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Tuesday, March 26, 2024

Encoding (memory)

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Encoding_(memory)

Memory has the ability to encode, store and recall information. Memories give an organism the capability to learn and adapt from previous experiences as well as build relationships. Encoding allows a perceived item of use or interest to be converted into a construct that can be stored within the brain and recalled later from long-term memory. Working memory stores information for immediate use or manipulation, which is aided through hooking onto previously archived items already present in the long-term memory of an individual.

History

Hermann Ebbinghaus
Hermann Ebbinghaus (1850-1909)

Encoding is still relatively new and unexplored but origins of encoding date back to age old philosophers such as Aristotle and Plato. A major figure in the history of encoding is Hermann Ebbinghaus (1850–1909). Ebbinghaus was a pioneer in the field of memory research. Using himself as a subject he studied how we learn and forget information by repeating a list of nonsense syllables to the rhythm of a metronome until they were committed to his memory. These experiments led him to suggest the learning curve. He used these relatively meaningless words so that prior associations between meaningful words would not influence learning. He found that lists that allowed associations to be made and semantic meaning was apparent were easier to recall. Ebbinghaus' results paved the way for experimental psychology in memory and other mental processes.

During the 1900s, further progress in memory research was made. Ivan Pavlov began research pertaining to classical conditioning. His research demonstrated the ability to create a semantic relationship between two unrelated items. In 1932, Frederic Bartlett proposed the idea of mental schemas. This model proposed that whether new information would be encoded was dependent on its consistency with prior knowledge (mental schemas). This model also suggested that information not present at the time of encoding would be added to memory if it was based on schematic knowledge of the world. In this way, encoding was found to be influenced by prior knowledge. With the advance of Gestalt theory came the realization that memory for encoded information was often perceived as different from the stimuli that triggered it. It was also influenced by the context that the stimuli were embedded in.

With advances in technology, the field of neuropsychology emerged and with it a biological basis for theories of encoding. In 1949, Donald Hebb looked at the neuroscience aspect of encoding and stated that "neurons that fire together wire together," implying that encoding occurred as connections between neurons were established through repeated use. The 1950s and 60's saw a shift to the information processing approach to memory based on the invention of computers, followed by the initial suggestion that encoding was the process by which information is entered into memory. In 1956, George Armitage Miller wrote his paper on how short-term memory is limited to seven items, plus-or-minus two, called The Magical Number Seven, Plus or Minus Two. This number was appended when studies done on chunking revealed that seven, plus or minus two could also refer to seven "packets of information". In 1974, Alan Baddeley and Graham Hitch proposed their model of working memory, which consists of the central executive, visuo-spatial sketchpad, and phonological loop as a method of encoding. In 2000, Baddeley added the episodic buffer. Simultaneously Endel Tulving (1983) proposed the idea of encoding specificity whereby context was again noted as an influence on encoding.

Types

There are two main approaches to coding information: the physiological approach, and the mental approach. The physiological approach looks at how a stimulus is represented by neurons firing in the brain, while the mental approach looks at how the stimulus is represented in the mind.

There are many types of mental encoding that are used, such as visual, elaborative, organizational, acoustic, and semantic. However, this is not an extensive list.

Visual encoding

Visual encoding is the process of converting images and visual sensory information to memory stored in the brain. This means that people can convert the new information that they stored into mental pictures (Harrison, C., Semin, A.,(2009). Psychology. New York p. 222) Visual sensory information is temporarily stored within our iconic memory and working memory before being encoded into permanent long-term storage. Baddeley's model of working memory suggests that visual information is stored in the visuo-spatial sketchpad. The visuo-spatial sketchpad is connected to the central executive, which is a key area of working memory. The amygdala is another complex structure that has an important role in visual encoding. It accepts visual input in addition to input, from other systems, and encodes the positive or negative values of conditioned stimuli.

Elaborative encoding

Elaborative encoding is the process of actively relating new information to knowledge that is already in memory. Memories are a combination of old and new information, so the nature of any particular memory depends as much on the old information already in our memories as it does on the new information coming in through our senses. In other words, how we remember something depends on how we think about it at the time. Many studies have shown that long-term retention is greatly enhanced by elaborative encoding.

Semantic encoding

Semantic encoding is the processing and encoding of sensory input that has particular meaning or can be applied to a context. Various strategies can be applied such as chunking and mnemonics to aid in encoding, and in some cases, allow deep processing, and optimizing retrieval.

Words studied in semantic or deep encoding conditions are better recalled as compared to both easy and hard groupings of nonsemantic or shallow encoding conditions with response time being the deciding variable. Brodmann's areas 45, 46, and 47 (the left inferior prefrontal cortex or LIPC) showed significantly more activation during semantic encoding conditions compared to nonsemantic encoding conditions regardless of the difficulty of the nonsemantic encoding task presented. The same area showing increased activation during initial semantic encoding will also display decreasing activation with repetitive semantic encoding of the same words. This suggests the decrease in activation with repetition is process specific occurring when words are semantically reprocessed but not when they are nonsemantically reprocessed. Lesion and neuroimaging studies suggest that the orbitofrontal cortex is responsible for initial encoding and that activity in the left lateral prefrontal cortex correlates with the semantic organization of encoded information.

Acoustic encoding

Acoustic encoding is the encoding of auditory impulses. According to Baddeley, processing of auditory information is aided by the concept of the phonological loop, which allows input within our echoic memory to be sub vocally rehearsed in order to facilitate rememberingen we hear any word, we do so by hearing individual sounds, one at a time. Hence the memory of the beginning of a new word is stored in our echoic memory until the whole sound has been perceived and recognized as a word. Studies indicate that lexical, semantic and phonological factors interact in verbal working memory. The phonological similarity effect (PSE), is modified by word concreteness. This emphasizes that verbal working memory performance cannot exclusively be attributed to phonological or acoustic representation but also includes an interaction of linguistic representation. What remains to be seen is whether linguistic representation is expressed at the time of recall or whether the representational methods used (such as recordings, videos, symbols, etc.) participate in a more fundamental role in encoding and preservation of information in memory. The brain relies primarily on acoustic (aka phonological) encoding for use in short-term storage and primarily semantic encoding for use in long-term storage.

Other senses

Tactile encoding is the processing and encoding of how something feels, normally through touch. Neurons in the primary somatosensory cortex (S1) react to vibrotactile stimuli by activating in synchronization with each series of vibrations. Odors and tastes may also lead to encode.

Organizational encoding is the course of classifying information permitting to the associations amid a sequence of terms.

Long-Term Potentiation

Early LPT Mechanism

Encoding is a biological event that begins with perception. All perceived and striking sensations travel to the brain's thalamus where all these sensations are combined into one single experience. The hippocampus is responsible for analyzing these inputs and ultimately deciding if they will be committed to long-term memory; these various threads of information are stored in various parts of the brain. However, the exact way in which these pieces are identified and recalled later remains unknown.

Encoding is achieved using a combination of chemicals and electricity. Neurotransmitters are released when an electrical pulse crosses the synapse which serves as a connection from nerve cells to other cells. The dendrites receive these impulses with their feathery extensions. A phenomenon called long-term potentiation allows a synapse to increase strength with increasing numbers of transmitted signals between the two neurons. For that to happen, NMDA receptor, which influences the flow of information between neurons by controlling the initiation of long-term potentiation in most hippocampal pathways, need to come to the play. For these NMDA receptors to be activated, there must be two conditions. Firstly, glutamate has to be released and bound to the NMDA receptor site on postsynaptic neurons. Secondly, excitation has to take place in postsynaptic neurons. These cells also organize themselves into groups specializing in different kinds of information processing. Thus, with new experiences the brain creates more connections and may 'rewire'. The brain organizes and reorganizes itself in response to one's experiences, creating new memories prompted by experience, education, or training. Therefore, the use of a brain reflects how it is organised. This ability to re-organize is especially important if ever a part of the brain becomes damaged. Scientists are unsure of whether the stimuli of what we do not recall are filtered out at the sensory phase or if they are filtered out after the brain examines their significance.

Mapping Activity

Positron emission tomography (PET) demonstrates a consistent functional anatomical blueprint of hippocampal activation during episodic encoding and retrieval. Activation in the hippocampal region associated with episodic memory encoding has been shown to occur in the rostral portion of the region whereas activation associated with episodic memory retrieval occurs in the caudal portions. This is referred to as the Hippocampal memory encoding and retrieval model or HIPER model.

One study used PET to measure cerebral blood flow during encoding and recognition of faces in both young and older participants. Young people displayed increased cerebral blood flow in the right hippocampus and the left prefrontal and temporal cortices during encoding and in the right prefrontal and parietal cortex during recognition. Elderly people showed no significant activation in areas activated in young people during encoding, however they did show right prefrontal activation during recognition. Thus it may be concluded that as we grow old, failing memories may be the consequence of a failure to adequately encode stimuli as demonstrated in the lack of cortical and hippocampal activation during the encoding process.

Recent findings in studies focusing on patients with post traumatic stress disorder demonstrate that amino acid transmitters, glutamate and GABA, are intimately implicated in the process of factual memory registration, and suggest that amine neurotransmitters, norepinephrine-epinephrine and serotonin, are involved in encoding emotional memory.

Molecular Perspective

The process of encoding is not yet well understood, however key advances have shed light on the nature of these mechanisms. Encoding begins with any novel situation, as the brain will interact and draw conclusions from the results of this interaction. These learning experiences have been known to trigger a cascade of molecular events leading to the formation of memories. These changes include the modification of neural synapses, modification of proteins, creation of new synapses, activation of gene expression and new protein synthesis. One study found that high central nervous system levels of acetylcholine during wakefulness aided in new memory encoding, while low levels of acetylcholine during slow-wave sleep aided in consolidation of memories. However, encoding can occur on different levels. The first step is short-term memory formation, followed by the conversion to a long-term memory, and then a long-term memory consolidation process.

