The document discusses advanced MRI techniques, focusing on sequences like FIESTA, compressed sensing, and diffusion tensor imaging. It details the benefits and limitations of each method, including their applications in visualizing cranial nerves, accelerating image acquisition, and improving contrast in brain imaging. Additionally, it highlights emerging techniques such as amide proton transfer imaging and double inversion recovery for specific clinical applications.

1. Advanced MRI Sequences
P.R.SAI PRASHANTH
FINAL YEAR DM PG
DEPT. OF NEUROLOGY
GRH

2. FIESTA vs FIESTA C
• FIESTA (Fast Imaging Employing Steady-state Acquisition) is the GE name
for a balanced steady-state gradient echo sequence that Siemens
calls TrueFISP and Philips calls balanced-FFE.
• these sequences may be affected by phase shift errors across the image
that produce banding artifacts.
• artifacts are prominent at the skull base and other locations where there
are susceptibility distortions of the main magnetic field. T
• They are also more problematic in 3D acquisitions where TR values may
exceed 10-15 msec.

3. • 3D FIESTA (TrueFISP) shows phase artifacts at
skull base

4. • FIESTA-C is a modification of the basic FIESTA/TrueFISP sequence.
• The equivalent Siemens product is called CISS (Constructive Interference
Steady State).
• FIESTA-C/CISS is composed of a pair of TrueFISP acquisitions run back-to-back
preceded by an automatic shimming procedure.
• The first uses phase alternation of the RF-pulses (+α, −α, +α, −α, ...) while the
second does not (+α, +α, +α, etc).
• When the paired data sets are combined in maximum intensity projection, the
phase errors cancel, resulting in an image largely free of dispersion banding.
• This combination of paired signals is performed automatically after data
collection (which increases reconstruction time slightly).

5. • 3D FIESTA-C (CISS) with reduced artifacts

6. • FIESTA-C/CISS is currently the sequence of choice for CSF-
cisternography for visualizing cranial nerves at the skull base.
• When used in the 3D mode, it provides high signal from CSF
based on T2/T1 contrast and high spatial resolution.
• Furthermore, like FIESTA/TrueFISP, it has inherent flow
compensation because of its perfectly balanced gradients.

7. MultiBand/Simultaneous Multi-Slice Imaging
• Simultaneous Multi-Slice (SMS) imaging, also
known as MultiBand (MB) imaging, employs
complex RF-pulses together with parallel imaging
coil arrays to acquire several sections along the z-
axis simultaneously.
• This allows a significant reduction in image
acquisition time with little signal-to-noise penalty.

8. • MultiBand, like POMP, begins with a composite
pulse that excites several slices simultaneously.
• sum several standard RF waveforms with different
phase offsets together.
• The number of simultaneous slices is referred to as
the MB or SMS acceleration factor.
• In current commercial implementations
(Siemens' SMS, GE's HyperBand, and Philips' Multi-
band SENSE), acceleration factors of 2-4 are typical.

9. • To take advantage of parallel imaging acceleration, MB uses coil encoding together
with either gradient- or RF-encoding to resolve data along the slice-select (z)-axis.
• Because modern coil arrays typically have only a few coil elements in the z-
direction, coil sensitivity differences along that axis are rather poor.
• Accordingly the simultaneously excited slices must be spaced widely apart (typically
at least 25−30 mm) as shown in the diagram.
• An interleaving technique is then used to excite missing slices in the gaps.

10. The blipped-CAIPI method for echo-
planar imaging. A MB pulse
simultaneously excites three (3) slices
defined together with the slice-select
gradient.
In-plane k-space is traversed by oscillation
of the frequency (readout) gradient with
stepping along the phase-encode
direction. "Blipped" gradients pulses (red)
are applied along the slice-select direction
during the readout gradient switching and
simultaneously with the phase encoding
pulses. This creates the constant required
phase modulation between the
simultaneously excited slices.
Every third blipped pulse is of larger
magnitude and opposite polarity serving
to rewind the net phase and normalize
the gradient moment. The end result is
"controlled" aliasing over FOV/3.

