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Encyclopedia > Functional magnetic resonance imaging

Functional magnetic resonance imaging (fMRI) is the use of MRI to measure the haemodynamic response related to neural activity in the brain or spinal cord of humans or other animals. It is one of the most recently developed forms of neuroimaging. The mri are a fictional alien species in the Faded Sun Trilogy of C.J. Cherryh. ... Neurons, like all other cells, require energy to function. ... Drawing by Santiago Ramón y Cajal of neurons in the pigeon cerebellum. ... Italic text // ahh addiing sum spiice iin hurr`` For other uses, see Brain (disambiguation). ... The Spinal cord nested in the vertebral column. ... Trinomial name Homo sapiens sapiens Linnaeus, 1758 Humans, or human beings, are bipedal primates belonging to the mammalian species Homo sapiens (Latin: wise man or knowing man) in the family Hominidae (the great apes). ... Neuroimaging includes the use of various techniques to either directly or indirectly image the structure, function, or pharmacology of the brain. ...

fMRI data (yellow) overlaid on an average of the brain anatomies of several humans (gray)
fMRI data (yellow) overlaid on an average of the brain anatomies of several humans (gray)


Sample fMRI data This example of fMRI data shows regions of activation including primary visual cortex (V1, BA17), extrastriate visual cortex and lateral geniculate body in a comparison between a task involving a complex moving visual stimulus and rest condition (viewing a black screen). ... Sample fMRI data This example of fMRI data shows regions of activation including primary visual cortex (V1, BA17), extrastriate visual cortex and lateral geniculate body in a comparison between a task involving a complex moving visual stimulus and rest condition (viewing a black screen). ...


It has been known for over 100 years (Roy and Sherrington, 1890) that changes in blood flow and blood oxygenation in the brain (collectively known as hemodynamics) are closely linked to neural activity. When nerve cells are active they consume oxygen carried by hemoglobin in red blood cells from local capillaries. The local response to this oxygen utilisation is an increase in blood flow to regions of increased neural activity, occurring after a delay of approximately 1-5 seconds. This hemodynamic response rises to a peak over 4-5 seconds, before falling back to baseline (and typically undershooting slightly). This leads to local changes in the relative concentration of oxyhemoglobin and deoxyhemoglobin and changes in local cerebral blood volume in addition to this change in local cerebral blood flow. Sherrington is considered one of the fathers of neuroscience. ... Blood flow is the flow of blood in the cardiovascular system. ... Italic text // ahh addiing sum spiice iin hurr`` For other uses, see Brain (disambiguation). ... Hemodynamics is concerned with the forces generated by the heart and the motion of blood through the cardiovascular system. ... General Name, Symbol, Number oxygen, O, 8 Chemical series nonmetals, chalcogens Group, Period, Block 16, 2, p Appearance colorless (gas) very pale blue (liquid) Standard atomic weight 15. ... Structure of hemoglobin. ... Human red blood cells Red blood cells are the most common type of blood cell and are the vertebrate bodys principal means of delivering oxygen to body tissues via the blood. ... This article does not cite any references or sources. ... Blood volume is a term describing the amout of blood (including both red blood cells and plasma) in a persons circulatory system. ... Cerebral blood flow, or CBF, is the amount of blood that enters the brain. ...