Synaptic Plasticity

Synaptic plasticity is the ability of the brain to strengthen, weaken, destroy and create neural synapses and is the basis for learning. These molecular distinctions will identify and indicate the strength of each neural connection. The effect of a learning experience depends on the content of such an experience. Reactions that are favored will be reinforced and those that are deemed unfavorable will be weakened. This shows that the synaptic modifications that occur can operate either way, in order to be able to make changes over time depending on the current situation of the organism. In the short term, synaptic changes may include the strengthening or weakening of a connection by modifying the preexisting proteins leading to a modification in synapse connection strength. In the long term, entirely new connections may form or the number of synapses at a connection may be increased, or reduced.

The Encoding Process

A significant short-term biochemical change is the covalent modification of pre-existing proteins in order to modify synaptic connections that are already active. This allows data to be conveyed in the short term, without consolidating anything for permanent storage. From here a memory or an association may be chosen to become a long-term memory, or forgotten as the synaptic connections eventually weaken. The switch from short to long-term is the same concerning both implicit memory and explicit memory. This process is regulated by a number of inhibitory constraints, primarily the balance between protein phosphorylation and dephosphorylation. Finally, long term changes occur that allow consolidation of the target memory. These changes include new protein synthesis, the formation of new synaptic connections, and finally the activation of gene expression in accordance with the new neural configuration. The encoding process has been found to be partially mediated by serotonergic interneurons, specifically in regard to sensitization as blocking these interneurons prevented sensitization entirely. However, the ultimate consequences of these discoveries have yet to be identified. Furthermore, the learning process has been known to recruit a variety of modulatory transmitters in order to create and consolidate memories. These transmitters cause the nucleus to initiate processes required for neuronal growth and long-term memory, mark specific synapses for the capture of long-term processes, regulate local protein synthesis, and even appear to mediate attentional processes required for the formation and recall of memories.

Encoding and Genetics

Human memory, including the process of encoding, is known to be a heritable trait that is controlled by more than one gene. In fact, twin studies suggest that genetic differences are responsible for as much as 50% of the variance seen in memory tasks. Proteins identified in animal studies have been linked directly to a molecular cascade of reactions leading to memory formation, and a sizable number of these proteins are encoded by genes that are expressed in humans as well. In fact, variations within these genes appear to be associated with memory capacity and have been identified in recent human genetic studies.

Complementary Processes

The idea that the brain is separated into two complementary processing networks (task positive and task negative) has recently become an area of increasing interest. The task positive network deals with externally oriented processing whereas the task negative network deals with internally oriented processing. Research indicates that these networks are not exclusive and some tasks overlap in their activation. A study done in 2009 shows encoding success and novelty detection activity within the task-positive network have significant overlap and have thus been concluded to reflect common association of externally oriented processing. It also demonstrates how encoding failure and retrieval success share significant overlap within the task negative network indicating common association of internally oriented processing. Finally, a low level of overlap between encoding success and retrieval success activity and between encoding failure and novelty detection activity respectively indicate opposing modes or processing. In sum task positive and task negative networks can have common associations during the performance of different tasks.

Depth of Processing

Different levels of processing influence how well information is remembered. This idea was first introduced by Craik and Lockhart (1972). They claimed that the level of processing information was dependent upon the depth at which the information was being processed; mainly, shallow processing and deep processing. According to Craik and Lockhart, the encoding of sensory information would be considered shallow processing, as it is highly automatic and requires very little focus. Deeper level processing requires more attention being given to the stimulus and engages more cognitive systems to encode the information. An exception to deep processing is if the individual has been exposed to the stimulus frequently and it has become common in the individual’s life, such as the person’s name. These levels of processing can be illustrated by maintenance and elaborate rehearsal.

Maintenance and Elaborative Rehearsal

Maintenance rehearsal is a shallow form of processing information which involves focusing on an object without thought to its meaning or its association with other objects. For example, the repetition of a series of numbers is a form of maintenance rehearsal. In contrast, elaborative or relational rehearsal is a process in which you relate new material to information already stored in Long-term memory. It's a deep form of processing information and involves thought of the object's meaning as well as making connections between the object, past experiences and the other objects of focus. Using the example of numbers, one might associate them with dates that are personally significant such as your parents' birthdays (past experiences) or perhaps you might see a pattern in the numbers that helps you to remember them.

American Penny

Due to the deeper level of processing that occurs with elaborative rehearsal it is more effective than maintenance rehearsal in creating new memories. This has been demonstrated in people's lack of knowledge of the details in everyday objects. For example, in one study where Americans were asked about the orientation of the face on their country's penny few recalled this with any degree of certainty. Despite the fact that it is a detail that is often seen, it is not remembered as there is no need to because the color discriminates the penny from other coins. The ineffectiveness of maintenance rehearsal, simply being repeatedly exposed to an item, in creating memories has also been found in people's lack of memory for the layout of the digits 0-9 on calculators and telephones.

Maintenance rehearsal has been demonstrated to be important in learning but its effects can only be demonstrated using indirect methods such as lexical decision tasks, and word stem completion which are used to assess implicit learning. In general, however previous learning by maintenance rehearsal is not apparent when memory is being tested directly or explicitly with questions like " Is this the word you were shown earlier?"

Intention to Learn

Studies have shown that the intention to learn has no direct effect on memory encoding. Instead, memory encoding is dependent on how deeply each item is encoded, which could be affected by intention to learn, but not exclusively. That is, intention to learn can lead to more effective learning strategies, and consequently, better memory encoding, but if you learn something incidentally (i.e. without intention to learn) but still process and learn the information effectively, it will get encoded just as well as something learnt with intention.

The effects of elaborative rehearsal or deep processing can be attributed to the number of connections made while encoding that increase the number of pathways available for retrieval.

Optimal Encoding

Organization

Organization is key to memory encoding. Researchers have discovered that our minds naturally organize information if the information received is not organized. One natural way information can be organized is through hierarchies. For example, the grouping mammals, reptiles, and amphibians is a hierarchy of the animal kingdom.

Depth of processing is also related to the organization of information. For example, the connections that are made between the to-be-remembered item, other to-be-remembered items, previous experiences, and context generate retrieval paths for the to-be-remembered item and can act as retrieval cues. These connections create organization on the to-be-remembered item, making it more memorable.

Visual Images

Another method used to enhance encoding is to associate images with words. Gordon Bower and David Winzenz (1970) demonstrated the use of imagery and encoding in their research while using paired-associate learning. Researchers gave participants a list of 15-word-pairs, showing each participant the word pair for 5 seconds for each pair. One group was told to create a mental image of the two words in each pair in which the two items were interacting. The other group was told to use maintenance rehearsal to remember the information. When participants were later tested and asked to recall the second word in each word pairing, researchers found that those who had created visual images of the items interacting remembered over twice as many of the word pairings than those who used maintenance rehearsal.  

Mnemonics

Red Orange Yellow Green Blue Indigo Violet
The mnemonic "Roy G. Biv" can be used to remember the colors of the rainbow

When memorizing simple material such as lists of words, mnemonics may be the best strategy, while "material already in long-term store [will be] unaffected". Mnemonic Strategies are an example of how finding organization within a set of items helps these items to be remembered. In the absence of any apparent organization within a group, organization can be imposed with the same memory enhancing results. An example of a mnemonic strategy that imposes organization is the peg-word system which associates the to-be-remembered items with a list of easily remembered items. Another example of a mnemonic device commonly used is the first letter of every word system or acronyms. When learning the colours in a rainbow most students learn the first letter of every color and impose their own meaning by associating it with a name such as Roy. G. Biv which stands for red, orange, yellow, green, blue, indigo, violet. In this way mnemonic devices not only help the encoding of specific items but also their sequence. For more complex concepts, understanding is the key to remembering. In a study done by Wiseman and Neisser in 1974 they presented participants with a picture (the picture was of a Dalmatian in the style of pointillism making it difficult to see the image). They found that memory for the picture was better if the participants understood what was depicted.

Chunking

Chunking is a memory strategy used to maximize the amount of information stored in short term memory in order to combine it into small, meaningful sections.  By organizing objects into meaningful sections, these sections are then remembered as a unit rather than separate objects. As larger sections are analyzed and connections are made, information is weaved into meaningful associations and combined into fewer, but larger and more significant pieces of information. By doing so, the ability to hold more information in short-term memory increases. To be more specific, the use of chunking would increase recall from 5 to 8 items to 20 items or more as associations are made between these items.

Words are an example of chunking, where instead of simply perceiving letters we perceive and remember their meaningful wholes: words. The use of chunking increases the number of items we are able to remember by creating meaningful "packets" in which many related items are stored as one. The use of chunking is also seen in numbers. One of the most common forms of chunking seen on a daily basis is that of phone numbers. Generally speaking, phone numbers are separated into sections. An example of this would be 909 200 5890, in which numbers are grouped together to make up one whole. Grouping numbers in this manner, allows them to be recalled with more facility because of their comprehensible acquaintanceship.

State-Dependent Learning

For optimal encoding, connections are not only formed between the items themselves and past experiences, but also between the internal state or mood of the encoder and the situation they are in. The connections that are formed between the encoders internal state or the situation and the items to be remembered are State-dependent. In a 1975 study by Godden and Baddeley the effects of State-dependent learning were shown. They asked deep sea divers to learn various materials while either under water or on the side of the pool. They found that those who were tested in the same condition that they had learned the information in were better able to recall that information, i.e. those who learned the material under water did better when tested on that material under water than when tested on land. Context had become associated with the material they were trying to recall and therefore was serving as a retrieval cue. Results similar to these have also been found when certain smells are present at encoding.

However, although the external environment is important at the time of encoding in creating multiple pathways for retrieval, other studies have shown that simply creating the same internal state that was present at the time of encoding is sufficient to serve as a retrieval cue. Therefore, being in the same mindset as in at the time of encoding will help with recalling in the same way that being in the same situation helps recall. This effect called context reinstatement was demonstrated by Fisher and Craik 1977 when they matched retrieval cues with the way information was memorized.

