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Introduction to brain anatomy. The brain. The brain in FSLview. sagittal. coronal. ACPC. axial. Terminology. Dorsal/superior. Right?. Rostral /anterior. Left?. caudal/posterior. Ventral/inferior. Superior/Dorsal surface. Inferior/Ventral surface. Anterior. Anterior. Rostral.

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slide2

The brain in FSLview

sagittal

coronal

ACPC

axial

slide3

Terminology

Dorsal/superior

Right?

Rostral/anterior

Left?

caudal/posterior

Ventral/inferior

slide5

Superior/Dorsal surface

Inferior/Ventral surface

Anterior

Anterior

Rostral

Rostral

Left

Right

Right

Left

Posterior

Posterior

Caudal

Caudal

slide6

Grey Matter

White Matter

Constituent Tissues

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

- Grey Matter

- White Matter

Post-Mortem

MRI

Neurons

slide9

Cerebral cortex

Cerebral 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
slide10

Two major modulatory systems

cerebellum

basal ganglia

slide11

Principle of organization:

The cortex has sub-regions with different functions

slide12

The cortex can be divided into 4 lobes

Central sulcus

frontal .

parietal

frontal

parietal

occipital

occipital

temporal

Sylvian fissure

Lateral surface

Medial surface

You should memorize these!

slide13

The cortex can be divided into 4 lobes

Central sulcus

parietal

frontal

parietal

frontal

occipital

occipital

temporal

Sylvian fissure

Lateral surface

Medial surface

You should memorize these!

slide14

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!

slide15

Modern cytoarchitectonics – Jülich atlas

  • Based on 10 brains
  • Registered into MNI space (affine)
  • Available in FSLview (atlas tools)
  • Disadvantage – subjects have to be dead
slide16

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

slide17

Principle of organization:

Function and connectivity are linked

slide18

Function and connectivity are linked

  • 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

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

slide19

Naming brain regions

  • A number of different systems are in use, most are arcane
  • Many areas will have a number of roughly-corresponding names
  • Brodmann areas (but only some of these are in common use)
  • 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

prefrontal

cortex

d=dorsal, v=ventral

l=lateral, m=medial

slide20

Humans ≠ monkeys

Monkey brain areas may have homologues in the human brain

Not quite that simple…

slide21

Principle of organization:

The brain contains maps of the outside world

slide22

The brain contains maps of the outside world

1. Somatotopy

Sereno et al 1995

  • Size of representation proportional to sensory/motor acuity
  • Adjacent parts of body are generally adjacent
slide23

The brain contains maps of the outside world

2. Retinotopy

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

slide25

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

slide26

Two major modulatory systems

  • Both interact heavily with cortex
  • Not just involved in motor system

cerebellum

basal ganglia

slide27

Basal ganglia

Pharmacological diversity

Many neurotransmitters and neuromodulators

Imbalance linked to psychiatric disorders

Two antagonistic pathways

Direct and indirect

Imbalance leads to disorders of movement and cognition

Parkinson’s disease

Huntington’s disease

slide28

Cerebellum

Extremely regular micro circuitry

Contains 50% of brain’s neurons

Important for motor coordination but not only that

slide29

Principle of organization:

Parallel circuits between cortex

& subcortical structures

slide30

Subcortical-cortical loops

1. Thalamus

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

  • 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
slide31

Subcortical-cortical loops

2. Basal ganglia

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

slide32

Subcortical-cortical loops

3. Cerebellum

Dum and Strick (2003) J. Neurophysiology

Lobules of the cerebellum connect to different cortical regions

slide33

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
slide36

How to identify brain structures:

2. Use the atlas toolbars in FSLview

slide37

How to identify brain structures:

3. Use a neuroscientist

slide38

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

slide39

Central sulcus

Find the central sulcus in the axial view

slide41

The end!

The brain