Hemoglobin is diamagnetic when oxygenated but paramagnetic when deoxygenated. The magnetic resonance (MR) signal of blood is therefore slightly different depending on the level of oxygenation. These differential signals can be detected using an appropriate MR pulse sequence as blood-oxygen-level dependent (BOLD) contrast. Higher BOLD signal intensities arise from decreases in the concentration of deoxygenated hemoglobin since the blood magnetic susceptibility now more closely matches the tissue magnetic susceptibility. By collecting data in an MRI scanner with parameters sensitive to changes in magnetic susceptibility one can assess changes in BOLD contrast. These changes can be either positive or negative depending upon the relative changes in both cerebral blood flow (CBF) and oxygen consumption. Increases in CBF that outstrip changes in oxygen consumption will lead to increased BOLD signal, conversely decreases in CBF that outstrip changes in oxygen consumption will cause decreased BOLD signal intensity. Structure of hemoglobin. ... Diamagnetism is a very weak form of magnetism that is only exhibited in the presence of an external magnetic field. ... Paramagnetism is the tendency of the atomic magnetic dipoles, due to quantum-mechanical spin, in a material that is otherwise non-magnetic to align with an external magnetic field. ... Magnetic resonance can mean: Nuclear magnetic resonance Electron spin resonance This is a disambiguation page — a navigational aid which lists other pages that might otherwise share the same title. ... Blood-oxygen-level dependent or BOLD fMRI is a method of observing which areas of the brain are active at any given time. ... Structure of hemoglobin. ... In physics and electrical engineering, the magnetic susceptibility is the degree of magnetization of a material in response to an applied magnetic field. ... The mri are a fictional alien species in the Faded Sun Trilogy of C.J. Cherryh. ...

Neural correlates of BOLD

The precise relationship between neural signals and BOLD is under active research. In general, changes in BOLD signal are well correlated with changes in blood flow. Numerous studies during the past several decades have identified a coupling between blood flow and metabolic rate; that is, the blood supply is tightly regulated in space and time to provide the nutrients for brain metabolism. However, neuroscientists have been seeking a more direct relationship between the blood supply and the neural inputs/outputs that can be related to observable electrical activity and circuit models of brain function. A few of the metabolic pathways in a cell. ... Drawing of the cells in the chicken cerebellum by S. Ramón y Cajal Neuroscience is a field that is devoted to the scientific study of the nervous system. ...

While current data indicate that local field potentials, an index of integrated electrical activity, form a better correlation with blood flow than the spiking action potentials that are most directly associated with neural communication, no simple measure of electrical activity to date has provided an adequate correlation with metabolism and the blood supply across a wide dynamic range. Presumably, this reflects the complex nature of metabolic processes, which form a superset with regards to electrical activity. Some recent results have suggested that the increase in cerebral blood flow (CBF) following neural activity is not causally related to the metabolic demands of the brain region, but rather is driven by the presence of neurotransmitters, especially glutamate. A local field potential (LFP) is a particular class of electrophysiological signals, which is related to the sum of all dendritic synaptic activity within a volume of tissue. ... A. A schematic view of an idealized action potential illustrates its various phases as the action potential passes a point on a cell membrane. ... Chemical structure of D-aspartic acid, a common amino acid neurotransmitter. ... Glutamic acid (Glu), also referred to as glutamate (the anion), is one of the 20 proteinogenic amino acids. ...

Some other recent results suggest that an initial small, negative dip before the main positive BOLD signal is more highly localized and also correlates with measured local decreases in tissue oxygen concentration (perhaps reflecting increased local metabolism during neuron activation). Use of this more localized negative BOLD signal has enabled imaging of human ocular dominance columns in primary visual cortex, with resolution of about 0.5 mm. One problem with this technique is that the early negative BOLD signal is small and can only be seen using larger scanners with magnetic fields of at least 3 teslas. Further, the signal is much smaller than the normal BOLD signal, making extraction of the signal from noise that much more difficult. Also, this initial dip occurs within 1-2 seconds of stimulus initiation, which may not be captured when signals are recorded at long repetition (TR). If the TR is sufficiently low, increased speed of the cerebral blood flow response due to consumption of vasoactive drugs (such as caffeine[1]) or natural differences in vascular responsivnesses may further obscure observation of the initial dip. A few of the metabolic pathways in a cell. ... Ocular dominance columns are regions of neurons in the striate cortex that synapse with axons carrying transduced signals from either the left or right eye. ... Brodmann area 17 (primary visual cortex) is shown in red in this image which also shows area 18 (orange) and 19 (yellow) The visual cortex refers to the primary visual cortex (also known as striate cortex or V1) and extrastriate visual cortical areas such as V2, V3, V4, and V5. ... SI unit. ...