Transfer-Appropriate Processing

Transfer-appropriate processing is a strategy for encoding that leads to successful retrieval. An experiment conducted by Morris and coworkers in 1977 proved that successful retrieval was a result of matching the type of processing used during encoding. During their experiment, their main findings were that an individual's ability to retrieve information was heavily influenced on whether the task at encoding matched the task during retrieval. In the first task, which consisted of the rhyming group, subjects were given a target word and then asked to review a different set of words. During this process, they were asked whether the new words rhymed with the target word. They were solely focusing on the rhyming rather than the actual meaning of the words. In the second task, individuals were also given a target word, followed by a series of new words. Rather than identify the ones that rhymed, the individual was to focus more on the meaning. As it turns out, the rhyming group, who identified the words that rhymed, was able to recall more words than those in the meaning group, who focused solely on their meaning. This study suggests that those who were focusing on rhyming in the first part of the task and on the second, were able to encode more efficiently. In transfer-appropriate processing, encoding occurs in two different stages. This helps demonstrate how stimuli were processed. In the first phase, the exposure to stimuli is manipulated in a way that matches the stimuli. The second phase then pulls heavily from what occurred in the first phase and how the stimuli was presented; it will match the task during encoding.

Encoding Specificity

An ambiguous figure which can be perceived as either a vase or a pair of faces.
Vase or faces?

The context of learning shapes how information is encoded. For instance, Kanizsa in 1979 showed a picture that could be interpreted as either a white vase on a black background or 2 faces facing each other on a white background. The participants were primed to see the vase. Later they were shown the picture again but this time they were primed to see the black faces on the white background. Although this was the same picture as they had seen before, when asked if they had seen this picture before, they said no. The reason for this was that they had been primed to see the vase the first time the picture was presented, and it was therefore unrecognizable the second time as two faces. This demonstrates that the stimulus is understood within the context it is learned in as well the general rule that what really constitutes good learning are tests that test what has been learned in the same way that it was learned. Therefore, to truly be efficient at remembering information, one must consider the demands that future recall will place on this information and study in a way that will match those demands.

Generation Effect

Another principle that may have the potential to aid encoding is the generation effect. The generation effect implies that learning is enhanced when individuals generate information or items themselves rather than reading the content. The key to properly apply the generation effect is to generate information, rather than passively selecting from information already available like in selecting an answer from a multiple-choice question In 1978, researchers Slameka and Graf conducted an experiment to better understand this effect. In this experiment, the participants were assigned to one of two groups, the read group or the generate group. The participants assigned to the read group were asked to simply read a list of paired words that were related, for example, horse-saddle. The participants assigned to the generate group were asked to fill in the blank letters of one of the related words in the pair. In other words, if the participant was given the word horse, they would need to fill in the last four letters of the word saddle.The researchers discovered that the group that was asked to fill in the blanks had better recall for these word pairs than the group that was asked to simply remember the word pairs.

Self-Reference Effect

Research illustrates that the self-reference effect aids encoding. The self-reference effect is the idea that individuals will encode information more effectively if they can personally relate to the information. For example, some people may claim that some birth dates of family members and friends are easier to remember than others. Some researchers claim this may be due to the self-reference effect. For example, some birth dates are easier for individuals to recall if the date is close to their own birth date or any other dates they deem important, such as anniversary dates.

Research has shown that after being encoded, self-reference effect is more effective when it comes to recalling memory than semantic encoding. Researchers have found that the self-reference effect goes more hand and hand with elaborative rehearsal. Elaborative rehearsal is more often than not, found to have a positive correlation with the improvement of retrieving information from memories. Self-reference effect has shown to be more effective when retrieving information after it has been encoded when being compared to other methods such as semantic encoding. Also, it is important to know that studies have concluded that self-reference effect can be used to encode information among all ages. However, they have determined that older adults are more limited in their use of the self-reference effect when being tested with younger adults.

Salience

When an item or idea is considered "salient", it means the item or idea appears to noticeably stand out. When information is salient, it may be encoded in memory more efficiently than if the information did not stand out to the learner. In reference to encoding, any event involving survival may be considered salient. Research has shown that survival may be related to the self-reference effect due to evolutionary mechanisms. Researchers have discovered that even words that are high in survival value are encoded better than words that are ranked lower in survival value. Some research supports evolution, claiming that the human species remembers content associated with survival. Some researchers wanted to see for themselves whether or not the findings of other research was accurate. The researchers decided to replicate an experiment with results that supported the idea that survival content is encoded better than other content. The findings of the experiment further suggested that survival content has a higher advantage of being encoded than other content.

Retrieval Practice

Studies have shown that an effective tool to increase encoding during the process of learning is to create and take practice tests. Using retrieval in order to enhance performance is called the testing effect, as it actively involves creating and recreating the material that one is intending to learn and increases one’s exposure to it. It is also a useful tool in connecting new information to information already stored in memory, as there is a close association between encoding and retrieval. Thus, creating practice tests allows the individual to process the information at a deeper level than simply reading over the material again or using a pre-made test. The benefits of using retrieval practice have been demonstrated in a study done where college students were asked to read a passage for seven minutes and were then given a two-minute break, during which they completed math problems. One group of participants was given seven minutes to write down as much of the passage as they could remember while the other group was given another seven minutes to reread the material. Later all participants were given a recall test at various increments (five minutes, 2 days, and one week) after the initial learning had taken place. The results of these tests showed that those who had been assigned to the group that had been given a recall test during their first day of the experiment were more likely to retain more information than those that had simply reread the text. This demonstrates that retrieval practice is a useful tool in encoding information into long term memory.

Computational Models of Memory Encoding

Computational models of memory encoding have been developed in order to better understand and simulate the mostly expected, yet sometimes wildly unpredictable, behaviors of human memory. Different models have been developed for different memory tasks, which include item recognition, cued recall, free recall, and sequence memory, in an attempt to accurately explain experimentally observed behaviors.

Item recognition

In item recognition, one is asked whether or not a given probe item has been seen before. It is important to note that the recognition of an item can include context. That is, one can be asked whether an item has been seen in a study list. So even though one may have seen the word "apple" sometime during their life, if it was not on the study list, it should not be recalled.

Item recognition can be modeled using Multiple trace theory and the attribute-similarity model. In brief, every item that one sees can be represented as a vector of the item's attributes, which is extended by a vector representing the context at the time of encoding, and is stored in a memory matrix of all items ever seen. When a probe item is presented, the sum of the similarities to each item in the matrix (which is inversely proportional to the sum of the distances between the probe vector and each item in the memory matrix) is computed. If the similarity is above a threshold value, one would respond, "Yes, I recognize that item." Given that context continually drifts by nature of a random walk, more recently seen items, which each share a similar context vector to the context vector at the time of the recognition task, are more likely to be recognized than items seen longer ago.

Cued Recall

In cued recall, an individual is presented with a stimulus, such as a list of words and then asked to remember as many of those words as possible. They are then given cues, such as categories, to help them remember what the stimuli were. An example of this would be to give a subject words such as meteor, star, space ship, and alien to memorize. Then providing them with the cue of "outer space" to remind them of the list of words given. Giving the subject cues, even when never originally mentioned, helped them recall the stimulus much better. These cues help guide the subjects to recall the stimuli they could not remember for themselves prior to being given a cue. Cues can essentially be anything that will help a memory that is deemed forgotten to resurface. An experiment conducted by Tulvig suggests that when subjects were given cues, they were able to recall the previously presented stimuli.

Cued recall can be explained by extending the attribute-similarity model used for item recognition. Because in cued recall, a wrong response can be given for a probe item, the model has to be extended accordingly to account for that. This can be achieved by adding noise to the item vectors when they are stored in the memory matrix. Furthermore, cued recall can be modeled in a probabilistic manner such that for every item stored in the memory matrix, the more similar it is to the probe item, the more likely it is to be recalled. Because the items in the memory matrix contain noise in their values, this model can account for incorrect recalls, such as mistakenly calling a person by the wrong name.

Free Recall

In free recall, one is allowed to recall items that were learned in any order. For example, you could be asked to name as many countries in Europe as you can. Free recall can be modeled using SAM (Search of Associative Memory) which is based on the dual-store model, first proposed by Atkinson and Shiffrin in 1968. SAM consists of two main components: short-term store (STS) and long-term store (LTS). In brief, when an item is seen, it is pushed into STS where it resides with other items also in STS, until it displaced and put into LTS. The longer the item has been in STS, the more likely it is to be displaced by a new item. When items co-reside in STS, the links between those items are strengthened. Furthermore, SAM assumes that items in STS are always available for immediate recall.

SAM explains both primacy and recency effects. Probabilistically, items at the beginning of the list are more likely to remain in STS, and thus have more opportunities to strengthen their links to other items. As a result, items at the beginning of the list are made more likely to be recalled in a free-recall task (primacy effect). Because of the assumption that items in STS are always available for immediate recall, given that there were no significant distractors between learning and recall, items at the end of the list can be recalled excellently (recency effect).

Studies have shown that free recall is one of the most effective methods of studying and transferring information from short term memory to long term memory compared to item recognition and cued recall as greater relational processing is involved.

Incidentally, the idea of STS and LTS was motivated by the architecture of computers, which contain short-term and long-term storage.

Sequence Memory

Sequence memory is responsible for how we remember lists of things, in which ordering matters. For example, telephone numbers are an ordered list of one digit numbers. There are currently two main computational memory models that can be applied to sequence encoding: associative chaining and positional coding.

Associative chaining theory states that every item in a list is linked to its forward and backward neighbors, with forward links being stronger than backward links, and links to closer neighbors being stronger than links to farther neighbors. For example, associative chaining predicts the tendencies of transposition errors, which occur most often with items in nearby positions. An example of a transposition error would be recalling the sequence "apple, orange, banana" instead of "apple, banana, orange."

