Brain Anatomy: Cortex, Brodmann Areas, MNI Coordinates

Identifying Cerebral Cortex Regions

• Identification of cerebral cortex regions is possible through relative locations within lobes or large regions.

Brodmann Areas

• These areas are defined by the layered composition of cells, known as cytoarchitecture.

Gyri and Sulci

• Each lobe is characterized by a set of gyri (ridges) and sulci (grooves).

Functional Divisions

• Primary sensory cortices for vision, hearing, and body sensations are functional divisions.
• Primary motor cortex is included in functional divisions.
• The olfactory bulb, responsible for the sense of smell, is a functional division.

MNI Coordinates

• Montreal Neurological Institute (MNI) coordinates are a coordinate system.
• It’s a standard for precise brain localization.
• NI coordinates extend to subcortical areas.
• The majority of fMRI research articles use MNI coordinates.

Navigating Brain Anatomy

• Planes of section include sagittal, horizontal (axial or transverse), frontal (coronal), and cross-sections.
• Horizontal planes show brain structure from above.
• Sagittal planes display brain structures from the side.
• Coronal planes show brain structures from the front.

Terms of Reference

• Dorsal: Towards the back or away from the stomach side, the brain's top in four-legged animals.
• Ventral: Towards the stomach or away from the back.
• Anterior: Towards the front end.
• Posterior: Towards the rear end.
• Superior: Above another part.
• Inferior: Below another part.
• Lateral: Towards the side, away from the midline.
• Medial: Towards the midline, away from the side.
• Ipsilateral: On the same side of the body.
• Contralateral: On the opposite side of the body.
• The dorsal and ventral axes of the body align in four-legged animals.
• Upright posture in humans shifts the head's dorsal/ventral directions at right angles.

Coarse Organization of the Nervous System

• CNS consists of the brain and the spinal cord.
• PNS connects the brain and spinal cord to the body's periphery.

Peripheral Nervous System (PNS)

• The PNS connects the brain and spinal cord to the rest of the body.
• The somatic nervous system controls voluntary muscles and conveys sensory information to the CNS.
• The autonomic nervous system controls the heart, intestines, and other organs.
• It sends and receives messages, regulating automatic behaviors like heart rate and digestion, and is divided into two subsystems.

Sympathetic Nervous System

• Known as "fight or flight."
• A network prepares organs for activity, increasing heart rate and respiration.
• It is composed of ganglia extending from the spinal cord to organs.
• Dominant during vigorous activity.

Parasympathetic Nervous System

• Known as "rest and digest."
• Facilitates vegetative and nonemergency responses.
• Decreases functions increased by the sympathetic nervous system.
• Composed of ganglia extending from the spinal cord to the organs, it is dominant during relaxed states.

Central Nervous System

• It consists of the brain and spinal cord.

Gray and White Matter

• Gray matter consists of neuronal cell bodies and dendrites.
• White matter consists of axons, myelin, and glia cells.
• Axon tracts exist within hemispheres, between hemispheres, and connecting cortical and subcortical regions.
• The corpus collosum is a large white matter tract linking the two hemispheres.

Ventricles

• Four fluid-filled cavities within the brain's central canal contain cerebrospinal fluid.
• The cerebrospinal fluid (CSF) is a clear fluid in the brain and spinal cord.
• CSF provides “cushioning" and acts as a reservoir for hormones and nutrition.

Meninges

• Membranes surround the brain and spinal cord.
• They contain pain receptors.
• Meningitis is an inflammation of the meninges.
• Swollen blood vessels in the meninges cause migraine headaches.

Major Divisions of the Vertebrate Brain

• The forebrain contains the prosencephalon, which includes the diencephalon ("between-brain" containing the thalamus and hypothalamus) and the telencephalon ("end-brain" containing the cerebral cortex, hippocampus, and basal ganglia).
• The midbrain is the mesencephalon ("middle brain").
• The hindbrain is the rhombencephalon ("parallelogram brain"- medulla, pons, and cerebellum).

Fish vs. Mammal Brain Development

• In fish, forebrain, midbrain, and hindbrain are distinct bulges.
• In adult mammals, the forebrain grows and surrounds the midbrain and part of the hindbrain.

Spinal Cord

• Two types of matter are in the spinal cord.
• Gray matter is located centrally within the spinal cord and contains densely packed cell bodies and dendrites.

White Matter

• White matter is composed of myelinated axons carrying information from gray matter to the brain or other areas of the spinal cord.
• The spinal cord communicates with sense organs and muscles, excluding those of the head.
• The dorsal root conveys sensory information to the spinal cord
• The ventral root conveys motor commands to the muscles.

Cranial Nerves

• Cranial nerves II through XII are shown.
• Cranial nerve I, the olfactory nerve, connects to the forebrain's olfactory bulbs.

Hindbrain

• Consists of the medulla, pons, and cerebellum.
• Located at the posterior portion of the brain.
• It combines hindbrain structures, the midbrain, and other central structures to form the brain stem.