The BOLD signal is composed of CBF contributions from larger arteries and veins, smaller arterioles and venules, and capillaries. Experimental results indicate that the BOLD signal can be weighted to the smaller vessels, and hence closer to the active neurons, by using larger magnetic fields. For example, whereas about 70% of the BOLD signal arises from larger vessels in a 1.5 tesla scanner, about 70% arises from smaller vessels in a 4 tesla scanner. Furthermore, the size of the BOLD signal increases roughly as the square of the magnetic field strength. Hence there has been a push for larger field scanners to both improve localization and increase the signal. A few 7 tesla commercial scanners have become operational, and experimental 8 and 9 tesla scanners are under development.

A sagittal slice of a Structural MRI scan of a human head. The nose is to the left.Click here to view an animated sequence of slices.
A sagittal slice of a Structural MRI scan of a human head. The nose is to the left. Click here to view an animated sequence of slices.
A slice of an MRI scan of the brain. The forehead is at the top and the back of the head is at the bottom. Click here to view an animation of the scan from top to bottom.
A slice of an MRI scan of the brain. The forehead is at the top and the back of the head is at the bottom. Click here to view an animation of the scan from top to bottom.

Image File history File links Download high resolution version (860x860, 69 KB) Description: saggital transection through the human brain Source: this is my very own brain. ... Image File history File links Download high resolution version (860x860, 69 KB) Description: saggital transection through the human brain Source: this is my very own brain. ... The mri are a fictional alien species in the Faded Sun Trilogy of C.J. Cherryh. ... Image File history File links Description: animated sequence of saggital transections through the human brain. ... Extracted from Image:User-FastFission-brain. ... Extracted from Image:User-FastFission-brain. ... The mri are a fictional alien species in the Faded Sun Trilogy of C.J. Cherryh. ... Made from an fMRI scan I had done. ...


BOLD effects are measured using rapid volumetric acquisition of images with contrast weighed by T2 or T2* (see MRI). Such images can be acquired with moderately good spatial and temporal resolution; images are usually taken every 1–4 seconds, and the voxels in the resulting image typically represent cubes of tissue about 2–4 millimeters on each side in humans. Recent technical advancements, such as the use of high magnetic fields and advanced "multichannel" RF reception, have advanced spatial resolution to the millimeter scale. Although responses to stimuli presented as close together as one or two seconds can be distinguished from one another, using a method known as event-related fMRI, the full time course of a BOLD response to a briefly presented stimulus lasts about 15 seconds for the robust positive response. The mri are a fictional alien species in the Faded Sun Trilogy of C.J. Cherryh. ... A voxel (a portmanteau of the words volumetric and pixel) is a volume element, representing a value on a regular grid in three dimensional space. ...

fMRI draws from many disciplines

To use fMRI effectively, an investigator must have a firm grasp of the relevant principles from all of these fields:

  • Physics: Researchers should have a reasonable understanding of the tools they are using in their own studies.
  • Electrophysiology: Familiarity with neuronal behavior at the electrophysiological level can help investigators design a useful fMRI study.
  • Psychology: Most fMRI studies are grounded experimental paradigms from cognitive psychology and psychophysics which allow quantitative measurement of the effect being studied.
  • Statistics: Correct application of statistics is essential to "tease out" observations and avoid false-positive results.
  • Neuroanatomy: The fMRI signals can be put into the context of previous knowledge only with an understanding of the neuroanatomy. Ultimately, the goal of all functional imaging experiments is to explain human cognition and behavior in terms of physical (anatomical) mechanisms.