Positional coding theory suggests that every item in a list is associated to its position in the list. For example, if the list is "apple, banana, orange, mango" apple will be associated to list position 1, banana to 2, orange to 3, and mango to 4. Furthermore, each item is also, albeit more weakly, associated to its index +/- 1, even more weakly to +/- 2, and so forth. So banana is associated not only to its actual index 2, but also to 1, 3, and 4, with varying degrees of strength. For example, positional coding can be used to explain the effects of recency and primacy. Because items at the beginning and end of a list have fewer close neighbors compared to items in the middle of the list, they have less competition for correct recall.

Although the models of associative chaining and positional coding are able to explain a great amount of behavior seen for sequence memory, they are far from perfect. For example, neither chaining nor positional coding is able to properly illustrate the details of the Ranschburg effect, which reports that sequences of items that contain repeated items are harder to reproduce than sequences of unrepeated items. Associative chaining predicts that recall of lists containing repeated items is impaired because recall of any repeated item would cue not only its true successor but also the successors of all other instances of the item. However, experimental data have shown that spaced repetition of items resulted in impaired recall of the second occurrence of the repeated item. Furthermore, it had no measurable effect on the recall of the items that followed the repeated items, contradicting the prediction of associative chaining. Positional coding predicts that repeated items will have no effect on recall, since the positions for each item in the list act as independent cues for the items, including the repeated items. That is, there is no difference between the similarity between any two items and repeated items. This, again, is not consistent with the data.

Because no comprehensive model has been defined for sequence memory to this day, it makes for an interesting area of research.

Functional magnetic resonance imaging

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Functional magnetic resonance imaging
An fMRI image with yellow areas showing increased activity compared with a control condition
PurposeMeasures brain activity detecting changes due to blood flow.

Functional magnetic resonance imaging or functional MRI (fMRI) measures brain activity by detecting changes associated with blood flow. This technique relies on the fact that cerebral blood flow and neuronal activation are coupled. When an area of the brain is in use, blood flow to that region also increases.

The primary form of fMRI uses the blood-oxygen-level dependent (BOLD) contrast, discovered by Seiji Ogawa in 1990. This is a type of specialized brain and body scan used to map neural activity in the brain or spinal cord of humans or other animals by imaging the change in blood flow (hemodynamic response) related to energy use by brain cells. Since the early 1990s, fMRI has come to dominate brain mapping research because it does not involve the use of injections, surgery, the ingestion of substances, or exposure to ionizing radiation. This measure is frequently corrupted by noise from various sources; hence, statistical procedures are used to extract the underlying signal. The resulting brain activation can be graphically represented by color-coding the strength of activation across the brain or the specific region studied. The technique can localize activity to within millimeters but, using standard techniques, no better than within a window of a few seconds. Other methods of obtaining contrast are arterial spin labeling and diffusion MRI. Diffusion MRI is similar to BOLD fMRI but provides contrast based on the magnitude of diffusion of water molecules in the brain.

In addition to detecting BOLD responses from activity due to tasks or stimuli, fMRI can measure resting state, or negative-task state, which shows the subjects' baseline BOLD variance. Since about 1998 studies have shown the existence and properties of the default mode network, a functionally connected neural network of apparent resting brain states.

fMRI is used in research, and to a lesser extent, in clinical work. It can complement other measures of brain physiology such as electroencephalography (EEG), and near-infrared spectroscopy (NIRS). Newer methods which improve both spatial and time resolution are being researched, and these largely use biomarkers other than the BOLD signal. Some companies have developed commercial products such as lie detectors based on fMRI techniques, but the research is not believed to be developed enough for widespread commercial use.

Overview

The fMRI concept builds on the earlier MRI scanning technology and the discovery of properties of oxygen-rich blood. MRI brain scans use a strong, permanent, static magnetic field to align nuclei in the brain region being studied. Another magnetic field, the gradient field, is then applied to spatially locate different nuclei. Finally, a radiofrequency (RF) pulse is played to kick the nuclei to higher magnetization levels, with the effect now depending on where they are located. When the RF field is removed, the nuclei go back to their original states, and the energy they emit is measured with a coil to recreate the positions of the nuclei. MRI thus provides a static structural view of brain matter. The central thrust behind fMRI was to extend MRI to capture functional changes in the brain caused by neuronal activity. Differences in magnetic properties between arterial (oxygen-rich) and venous (oxygen-poor) blood provided this link.

Researcher checking fMRI images.
Researcher checking fMRI images

Since the 1890s it has been known that changes in blood flow and blood oxygenation in the brain (collectively known as hemodynamics) are closely linked to neural activity. When neurons become active, local blood flow to those brain regions increases, and oxygen-rich (oxygenated) blood displaces oxygen-depleted (deoxygenated) blood around 2 seconds later. This rises to a peak over 4–6 seconds, before falling back to the original level (and typically undershooting slightly). Oxygen is carried by the hemoglobin molecule in red blood cells. Deoxygenated hemoglobin (dHb) is more magnetic (paramagnetic) than oxygenated hemoglobin (Hb), which is virtually resistant to magnetism (diamagnetic). This difference leads to an improved MR signal since the diamagnetic blood interferes with the magnetic MR signal less. This improvement can be mapped to show which neurons are active at a time.

History

Michael Faraday first noted that dried blood is not magnetic and "Must try recent fluid blood." in diary dated 8th November 1845. This was cited in Pauling & Coryell (1945).
Michael Faraday first noted that dried blood is not magnetic and "Must try recent fluid blood." in diary dated 8th November 1845. This was cited in Pauling & Coryell (1945).

During the late 19th century, Angelo Mosso invented the 'human circulation balance', which could non-invasively measure the redistribution of blood during emotional and intellectual activity. However, although briefly mentioned by William James in 1890, the details and precise workings of this balance and the experiments Mosso performed with it remained largely unknown until the recent discovery of the original instrument as well as Mosso's reports by Stefano Sandrone and colleagues. Angelo Mosso investigated several critical variables that are still relevant in modern neuroimaging such as the 'signal-to-noise ratio', the appropriate choice of the experimental paradigm and the need for the simultaneous recording of differing physiological parameters. Mosso's manuscripts do not provide direct evidence that the balance was really able to measure changes in cerebral blood flow due to cognition, however a modern replication performed by David T Field has now demonstrated—using modern signal processing techniques unavailable to Mosso—that a balance apparatus of this type is able to detect changes in cerebral blood volume related to cognition.

In 1890, Charles Roy and Charles Sherrington first experimentally linked brain function to its blood flow, at Cambridge University. The next step to resolving how to measure blood flow to the brain was Linus Pauling's and Charles Coryell's discovery in 1936 that oxygen-rich blood with Hb was weakly repelled by magnetic fields, while oxygen-depleted blood with dHb was attracted to a magnetic field, though less so than ferromagnetic elements such as iron. Seiji Ogawa at AT&T Bell labs recognized that this could be used to augment MRI, which could study just the static structure of the brain, since the differing magnetic properties of dHb and Hb caused by blood flow to activated brain regions would cause measurable changes in the MRI signal. BOLD is the MRI contrast of dHb, discovered in 1990 by Ogawa. In a seminal 1990 study based on earlier work by Thulborn et al., Ogawa and colleagues scanned rodents in a strong magnetic field (7.0 T) MRI. To manipulate blood oxygen level, they changed the proportion of oxygen the animals breathed. As this proportion fell, a map of blood flow in the brain was seen in the MRI. They verified this by placing test tubes with oxygenated or deoxygenated blood and creating separate images. They also showed that gradient-echo images, which depend on a form of loss of magnetization called T2* decay, produced the best images. To show these blood flow changes were related to functional brain activity, they changed the composition of the air breathed by rats, and scanned them while monitoring brain activity with EEG. The first attempt to detect the regional brain activity using MRI was performed by Belliveau and colleagues at Harvard University using the contrast agent Magnevist, a paramagnetic substance remaining in the bloodstream after intravenous injection. However, this method is not popular in human fMRI, because of the inconvenience of the contrast agent injection, and because the agent stays in the blood only for a short time.

Three studies in 1992 were the first to explore using the BOLD contrast in humans. Kenneth Kwong and colleagues, using both gradient-echo and inversion recovery echo-planar imaging (EPI) sequence at a magnetic field strength of 1.5 T published studies showing clear activation of the human visual cortex. The Harvard team thereby showed that both blood flow and blood volume increased locally in activity neural tissue. Ogawa and Ugurbil conducted a similar study using a higher magnetic field (4.0 T) in Ugurbil's laboratory at the University of Minnesota, generating higher resolution images that showed activity largely following the gray matter of the brain, as would be expected; in addition, they showed that fMRI signal depended on a decrease in T2*, consistent with the BOLD mechanism. T2* decay is caused by magnetized nuclei in a volume of space losing magnetic coherence (transverse magnetization) from both bumping into one another and from experiencing differences in the magnetic field strength across locations (field inhomogeneity from a spatial gradient). Bandettini and colleagues used EPI at 1.5 T to show activation in the primary motor cortex, a brain area at the last stage of the circuitry controlling voluntary movements. The magnetic fields, pulse sequences and procedures and techniques used by these early studies are still used in current-day fMRI studies. But today researchers typically collect data from more slices (using stronger magnetic gradients), and preprocess and analyze data using statistical techniques.

Physiology

The brain does not store a lot of glucose, its primary source of energy. When neurons become active, getting them back to their original state of polarization requires actively pumping ions across the neuronal cell membranes, in both directions. The energy for those ion pumps is mainly produced from glucose. More blood flows in to transport more glucose, also bringing in more oxygen in the form of oxygenated hemoglobin molecules in red blood cells. This is from both a higher rate of blood flow and an expansion of blood vessels. The blood-flow change is localized to within 2 or 3 mm of where the neural activity is. Usually the brought-in oxygen is more than the oxygen consumed in burning glucose (it is not yet settled whether most glucose consumption is oxidative), and this causes a net decrease in deoxygenated hemoglobin (dHb) in that brain area's blood vessels. This changes the magnetic property of the blood, making it interfere less with the magnetization and its eventual decay induced by the MRI process.