Medulla

• It's in the hindbrain, also known as the medulla oblongata.
• It's just above the spinal cord.
• Axons from each brain half cross to control the opposite body side.
• It is responsible for vital reflexes like breathing, heart rate, vomiting, and sneezing.

Pons

• In the hindbrain.
• It lies on each side of the medulla (ventral and anterior).
• Pons means "bridge" in Latin.
• Relays signals from the forebrain to the cerebellum.
• Functions include sleep, respiration, swallowing, bladder control, hearing, equilibrium, taste, eye movement, facial expressions, facial sensation, and posture.

Cerebellum

• In the hindbrain occupies 10% of mass and contains ~80% of the neurons.
• It integrates motor commands and sensory feedback for smooth movement and dexterity.
• Fine-tunes motor movement and coordination and corrects unintended movements.
• Important for attention shifting between auditory and visual stimuli.
• Cerebellum-damaged people struggle with timing and shifting attention.

Midbrain

• The tectum is the roof of the midbrain and includes the superior & inferior colliculi
• The inferior colliculus is a subcortical route for hearing
• The superior colliculus is a subcortical route for gaze orienting
• The tegmentum include the red nucleus (motor coordination) and substantia nigra (dopamine).
• The substantia gives rise to a dopamine pathway facilitating readiness for movement and include the periaqueductal gray (pain signals)
• The Cerebral Peduncles include ascending (sensory) and descending (motor) white matter tracts
• It connects the pons (hindbrain/brainstem) to the thalamus (forebrain).

Brainstem

• The midbrain, pons, and medulla comprise the the brainstem
• Zombies have a brainstem but lack a forebrain.

Forebrain (Telencephalon and Diencephalon)

• It’s the most anterior and prominent area of mammalian brains, with two cerebral hemispheres.
• Consists of the outer cortex and subcortical regions with outer portion known as the “cerebral cortex."
• Each side receives sensory information and controls the contralateral side of the body.

Limbic System

• A set of subcortical structures that form a border (or limbus) around the brainstem.
• Includes the hippocampus, olfactory bulb, hypothalamus, amygdala, and cingulate gyrus of the cerebral cortex.
• Associated with motivation-emotions, such as eating, drinking, sexual activity, anxiety, and aggression.

Hippocampus

• A large structure located between the thalamus and cerebral cortex critical for certain types of memories, especially those of individual events.

Hypothalamus

• Conveys messages to the pituitary gland to alter the release of hormones.
• The pituitary gland is a hormone-producing gland found at the base of the hypothalamus.
• Associated with behaviors include eating, drinking, sexual activity, and other motivated behaviors.
• The thalamus and the hypothalamus together form the “diencephalon."

Thalamus

• A relay station from the sensory organs and the main source of input to the cortex.
• Information routes from the thalamus to the cerebral cortex.
• Each thalamic nucleus projects its axons to a different part of the cortex.

Basal Ganglia

• Includes the caudate nucleus, the putamen (collectively called the striatum), and the globus pallidus.
• Associated with planning of motor movement, and with aspects of memory and emotional expression.
• Involved in modulating both action and thought through reciprocal interaction with frontal lobes.
• Disease of the basal ganglia results in abnormalities including hypokinesia and hyperkinesia understood via the basal ganglia.
• Hypokinesia (e.g., Parkinson's disease) is characterized by impairment in initiating movements and reduction in strength of voluntary movements.
• Hyperkinesia (e.g., Huntington's disease) is defined as excessive motor activity, involuntary movements, hypotonia.

Brain Imaging and Brain Damage; Structural Imaging

• Brian anatomy and behavior correlates via CAT or MRI.
• Phrenology was a pseudoscience that attempts to relate skull anatomy to behavior but didn't follow the scientific method and has a minimal relationship between skull anatomy and brain anatomy

Computerized Axial Tomography (CT/CAT)

• Maps brain areas, but requires exposure to X-rays.
• Used to identify tumors and abnormalities as well as requiring injected contrast agents and X-rays through the head.
• A person's head is placed into a rotating scanner.

Magnetic Resonance Imaging (MRI)

• Magnetic field aligns axes of rotation of hydrogen atoms.
• Radio frequency field makes atoms spin.
• When radio frequency field is turned off, atomic nuclei release electromagnetic energy as they relax.
• Measure released energy to obtain an image of the brain or other structure.

Diffusion-weighted MRI

• Diffusion-tensor imaging (DTI) data can be analyzed to trace white matter connections in the brain.
• Based on limited diffusion of water molecules in axons, it measures diffusion of water in axons (more likely to move parallel to axon than perpendicular).

