MRI PULSE SEQUANCE ARE DESCRIBED IN DETAILIN THIS PPT. CONTENT TAKEN FROM MUTIPLE BOOKS AND GENERALS.

1. MRI PULSE SEQUENCE
ROHIT BANSAL
Assistant Professor
Department of Radio-Diagnosis
MAMC, Agroha

2. An MRI pulse sequence is a programmed set of changing magnetic
gradients. Each sequence will have a number of parameters, and multiple
sequences grouped together into an MRI protocol. A pulse sequence is
generally defined by multiple parameters, including: Different combinations
of these parameters affect tissue contrast and spatial resolution.
The different steps that make up an MR pulse sequence.
•Excitation of the target area
•Switching on the slice-selection gradient,
•Delivering the excitation pulse (RF pulse),
•Switching off the slice-selection gradient.
Phase encoding
•Switching on the phase-encoding gradient repeatedly, each time with a
different strength, to create the desired number of phase shifts across the
image.
Formation of the echo or MR signal
•Generating an echo, this can be done in two ways (discussed below).
Collection of the signal
•Switching on the frequency-encoding or readout gradient,
•Recording the echo.

4. These steps are repeated many times, depending on the desired
image quality. A wide variety of sequences are used in medical MR
imaging. The most important ones are the spin echo (SE) sequence,
the inversion recovery (IR) sequence, and the gradient echo (GRE)
sequence, which are the basic MR pulse sequences.
We have already briefly mentioned echoes and said that some time
must elapse before an MR signal form after the hydrogen protons
have been excited. Now we can explain why this is so:
Before an MR signal can be collected, the phase-encoding gradient
must be switched on for spatial encoding of the signal.
Some time is also needed to switch off the slice-selection gradient
and switch on the frequency-encoding gradient.
Finally, formation of the echo itself also takes time, which varies
with the pulse sequence used.

5. Conventional spin echo
Dual Spin echo
Fast or turbo spin echo
Inversion Recovery
Spin echo pulse sequences

6. Spin echo uses a 90° excitation pulse followed by one or more 180°
rephasing pulses to generate a spin echo.
This pulse sequence can be used to produce T1 weighted images if a short
TR andTE are used.
One 180° RF pulse is applied after the 90° excitation pulse.
The single 180° RF pulse generates a single spin echo.
Conventional Spin Echo

7. This can be used to produce both a proton density and a T2 weighted
image in theTR time.
Dual Spin echo uses a 90° excitation pulse followed by two 180° rephasing
pulses to generate a spin echo.
Dual Spin Echo

8. The first echo has a short TE (TE1) and a long TR and results in a set of
proton density weighted images.
The second echo has a long TE (TE2) and a long TR and results in a T2
weighted set of images. This echo has less amplitude than the first echo
because moreT2 decay has occurred by this point.
Typical parameters
Single echo (forT1 weighting)
•TR 300–500ms
•TE 10–30 ms
Dual echo (for PD/T2 weighting)
•TR 2000+ms
•TE1 20ms
•TE2 80 ms

9. FSE employs a train of 180° rephasing pulses, each one producing
a spin echo. This train of spin echoes is called an echo train. The
number of 180° RF pulses and resultant echoes is called the echo
train length (ETL) or turbo factor. The spacing between each
echo is called the echo spacing.
After each rephasing, a phase encoding step is performed and
data from the resultant echo are stored in K space. Therefore
several lines of K space are filled every TR instead of one line as in
conventional spin echo. As K space is filled more rapidly, the scan
time decreases.
Typically 2, 4, 8 or 16, 180° RF pulses are applied during every TR.
As 2, 4, 8 or 16 phase encodings are also performed during each TR,
the scan time is reduced to 1/2, 1/4, 1/8 or 1/16 of the original scan
time.
The higher the turbo factor the shorter the scan time.
Fast or Turbo Spin Echo

11. Typical parameters
Dual echo
TR 2500–4500 ms (for weighting and slice number)
effectiveTE1 17ms
effectiveTE2 102ms
ETL 8 –This may be split so that the PD image is acquired with the first
four echoes and theT2 with the second four.
Single echoT2 weighting
TR 4000–8000ms
TE 102ms
ETL 16
Single echoT1 weighting
TR 600ms
TE 17ms
ETL 4

12. Uses
FSE produces T1, T2 or proton density scans in a fraction of the time of
Conventional Spin Echo. Because the scan times are reduced, matrix size
can be increased to improve spatial resolution.
FSE is usually used for brains, spines, joints, extremities and the pelvis.
As FSE is incompatible with respiratory compensation techniques, it can
only be used in the chest and abdomen with respiratory triggering or
multiple NEX.