The cerebral blood flow (CBF) corresponds to the consumed glucose differently in different brain regions. Initial results show there is more inflow than consumption of glucose in regions such as the amygdala, basal ganglia, thalamus and cingulate cortex, all of which are recruited for fast responses. In regions that are more deliberative, such as the lateral frontal and lateral parietal lobes, it seems that incoming flow is less than consumption. This affects BOLD sensitivity.

Hemoglobin differs in how it responds to magnetic fields, depending on whether it has a bound oxygen molecule. The dHb molecule is more attracted to magnetic fields. Hence, it distorts the surrounding magnetic field induced by an MRI scanner, causing the nuclei there to lose magnetization faster via the T2* decay. Thus MR pulse sequences sensitive to T2* show more MR signal where blood is highly oxygenated and less where it is not. This effect increases with the square of the strength of the magnetic field. The fMRI signal hence needs both a strong magnetic field (1.5 T or higher) and a pulse sequence such as EPI, which is sensitive to T2* contrast.

The physiological blood-flow response largely decides the temporal sensitivity, that is how accurately we can measure when neurons are active, in BOLD fMRI. The basic time resolution parameter (sampling time) is designated TR; the TR dictates how often a particular brain slice is excited and allowed to lose its magnetization. TRs could vary from the very short (500 ms) to the very long (3 s). For fMRI specifically, the hemodynamic response lasts over 10 seconds, rising multiplicatively (that is, as a proportion of current value), peaking at 4 to 6 seconds, and then falling multiplicatively. Changes in the blood-flow system, the vascular system, integrate responses to neuronal activity over time. Because this response is a smooth continuous function, sampling with ever-faster TRs does not help; it just gives more points on the response curve obtainable by simple linear interpolation anyway. Experimental paradigms such as staggering when a stimulus is presented at various trials can improve temporal resolution, but reduces the number of effective data points obtained.

BOLD hemodynamic response

Main brain functional imaging technique resolutions

The change in the MR signal from neuronal activity is called the hemodynamic response (HR). It lags the neuronal events triggering it by a couple of seconds, since it takes a while for the vascular system to respond to the brain's need for glucose. From this point it typically rises to a peak at about 5 seconds after the stimulus. If the neurons keep firing, say from a continuous stimulus, the peak spreads to a flat plateau while the neurons stay active. After activity stops, the BOLD signal falls below the original level, the baseline, a phenomenon called the undershoot. Over time the signal recovers to the baseline. There is some evidence that continuous metabolic requirements in a brain region contribute to the undershoot.

The mechanism by which the neural system provides feedback to the vascular system of its need for more glucose is partly the release of glutamate as part of neuron firing. This glutamate affects nearby supporting cells, astrocytes, causing a change in calcium ion concentration. This, in turn, releases nitric oxide at the contact point of astrocytes and intermediate-sized blood vessels, the arterioles. Nitric oxide is a vasodilator causing arterioles to expand and draw in more blood.

A single voxel's response signal over time is called its timecourse. Typically, the unwanted signal, called the noise, from the scanner, random brain activity and similar elements is as big as the signal itself. To eliminate these, fMRI studies repeat a stimulus presentation multiple times.

Spatial resolution

Spatial resolution of an fMRI study refers to how well it discriminates between nearby locations. It is measured by the size of voxels, as in MRI. A voxel is a three-dimensional rectangular cuboid, whose dimensions are set by the slice thickness, the area of a slice, and the grid imposed on the slice by the scanning process. Full-brain studies use larger voxels, while those that focus on specific regions of interest typically use smaller sizes. Sizes range from 4 to 5 mm, or with laminar resolution fMRI (lfMRI), to submillimeter. Smaller voxels contain fewer neurons on average, incorporate less blood flow, and hence have less signal than larger voxels. Smaller voxels imply longer scanning times, since scanning time directly rises with the number of voxels per slice and the number of slices. This can lead both to discomfort for the subject inside the scanner and to loss of the magnetization signal. A voxel typically contains a few million neurons and tens of billions of synapses, with the actual number depending on voxel size and the area of the brain being imaged.

The vascular arterial system supplying fresh blood branches into smaller and smaller vessels as it enters the brain surface and within-brain regions, culminating in a connected capillary bed within the brain. The drainage system, similarly, merges into larger and larger veins as it carries away oxygen-depleted blood. The dHb contribution to the fMRI signal is from both the capillaries near the area of activity and larger draining veins that may be farther away. For good spatial resolution, the signal from the large veins needs to be suppressed, since it does not correspond to the area where the neural activity is. This can be achieved either by using strong static magnetic fields or by using spin-echo pulse sequences. With these, fMRI can examine a spatial range from millimeters to centimeters, and can hence identify Brodmann areas (centimeters), subcortical nuclei such as the caudate, putamen and thalamus, and hippocampal subfields such as the combined dentate gyrus/CA3, CA1, and subiculum.

Temporal resolution

Temporal resolution is the smallest time period of neural activity reliably separated out by fMRI. One element deciding this is the sampling time, the TR. Below a TR of 1 or 2 seconds, however, scanning just generates sharper hemodynamic response (HR) curves, without adding much additional information (e.g. beyond what is alternatively achieved by mathematically interpolating the curve gaps at a lower TR). Temporal resolution can be improved by staggering stimulus presentation across trials. If one-third of data trials are sampled normally, one-third at 1 s, 4 s, 7 s and so on, and the last third at 2 s, 5 s and 8 s, the combined data provide a resolution of 1 s, though with only one-third as many total events.

The time resolution needed depends on brain processing time for various events. An example of the broad range here is given by the visual processing system. What the eye sees is registered on the photoreceptors of the retina within a millisecond or so. These signals get to the primary visual cortex via the thalamus in tens of milliseconds. Neuronal activity related to the act of seeing lasts for more than 100 ms. A fast reaction, such as swerving to avoid a car crash, takes around 200 ms. By about half a second, awareness and reflection of the incident sets in. Remembering a similar event may take a few seconds, and emotional or physiological changes such as fear arousal may last minutes or hours. Learned changes, such as recognizing faces or scenes, may last days, months, or years. Most fMRI experiments study brain processes lasting a few seconds, with the study conducted over some tens of minutes. Subjects may move their heads during that time, and this head motion needs to be corrected for. So does drift in the baseline signal over time. Boredom and learning may modify both subject behavior and cognitive processes.

Linear addition from multiple activation

When a person performs two tasks simultaneously or in overlapping fashion, the BOLD response is expected to add linearly. This is a fundamental assumption of many fMRI studies that is based on the principle that continuously differentiable systems can be expected to behave linearly when perturbations are small; they are linear to first order. Linear addition means the only operation allowed on the individual responses before they are combined (added together) is a separate scaling of each. Since scaling is just multiplication by a constant number, this means an event that evokes, say, twice the neural response as another, can be modeled as the first event presented twice simultaneously. The HR for the doubled-event is then just double that of the single event.

To the extent that the behavior is linear, the time course of the BOLD response to an arbitrary stimulus can be modeled by convolution of that stimulus with the impulse BOLD response. Accurate time course modeling is important in estimating the BOLD response magnitude.

This strong assumption was first studied in 1996 by Boynton and colleagues, who checked the effects on the primary visual cortex of patterns flickering 8 times a second and presented for 3 to 24 seconds. Their result showed that when visual contrast of the image was increased, the HR shape stayed the same but its amplitude increased proportionally. With some exceptions, responses to longer stimuli could also be inferred by adding together the responses for multiple shorter stimuli summing to the same longer duration. In 1997, Dale and Buckner tested whether individual events, rather than blocks of some duration, also summed the same way, and found they did. But they also found deviations from the linear model at time intervals less than 2 seconds.

A source of nonlinearity in the fMRI response is from the refractory period, where brain activity from a presented stimulus suppresses further activity on a subsequent, similar, stimulus. As stimuli become shorter, the refractory period becomes more noticeable. The refractory period does not change with age, nor do the amplitudes of HRs. The period differs across brain regions. In both the primary motor cortex and the visual cortex, the HR amplitude scales linearly with duration of a stimulus or response. In the corresponding secondary regions, the supplementary motor cortex, which is involved in planning motor behavior, and the motion-sensitive V5 region, a strong refractory period is seen and the HR amplitude stays steady across a range of stimulus or response durations. The refractory effect can be used in a way similar to habituation to see what features of a stimulus a person discriminates as new. Further limits to linearity exist because of saturation: with large stimulation levels a maximum BOLD response is reached.

Matching neural activity to the BOLD signal

Researchers have checked the BOLD signal against both signals from implanted electrodes (mostly in monkeys) and signals of field potentials (that is the electric or magnetic field from the brain's activity, measured outside the skull) from EEG and MEG. The local field potential, which includes both post-neuron-synaptic activity and internal neuron processing, better predicts the BOLD signal. So the BOLD contrast reflects mainly the inputs to a neuron and the neuron's integrative processing within its body, and less the output firing of neurons. In humans, electrodes can be implanted only in patients who need surgery as treatment, but evidence suggests a similar relationship at least for the auditory cortex and the primary visual cortex. Activation locations detected by BOLD fMRI in cortical areas (brain surface regions) are known to tally with CBF-based functional maps from PET scans. Some regions just a few millimeters in size, such as the lateral geniculate nucleus (LGN) of the thalamus, which relays visual inputs from the retina to the visual cortex, have been shown to generate the BOLD signal correctly when presented with visual input. Nearby regions such as the pulvinar nucleus were not stimulated for this task, indicating millimeter resolution for the spatial extent of the BOLD response, at least in thalamic nuclei. In the rat brain, single-whisker touch has been shown to elicit BOLD signals from the somatosensory cortex.

However, the BOLD signal cannot separate feedback and feedforward active networks in a region; the slowness of the vascular response means the final signal is the summed version of the whole region's network; blood flow is not discontinuous as the processing proceeds. Also, both inhibitory and excitatory input to a neuron from other neurons sum and contribute to the BOLD signal. Within a neuron these two inputs might cancel out. The BOLD response can also be affected by a variety of factors, including disease, sedation, anxiety, medications that dilate blood vessels, and attention (neuromodulation).