The discoverer of the key principle behind BOLD and fMRI is widely credited to be Seiji Ogawa and Kenneth Kwong. The first few hydrogen atom electron orbitals shown as cross-sections with color-coded probability density Physics (Greek: (phúsis), nature and (phusiké), knowledge of nature) is the branch of science concerned with the discovery and characterization of universal laws which govern matter, energy, space, and time. ... Current Clamp is a common technique in electrophysiology. ... Psychology (from Greek: ψυχή, psukhē, spirit, soul; and λόγος, logos, knowledge) is an academic / applied discipline involving the scientific study of mental processes and behavior of humans and animals. ... Cognitive Psychology is the school of psychology that examines internal mental processes such as problem solving, memory, and language. ... Psychophysics is the branch of cognitive psychology dealing with the relationship between physical stimuli and their perception. ... A graph of a normal bell curve showing statistics used in educational assessment and comparing various grading methods. ... Type I errors (or α error, or false positive) and type II errors (β error, or a false negative) are two terms used to describe statistical errors. ... Neuroanatomy is the anatomy of the nervous system. ... Human cognition is the study of how the human brain thinks. ... Seiji Ogawa (born January 19th, 1934) is a Japanese researcher best known for discovering the technique that underlies Functional Magnetic Resonance Imaging. ... On May 9, 1991, Dr. Kenneth Kwong, working at the Massachusetts General Hospital, succeeded in imaging the changing MR signal at the visual cortex in response to flickering visual stimuli, using MR echo-planar imaging technology to acquire images of T1-weighted perfusion contrast and T2* weighted BOLD contrast. ...

Is fMRI worthwhile?

Since its inception, fMRI has been strongly criticised, both as a research technique and in the way its results have been interpreted.

Criticisms leveled at fMRI

  • The BOLD signal is only an indirect measure of neural activity, and is therefore susceptible to influence by non-neural changes in the body.
  • BOLD signals are most strongly associated with the input to a given area than with the output. It is therefore possible (although unlikely) that a BOLD signal could be present in a given area even if there is no single unit activity.[2]
  • Different brain areas may have different hemodynamic responses, which would not be accurately reflected by the general linear model often used to filter fMRI time signals.
  • fMRI has often been used to ask "where" activations take place in the brain. This has led to the charge that it is simply a modern-day phrenology. Most scientists prefer models which explain "how" psychological mechanisms function. The counter-argument to this criticism is that knowing "where" a cognitive function is located is vitally important. Neuropsychology, invasive manipulation of brain function and functional imaging each give us different windows of understanding into what each brain region does. The analogy to phrenology is somewhat misleading: Phrenology has little or no basis in science, but fMRI permits strong inferences to be made and tested within the scientific method.
  • fMRI has often been used to show activation localized to specific regions, and do not reflect the distributed nature of processing in neural networks. Several recent multivariate statistical techniques work around this issue by characterizing interactions between "active" regions found via traditional univariate techniques. Such techniques might prove useful in the future.
  • For a non-invasive scan, fMRI has moderately good spatial resolution. However, the temporal response of the blood supply, which is the basis of fMRI, is poor relative to the electrical signals that define neuronal communication. Therefore, some research groups are working around this issue by combining fMRI with data collection techniques such as electroencephalography (EEG) or magnetoencephalography (MEG). EEG has much higher temporal resolution but rather poor spatial resolution, whereas MEG has much higher temporal resolution and similar spatial resolution. This has led some to suggest MEG is a more valuable tool than fMRI.
  • Many theoretical models used to explain fMRI signals are so poorly specified that they are not falsifiable (a central tenet from the scientific method). Hence, some argue, fMRI is not really a "science". The counter-argument is that a fMRI study can provide evidence to falsify a prior theory if it is well-designed. Also, well-specified mathematical and computational models of the neural processes underlying fMRI can make theories more concrete, allowing them to make predictions that can be verified or falsified by fMRI (see also, Dualism in modern science, in Dualism (philosophy of mind)).