11. Compressed Sensing
• Compressed sensing (CS)​refers to a group of methods
for accelerated MR data acquisition based on semi-
random, incomplete sampling of k-space.
• A final image is created through an iterative optimization
process using non-Fourier transformation and
thresholding of intermediately reconstructed images.
• CS methods appear especially promising for MRA, 3D/4D
MRI, dynamic contrast enhanced (DCE) studies, and
cardiac MR imaging applications.

12. Cine cardiac study using compressed sensing with acceleration
factors up to 15-fold. (Adapted from Abascal et al under CC BY)

13. • Most readers will be aware that file size of photos can be
reduced as much as 10:1 while maintaining good quality
using a format like jpeg.
• Such compression is possible because photographic (as well
as MR) images contain many pixels lacking unique
information content (e.g., those in the background with zero
intensity and those with nearly the same values as their
neighbors).

14. • why not save time up front and only collect only
the "essential" components of the MR signal
rather than all k-space data?
• three factors are required:
• incoherent undersampling, sparsifying
transformation, and iterative reconstruction.

15. • Sparsity reflects the extent to which an imaging matrix is filled with
meaningful data.
• Some matrices are intrinsically sparse, such as those associated with
MRAs, containing mostly zeros (corresponding to black/nonvascular
regions).
• Images of solid organs may not appear sparse in their conventional
display, but can be mathematically transformed/decomposed into
representations having relatively sparse components.
• The application of so-called sparsifying transforms (such as wavelets)
are an essential feature of CS reconstruction methods described
below.

17. Use and Limitations of CS
• CS methods are only now just beginning to be offered as
commercial products: Compressed
Sensing (Siemens), Compressed SENSE (Philips),
and HyperSense (GE).
• Expect to see many more in the future. Limitations include
longer reconstruction times (sometimes requiring offline
postprocessing) and CS-related artifacts (blurring of fine
detail and global ringing).

18. Amide Proton Transfer (APT) Imaging
• Amide Proton Transfer (APT) imaging is a relatively
new method using off-resonance saturation pulses to
detect mobile proteins and peptides in biological
tissues.
• The premise underlying its potential utility is that
certain diseases such as malignant tumors with high
cellularity and processes that denature proteins (like
multiple sclerosis) may exhibit elevated APT values.

20. • APT, like Magnetization Transfer (MT) imaging, is a subset of a more
general class of methods known as Chemical Exchange Saturation
Techniques (CEST).
• The basic concept is that proteins and other macromolecules can absorb RF
energy at frequencies applied a few hundred to a few thousand Hz away
from the pure water resonance.
• When such an "off-resonance" RF-pulse is applied, energy absorbed by
macromolecules is then transferred via chemical exchange and dipolar
interactions to the water resonance, lowering its signal.
• The degree of signal suppression will be greatest for tissues with high
protein content and high rates of water-macromolecular interactions.

21. • To isolate the effect of amide proton transfer from that of other
background macromolecules, the APT pulse sequence uses 8-10
RF-pulses of slightly different off-resonance frequencies
clustered near both +3.5 ppm (at δ ≈ 8.2) and −3.5 ppm (at δ ≈
1.2) symmetrically on each side of the water resonance.
• After correction for Bo nonuniformities and measurement of
baseline signal (So) in the absence of RF-pulses, APT suppression
is calculated using subtraction on a pixel-by-pixel basis.
• Such APT values in tissues typically range between 0 and 5% and
can be displayed as color maps overlaid on conventional images.

22. An amide functional group is defined as a nitrogen (N)
attached to a carbonyl (C=O) group. The R's may be
hydrogens (H) or an alkane.