The amplitude of the BOLD signal does not necessarily affect its shape. A higher-amplitude signal may be seen for stronger neural activity, but peaking at the same place as a weaker signal. Also, the amplitude does not necessarily reflect behavioral performance. A complex cognitive task may initially trigger high-amplitude signals associated with good performance, but as the subject gets better at it, the amplitude may decrease with performance staying the same. This is expected to be due to increased efficiency in performing the task. The BOLD response across brain regions cannot be compared directly even for the same task, since the density of neurons and the blood-supply characteristics are not constant across the brain. However, the BOLD response can often be compared across subjects for the same brain region and the same task.

More recent characterization of the BOLD signal has used optogenetic techniques in rodents to precisely control neuronal firing while simultaneously monitoring the BOLD response using high field magnets (a technique sometimes referred to as "optofMRI"). These techniques suggest that neuronal firing is well correlated with the measured BOLD signal including approximately linear summation of the BOLD signal over closely spaced bursts of neuronal firing. Linear summation is an assumption of commonly used event-related fMRI designs.

Medical use

Composite images from an fMRI scan

Physicians use fMRI to assess how risky brain surgery or similar invasive treatment is for a patient and to learn how a normal, diseased or injured brain is functioning. They map the brain with fMRI to identify regions linked to critical functions such as speaking, moving, sensing, or planning. This is useful to plan for surgery and radiation therapy of the brain.

fMRI image of the brain of a participant in the Personal Genome Project

Clinical use of fMRI still lags behind research use. Patients with brain pathologies are more difficult to scan with fMRI than are young healthy volunteers, the typical research-subject population. Tumors and lesions can change the blood flow in ways not related to neural activity, masking the neural HR. Drugs such as antihistamines and even caffeine can affect HR. Some patients may have disorders such as compulsive lying, which makes certain studies impossible. It is harder for those with clinical problems to stay still for long. Using head restraints or bite bars may injure epileptics who have a seizure inside the scanner; bite bars may also discomfort those with dental prostheses.

Despite these difficulties, fMRI has been used clinically to map functional areas, check left-right hemispherical asymmetry in language and memory regions, check the neural correlates of a seizure, study how the brain recovers partially from a stroke, and test how well a drug or behavioral therapy works. Mapping of functional areas and understanding lateralization of language and memory help surgeons avoid removing critical brain regions when they have to operate and remove brain tissue. This is of particular importance in removing tumors and in patients who have intractable temporal lobe epilepsy. Lesioning tumors requires pre-surgical planning to ensure no functionally useful tissue is removed needlessly. Recovered depressed patients have shown altered fMRI activity in the cerebellum, and this may indicate a tendency to relapse. Pharmacological fMRI, assaying brain activity after drugs are administered, can be used to check how much a drug penetrates the blood–brain barrier and dose vs effect information of the medication.

Animal research

Research is primarily performed in non-human primates such as the rhesus macaque. These studies can be used both to check or predict human results and to validate the fMRI technique itself. But the studies are difficult because it is hard to motivate an animal to stay still and typical inducements such as juice trigger head movement while the animal swallows it. It is also expensive to maintain a colony of larger animals such as the macaque.

Analyzing the data

The goal of fMRI data analysis is to detect correlations between brain activation and a task the subject performs during the scan. It also aims to discover correlations with the specific cognitive states, such as memory and recognition, induced in the subject. The BOLD signature of activation is relatively weak, however, so other sources of noise in the acquired data must be carefully controlled. This means that a series of processing steps must be performed on the acquired images before the actual statistical search for task-related activation can begin. Nevertheless, it is possible to predict, for example, the emotions a person is experiencing solely from their fMRI, with a high degree of accuracy.

Sources of noise

Noise is unwanted changes to the MR signal from elements not of interest to the study. The five main sources of noise in fMRI are thermal noise, system noise, physiological noise, random neural activity and differences in both mental strategies and behavior across people and across tasks within a person. Thermal noise multiplies in line with the static field strength, but physiological noise multiplies as the square of the field strength. Since the signal also multiplies as the square of the field strength, and since physiological noise is a large proportion of total noise, higher field strengths above 3 T do not always produce proportionately better images.

Heat causes electrons to move around and distort the current in the fMRI detector, producing thermal noise. Thermal noise rises with the temperature. It also depends on the range of frequencies detected by the receiver coil and its electrical resistance. It affects all voxels similarly, independent of anatomy.

System noise is from the imaging hardware. One form is scanner drift, caused by the superconducting magnet's field drifting over time. Another form is changes in the current or voltage distribution of the brain itself inducing changes in the receiver coil and reducing its sensitivity. A procedure called impedance matching is used to bypass this inductance effect. There could also be noise from the magnetic field not being uniform. This is often adjusted for by using shimming coils, small magnets physically inserted, say into the subject's mouth, to patch the magnetic field. The nonuniformities are often near brain sinuses such as the ear and plugging the cavity for long periods can be discomfiting. The scanning process acquires the MR signal in k-space, in which overlapping spatial frequencies (that is repeated edges in the sample's volume) are each represented with lines. Transforming this into voxels introduces some loss and distortions.

Physiological noise is from head and brain movement in the scanner from breathing, heart beats, or the subject fidgeting, tensing, or making physical responses such as button presses. Head movements cause the voxel-to-neurons mapping to change while scanning is in progress. Noise due to head movement is a particular issue when working with children, although there are measures that can be taken to reduce head motion when scanning children, such as changes in experimental design and training prior to the scanning session. Since fMRI is acquired in slices, after movement, a voxel continues to refer to the same absolute location in space while the neurons underneath it would have changed. Another source of physiological noise is the change in the rate of blood flow, blood volume, and use of oxygen over time. This last component contributes to two-thirds of physiological noise, which, in turn, is the main contributor to total noise.

Even with the best experimental design, it is not possible to control and constrain all other background stimuli impinging on a subject—scanner noise, random thoughts, physical sensations, and the like. These produce neural activity independent of the experimental manipulation. These are not amenable to mathematical modeling and have to be controlled by the study design.

A person's strategies to respond or react to a stimulus, and to solve problems, often change over time and over tasks. This generates variations in neural activity from trial to trial within a subject. Across people too neural activity differs for similar reasons. Researchers often conduct pilot studies to see how participants typically perform for the task under consideration. They also often train subjects how to respond or react in a trial training session prior to the scanning one.

Preprocessing

The scanner platform generates a 3 D volume of the subject's head every TR. This consists of an array of voxel intensity values, one value per voxel in the scan. The voxels are arranged one after the other, unfolding the three-dimensional structure into a single line. Several such volumes from a session are joined to form a 4 D volume corresponding to a run, for the time period the subject stayed in the scanner without adjusting head position. This 4 D volume is the starting point for analysis. The first part of that analysis is preprocessing.

The first step in preprocessing is conventionally slice timing correction. The MR scanner acquires different slices within a single brain volume at different times, and hence the slices represent brain activity at different timepoints. Since this complicates later analysis, a timing correction is applied to bring all slices to the same timepoint reference. This is done by assuming the timecourse of a voxel is smooth when plotted as a dotted line. Hence the voxel's intensity value at other times not in the sampled frames can be calculated by filling in the dots to create a continuous curve.

Head motion correction is another common preprocessing step. When the head moves, the neurons under a voxel move and hence its timecourse now represents largely that of some other voxel in the past. Hence the timecourse curve is effectively cut and pasted from one voxel to another. Motion correction tries different ways of undoing this to see which undoing of the cut-and-paste produces the smoothest timecourse for all voxels. The undoing is by applying a rigid-body transform to the volume, by shifting and rotating the whole volume data to account for motion. The transformed volume is compared statistically to the volume at the first timepoint to see how well they match, using a cost function such as correlation or mutual information. The transformation that gives the minimal cost function is chosen as the model for head motion. Since the head can move in a vastly varied number of ways, it is not possible to search for all possible candidates; nor is there right now an algorithm that provides a globally optimal solution independent of the first transformations we try in a chain.

Distortion corrections account for field nonuniformities of the scanner. One method, as described before, is to use shimming coils. Another is to recreate a field map of the main field by acquiring two images with differing echo times. If the field were uniform, the differences between the two images also would be uniform. Note these are not true preprocessing techniques since they are independent of the study itself. Bias field estimation is a real preprocessing technique using mathematical models of the noise from distortion, such as Markov random fields and expectation maximization algorithms, to correct for distortion.

In general, fMRI studies acquire both many functional images with fMRI and a structural image with MRI. The structural image is usually of a higher resolution and depends on a different signal, the T1 magnetic field decay after excitation. To demarcate regions of interest in the functional image, one needs to align it with the structural one. Even when whole-brain analysis is done, to interpret the final results, that is to figure out which regions the active voxels fall in, one has to align the functional image to the structural one. This is done with a coregistration algorithm that works similar to the motion-correction one, except that here the resolutions are different, and the intensity values cannot be directly compared since the generating signal is different.

Typical MRI studies scan a few different subjects. To integrate the results across subjects, one possibility is to use a common brain atlas, and adjust all the brains to align to the atlas, and then analyze them as a single group. The atlases commonly used are the Talairach one, a single brain of an elderly woman created by Jean Talairach, and the Montreal Neurological Institute (MNI) one. The second is a probabilistic map created by combining scans from over a hundred individuals. This normalization to a standard template is done by mathematically checking which combination of stretching, squeezing, and warping reduces the differences between the target and the reference. While this is conceptually similar to motion correction, the changes required are more complex than just translation and rotation, and hence optimization even more likely to depend on the first transformations in the chain that is checked.

Temporal filtering is the removal of frequencies of no interest from the signal. A voxel's intensity change over time can be represented as the sum of a number of different repeating waves with differing periods and heights. A plot with these periods on the x-axis and the heights on the y-axis is called a power spectrum, and this plot is created with the Fourier transform technique. Temporal filtering amounts to removing the periodic waves not of interest to us from the power spectrum, and then summing the waves back again, using the inverse Fourier transform to create a new timecourse for the voxel. A high-pass filter removes the lower frequencies, and the lowest frequency that can be identified with this technique is the reciprocal of twice the TR. A low-pass filter removes the higher frequencies, while a band-pass filter removes all frequencies except the particular range of interest.

