Optogenetics refers to using light to control cell activation (e.g: neurons) in living tissue. The cognitive approach to psychology uses two key concepts: information processing depends on internal representations (1) and these mental representations undergo transformations (2). People derive multiple representations from stimuli. Physical representations are activated first, phonetic representations next and category representations last.

The chronometric method refers to measuring reaction time. Information perception is biased by memory and attention. People engage in four primary mental operations: encode (1), compare (2), decide (3) and respond (4). The word superiority effect refers to the fact that participants are most accurate in identifying the target letter when the stimuli are words. Letter and word representation are activated in parallel.

There are four broad groups of study populations. Neurologically intact animals and humans and neurologically abnormal animals and humans. There are several types of brain disorders:

1. Vascular disorders
   Cerebral vascular accidents (stroke) occur when blood flow to the brain is suddenly disrupted. The cause is occlusion of the normal passage of blood by a foreign substance. Ischemia is a restriction in blood supply to tissues and is the result of partial occlusion. Cerebral arteriosclerosis is a chronic condition in which cerebral blood vessels become narrow because of thickening and hardening of the arteries.
2. Tumours
   A tumour is a mass of tissue that grows abnormally and has no physiological function. Brain lesions can result from tumours. Benign tumours are non-recurring tumours and tumours that don’t spread. Malignant tumours are recurring tumours and likely to distribute over several areas.
3. Degenerative and infectious disorders
   Many neurological disorders result from progressive disease (e.g: Alzheimer’s). This can be the result of genetic or environmental factors but also viruses.
4. Traumatic brain injury
   This is the result of an accident. Closed head injuries refer to injuries in which the skull remains intact but the brain is damaged. A coup is damage at the place of the blow and a countercoup is damage at the place opposite of the blow.
5. Epilepsy
   This is a condition characterized by excessive and abnormally patterned activity in the brain.

Angiography is a clinical imaging method used to evaluate the circulatory system in the brain and diagnose disruptions in circulation. In a single dissociation, a between-group difference is apparent in only one task. A double dissociation identifies whether two cognitive functions are independent of each other. Researchers can choose people with similar anatomical lesions or people with similar behavioural deficits. Many diseases of the nervous system are not usually related to problems with neurons, but rather with how the flow of information is altered by the disease process.

Perturbing neural function refers to disturb interactions between neurons. There are several methods to perturb neural function:

1. Pharmacology
   This involves the use of psychoactive drugs (e.g: caffeine and medicine). The problem is that the drugs affect the entire body and we don’t know the effect on one specific area.
2. Transcranial magnetic stimulation (TMS)
   This is non-invasively produce focal stimulation of the human brain. It is safe and people can act as their control group. It looks like sunglasses on someone’s head.
3. Transcranial direct current stimulation (tDCS)
   It sends a current between two small electrodes, an anode and a cathode, placed on the scalp. Neurons under the anode become depolarized. Neurons under the cathode become hyperpolarized and are less likely to fire.
4. Genetic manipulation
   This is altering genes in animals. It makes use of the knockout procedure: researchers knock out certain genes to study the effects.

There are several methods to analyse the structure of the brain:

1. Computed Tomography (CT/CAT)
   This involves making a 3D image of the brain using x-rays. It can be used to distinguish large structures.
2. Magnetic resonance imaging (MRI)
   This creates a magnetic field and then sends radio-waves through someone’s brain to make an image of the brain. It can be used to distinguish small structures.
3. Diffusion tensor imaging (DTI)
   This is an MRI scan that measures the white matter tracts in the brain by looking at water in the axons. It can be used to study anatomical connectivity between regions.

There are several methods to analyse the function of brain regions:

1. Single-cell recording
   A thin electrode is inserted and changes in electrical activity in the neuron can be measured. It can also detect electrical activity in cells nearby, but that electrical activity will be weaker than the intended cell. Cell activity can best be understood in relation to other cells around it.
2. Electroencephalography (EEG)
   This measures electrical potentials of populations of neurons. The scalp passively conducts the electrical activity conducted by synaptic activity and this is measured by electrodes on the scalp. It can be used to detect abnormalities in brain function.
3. Event-related potential (ERP)
   EEG traces recorded from a series of trials are averaged together aligning them relative to an external event (e.g: the onset of a stimulus). This reflects neural activity that is specifically related to the external event.
4. Magnetoencephalography (MEG)
   This measures small magnetic fields that are associated with synaptic activity and averages them over a series of trials to obtain event-related fields. MEG is more specific than EEG because magnetic fields are not distorted by the scalp. MEG only tends to be able to record neurons within sulci and MEG requires a room that is shielded from all external magnetic fields.
5. Electrocortogram (ECoG)
   It is similar to EEG, but the electrode is placed on the surface of the brain, instead of the scalp. There is less distortion than with EEG. It has a good temporal and spatial resolution.

The region of space a visual cell responds to is the cell’s receptive field. Retinotopic refers to topographic representations in vision.

There are several methods that accurately measure the structure and the function of the brain. These methods do not measure neural activity directly.

1. Positron emission tomography (PET)
   This measures local variations in cerebral blood flow that are correlated with mental activity. A radioactive substance is introduced in the bloodstream and the radiation emitted from this substance is monitored. The results are reported as a change in regional cerebral blood flow.
2. Functional magnetic resonance imaging (fMRI)
   This measures the oxygen levels at certain parts of the brain. It detects the ratio of oxygenated to deoxygenated haemoglobin. This value is the blood oxygen level-dependent (BOLD). The more an area is used, the more deoxygenated haemoglobin there is.

In a block design experiment, the recorded neural activity is integrated over a block of time during which the participant either is presented a stimulus or performs a task. PET and fMRI have poor temporal resolution compared with single-cell recordings or ERPs. Interpreting the data from a PET or fMRI study is also difficult because the data sets are enormous. fMRI can be used to check for functional connectivity: how the activation changes of one brain area correlate with the activation changes of another.