Introduction to brain anatomy

The brain

The brain in FSLview

coronal sagittal

axial

ACPC

Rostral/anterior

caudal/posterior

Dorsal/superior

Ventral/inferior

Left?

Right?

Terminology

Left Right Right Left

Posterior PosteriorCaudalCaudal

Superior/Dorsal surface Inferior/Ventral surface

Rostral RostralAnterior Anterior

The brain is full of neurons. These are organised into two types of “tissues”: - Grey Matter - White Matter

Grey Matter

White Matter

MRIPost-Mortem

Neurons

Constituent Tissues

Parts of the Brain

The human brain is big and most of it is cortex

Cerebral cortexCerebral cortex

• Makes up the bulk of the brain in humans• Newest part of the brain (in evolutionary terms)• Does thinking• Also most adaptable and variable part of brain

Two major modulatory systems

cerebellum basal ganglia

Principle of organization:The cortex has sub-regions with different functions

Lateral surface Medial surface

Central sulcus

Sylvian fissure

frontal .

The cortex can be divided into 4 lobes

parietalparietal

occipitaltemporal

occipital

frontal

You should memorize these!

Lateral surface Medial surface

Central sulcus

Sylvian fissure

The cortex can be divided into 4 lobes

parietalparietal

occipitaltemporal

occipital

frontal

You should memorize these!

frontal

Brodmann’s areas –(1909) • Divides cortex into 52 areas

• Based on cytoarchitecture (which types of cells are present?)

• Largely symmetrical (across two cerebral hemispheres)

Don’t try to memorize these!

Modern cytoarchitectonics – Jülich atlas

• Based on 10 brains• Registered into MNI space (affine)• Available in FSLview (atlas tools)

• Disadvantage – subjects have to be dead

Gross anatomical features(sulci and gyri)

e.g. Harvard-Oxford atlas in FSLview

Problem – gyri do not correspond to functional regions

Even if we could work out correspondence in one person,gyrification differs between individuals

Principle of organization:Function and connectivity are linked

Function and connectivity are linked

Johansen-Berg et al (2004) PNAS 101(36):13335-40

• SMA and pre SMA

• No obvious anatomical boundary

• Different functional regions (top row) – for finger tapping and counting backwards in 3’s

• Connectivity (DTI) based parcellation (bottom row)

• Structure and function same dividing line between SMA and pre SMA

Naming brain regionsA number of different systems are in use, most are arcaneMany areas will have a number of roughly-corresponding names

1. Brodmann areas (but only some of these are in common use)2. Descriptive anatomical names e.g. dlPFC

Decoding: dl PF C

… but beware, some of these anatomical descriptions relate to the monkey brain!!!

3. Descriptive names (often in Latin, e.g. cingulate)4. Functional names, e.g. visual cortex

d=dorsal, v=ventrall=lateral, m=medial

prefrontal

cortex

Monkey brain areas may have homologues in the human brain

Not quite that simple…

Humans ≠ monkeys

Principle of organization:The brain contains maps of the outside world

Sereno et al 1995

• Size of representation proportional to sensory/motor acuity• Adjacent parts of body are generally adjacent

The brain contains maps of the outside world1. Somatotopy

The brain contains maps of the outside world2. Retinotopy

Dougherty et al (2003), Journal of Vision 3(10):586-598

What about sub-cortical brain areas?

What about the sub-cortical brain structures?Some software only shows the cortex

Freesurfer Caret

Advantage: can do cortical flattening,easier to compare

cortical surface

Disadvantage: gets rid of sub-cortical systems

Two major modulatory systems• Both interact heavily with cortex• Not just involved in motor system

cerebellum basal ganglia

Basal ganglia Pharmacological diversity

Many neurotransmitters and neuromodulators

Imbalance linked to psychiatric disorders

Two antagonistic pathwaysDirect and indirect

Imbalance leads to disorders of movement and cognition

Parkinson’s diseaseHuntington’s disease

CerebellumExtremely regular micro circuitryContains 50% of brain’s neuronsImportant for motor coordination but not only that

Principle of organization:Parallel circuits between cortex

& subcortical structures

Subcortical-cortical loops1. Thalamus

• Correspondence between cortical regions and thalamic nuclei• They have reciprocal connections (thalamo-cortical and cortico-thalamic)• Thalamus also relays information from senses, basal ganglia and cerebellum to cortex

Behrens et al (2003). Nat Neurosci. 6(7):750-7.

Subcortical-cortical loops2. Basal ganglia

Draganski et al (2008) J Neurosci. 28(28):7143-52

Subcortical-cortical loops3. Cerebellum

Lobules of the cerebellum connect to different cortical regions

Dum and Strick (2003) J. Neurophysiology

Principle of organization:Loops between cortex & subcortical structures

• Each subcortical structure has a different contribution to information processing

• This information processing function may be applied to many cortical areas

• We can see many of the same principles of organization (functional localization, somatotopy) in subcortical structures

• The corresponding bits of cortex & subcortical structures are interconnected in parallel & integrative loops

Top tips for finding your wayaround the brain

How to identify brain structures:1. Use a brain atlas

How to identify brain structures:

2. Use the atlas toolbars in FSLview

How to identify brain structures:

3. Use a neuroscientist

Using a brain atlas

These generally have axial, sagittal and coronal views

Some structures are easier to identify in one view than another

There are specialized atlases for some structures e.g. cerebellum and brainstem

Central sulcus

Find the central sulcus in the axial view

Find the intra- parietal sulcus in the coronal view

The end!

The brain