13. T1 weighted images best demonstrate anatomy but also show pathology
if used after contrast enhancement.
Typical parameters
•TR 300–600 ms (shorter in gradient echo sequences)
•TE 10–30 ms (shorter in gradient echo sequences)
Signal intensities seen inT1 weighted images.
High signal fat
•Haemangioma
•Intra-osseous lipoma
•Radiation change
•Degeneration fatty deposition
•Methaemoglobin
•Cysts with proteinaceous fluid
•Paramagnetic contrast agents
•Slow flowing blood
T1 Weighted Image

14. Low signal
•Cortical bone
•Avascular necrosis
•Infarction
•Infection
•Tumors
•Sclerosis
•Cysts
•Calcification
No signal air
•Fast flowing blood
•Tendons
•Cortical bone
•Scar tissue
•Calcification

16. T2 weighted images best demonstrate pathology as most pathology has an
increased water content and is therefore bright onT2 weighted images.
Typical parameters
•TR 2000 ms +
•TE 70 ms +
Signal intensities seen inT2 weighted images.
•High signal CSF
•Synovial fluid
•Haemangioma
•Infection
•Inflammation
•Oedema
•Some tumors
•Hemorrhage
•Slow-flowing blood
•Cysts
T2 Weighted Image

17. Low signal
•Cortical bone
•Bone islands
•De-oxyhaemoglobin
•Haemosiderin
•Calcification
•T2 paramagnetic agents
No signal air
•Fast flowing blood
•Tendons
•Cortical bone
•Scar tissue
•Calcification

19. Cortical bone and air are always dark on MR images regardless of the
weighting as they have a low proton density and therefore return little
signal.
Proton density weighted images show anatomy and some pathology.
Typical values
•TR 2000ms+
•TE 10–30ms
Proton Density Images

21. Inversion recovery (IR) is a spin-echo pulse sequence that uses an RF
inverting pulse to suppress signal from certain tissues, although it is also
sometimes used to generate heavy T1 contrast.
The IR pulse sequence begins with a 180° RF pulse. This is applied at the
beginning of the TR period when the NMV is aligned in the same direction as
B0 in the longitudinal plane (termed +z).
The RF pulse inverts the NMV through 180°, which means that after the
pulse, the NMV still lies in the longitudinal plane but in the opposite
direction to B0 (termed−z).
When the RF inverting pulse is removed, the NMV relaxes back to B0
because ofT1 recovery processes.
At a certain time-point during this recovery, a 90° RF excitation pulse is
applied and then switched off.
The resultant FID is then rephased by another 180° RF rephasing pulse to
produce a spin echo at timeTE.
Inversion Recovery

23. The time from the 180° RF inverting pulse to the 90° RF
excitation pulse is known as the TI (time from inversion).
Image contrast depends primarily on theTI.
If the 90° RF excitation pulse is applied after the NMV has
relaxed back through the transverse plane, image contrast
depends on the amount of longitudinal recovery of each
vector (as in spin-echo).The resultant image isT1-weighted.
If the 90° RF excitation pulse is not applied until the NMV
has reached full recovery, a PD-weighted image is produced,
as both fat and water are fully relaxed.