Smoothing, or spatial filtering, is the idea of averaging the intensities of nearby voxels to produce a smooth spatial map of intensity change across the brain or region of interest. The averaging is often done by convolution with a Gaussian filter, which, at every spatial point, weights neighboring voxels by their distance, with the weights falling exponentially following the bell curve. If the true spatial extent of activation, that is the spread of the cluster of voxels simultaneously active, matches the width of the filter used, this process improves the signal-to-noise ratio. It also makes the total noise for each voxel follow a bell-curve distribution, since adding together a large number of independent, identical distributions of any kind produces the bell curve as the limit case. But if the presumed spatial extent of activation does not match the filter, signal is reduced.

Statistical analysis

fMRI images from a study showing parts of the brain lighting up on seeing houses and other parts on seeing faces
These fMRI images are from a study showing parts of the brain lighting up on seeing houses and other parts on seeing faces. The 'r' values are correlations, with higher positive or negative values indicating a stronger relationship (i.e., a better match).

One common approach to analysing fMRI data is to consider each voxel separately within the framework of the general linear model. The model assumes, at every time point, that the hemodynamic response (HR) is equal to the scaled and summed version of the events active at that point. A researcher creates a design matrix specifying which events are active at any timepoint. One common way is to create a matrix with one column per overlapping event, and one row per time point, and to mark it if a particular event, say a stimulus, is active at that time point. One then assumes a specific shape for the HR, leaving only its amplitude changeable in active voxels. The design matrix and this shape are used to generate a prediction of the exact HR of the voxel at every timepoint, using the mathematical procedure of convolution. This prediction does not include the scaling required for every event before summing them.

The basic model assumes the observed HR is the predicted HR scaled by the weights for each event and then added, with noise mixed in. This generates a set of linear equations with more equations than unknowns. A linear equation has an exact solution, under most conditions, when equations and unknowns match. Hence one could choose any subset of the equations, with the number equal to the number of variables, and solve them. But, when these solutions are plugged into the left-out equations, there will be a mismatch between the right and left sides, the error. The GLM model attempts to find the scaling weights that minimize the sum of the squares of the error. This method is provably optimal if the error were distributed as a bell curve, and if the scaling-and-summing model were accurate. For a more mathematical description of the GLM model, see generalized linear models.

The GLM model does not take into account the contribution of relationships between multiple voxels. Whereas GLM analysis methods assess whether a voxel or region's signal amplitude is higher or lower for one condition than another, newer statistical models such as multi-voxel pattern analysis (MVPA), utilize the unique contributions of multiple voxels within a voxel-population. In a typical implementation, a classifier or more basic algorithm is trained to distinguish trials for different conditions within a subset of the data. The trained model is then tested by predicting the conditions of the remaining (independent) data. This approach is most typically achieved by training and testing on different scanner sessions or runs. If the classifier is linear, then the training model is a set of weights used to scale the value in each voxel before summing them to generate a single number that determines the condition for each testing set trial. More information on training and testing classifiers is at statistical classification. MVPA allows for inferences about the information content of the underlying neural representations reflected in the BOLD signal, though there is a controversy about whether information detected by this method reflects information encoded at the level of columns, or higher spatial scales. Moreover, its harder to decode information from the prefrontal cortex compared to visual cortex and such differences in sensitivity across regions makes comparisons across regions problematic. Another method used the same fMRI dataset for visual object recognition in the human brain is depending on multi-voxel pattern analysis (fMRI voxels) and multi-view learning which is described in, this method used meta-heuristic search and mutual information to eliminate noisy voxels and select the significant BOLD signals.

Combining with other methods

It is common to combine fMRI signal acquisition with tracking of participants' responses and reaction times. Physiological measures such as heart rate, breathing, skin conductance (rate of sweating), and eye movements are sometimes captured simultaneously with fMRI. The method can also be combined with other brain-imaging techniques such as transcranial stimulation, direct cortical stimulation and, especially, EEG. The fMRI procedure can also be combined with near-infrared spectroscopy (NIRS) to have supplementary information about both oxyhemoglobin and deoxyhemoglobin.

The fMRI technique can complement or supplement other techniques because of its unique strengths and gaps. It can noninvasively record brain signals without risks of ionising radiation inherent in other scanning methods, such as CT or PET scans. It can also record signal from all regions of the brain, unlike EEG/MEG, which are biased toward the cortical surface. But fMRI temporal resolution is poorer than that of EEG since the HR takes tens of seconds to climb to its peak. Combining EEG with fMRI is hence potentially powerful because the two have complementary strengths—EEG has high temporal resolution, and fMRI high spatial resolution. But simultaneous acquisition needs to account for the EEG signal from varying blood flow triggered by the fMRI gradient field, and the EEG signal from the static field. For details, see EEG vs fMRI.

While fMRI stands out due to its potential to capture neural processes associated with health and disease, brain stimulation techniques such as transcranial magnetic stimulation (TMS) have the power to alter these neural processes. Therefore, a combination of both is needed to investigate the mechanisms of action of TMS treatment and on the other hand introduce causality into otherwise pure correlational observations. The current state-of-the-art setup for these concurrent TMS/fMRI experiments comprises a large-volume head coil, usually a birdcage coil, with the MR-compatible TMS coil being mounted inside that birdcage coil. It was applied in a multitude of experiments studying local and network interactions. However, classic setups with the TMS coil placed inside MR birdcage-type head coil are characterised by poor signal to noise ratios compared to multi-channel receive arrays used in clinical neuroimaging today. Moreover, the presence of the TMS coil inside the MR birdcage coil causes artefacts beneath the TMS coil, i.e. at the stimulation target. For these reasons new MR coil arrays were currently developed dedicated to concurrent TMS/fMRI experiments.

Issues in fMRI

Design

If the baseline condition is too close to maximum activation, certain processes may not be represented appropriately. Another limitation on experimental design is head motion, which can lead to artificial intensity changes of the fMRI signal.

Block versus event-related design

In a block design, two or more conditions are alternated by blocks. Each block will have a duration of a certain number of fMRI scans and within each block only one condition is presented. By making the conditions differ in only the cognitive process of interest, the fMRI signal that differentiates the conditions should represent this cognitive process of interest. This is known as the subtraction paradigm. The increase in fMRI signal in response to a stimulus is additive. This means that the amplitude of the hemodynamic response (HR) increases when multiple stimuli are presented in rapid succession. When each block is alternated with a rest condition in which the HR has enough time to return to baseline, a maximum amount of variability is introduced in the signal. As such, we conclude that block designs offer considerable statistical power. There are however severe drawbacks to this method, as the signal is very sensitive to signal drift, such as head motion, especially when only a few blocks are used. Another limiting factor is a poor choice of baseline, as it may prevent meaningful conclusions from being drawn. There are also problems with many tasks lacking the ability to be repeated. Since within each block only one condition is presented, randomization of stimulus types is not possible within a block. This makes the type of stimulus within each block very predictable. As a consequence, participants may become aware of the order of the events.

Event-related designs allow more real world testing, however, the statistical power of event related designs is inherently low, because the signal change in the BOLD fMRI signal following a single stimulus presentation is small.

Both block and event-related designs are based on the subtraction paradigm, which assumes that specific cognitive processes can be added selectively in different conditions. Any difference in blood flow (the BOLD signal) between these two conditions is then assumed to reflect the differing cognitive process. In addition, this model assumes that a cognitive process can be selectively added to a set of active cognitive processes without affecting them.

Baseline versus activity conditions

The brain is never completely at rest. It never stops functioning and firing neuronal signals, as well as using oxygen as long as the person in question is alive. In fact, in Stark and Squire's, 2001 study When zero is not zero: The problem of ambiguous baseline conditions in fMRI, activity in the medial temporal lobe (as well as in other brain regions) was substantially higher during rest than during several alternative baseline conditions. The effect of this elevated activity during rest was to reduce, eliminate, or even reverse the sign of the activity during task conditions relevant to memory functions. These results demonstrate that periods of rest are associated with significant cognitive activity and are therefore not an optimal baseline for cognition tasks. In order to discern baseline and activation conditions it is necessary to interpret a lot of information. This includes situations as simple as breathing. Periodic blocks may result in identical data of other variance in the data if the person breathes at a regular rate of 1 breath/5sec, and the blocks occur every 10s, thus impairing the data.

Reverse inference

Neuroimaging methods such as fMRI and MRI offer a measure of the activation of certain brain areas in response to cognitive tasks engaged in during the scanning process. Data obtained during this time allow cognitive neuroscientists to gain information regarding the role of particular brain regions in cognitive function. However, an issue arises when certain brain regions are alleged by researchers to identify the activation of previously labeled cognitive processes. Poldrack clearly describes this issue:

The usual kind of inference that is drawn from neuroimaging data is of the form 'if cognitive process X is engaged, then brain area Z is active.' Perusal of the discussion sections of a few fMRI articles will quickly reveal, however, an epidemic of reasoning taking the following form:
(1) In the present study, when task comparison A was presented, brain area Z was active.
(2) In other studies, when cognitive process X was putatively engaged, then brain area Z was active.
(3) Thus, the activity of area Z in the present study demonstrates engagement of cognitive process X by task comparison A.
This is a 'reverse inference', in that it reasons backwards from the presence of brain activation to the engagement of a particular cognitive function.

Reverse inference demonstrates the logical fallacy of affirming what you just found, although this logic could be supported by instances where a certain outcome is generated solely by a specific occurrence. With regard to the brain and brain function it is seldom that a particular brain region is activated solely by one cognitive process. Some suggestions to improve the legitimacy of reverse inference have included both increasing the selectivity of response in the brain region of interest and increasing the prior probability of the cognitive process in question. However, Poldrack suggests that reverse inference should be used merely as a guide to direct further inquiry rather than a direct means to interpret results.

