• Protects brain from harm
• Shields brain from direct observation

•  is to understand human behavior by performing physical measurements of brain function 
• the greatest obstacle is that we must understand human brain function using our human brains
• This goal is made possible by, and limited by, the tools and methods that we have at our disposal.

• noninvasive
• Basic belief: the brain is like a muscle, the bumps on outside of skull should reflect cognitive strengths
• Problem with theory: the inside of the skull is actually smooth, not the same as the outside of skull.
• However, phrenology concept of localized function was correct

• CAT scan = Computed Axial Tomography
• structure (some functional information can be garnered from lesions and malformations)
• noninvasive
• no telemetry
• good (<1mm spatial resolution)
• Similar to X-ray except array of beams are directed through head at all angles
• Detected by highly sensitive scintillation counters
• 1mm planar slices reconstructed by computer showing hard and soft tissues
• Little radiation actually used (although radiation can accumulate in brain with repeated use)
• right and left switched

• MRI = Magnetic Resonance Imaging
• no telemetry
• noninvasive
• Excellent (10s of microns) spatial resolution (resolution gets better every year - wiping out CT)
• Shows structure not function
• used to be NMRI but people don't like nuclear
• Subject placed in strong magnetic field to align polarized molecules (i.e. water) - coils of solenoid
• Weak perpendicular magnetic field pulsed to cause resonance of aligned molecules
• dangerous to have metal around
• orthogonal magnetic field in other direction makes pounding sound
• Resonance frequency related to molecule

• fMRI = Functional MRI
• Allows function to be measured by a MRI
• Same excellent spatial resolution as MRI (10s of microns)
• Lousy temporal resolution (many seconds to minutes)
• noninvasive
• no telemetry
• Measures changes in blood oxygen due to local brain activity
• ambiguous about excitation or inhibition
• ultra low field fMRI may measure neuronal current (electrical currents flowing through cells, cause transmission between cells)

• PET = Positron Emission Tomography
• Shows both structure and function
• Good spatial resolution (~ 3 mm)
• Bad temporal resolution (minutes of repeated stimulation)
• no telemetry
• ambiguous excitation/inhibition
• Injected or inhaled positron emitting isotope
• Isotopes bind to glucose taken up by active brain cells
• showed amygdala activated first due to anxiety
• outdated by fMRI
• Break down of isotope produces positrons
• Collision of positron with electron = 2 gamma rays at 180 degrees
• Coincidence detectors permit precise localization
• for suspected tumors/cancer

• EEG = Electroencephalogram
• Not historically thought of as a imaging method
• Shows both structure and function
• Excellent temporal resolution (< 1 ms)
• Fair - Poor spatial resolution (~ 1 cm)
• telemetry
• NOT ambiguous excitation/inhibition by correlating what's happening in cells w/ evoked potential
• noninvasive
• Many electrodes pasted on the scalp serve to record electric potentials outside the head
• EEG produced by active brain cells (postsynaptic currents in dendrites)
• Computerized EEG maps may indicate focally active regions

• MEG = Magnetoencephalogram
• Shows both structure and function
• Excellent temporal resolution (< 1 ms)
• Excellent spatial resolution (~ 1 mm)
• no telemetry
• NOT ambiguous about excitation/inhibition
• Measures magnetic field outside the head produced by active brain cells
• neuronal currents make magnetic fields - not smeared out by skull
• May be mapped with multichannel (100 - 200 channels) systems
• cryogenic

• MEG
• works at room temperature
• heat up atoms
• exqusite imaging
• mobile
• made by Barth & co

• ECoG = Electrocorticography
• Shows both structure and function
• invasive
• Excellent temporal resolution (< 1 ms)
• Excellent spatial resolution (~ 1 mm; governed by electrode size)
• used for telemetry
• not ambiguous about exciation/inhibition
• can stimulater other areas of cortex, too
• Measurement of electrical potential on the surface of the brain
• Metal electrodes put on surface of the brain (skull pulled back)
• Method used when all other methods fail to help patient
• Also may involve selective brain stimulation
• Measures all activity at the brain surface, not in the depth
• Measurements can be performed chronically

• SEEG = Stereotaxic Electroencephalography
• invasive
• Shows both structure and function
• Excellent temporal resolution (< 1 ms)
• Excellent spatial resolution (10 µm; governed by electrode size - down to individual cells, measure action potentials)
• not ambiguous about excitation/inhibition
• telemetry
• can stimulate  many brain areas
• Measurement of electrical potentials using fine wire electrodes implanted in the brain
• Also may involve selective brain stimulation
• Measurements can be performed chronically

• invasive
• Relate structural damage to functional loss
• “Experiments of nature” not very precise
• Difficulty relating deficit to normal function
• much early knowledge of brain function from experiments of war

• Macroscopic and microscopic study of brain anatomy postmortem or from biopsy
• invasive

• Shows structure only
• invasive
• Nissl stains: cell bodies
• Myelin stains: cell processes