24. T1 weighting:
• MediumTI 400–800 ms (varies at different field strengths)
• ShortTE 10–20 ms
• LongTR 3000 ms+.
Proton density weighting:
• LongTI 1800 ms
• ShortTE 10–20 ms
• LongTR 3000 ms+.
Pathology weighting:
• MediumTI 400–800 ms
• LongTE 70 ms+
• LongTR 3000 ms+.
Suggested Parameters

25. In this sequence, the 180° RF inverting pulse is followed at
time TI by the 90° RF excitation pulse and a train of 180° RF
rephasing pulses to fill out multiple lines of k-space as inTSE.
This reduces the scan time compared to conventional IR.
However, instead of T1-weighted images, fast IR is usually
used to suppress signal from certain tissues in conjunction
with T2 weighting so that water and pathology return a high
signal.
The two main sequences in this category are STIR and
FLAIR.
Fast Inversion Recovery

26. Mechanism
STIR is an IR pulse sequence that uses a TI that corresponds to the time it
takes the fat vector to recover from full inversion to the transverse plane so
that there is no longitudinal magnetization corresponding to fat. This is called
the null point.
As there is no longitudinal component of fat when the 90° RF excitation
pulse is applied, there is no transverse component after excitation, and signal
from fat is nulled.
 A TI of 100–175 ms usually achieves fat suppression, although this value
varies slightly at different field strengths.
Uses
STIR is an extremely important sequence in musculoskeletal imaging
because normal bone, which contains fatty marrow, is suppressed, and
lesions within bone such as bone bruising and tumours are seen more clearly.
It is also a very useful sequence for suppressing fat in general MR imaging.
STIR (Short Tau Inversion Recovery)

27. Suggested parameters
• ShortTI (tau) 150–175 ms (to suppress fat depending on field
strength)
• LongTE 50 ms+ (to enhance signal from pathology)
• LongTR 4000 ms+ (to allow full longitudinal recovery)
• Long turbo factor 16–20 (to enhance signal from
pathology).
Scan tip: When not to use STIR
STIR should not be used in conjunction with contrast enhancement, which
shortens the T1 recovery times of enhancing tissues, making them relatively
hyperintense. The T1 recovery times of these structures are shortened by the
contrast agent so that they approach the T1 recovery time of fat. In a STIR
sequence, therefore, enhancing tissue may also be nulled.

28. Mechanism
FLAIR is another variation of the IR sequence. In FLAIR, a TI
corresponding to the recovery of the vector in CSF from full inversion to
the transverse plane is selected.
This TI nulls signal from CSF because there is no longitudinal
magnetization present in CSF. As there is no longitudinal component of
CSF when the 90° RF excitation pulse is applied, there is no transverse
component after excitation, and signal from CSF is nulled.
FLAIR is used to suppress high CSF signal in T2 weighted images so that
the pathology adjacent to CSF is seen more clearly.
A TI of 1700–2200 ms usually achieves CSF suppression (although this
varies slightly at different field strengths).
FLAIR (Fluid Attenuated
Inversion Recovery)

29. Uses
FLAIR is used in brain and spine imaging to see periventricular and cord
lesions more clearly because high signal from CSF that lies adjacent is
nulled.
It is especially useful in visualizing multiple sclerosis plaques, acute
subarachnoid haemorrhage, and meningitis.
Another modification of this sequence in brain imaging is selecting a TI
that corresponds to the null point of white matter. This TI value nulls signal
from normal white matter so that lesions within it appear much brighter by
comparison.
This sequence (which requires a TI of about 300 ms) is very useful for
white matter lesions such as periventricular leukomalacia and for congenital
grey/white matter abnormalities.

30. Suggested parameters
• LongTI 1700–2200 ms (to suppress CSF depending on
field strength)
• LongTE 70 ms+ (to enhance signal from pathology)
• LongTR 6000 ms+ (to allow full longitudinal recovery)
• Long turbo factor 16–20 (to enhance signal from pathology).
Learning tip: FLAIR and gadolinium
Sometimes gadolinium is given to enhance pathology in the FLAIR
sequence. This oddity (gadolinium enhancement in T2-weighted images)
may be due to the long echo trains used in FLAIR sequences that cause fat
to remain bright on T2-weighted images. As gadolinium reduces the T1
recovery time of enhancing tissue so that it is similar to fat, enhancing
tissue may appear brighter than when gadolinium is not given.