Forward inference

Forward inference is a data driven method that uses patterns of brain activation to distinguish between competing cognitive theories. It shares characteristics with cognitive psychology's dissociation logic and philosophy's forward chaining. For example, Henson discusses forward inference's contribution to the "single process theory vs. dual process theory" debate with regard to recognition memory. Forward inference supports the dual process theory by demonstrating that there are two qualitatively different brain activation patterns when distinguishing between "remember vs. know judgments". The main issue with forward inference is that it is a correlational method. Therefore, one cannot be completely confident that brain regions activated during cognitive process are completely necessary for that execution of those processes. In fact, there are many known cases that demonstrate just that. For example, the hippocampus has been shown to be activated during classical conditioning, however lesion studies have demonstrated that classical conditioning can occur without the hippocampus.

Health risks

The most common risk to participants in an fMRI study is claustrophobia and there are reported risks for pregnant women to go through the scanning process. Scanning sessions also subject participants to loud high-pitched noises from Lorentz forces induced in the gradient coils by the rapidly switching current in the powerful static field. The gradient switching can also induce currents in the body causing nerve tingling. Implanted medical devices such as pacemakers could malfunction because of these currents. The radio-frequency field of the excitation coil may heat up the body, and this has to be monitored more carefully in those running a fever, the diabetic, and those with circulatory problems. Local burning from metal necklaces and other jewellery is also a risk.

The strong static magnetic field can cause damage by pulling in nearby heavy metal objects converting them to projectiles.

There is no proven risk of biological harm from even very powerful static magnetic fields. However, genotoxic (i.e., potentially carcinogenic) effects of MRI scanning have been demonstrated in vivo and in vitro, leading a recent review to recommend "a need for further studies and prudent use in order to avoid unnecessary examinations, according to the precautionary principle". In a comparison of genotoxic effects of MRI compared with those of CT scans, Knuuti et al. reported that even though the DNA damage detected after MRI was at a level comparable to that produced by scans using ionizing radiation (low-dose coronary CT angiography, nuclear imaging, and X-ray angiography), differences in the mechanism by which this damage takes place suggests that the cancer risk of MRI, if any, is unknown.

Advanced methods

The first fMRI studies validated the technique against brain activity known, from other techniques, to be correlated to tasks. By the early 2000s, fMRI studies began to discover novel correlations. Still their technical disadvantages have spurred researchers to try more advanced ways to increase the power of both clinical and research studies.

Better spatial resolution

MRI, in general, has better spatial resolution than EEG and MEG, but not as good a resolution as invasive procedures such as single-unit electrodes. While typical resolutions are in the millimeter range, ultra-high-resolution MRI or MR spectroscopy works at a resolution of tens of micrometers. It uses 7 T fields, small-bore scanners that can fit small animals such as rats, and external contrast agents such as fine iron oxide. Fitting a human requires larger-bore scanners, which make higher fields strengths harder to achieve, especially if the field has to be uniform; it also requires either internal contrast such as BOLD or a non-toxic external contrast agent unlike iron oxide.

Parallel imaging is another technique to improve spatial resolution. This uses multiple coils for excitation and reception. Spatial resolution improves as the square root of the number of coils used. This can be done either with a phased array where the coils are combined in parallel and often sample overlapping areas with gaps in the sampling or with massive coil arrays, which are a much denser set of receivers separate from the excitation coils. These, however, pick up signals better from the brain surface, and less well from deeper structures such as the hippocampus.

Better temporal resolution

Temporal resolution of fMRI is limited by: (1) the feedback mechanism that raises the blood flow operating slowly; (2) having to wait until net magnetization recovers before sampling a slice again; and (3) having to acquire multiple slices to cover the whole brain or region of interest. Advanced techniques to improve temporal resolution address these issues. Using multiple coils speeds up acquisition time in exact proportion to the coils used. Another technique is to decide which parts of the signal matter less and drop those. This could be either those sections of the image that repeat often in a spatial map (that is small clusters dotting the image periodically) or those sections repeating infrequently (larger clusters). The first, a high-pass filter in k-space, has been proposed by Gary H. Glover and colleagues at Stanford. These mechanisms assume the researcher has an idea of the expected shape of the activation image.

Typical gradient-echo EPI uses two gradient coils within a slice, and turns on first one coil and then the other, tracing a set of lines in k-space. Turning on both gradient coils can generate angled lines, which cover the same grid space faster. Both gradient coils can also be turned on in a specific sequence to trace a spiral shape in k-space. This spiral imaging sequence acquires images faster than gradient-echo sequences, but needs more math transformations (and consequent assumptions) since converting back to voxel space requires the data be in grid form (a set of equally spaced points in both horizontal and vertical directions).

New contrast mechanisms

BOLD contrast depends on blood flow, which is both sluggish in response to stimulus and subject to noisy influences. Other biomarkers now looked at to provide better contrast include temperature, acidity/alkalinity (pH), calcium-sensitive agents, neuronal magnetic field, and the Lorentz effect. Temperature contrast depends on changes in brain temperature from its activity. The initial burning of glucose raises the temperature, and the subsequent inflow of fresh, cold blood lowers it. These changes alter the magnetic properties of tissue. Since the internal contrast is too difficult to measure, external agents such as thulium compounds are used to enhance the effect. Contrast based on pH depends on changes in the acid/alkaline balance of brain cells when they go active. This too often uses an external agent. Calcium-sensitive agents make MRI more sensitive to calcium concentrations, with calcium ions often being the messengers for cellular signalling pathways in active neurons. Neuronal magnetic field contrast measures the magnetic and electric changes from neuronal firing directly. Lorentz-effect imaging tries to measure the physical displacement of active neurons carrying an electric current within the strong static field.

Commercial use

Some experiments have shown the neural correlates of peoples' brand preferences. Samuel M. McClure used fMRI to show the dorsolateral prefrontal cortex, hippocampus and midbrain were more active when people knowingly drank Coca-Cola as opposed to when they drank unlabeled Coke. Other studies have shown the brain activity that characterizes men's preference for sports cars, and even differences between Democrats and Republicans in their reaction to campaign commercials with images of the 9/11 attacks. Neuromarketing companies have seized on these studies as a better tool to poll user preferences than the conventional survey technique. One such company was BrightHouse, now shut down. Another is Oxford, UK-based Neurosense, which advises clients how they could potentially use fMRI as part of their marketing business activity. A third is Sales Brain in California.

At least two companies have been set up to use fMRI in lie detection: No Lie MRI and the Cephos Corporation. No Lie MRI charges close to $5000 for its services. These companies depend on evidence such as that from a study by Joshua Greene at Harvard University suggesting the prefrontal cortex is more active in those contemplating lying.

However, there is still a fair amount of controversy over whether these techniques are reliable enough to be used in a legal setting. Some studies indicate that while there is an overall positive correlation, there is a great deal of variation between findings and in some cases considerable difficulty in replicating the findings. A federal magistrate judge in Tennessee prohibited fMRI evidence to back up a defendant's claim of telling the truth, on the grounds that such scans do not measure up to the legal standard of scientific evidence.. Most researchers agree that the ability of fMRI to detect deception in a real life setting has not been established.

Use of the fMRI has been left out of legal debates throughout its history. Use of this technology has not been allowed due to holes in the evidence supporting fMRI. First, most evidence supporting fMRIs accuracy was done in a lab under controlled circumstances with solid facts. This type of testing does not pertain to real life. Real-life scenarios can be much more complicated with many other affecting factors. It has been shown that many other factors affect BOLD other than a typical lie. There have been tests done showing that drug use alters blood flow in the brain, which drastically affects the outcome of BOLD testing. Furthermore, individuals with diseases or disorders such as schizophrenia or compulsive lying can lead to abnormal results as well. Lastly, there is an ethical question relating to fMRI scanning. This testing of BOLD has led to controversy over if fMRIs are an invasion of privacy. Being able to scan and interpret what people are thinking may be thought of as immoral and the controversy still continues.

Because of these factors and more, fMRI evidence has been excluded from any form of legal system. The testing is too uncontrolled and unpredictable. Therefore, it has been stated that fMRI has much more testing to do before it can be considered viable in the eyes of the legal system.

Criticism

Some scholars have criticized fMRI studies for problematic statistical analyses, often based on low-power, small-sample studies. Other fMRI researchers have defended their work as valid. In 2018, Turner and colleagues have suggested that the small sizes affect the replicability of task-based fMRI studies and claimed that even datasets with at least 100 participants the results may not be well replicated, although there are debates on it.

In one real but satirical fMRI study, a dead salmon was shown pictures of humans in different emotional states. The authors provided evidence, according to two different commonly used statistical tests, of areas in the salmon's brain suggesting meaningful activity. The study was used to highlight the need for more careful statistical analyses in fMRI research, given the large number of voxels in a typical fMRI scan and the multiple comparisons problem. Before the controversies were publicized in 2010, between 25 and 40% of studies on fMRI being published were not using the corrected comparisons. But by 2012, that number had dropped to 10%. Dr. Sally Satel, writing in Time, cautioned that while brain scans have scientific value, individual brain areas often serve multiple purposes and "reverse inferences" as commonly used in press reports carry a significant chance of drawing invalid conclusions. In 2015, it was discovered that a statistical bug was found in the fMRI computations which likely invalidated at least 40,000 fMRI studies preceding 2015, and researchers suggest that results prior to the bug fix cannot be relied upon. Furthermore, it was later shown that how one sets the parameters in the software determines the false positive rate. In other words, study outcome can be determined by changing software parameters.

In 2020 professor Ahmad Hariri, (Duke University) one of the first researchers to use fMRI, performed a largescale experiment that sought to test the reliability of fMRI on individual people. In the study, he copied protocols from 56 published papers in psychology that used fMRI. The results suggest that fMRI has poor reliability when it comes to individual cases, but good reliability when it comes to general human thought patterns.

List of human positions

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