephalon including the thalamus, the pulvinar nuclei, the habenula, the pineal gland, the infundibulum (formerly the pituitary stalk) and the neurohypophysis (the anterior lobe of the pituitary gland not forming part of the central nervous system).


Anatomy of the brain (MRI)

Anatomy of the brain (MRI)


  • Cerebellum with its various fissures and lobes as well as the structures of the cerebellar vermis.
Cerebellum: Cerebellar fissures, Vermis of cerebellum [I-X], Hemisphere of cerebellum [H II - H X]



  • The brain stem subdivided into midbrain, pons and medulla oblongata (bulb, myelencephalon).


Brainstem: Pons, Myelencephalon; Medulla oblongata; Bulb,



  • The cranial nerves at the level of their emergence, and the cranial nerve nuclei with a projection of their supposed position on the brain stem.
  • The brain ventricles (lateral ventricles, third ventricle, fourth ventricle) with the choroid plexus.


Lateral ventricle, Third ventricle, Fourth ventricle, Aqueduct of midbrain; Cerebral aqueduct

Lateral ventricle, Third ventricle, Fourth ventricle, Aqueduct of midbrain; Cerebral aqueduct


  • The meninges with sacs containing the cerebrospinal fluid (CSF) but also the different layers and pericerebral spaces (of course, the dura mater, the pia mater, the arachnoid and the spaces between them are very difficult to identify in a healthy subject and the labels on it are approximate).
  • The arteries of encephalic destination emerging from the internal carotid arteries and vertebral arteries and forming the circle of Willis (arterial circle of the brain). It should be noted that this MRI is without gadolinium injection; the large arteries are visible by hyperintense flow phenomenon but the small arteries are not visible and we have preferred not to label them.


Cerebral arterial circle (Willis): Superior aspect; Vertical aspect

Cerebral arterial circle (Willis): Superior aspect; Vertical aspect


  • The main deep and superficial, diploid and emissary veins (subject to the same restrictions as arteries on this MRI without injection), as well as the various venous sinuses (superior sagittal sinus and lower sigmoid sinus, straight sinus, cavernous sinus, lower and upper petrosal sinus).


Dural venous sinuses: Superior sagittal sinus, Cavernous sinus, Sigmoid sinus

Dural venous sinuses


View of MRI and 3D brain images

The "plans" tab provides access to groups of images (axial, coronal, sagittal and 3D image series), but the images on the left can be accessed directly by a simple click.


The anatomy of the brain in several languages

The anatomical structures are all translated from the Terminologia Anatomica into English, French, Spanish, Portuguese, Chinese, Italian, Polish, German and Japanese.
Please note that the neuroanatomical and radioanatomical vocabulary can vary, depending on the structures and languages, and that therefore we use the Terminologia Anatomica to its maximum.

Download e-Anatomy

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e-Anatomy on Appstore e-Anatomy on Googleplay

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