32. Gradient-echo pulse sequences differ from spin-echo pulse
sequences in two ways:
• They use variable RF excitation pulse flip angles as opposed
to 90° RF excitation pulse flip angles that are common in spin-
echo pulse sequences.
• They use gradients rather than RF pulses to rephase the
magnetic moments of hydrogen nuclei to form an echo.
The main purpose of these two mechanisms is to enable
shorter TRs and therefore scan times than are common with
spin-echo pulse sequences.
Gradient Echo Pulse Sequence

33. Variable flip angle
A gradient-echo pulse sequence uses an RF excitation pulse
that is variable and therefore flips the NMV through any angle
(not just 90°).
Typically, a flip angle of less than 90° is used. This means that
the NMV is flipped through a lower angle than it is in spin-echo
sequences when a larger 90° flip angle is usually applied.
As the NMV is moved through a smaller angle in the
excitation phase of the pulse sequence, it does not take as long
for the NMV to achieve full relaxation once the RF excitation
pulse is removed.
Therefore, full T1 recovery is achieved in a much shorter TR
than in spin-echo pulse sequences.
As the TR is a scan time parameter, this leads to shorter scan
times.

34. Gradient rephasing
After the RF excitation pulse is withdrawn, the FID immediately occurs due to
inhomogeneities in the magnetic field andT2* decay.
In spin-echo pulse sequences, the magnetic moments of hydrogen nuclei are
rephased by an RF pulse.
As a relatively large flip angle is used in spin-echo pulse a sequence, most of the
magnetization is still in the transverse plane when the 180° RF rephasing pulse
is applied.
Consequently, this pulse rephases this transverse magnetization to create a
spin-echo.
In gradient-echo pulse sequences, an RF pulse cannot rephase transverse
magnetization to create an echo.
The low flip angles used in gradient-echo pulse sequences result in a large
component of magnetization remaining in the longitudinal plane after the RF
excitation pulse is switched off.
The 180° RF pulse would therefore largely invert this magnetization into the−z
direction (the direction that is opposite to B0) rather than rephase the
transverse magnetization. Therefore, in gradient-echo pulse sequences, a
gradient is used to rephase transverse magnetization instead.

35. How gradients diphase
Look at Figure, with no gradient applied, all the magnetic moments of hydrogen
nuclei precess at the same frequency, as they experience the same field strength
(in reality they do not because of magnetic field inhomogeneities, but these
changes are relatively small compared with those imposed by a gradient).
A gradient is applied to coherent (in phase) magnetization (all the magnetic
moments are in the same place at the same time). The gradient alters the magnetic
field strength experienced by the coherent magnetization. Some of the magnetic
moments speed up, and some slow down, depending on their position along the
gradient axis. Thus, the magnetic moments fan out or dephase because their
frequencies are changed by the gradient.
The trailing edge of the fan (shown in purple) consists of nuclei whose magnetic
moments slow down because they are situated on the gradient axis that has a
lower magnetic field strength relative to isocenter.
The leading edge of the fan (shown in red) consists of nuclei whose magnetic
moments speed up because they are situated on the gradient axis that has a higher
magnetic field strength relative to isocenter.
The magnetic moments of nuclei are therefore no longer in the same place at the
same time, and so magnetization is dephased by the gradient. Gradients that
dephase in this way are called spoilers, and the process of dephasing magnetic
moments with gradients is called gradient spoiling.

37. How gradients rephase
Look at Figure, A gradient is applied to incoherent (out of phase)
magnetization to rephase it. The magnetic moments initially fan out due to
T2* decay, and the fan has a trailing edge consisting of nuclei with slowly
precessing magnetic moments (shown in purple) and a leading edge consisting
of nuclei with faster precessing magnetic moments (shown in red).
 A gradient is then applied so that the magnetic field strength is altered in a
linear fashion along the axis of the gradient.
The direction of this altered field strength is such that the slowly precessing
magnetic moments in the trailing edge of the fan experience an increased
magnetic and speed up.
In figure, these are the purple spins that experience the red “high end” of the
gradient. At the same time, the faster precessing magnetic moments in the
leading edge of the fan experience a decreased magnetic field strength and
slow down.
In Figure, these are the red magnetic moments that experience the purple
“low end” of the gradient. After a short period of time, the slow magnetic
moments speed up sufficiently to meet the faster ones that are slowing down.