23. Diffusion Tensor Imaging
• Biological tissues are highly anisotropic,
meaning that their diffusion rates are not the
same in every direction.
• For routine DW imaging we often ignore this
complexity and reduce diffusion to a single
average value, the apparent diffusion
coefficient (ADC), but this is overly simplistic.

24. • A superior method to model diffusion in complex
materials is to use the diffusion tensor, a [3 x 3] array of
numbers corresponding to diffusion rates in each
combination of directions.
• The three diagonal elements (Dxx, Dyy, Dzz) represent
diffusion coefficients measured along each of the
principal (x-, y- and z-) laboratory axes.
• The six off-diagonal terms (Dxy, Dyz, etc) reflect reflect
the correlation of random motions between each pair of
principal directions.

26. • For the special case of perfect isotropic diffusion (such as seen in pure
liquids), the off-diagonal elements are all zero.
• The diagonal elements are all the same and equal the single diffusion
coefficient, D, for the isotropic material (i.e., Dxx = Dyy = Dzz = D).
• For anisotropic diffusion, however, the diagonal elements are unequal
and the off-diagonal elements cannot be ignored.
• An additional complicating factor is that the value of each tensor
element depends upon the frame of reference in which it is measured.

27. • typically begin in the so-called laboratory (x-y-z) frame, which for clinical
MRI is typically aligned with the patient's body and main magnetic field.
• Gradients are applied in different directions and several sets of raw data
(source) images are obtained.
• After some filtering and other mathematical corrections, linear
regression techniques are applied to the data to create estimates for
each tensor component.
• Because x→y and y→x diffusivities should be the same, mirror-image
off-diagonal elements are equal (Dxy = Dyx, Dyz = Dzy, and Dxz = Dzx).
• This means the diffusion tensor matrix is symmetric with only 6 unique
elements. To estimate all of them we need a minimum of 7
measurements: one baseline (b0) and 6 source data sets.

28. • The values we calculate for each tensor
component (such as Dxx or Dxy), however, are
not unique, being dependent on the (x-y-
z) frame of reference chosen for
measurement.
• Had we selected a different coordinate
system (x'-y'-z') not aligned with the patient
but at some arbitrary angle, the calculated
values (Dx'x' or Dx'y') would have been
completely different.

29. • This optimal coordinate system is based upon
the diffusion ellipsoid, whose main axis is parallel
to the principal diffusion direction within a voxel.
• This principal axis often corresponds to anatomic
features such as white matter tracts or fascial
planes.

30. • The major and minor axes of the diffusion ellipsoid are defined by
thee orthogonal unit vectors (ε1, ε2, and ε3) known
as eigenvectors.
• The length of each eigenvector (εi) is multiplied by a factor λi,
called the eigenvalue.
• The eigenvalues of the ellipsoid are proportional to Einstein's root
mean squared diffusion displacement in each direction.
• By convention, eigenvalues are labeled in descending order of
magnitude (λ1 ≥ λ2 ≥ λ3).

32. – An additional benefit to using the diffusion
ellipsoid is that in this frame of reference, the off-
diagonal elements disappear.
– The set of eigenvalues define a matrix with only 3
diagonal elements denoted by the
symbol Λ ("capital lambda") that appears in many
advanced treatises about diffusion tensors.
– As a bonus, you may wish to watch this math
professor explaining tensor and vectors. It's pretty
good and only 12 minutes long.

33. Color-coded diffusion ellipsoids in the brain,
The reddish boomerang-shaped structure is
the posterior corpus callosum just behind the
black lateral ventricles.

34. MP-RAGE v MP2RAGE
• MP-RAGE has become the dominant sequence for 3D-T1-
weighted imaging especially on Siemens scanners.
• MP-RAGE consists of a non-selective (180º) inversion
pulse followed by a collection of rapidly acquired gradient
echoes obtained at short TE's (2-4 ms) and small flip
angles α (5- 12º).
• A medium inversion time (TI) of 600-900 ms and long
repetition time (TR) of approximately 2000 ms are typical.