The general linear model (GLM) is a statistical, linear model. ... A 19th century Phrenology chart. ... A 19th century Phrenology chart. ... Scientific method is a body of techniques for investigating phenomena and acquiring new knowledge, as well as for correcting and integrating previous knowledge. ... In cognitive neuroscience, a neural network (also known as a neuronal network or biological neural network to distinguish from artificial neural networks) is a population of interconnected neurons. ... In statistics, in multivariate data, each data point has more than one scalar component, and often one is concerned with correlations between the components. ... Univariate describes a concept in statistics or econometrics. ... Girl wearing electrodes for electroencephalography Person wearing electrodes for electroencephalography Portable recording device for electroencephalography Electroencephalography is the neurophysiologic measurement of the electrical activity of the brain by recording from electrodes placed on the scalp or, in special cases, subdurally or in the cerebral cortex. ... Magnetoencephalography (MEG) is the measurement of the magnetic fields produced by electrical activity in the brain, usually conducted externally, using extremely sensitive devices such as SQUIDs. ... This page discusses how a theory or assertion is falsifiable (disprovable opp: verifiable), rather than the non-philosophical use of falsification, meaning counterfeiting. ... Scientific method is a body of techniques for investigating phenomena and acquiring new knowledge, as well as for correcting and integrating previous knowledge. ... René Descartes illustration of dualism. ...

General counterargument

Like any other technique, fMRI is as worthwhile as the design of the experiment using it. Many investigators have used fMRI ineffectively because they were not familiar with all aspects of the technique, or because they received their academic training in disciplines characterized by less rigor than some other branches of psychology and neuroscience. Ineffective use of the technique is a problem for the field, but it is not a consequence of the technique itself.

Advantages of fMRI

  • It can noninvasively record brain signals (of humans and other animals) without risks of radiation inherent in other scanning methods, such as CT scans.
  • It can record on a spatial resolution in the region of 3-6 millimeters, but with relatively poor temporal resolution (in the order of seconds) compared with techniques such as EEG. However, this is mainly because of the phenomena being measured, not because of the technique. EEG measures electrical/neural activity while fMRI measures blood activity, which has a longer response. The MRI equipment used for fMRI can be used for high temporal resolution, if you measure different phenomena.

This article does not cite any references or sources. ...

Commercial use

Imagilys [1] is a company specialized in clinical and research fMRI.

At least two companies have been set up to use fMRI in lie detection. They are No Lie MRI, Inc [2] and Cephos Corporation [3]. Lie detection is the practice of determining whether someone is practicing deception. ...

The signals are extrapolated from the fMRI machine onto a screen, displaying the active regions of the brain. Depending on what regions are the most active, the technician can determine whether a subject is telling the truth or not. This technology is in its early stages of development, and many of its proponents hope to replace older lie detection techniques.

Scanning in practice

Berkeley's 4T fMRI scanner.

Subjects participating in a fMRI experiment are asked to lie still and are usually restrained with soft pads to prevent small motions from disturbing measurements. Some labs also employ bite bars to reduce motion, although these are unpopular as they can cause some discomfort to subjects. It is possible to correct for some amount of head movement with post-processing of the data, but large transient motion can render these attempts futile. Generally motion in excess of 3 millimeters will result in unusable data. The issue of motion is present for all populations, but most notably within populations that are not physically or emotionally equipped for even short MRI sessions (e.g., those with Alzheimer's Disease or schizophrenia, or young children). In these populations, various and negative reinforcement strategies can be employed in an attempt to attenuate motion artifacts, but in general the solution lies in designing a compatible paradigm with these populations. ImageMetadata File history File links Download high resolution version (2048x1536, 855 KB) Varian 4T fMRI, part of the Brain Imaging Center, Helen Wills Neuroscience Institute at the University of California, Berkeley. ... ImageMetadata File history File links Download high resolution version (2048x1536, 855 KB) Varian 4T fMRI, part of the Brain Imaging Center, Helen Wills Neuroscience Institute at the University of California, Berkeley. ... Sather tower (the Campanile) looking out over the San Francisco Bay and Mount Tamalpais. ... In operant conditioning, reinforcement is an increase in the strength of a response following the presentation of a stimulus contingent on that response. ...