38. At this point, all the magnetic moments are in the same place at the same
time and are therefore rephased by the gradient. A maximum signal is
induced in the receiver coil, and this signal is called a gradient-echo.
Gradients that rephase in this way are called rewinders. Whether a gradient
field adds or subtracts from the main magnetic field depends on the direction
of current that passes through the gradient coils. This is called the polarity of
the gradient.
Gradient-echoes are created by a bipolar gradient. This means that it
consists of two lobes, one negative and one positive.
The frequency-encoding gradient is used for this purpose.
It is initially applied negatively, which increases dephasing and eliminates
the FID. Its polarity is then reversed, which rephases only those magnetic
moments that were dephased by the negative lobe. It is only these nuclei
(those whose magnetic moments are dephased by the negative lobe of the
gradient and are then rephased by the positive lobe) that create the gradient-
echo at timeTE.
The area under the negative lobe of the gradient is half that of the area
under the positive lobe.

41. ForT1 weighting
TR less than 50 ms (short)
Flip angle 60–120° (large)
TE 5–10 ms (short)
ForT2* weighting
TR less than 500 ms (long)
Flip angle less than 30° (small)
TE 15–20 ms (relatively long)
For proton density weighting
TR 200–600 ms (long)
Flip angle 5–20° (small)
TE 5–15 ms (short)

42. It is a MRI sequence which uses steady state of magnetization.
This is a situation when theTR is shorter than both theT1 andT2 relaxation
times of all the tissues.Therefore there is no time for the transverse
magnetization to decay before the pulse pattern is repeated again.The
only process that has time to occur isT2*.Therefore the NMV does not
move between repetition times.This is called steady state
In general, SSFP MRI sequence are based on gradient echo with a short
repetition time, it is also called FLASH MRITechnique.
SSFP is beneficial for localizer sequence.
This sequence also named as FFE (Fast Field Echo) and FISP (Fast Imaging
with Steady State Precession) in many commercials.
Useful for blood vessels and fluid field spaces in body.
Fluid = Bright
Fat = Intermediate Signal
Steady State Free Precession
Imaging (SSFP)

43. GRADIENT ECHO SHOWING EXCESSIVE IROM DEPOSITION

44. EPI is an MR acquisition method that collects all the data required to fill all
the lines of K space from a single echo train.
In order to achieve this, multiple echoes are generated and each is phase
encoded by a different slope of gradient to fill all the required lines of K space.
Echoes are generated either by 180° rephasing pulses (termed spin echo
EPI), or by gradients (termed gradient echo EPI).
Gradient rephasing is much faster and involves no RF deposition to the
patient but does require high speed gradients. In order to fill all of K space in
one repetition, the readout and phase encode gradients must rapidly switch on
and off.
As data acquisition is so rapid in EPI, images may be acquired in 50 ms to 80
ms.
Axial images of the whole brain are possible in 2s to 3s and whole body
imaging in about 30 s.
EPI sequences place exceptional strains on the gradients and therefore
gradient modifications are required.
Echo Planar Imaging (EPI)

45. Typical parameters
Either proton density or T2 weighting is achieved by selecting either a
short or long effective TE which corresponds to the time interval between
the excitation pulse and when the centre of K space is filled.
T1 weighting is possible by applying an inverting pulse prior to the
excitation pulse to produce saturation.
Uses
Functional imaging
Real time cardiac imaging
Perfusion/diffusion

48. Diffusion weighted imaging measures the motion of spins
(specifically in water).
The signal is dependent on the diffusion coefficient within the
material i.e. how freely the water can diffuse. The more a particle
can move in a given amount of time, the higher the diffusion
coefficient.
Water diffuses randomly via Brownian motion. In pure water and
gel, water can diffuse freely with no impediment or restriction.
within soft tissues, water diffusion is impeded by cell membranes
and intracellular organelles.
A spin-echo sequence is typically used, specifically echo-planar
imaging (EPI). EPI minimizes the effect of patient motion as it is a
very quick sequence. This is important as DWI images the very small
motion of water molecules which will be masked by any macroscopic
body motion.
Diffusion-Weighted Imaging (DWI)