• Shows structure only
• invasive
• HRP (Horse Radish Peroxidase): retrograde transport to cell bodies
• Autoradiography: radioactive acid transport to cell terminals
• And many more tracing methods too numerous to mention here
• anterograde vs retrograde

• invasive
• versions of Rhodopsins that open ion channels by light
• insert through viral vector
• targets in vivo cells individually

• 2DG = 2-deoxyglucose
• Shows function and structure
• Excellent spatial resolution (10 µm)
• Lousy temporal resolution (many minutes of repeated trials)
• invasive
• Accumulates in active cells
• when busy, cells use glucose ~ radioactive

• Both intrinsic signals and voltage senstive dyes
• Can be “noninvasive” (study development)
• Ambiguous about excitation or inhibition
• Excellent spatial resolution (10 μm; but can’t image below cortical surface)
• Lousy temporal resolution (seconds - minutes) but getting better

• Forebrain = Telencephalon + Diencephalon
• Telencephalon = cerebral cortex + limbic system + basal ganglia
• Diencephalon = thalamus & hypothalamus
• Midbrain = Mesencephalon
• Mesencephalon = tectum + tegmentum
• tectum = superior & inferior colliculi
• tegmentum = reticular formation, periacqueductal grey matter, red nucleus, substantia nigra
• Hindbrain = Metencephalon + Myelencephalon
• Metencephalon = pons + cerebellum
• Myelencephalon = medulla

• Brain appears as a folded balloon
• If inflated, would appear almost three time this size
• 1mm3 = 50K neurons = 6K syn/neuron = 300 mill synapses
• 1 hemisphere = 100,000 mm2 = 10 billion cells = 60 trillion synapses
• Each cell is far more powerful than a PC
• most processing unconscious
• Computational capacity of the cortex is truly unimaginable
• Fortunately the brain is folded - act as anatomical landmarks

• Central Sulcus - divides the frontal and parietal lobes
• Lateral/Sylvian Sulcus - separates temporal lobe from frontal/parietal
• Parietal/Occipital Sulcus - divides occipital and parietal lobes
• Preoccipital notch - divides occipital and temporal lobes

Telencephalon Landmarks

- Lobes

• Frontal Lobe
• Precentral Gyrus - just anterior to central sulcus (“motor strip”) = motor execution
• Anterior to this - secondary motor cortex = motor planning
• Anterior to this - prefrontal cortex = pretty much a functional grab bag
• Frontal lobectomies produce mixed results
• Appropriate social behavior? 
• Attention?
• Working memory?
• Parietal Lobe
• Postcentral Gyrus - just posterior to central sulcus (“somatosensory strip”) = primary somatosensory cortex
• Posterior to this - “association cortex” = polysensory processing?
• Occipital Lobe - primary and secondary visual cortex
• retinotopic - upside down & inside out
• Temporal Lobe
• Superior Temporal Gyrus - primary and secondary auditory cortex
• Middle and Inferior Temporal Gyrus - secondary visual cortex
• Hippocampus - short term memory

I. Olfactory - sensory, smell

II. Optic - sensory, vision

III. Oculomotor - motor, all eye muscles except for IV and VI, also cillary, iris, and sphincter

IV. Trochlear - motor, superior oblique

V. Trigeminal - both, sensory to face, sinuses, teeth; muscles of mastication

VI. Abducens - motor, lateral rectus

VII. Facial - both, muscles of face (submaxilary, sublingual, lacrimal glands); anterior 2/3 of tongue, soft palate

VIII. Vestibulocochlear - sensory, hearing & balance

IX. Glossopharyngeal - both, posterior 1/3 of tonge, tonsil, pharynx, middle ear; stylopharngeus, pharyngeal musculature

X. Vagus - both, motor: pharynx, heart, lungs, bronchi, GI tract; sensory: pharynx, heart, lungs, bronchi, GI tract, trachea, larynx, external ear

XI. Spinal Accessory - motor, sternocleidomastoid, trapezius

XII. Hypoglossal - motor, tongue muscles, strap muscles

Calcarine Sulcus

Corpus callosum

Cingulate Gyrus

Uncus

• Calcarine Sulcus- divides the uper and lower half of visual world
• Corpus Callosum + anterior + posterior commissures - fiber paths linking hemipsheres on point for point basis (split brain patients done so their seizures couldn't spread)
• Cingulate Gyrus - part of Limbic system, influence of emotion on cognition?, largest white matter bundle in CNS
• Uncus - external landmark above the amygdala

Thalamus

Cerebral Peduncles

Insula

• Thalamus - major interface to cerebral cortex
• Cerebral Peduncles - descending motor output from cortex down neural axis, 3rdlargest fiber bundle in CNS
• Insula - sensory of guts/inside body, lots to do with pain, heavy input to  anxiety, arousal