Functional Imaging

• PET measures local blood flow (rCBF), injecting a radioactive tracer into the blood stream.
• PET tracer uptake takes up to 30 seconds to peak.
• Over the last 20 years, functional magnetic resonance imaging (fMRI) has overtaken PET scans in functional imaging experiments with the first fMRI experiment (Kwong et al, 1992)

BOLD signal (fMRI)

• Deoxygenated hemoglobin is magnetic; oxygenated is not
• The extent of magnetic field disruption varies with the proportion of deoxygenated hemoglobin in the blood
• Low Oxygenated: Deoxygenated ratio correlates to Lower MR signal
• High Oxygenated: Deoxygenated ratio correlates to Higher MR signal
• fMRI directly measures deoxyhemoglobin, not radioactivity concentration.
• This is called the BOLD response (Blood Oxygen Level Dependent contrast).
• Neural activity consumes oxygen which compensate for increased oxygen consumption, more blood is pumped into active regions.

Hemodynamic Response Function (fMRI)

• The change in BOLD response over time is the hemodynamic response function.
• Peaks in 6–8 seconds, which limits temporal resolution.
• Unless stimuli are far apart in time (e.g., every 16 sec), the BOLD response resembles superimposed HRFs.

FMRI Experimental Design and Analysis

• Preprocessing includes:
  • Data acquisition à correct for head movement à stereotactic normalization à smoothing à Divide data according to the design and perform a statistical comparison before raw data is cleaned.

Event-Related Designs

• Random ordering of stimuli with events determined by the subject via Oddball (or unexpected events)
• Stimuli are presented as individual events that model the brain's response individually, creating responses that are reordered over time.
• The models averages responses to get general patterns with either a slow or rapid event-related design.

Statistics

• Can predict how hemodynamic response and what the event will reflect
• Relies on linearity to separate signals.
• Statistical data model contains a regressor for each condition.
• Find which voxels show the predicted changes in the BOLD response over time, according to experimental design and HRF shape.

Subtraction Logic

• The effect is that the brian imaging subtracts brain activity in one condition from another to isolate effect of cognitive or sensory process in relation to the comparative nature of everything: RELATIVE differences in brain activity between two or more conditions.

Multivoxel Pattern Analysis (MVPA)

• MVPA looks at brain activity patterns across multiple voxels instead of focusing on individual regions which decodes information by guessing which image the person is looking at based on scan

Effects of Brain Damage

• Brain damage constrained by blood supply and blood is disrupted.
• Single dissociation occurs because of the spared nature of of of one task relative to another, either classically or strongly.

Double Dissociation

• Two single dissociations that have complementary profile of abilities
• Syndromes are based on the associations between the symptoms in a certain group during a structure function relatiionshio with more precision by syndromes or a single specific behavioral symptom

Functional Connectivity with Group Lesions

• In Group lesions, you can assess structure-function relationships with more precision which enables investigation neural correlates of a disease of a speicfic pathology while identifying regions that are implicated in a behavior, and focusing on the role of particular structures.
• Animal models of brain damage produce an inability to recognize faces, inability to perceive motion, changes in emotional responses
• Ablation: removal of a brain area
• Lesion: damage to a brain area, often done for research
• Gene knockout: one of an organism's genes is made inoperative ("knocked out" of the organism)
• Stereotaxic instrument: used to damage structures in the interior of the brain and have a greater focus on disconnections.

Brain Stimulation

• Transcranial Magnetic Stimulation (TMS)*
• TMS is is a noninvasive technique that stimulate the brain so virtual, reversible lesions are possible to produce. A wire carrying electric current is placed near the participant's head where a magnetic field induces a current in neraby neurons which effects cognitive function (creates a “virtual lesion”). Experimental controls in TMS research consist of utilizing varying time windows, tasks, stimulation location and differing stimuli , for better experimental standards

Advantages and disadvatages of TMS

• Temporary effects remove the lesion confound of brain reorganization with Focal lesions that are controlled by the experimenter. However, the disadvantages include that many areas cannot be stimulated, there can be some overestimation in the stimulation and affects may be either be of an excitatory or inhibitory area.

Transcranial Direct Current Stimulation (TDCS)

• TDCS is a Noninvasive stimulation of the brain where the brain passis weak electrical currents and applies very weak electric current applied between two stimulating electrodes (one anodal, one cathodal) to the the region of interst.
• Andol increases neuron firing rate and causes performance enhancement
• Cathodal decreases neuron firing rate and disrupts Performance and its actions rely on GABA and glutamate activity

Intracranial stimulation

• Invasive Stimulating electrodes can be observed during laboratory animals and for clinical purposes with humans such as deep brain stimulation to treat Parkinson's disease should increase behavior. however complexity has limited electrode probing of the brain during brain surgery because the are complex

Optogenetic stimulation

• Can pinpoint function to particular cell types in laboratory animals via light to control a a specific neuron population through virally inserting proteins the in a certain neuron type where optical shines fibers to control excititation or inhibition with millisecond accuarcy being tested in humans

Deep Brain stimulation

• Deep brain stimulation (DBS) of the subthalamic nucleus (STN) helps treats motor symptoms in Parkinson disease

Explore cerebral cortex regions, Brodmann areas defined by cytoarchitecture, and gyri/sulci. Functional divisions like sensory and motor cortices, along with the olfactory bulb, are examined. Understand MNI coordinates for precise brain localization in fMRI research, and navigate brain anatomy through sagittal, horizontal, and frontal planes.