51. Two diffusion gradients are added either side of the 180º RF pulse.
The first diffusion gradient dephases the spins. The second diffusion
gradient rephases and returns a signal only from the spins that have
remained within the area i.e. those that are stationary. Any spins that
have moved out of the area aren’t rephased and do not return a signal.
The diffusion gradient is applied in multiple directions. The
minimum number of directions is 3 run perpendicular to each other
(e.g. x-, y-, and z-axes) but, usually, 6-20 directions are used. Each
voxel’s signal is an average of the signal from all directions.
Then, a standard sequence is run to generate echoes and create the
signal.
b-value
The degree of diffusion weighting is represented as the b-value. The
more sensitive the DWI sequence is to molecular motion, the higher
the b-value.
The strength, duration, and interval of the gradients (collectively
known as the b factor/value expressed in units of s/mm2). This is one
of the extrinsic contrast parameter.

52. Higher b-value:
•More sensitive to diffusion
•More noise
•Less signal
Increase the b-value by:
Larger diffusion gradient (increase the amplitude or the duration)
Increased time between dephasing and rephasing diffusion
gradients
b0 – A DW pulse sequence is first run with the diffusion gradients
switched off. This creates a T2*-weighted image that is used for the
calculated maps later.
b600-700 – Useful in neonatal brain imaging and body MRI.
b1000 – Strong diffusion weighting. Used to look for cerebral
infarcts.

53. Apparent diffusion coefficient
As DWI images have T2 weighting. Therefore, a lesion that shows
as bright on DWI may be bright because of restricted diffusion or
because of inherent high T2 signal. The apparent diffusion
coefficient (ADC) map is a calculated image that removes the
effects of inherent T2 signal.
The signal of a tissue decreases exponentially with increasing b-
values. If we plot the log of the signal against the b-value, the slope
will give us the diffusion characteristics without any T2 signal
influence i.e. the ADC signal.
Tissues with free diffusion will change signal over different b-
values much more than those with restricted diffusion. More
diffusion = greater change in signal = a steeper slope = a higher ADC
value. This is why restricting lesions will appear dark on the ADC
map.
Clinical applications
Diagnosis of stroke where areas of decreased diffusion, which
represent infarction, are either dark or bright depending on the
technique used.

54. Diffusion-weighted imaging has a major role in the following clinical
situations:
 early identification of ischemic stroke
 differentiation of acute from chronic stroke
 differentiation of acute stroke from other stroke mimics
 differentiation of epidermoid cyst from an arachnoid cyst
 differentiation of abscess from necrotic tumors
 assessment of cortical lesions in Creutzfeldt-Jakob disease (CJD)
 differentiation of herpes encephalitis from diffuse temporal gliomas
 assessment of the extent of diffuse axonal injury
 grading of diffuse gliomas and meningiomas
 assessment of active demyelination
 grading of prostate lesions (see PIRADS)
 differentiation between cholesteatoma and otitis media

55. B- value map calculation

57. If the probability of diffusion is the same in every direction, this is called isotropic
diffusion e.g. in CSF. Anisotropic diffusion is when diffusion is not equal in every
direction e.g. along nerve bundles and white matter tracts. In standard DWI we
remove this effect by averaging out the signal obtained from multiple directions.
However, we can use this asymmetry in diffusion tensor imaging. The three main
techniques are the fractional anisotropy map, the principal diffusion direction map
and fibre-tracking maps.
Fractional anisotropy map
Fractional anisotropy (FA) is a measure, from 0 to 1, of the amount of diffusion
asymmetry within a voxel. A sphere, which is isotropic, has an FA of 0. The more
asymmetric the diffusion becomes the closer it is to 1. The FA map is gray-scale. The
brighter the voxel, the more anisotropic the diffusion.
Principal diffusion direction map
Colours and brightness are assigned to the voxels based on the degree of
anisotropy (represented as brightness) and the direction (represented as colours).
Fibre tracking map
The direction of the asymmetry is used to compute fibre trajectories with
automated software. A “seed voxel” is selected by the user and the software follows
the direction of the adjacent voxels to create an image of the tracts.
Diffusion Tensor Imaging