Cerebral Longitudinal Fissure

Mammilary Bodies

Genu & Splenium of Corpus Callosum

Rhinal Sulcus

Parahippocampal Gyrus

• Cerebral Longitudinal Fissure - divides the hemispheres sagittally
• Mammillary Bodies - part of hypothalamus and Limbic System, ends of anterior arches of fornix, act as relay for impulses for amygdala & hippocampus via mamillo-thalamic tract to thalamus
• Genu and Splenium of the Corpus Callosum - Genu = anterior, Splenium = posterior
• Rhinal Sulcus - defines border of Parahippocampal Gyrus
• Parahippocampal Gyrus - outer landmark covering hippocampus

Amygdala

Hippocampus

Fornix

• Amygdala - emotions, smell (connections to hippocampus), memory, decision-making, anxiety, part of limbic system & basal ganglia
• Hippocampus - memory formation, short-term memory
• Fornix - connect hippocampus to mammilary bodies (to hypothalamus to mammilary bodies to anterior nucleus of thalamus to cingulate cortex), allow hippocampi to talk to each other

Globus Pallidus

Lentiform  Nucleus

Internal Capsule

• Basal Ganglia - role in motor function (intentional)
• Lentiform Nucleus - globus pallidus (medial) + putamen (lateral)
• Internal Capsule - separate thalamus & lentiform nucleus, anterior part moving motor fibers to peduncles; anterior = motor fibers, posterior = sensory fibers

• lots of gray matter - info processing
• evolves along with cortex
• 10x fibers coming down to thalamus as going up to cortex
• cortex communicates via thalamus when going to other cortical areas (cortico-thalamic-cortical)

• Hypothalamus - neuroendocrine organ of CNS
• ventromedial = satiety
• lateral = hunger
• head hanglion of autonomic nervous system:
• anterior = parasympathetic
• sympathetic
• Consists of a large number of nuclei for such a small area
• Presses definition of nuclei in that many are fiber tracks as well
• Direct influence on pituitary effects - neurosecretory role

• superior = map of visual space; inferior = map of auditory space
• inferior connects to medial geniculate body
• superior connects to lateral geniculate body

Cuneate & Gracile Fasciculi

Cuneate & Gracile Nuclei

Cerebellar Peduncles

Olive

• Cuneate & Gracile Fasciculi - ascending somatosensory (middle & caudal of medulla)

• Cuneate & Gracile Nuclei - relay of somatosensory info to VPL

• Cerebellar Peduncles - second largest fiber bundle in CNS, descending motor fibers
• Olive/Olivary Nuclei - secondary auditory system (top of medulla, lateral to pyramids), ascending audiory fibers

Substantia Nigra

Periaquaductal Grey  Matter

Reticular Activating System

Red Nuclei

• Substantia Nigra -  pimary DA generation, decline 1% myelin each year, dopamine to basal ganglia, when degenerated you get Parkinson's, lose 1% DA a year, resting vs. intentional tremor
• Periaquaductal Grey  Matter - pain modulation
• Reticular Activating System - arousal, if excited get general arousal
• Red Nuclei - motor

Reticular Formation

Rostral Ventral Medulla

Gracile Nucleus

Cuneate Nucleus

• Reticular Formation - sleep & posture in metencephalon (pons), then vital reflexesin medulla/myencephalon (heartbeat, respiration) & postural control
• Rostral Ventral Medulla - modulating descending pain
• Gracile Nucleus - legs
• Cuneate Nucleus - arms

Pons

Cerebellum

• pons - descending mitor fibers interdigitated by transverse collaterals to cerebellum via cerebellar peduncles
• cerebellum - miniature cerebral cortex, miniature gyri called folia, deep nuclei mediate connections with rest of CNS

• consists of 33 segments
• cervical = 7
• thoracic =12
• lumbar = 5
• sacral = 5
• coccyx = 4
• downward continuation of medulla
• approximately 46cm long
• cervical & lumbar enlargement = increased processing load for upper & lower limbs
• nerves emerge between segments
• info enters the spinal cord via the dorsal roots (dorsal root ganglion)
• info exits the spinal cord via ventral roots (gray matter)
• afferent & efferent fibers merge to share the same spinal nerve and innervate the same body region (2/3 dedicated)
• propriospinal fibers surroud grey matter = interconnections between spinal segments

• sympathetic = thoracolumbar, ganglia near spinal cord, divergent contact w/ organs, catabolic (expend energy)
• parasympathetic = craniosacral, ganglia near target organs, specific contact w/ organs, anabolic (store energy)
• usually opposite effects on same organs for speed, preciseness, balancing
• head ganglion is hypothalamus
• dorsal afferent info goes directly to insula, sensation from visceral afferent is largely unconscious but also visceral pain, nausea, hunger; visceral pain  may be reffered to skin area supplied by somatic fibers of same segment 
• feedback forcontrol evverywhere in nervous system
• negative feedback = stability, positive feedback = instability
• good segue to neural circuits and neurophysioology sections