An fMRI experiment usually lasts between 15 minutes and 2 hours. Depending on the purpose of study, subjects may view movies, hear sounds, smell odors, perform cognitive tasks such as memorization or imagination, press a few buttons, or perform other tasks. Researchers are required to give detailed instructions and descriptions of the experiment plan to each subject, who must sign a consent form before the experiment.

Safety is a very important issue in all experiments involving MRI. Potential subjects must ensure that they are able to enter the MRI environment. Due to the nature of the MRI scanner, there is an extremely strong magnetic field surrounding the MRI scanner (at least 1.5 teslas, possibly stronger). Potential subjects must be thoroughly examined for any ferromagnetic objects (e.g. watches, glasses, hair pins, pacemakers, bone plates and screws, etc.) before entering the scanning environment. SI unit. ...

Related techniques

Aside from fMRI, there are other related ways to probe brain activity using magnetic resonance properties:

Contrast MR

An injected contrast agent such as an iron oxide that has been coated by a sugar or starch (to hide from the body's defense system), causes a local disturbance in the magnetic field that is measurable by the MRI scanner. The signals associated with these kinds of contrast agents are proportional to the cerebral blood volume. While this semi-invasive method presents a considerable disadvantage in terms of studying brain function in normal subjects, it enables far greater detection sensitivity than BOLD signal, which may increase the viability of fMRI in clinical populations. Other methods of investigating blood volume that do not require an injection are a subject of current research, although no alternative technique in theory can match the high sensitivity provided by injection of contrast agent. Radiocontrast agents (or simply contrast agents) are compounds used to improve the visibility of internal bodily structures in an X-ray image. ... Iron oxide pigment There are a number of iron oxides: Iron oxides Iron(II) oxide or ferrous oxide (FeO) The black-coloured powder in particular can cause explosions as it readily ignites. ... Magnification of grains of sugar, showing their monoclinic hemihedral crystalline structure. ... Starch (CAS# 9005-25-8) is a complex carbohydrate which is insoluble in water; it is used by plants as a way to store excess glucose. ... Magnetic field lines shown by iron filings In physics, a magnetic field is a solenoidal vector field in the space surrounding moving electric charges, such as those in electric currents and bar magnets. ...

Arterial spin labeling

By magnetic labeling the proximal blood supply using "arterial spin labeling" ASL, the associated signal is proportional to the cerebral blood flow, or perfusion. This method provides more quantitative physiological information than BOLD signal, and has the same sensitivity for detecting task-induced changes in local brain function In physiology, perfusion is the process of nutritive delivery of arterial blood to a capillary bed in the biological tissue. ...

Magnetic resonance spectroscopic imaging

Magnetic resonance spectroscopic imaging (MRS) is another, NMR-based process for assessing function within the living brain. MRS takes advantage of the fact that protons (hydrogen atoms) residing in differing chemical environments depending upon the molecule they inhabit (H2O vs. protein, for example) possess slightly different resonant properties. For a given volume of brain (typically > 1 cubic cm), the distribution of these H resonances can be displayed as a spectrum. Pacific Northwest National Laboratorys high magnetic field (800 MHz, 18. ... In physics, the proton (Greek proton = first) is a subatomic particle with an electric charge of one positive fundamental unit (1. ... General Name, Symbol, Number hydrogen, H, 1 Chemical series nonmetals Group, Period, Block 1, 1, s Appearance colorless Atomic mass 1. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Extremely high resolution spectrogram of the Sun showing thousands of elemental absorption lines (fraunhofer lines) Spectroscopy is the study of the interaction between radiation (electromagnetic radiation, or light, as well as particle radiation) and matter. ...