36. • The standard Siemens implementation of MP-
RAGE is as a 3DFT technique.
• Following the non-selective 180º pulse, Mz is
inverted and allowed to regrow via T1 relaxation
mechanisms over inversion time interval (TI), at
which time signal is acquired by using a spoiled
GRE (“Turbo-FLASH”) with low flip angle.

37. • Sequential ordering is typically used for both in-plane (Gy) and
slice-select (Gz) phase encoding.
• All the (Gz) phase-encoding lines are collected following the
inversion pulse, then repeated for the next value of the
Gy gradient, and so forth.
• Because the number of partitions (Gz phase steps) is usually
smaller than the number of Gy steps, this strategy results in the
shortest scan time.
• Image contrast is determined by the effective inversion time
(TIeff), which is the time between the 180º-pulse and the
central Gz phase steps (i.e., kz near 0).

38. • MP-RAGE contrast is determined strongly by T1-contrast, but
spin density and T2* effects are also present.
• Use of high bandwidth and short data collection period
reduces susceptibility effects including eddy currents
associated with metal.
• It is widely used in isotropic mode for T1-weighted brain
imaging.

40. • The MP2RAGE sequence, by comparison, uses two Turbo-
FLASH GRE readouts between each inversion pulse. The first
inversion time (TI1) is typically about 700 ms, producing a T1-
weighted image with the gray matter nulled at the center
of k-space.
• The second inversion time (TI2) is long (~2500 ms), which
combined with small flip angles (4-5º) and long TR (~5000
ms), produces spin-density-weighted contrast.
• By combining image data from the 1st and 2nd readouts, T2*
and B1 inhomogeneity effects can be largely cancelled out,
resulting in a strongly T1-weighted image with superior gray
matter to white matter contrast than available by MP-RAGE.

41. • Schematic of the MP2RAGE sequence
• Unlike MP-RAGE data acquisition occurs in two
separate readouts at different inversion times (TI1 and
TI2).
• Each TI is defined as the time between the middle of
the inversion pulse and the central echo of k-space.

42. Double Inversion Recovery
• Double Inversion Recovery (DIR) is an
inversion recovery variant that uses not one,
but two nonselective 180°-inverting pulses. T
• he time associated with each are commonly
denoted TI-1 and TI-2.

43. Double IR sequence suppressing CSF and white
matter. TR=11000, TE=30, TI-1=3400, TI-2=325.

44. • To date, most of the applications of this type
of DIR technique has been for brain imaging,
especially for detection of multiple sclerosis
plaques and lesions of the cerebral cortex.
• Here the first 180°-pulse suppresses CSF and
the second suppresses white matter.

45. • A differently structured DIR technique producing "black blood" is
commonly used in cardiovascular MRI.
• In this method, two 180°-pulses are applied very close together in
time.
• The first 180°-pulse is nonselective, meaning that it inverts the
magnetization for all slices within the imaging volume. The
second 180°-pulse, following immediately on the heels of the
first 180°-pulse, is slice selective, meaning it returns the magnetization
of all tissues in that slice only back to the +z-direction.
• Thus the myocardium and other relatively stationary tissues have their
signals preserved, but the blood flowing from adjacent slices has an
inverted magnetization. The TI is adjusted to null the signal from
inflowing blood, which appears "black" on magnitude reconstructed IR
images.

46. • Although two 180°-pulses are used, there is really only one
material (blood) being inverted and hence only one TI value
(measured from the time of the first inverting pulse). Thus this
sequence in many ways behaves more like a single IR sequence
than the DIR for brain imaging described above.
• It is possible to use a third (or even fourth) 180°-pulse in
conjunction with a black blood DIR technique. This third pulse is
commonly used to suppress pericardial fat, producing a triple
inversion recovery (TIR) sequence, that is a combination of STIR
plus black blood DIR.

47. THANK YOU