Introduction to brain anatomy
The brain
The brain in FSLview
coronal
sagittal
ACPC
axial
Terminology
Dorsal/superior
Right?
Rostral/anterior
Left?
caudal/posterior
Ventral/inferior
Superior/Dorsal surface
Inferior/Ventral surface
Anterior
Rostral
Left
Anterior
Rostral
Right
Posterior
Caudal
Right
Left
Posterior
Caudal
Constituent Tissues
The brain is full of neurons. These
are organised into two types of
“tissues”:
- Grey Matter
- White Matter
Grey Matter
Post-Mortem
MRI
Neurons
White Matter
Parts of the Brain
The human brain is big and most of it is cortex
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
Two major modulatory systems
cerebellum
basal ganglia
Principle of organization:
The cortex has sub-regions with different functions
The cortex can be divided into 4 lobes
Central sulcus
parietal
frontal
occipital
parietal frontal
occipital
temporal
Sylvian fissure
Lateral surface
You should memorize these!
Medial surface
The cortex can be divided into 4 lobes
Central sulcus
parietal
parietal frontal
frontal
occipital
occipital
temporal
Sylvian fissure
Lateral surface
You should memorize these!
Medial surface
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
• 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
Naming brain regions
A number of different systems are in use, most are arcane
Many 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
prefrontal
PF C
cortex
d=dorsal, v=ventral
l=lateral, m=medial
… 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
Humans ≠ monkeys
Monkey brain areas may have
homologues in the human
brain
Not quite that simple…
Principle of organization:
The brain contains maps of the outside world
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
The brain contains maps of the outside world
2. 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 pathways
Direct and indirect
Imbalance leads to disorders of
movement and cognition
Parkinson’s disease
Huntington’s disease
Cerebellum
Extremely regular micro
circuitry
Contains 50% of brain’s neurons
Important for motor
coordination but not only that
Principle of organization:
Parallel circuits between cortex
& subcortical structures
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
Subcortical-cortical loops
2. Basal ganglia
Draganski et al (2008) J Neurosci. 28(28):7143-52
Subcortical-cortical loops
3. Cerebellum
Dum and Strick (2003) J. Neurophysiology
Lobules of the
cerebellum connect
to different cortical
regions
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 way
around 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