59. Perfusion is a measure of the quality of vascular supply to a tissue. Since
vascular supply and metabolism are usually related, perfusion can also be used
to measure tissue activity. Perfusion imaging utilizes a bolus injection of
gadolinium administered intravenously during ultrafast T2 or T2* acquisitions.
The contrast agent causes transient decreases in T2 and T2* in and around the
microvasculature perfused with contrast. After data acquisition, a signal decay
curve can be used to ascertain blood volume, transient time and measurement
of perfusion. This curve is known as a time intensity curve. Time intensity curves
for multiple images acquired during and after injection are combined to
generate a cerebral blood volume (CBV) map. Mean transit times (MTT) of
contrast through an organ or tissue can also be calculated.
Clinical applications
This is used for evaluation of ischaemic disease or metabolism. On the CBV
map, areas of low perfusion appear dark (stroke) whereas areas of higher
perfusion appear bright (malignancies).
Perfusion Imaging

61. Functional MR imaging (fMRI) is a rapid MR imaging technique that acquires
images of the brain during activity or stimulus and at rest. The two sets of
images are then subtracted demonstrating functional brain activity as the
result of increased blood flow to the activated cortex. The most important
physiological effect that produces MR signal intensity changes between
stimulus and rest is called blood oxygenation level dependent (BOLD). BOLD
exploits differences in the magnetic susceptibility of oxyhaemoglobin and
deoxyhaemoglobin.
• Haemoglobin is a molecule that contains iron and transports oxygen in the
vascular system as oxygen binds directly to iron.
• Oxyhaemoglobin is a diamagnetic molecule in which the magnetic
properties of iron are largely suppressed.
• Deoxyhaemoglobin is a paramagnetic molecule that creates an
inhomogeneous magnetic field in its immediate vicinity that increasesT2*.
Functional MRI (fMRI)

62. At rest, tissue uses a substantial fraction of the blood flowing
through the capillaries, so venous blood contains an almost equal mix
of oxy and deoxyhaemoglobin.
During exercise however when metabolism is increased, more
oxygen is needed and hence more is extracted from the capillaries.
The brain is very sensitive to low concentrations of
oxyhaemoglobin and therefore the cerebral vascular system
increases blood flow to the activated area.
This causes a drop in deoxyhaemoglobin that result in a decrease in
dephasing and a corresponding increase in signal intensity.
Blood oxygenation increases during brain activity and specific
locations of the cerebral cortex are activated during specific tasks.
For example, seeing activates the visual cortex, hearing the
auditory cortex, finger tapping the motor cortex.

63. More sophisticated tasks, including maze paradigms and other
thought-provoking tasks, stimulate other brain cortices.
BOLD effects are very short lived and therefore require extremely
rapid sequences such as EPI or fast gradient echo.
The images are usually acquired with long TEs (40–70 ms) while the
task is modulated on and off.
The ‘off’ images are then subtracted from the ‘on’ images and a
more sophisticated statistical analysis is performed.
Regions that were activated above some threshold levels are
overlaid onto anatomic images.
Clinical applications
Primarily developments of the understanding of brain function
including evaluation of stroke, epilepsy, pain and behavioural
problems.

64. fMRI is becoming the diagnostic method of choice for learning how
a normal, diseased or injured brain is working, as well as for assessing
the potential risks of surgery or other invasive treatments of the
brain.
Physicians perform fMRI to:
Examine the functional anatomy of the brain.
Determine which part of the brain is handling critical functions such
as thought, speech, movement and sensation, which is called brain
mapping.
Help assess the effects of stroke, trauma, or degenerative disease
(such as Alzheimer's) on brain function.
Monitor the growth and function of brain tumors.
Guide the planning of surgery, radiation therapy, or other invasive
treatments for the brain.