The area under the peak for each resonance provides a quantitative measure of the relative abundance of that compound. The largest peak is composed of H2O. However, there are also discernible peaks for choline, creatine, n-acetylaspartate (NAA) and lactate. Fortuitously, NAA is mostly inactive within the neuron, serving as a precursor to glutamate and as storage for acetyl groups (to be used in fatty acid synthesis)—but its relative levels are a reasonable approximation of neuronal integrity and functional status. Brain diseases (schizophrenia, stroke, certain tumors, multiple sclerosis) can be characterized by the regional alteration in NAA levels when compared to healthy subjects. Creatine is used as a relative control value since its levels remain fairly constant, while choline and lactate levels have been used to evaluate brain tumors. Choline is an organic compound, classified as an essential nutrient and usually grouped within the Vitamin B complex. ... Creatine is a nitrogenous organic acid that naturally occurs in vertebrates and helps to supply energy to muscle cells. ... N-Acetyl aspartate (NAA) is a derivative of aspartic acid with a formula of C6H9NO5 and a molecular weight of 175. ... For the production of milk by mammals, see Lactation. ... In chemistry, especially biochemistry, a fatty acid is a carboxylic acid often with a long unbranched aliphatic tail (chain), which is either saturated or unsaturated. ... Stroke (or cerebrovascular accident or CVA) is the clinical designation for a rapidly developing loss of brain function due to an interruption in the blood supply to all or part of the brain. ... Tumor or tumour literally means swelling, and is sometimes still used with that meaning. ... A brain tumor is any intracranial tumor created by abnormal and uncontrolled cell division, normally either found in the brain itself (neurons, glial cells (astrocytes, oligodendrocytes, ependymal cells), lymphatic tissue, blood vessels), in the cranial nerves (myelin-producing Schwann cells), in the brain envelopes (meninges), skull, pituitary and pineal gland...

Diffusion tensor imaging

Diffusion tensor imaging (DTI) is a related use of MR to measure anatomical connectivity between areas. Although it is not strictly a functional imaging technique because it does not measure dynamic changes in brain function, the measures of inter-area connectivity it provides are complementary to images of cortical function provided by BOLD fMRI. White matter bundles carry functional information between brain regions. The diffusion of water molecules is hindered across the axes of these bundles, such that measurements of water diffusion can reveal information about the location of large white matter pathways. Illnesses that disrupt the normal organization or integrity of cerebral white matter (such as multiple sclerosis) have a quantitative impact on DTI measures. Diffusion tensor imaging (DTI) is a new magnetic resonance imaging (MRI)-based technique that allows us to visualize the location, the orientation, and the anisotropy of the brains white matter tracts. ... Location of the cerebral cortex Slice of the cerebral cortex, ca. ... White matter is one of the two main solid components of the central nervous system. ...

Approaches to fMRI data analysis

The ultimate goal of fMRI data analysis is to detect correlations between brain activation and the task the subject performs during the scan. 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 activation can begin.

For a typical fMRI scan using an EPI pulse sequence the 3D volume of the subject's head is imaged every one or two seconds, producing a few hundred to a few thousand complete images per scanning session. The nature of MR imaging is such that these images are acquired in Fourier transform space, so they must be transformed back to image space to be useful. Because of practical limitations of the scanner the Fourier samples are not acquired on a grid, and scanner imperfections like thermal drift and spike noise introduce additional distortions. Small motions on the part of the subject and the subject's pulse and respiration will also affect the images. In mathematics, the Fourier transform is a certain linear operator that maps functions to other functions. ...

The most common situation is that the researcher uses a pulse sequence supplied by the scanner vendor, for example a boustrophedonic boustrophedon EPI sequence. Software in the scanner platform itself then performs the reconstruction of images from Fourier transform space. During this stage some information is lost (specifically the complex phase of the reconstructed signal). Some types of artifacts, for example spike noise, become more difficult to remove after reconstruction, but if the scanner is working well these artifacts are thought to be relatively unimportant. For pulse sequences not provided by the vendor, for example spiral EPI, reconstruction must be done by software running on a separate platform. Boustrophedon is an ancient way of writing manuscripts and other inscriptions in which, rather than going from left to right as in modern English, or right to left as in Arabic, alternate lines must be read in opposite directions. ...

After reconstruction the output of the scanning session consists of a series of 3D images of the brain. The most common corrections performed on these images are motion correction and correction for physiological effects. Outlier correction and spatial and/or temporal filtering may also be performed. If the task performed by the subject is thought to produce bursts of activation which are short compared to the BOLD response time (on the order of 6 seconds), temporal filtering may be performed at this stage to attempt to deconvolve out the BOLD response and recover the temporal pattern of activation.

At this point the data provides a time series of samples for each voxel in the scanned volume. A variety of methods are used to correlate these voxel time series with the task in order to produce maps of task-dependent activation.

Some fMRI neuroimaging software: Neuroimaging software is used to study the structure and function of the brain. ...

Analysis of Functional NeuroImages (AFNI) is an open source environment for processing and displaying functional MRI data—a technique for mapping human brain activity. ... FreeSurfer is an MRI brain imaging software package developed by the Athinoula A. Martinos Center for Biomedical Imaging at Massachusetts General Hospital and CorTechs, Inc. ... Example FSL GUIs The FMRIB Software Library (FSL) is a software library containing image analysis and statistical tools for functional, structural and diffusion MRI brain imaging data. ... Statistical parametric mapping or SPM is a statistical technique for examining differences in brain activity recorded during functional neuroimaging experiments using neuroimaging technologies such as fMRI or PET. It may also refer to a specific piece of software created by the Wellcome Department of Imaging Neuroscience (part of University College...

See also

  • The fMRI Data Centre

The fMRI Data Centre website The fMRI Data Centre (fMRIDC) is a public repository of neuroimaging data. ...


  1. ^ Behzadi, Y. et al (2006). "Caffeine reduces the initial dip in the visual bold response at 3 t.". Neuroimage 32: 9-15. 
  2. ^ Logothetis, N.K. (2001). "Neurophysiological investigation of the basis of the fMRI signal.". Nature 412. 


Scott A. Huettel, Allen W. Song, Gregory McCarthy, Functional Magnetic Resonance Imaging, Sinauer Associates, 2004, ISBN 0-87893-288-7

Journal articles

Weiller C et al (2006). "Clinical potential of brain mapping using MRI". Journal of Magnetic Resonance Imaging 23 (6): 840–850. 

External links

  Results from FactBites:
Neuroguide.com - Functional Magnetic Resonance Imaging (1871 words)
Functional magnetic resonance imaging (fMRI) is used to visualize brain function, by visualizing changes in chemical composition of brain areas or changes in the flow of fluids that occur over timespans of seconds to minutes.
In magnetic resonance studies, an object is put in a strong, externally-imposed magnetic field ("main magnetic field"); the spin-axes of all the nuclei in the object line up with the field, with the north poles of the nuclei pointing in the "southward" direction of the field.
The amount by which the magnetization vector tilts away from the z-axis is controlled by the intensity and duration of the RF pulse; for example, if a 5 msec pulse at a certain intensity caused it to deviate 90 degrees from the z-axis, then a 10 msec pulse would cause a 180 degree deviation.
fMRI - About Functional MRI(General) (2162 words)
Functional MRI is based on the increase in blood flow to the local vasculature that accompanies neural activity in the brain.
During a typical functional imaging series, 30 images are acquired in a 90 sec run where the initial and last 10 images are baseline conditions and the middle 10 images (30 secs) are acquired during a task.
Functional imaging results are compared with all conventional mapping studies performed on each patient including the WADA test, intraoperative cortical stimulation, electrophysiological assessments, and neurologic assessments of surgical outcome.
  More results at FactBites »



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