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MR Image Formation. FMRI Graduate Course (NBIO 381, PSY 362) Dr. Scott Huettel, Course Director . Introductory Exercise. Write down the major steps involved in the generation of MR signal Just write an outline, not an essay Note what scanner component contributes to each step.

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mr image formation

MR Image Formation

FMRI Graduate Course (NBIO 381, PSY 362)

Dr. Scott Huettel, Course Director

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

introductory exercise
Introductory Exercise
  • Write down the major steps involved in the generation of MR signal
    • Just write an outline, not an essay
    • Note what scanner component contributes to each step

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

generation of mr signal
Generation of MR Signal

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

slide4

T1

T2

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

relaxation times and rates
Relaxation Times and Rates
  • Net magnetization changes in an exponential fashion
    • Constant rate (R) for a given tissue type in a given magnetic field
    • R = 1/T, leading to equations like e–Rt
  • T1 (recovery): Relaxation of Mback to alignment with B0
    • Usually 500-1000 ms in the brain (lengthens with bigger B0)
  • T2 (decay): Loss of transverse magnetization over a microscopic region ( 5-10 micron size)
    • Usually 50-100 ms in the brain (shortens with bigger B0)
  • T2*: Overall decay of the observable RF signal over a macroscopic region (millimeter size)
    • Usually about half of T2 in the brain (i.e., faster relaxation)

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

t 1 recovery
T1 Recovery

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

t 2 decay
T2 Decay

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

t 1 and t 2 parameters
T1 and T2 parameters

By selecting appropriate pulse sequence parameters (Week 4’s lecture), images can be made sensitive to tissue differences in T1, T2, or a combination.

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

slide9

I

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

slide10
FMRI – Week 3 – Image Formation Scott Huettel, Duke University
gradients change the strength not direction of the magnetic field
Gradients change the Strength, not Direction of the Magnetic Field

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

parts of 2d image formation
Parts of 2D Image Formation
  • Slice selection
    • Linear z-gradient
    • Tailored excitation pulse
  • Spatial encoding within the slice
    • Frequency encoding
    • Phase encoding

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

slice selection
Slice Selection

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

slide14
FMRI – Week 3 – Image Formation Scott Huettel, Duke University
linear z gradient
Linear z-gradient

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

why can t we just use an excitation pulse of a single frequency
Why can’t we just use an excitation pulse of a single frequency?

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

selecting a band of frequencies
Selecting a Band of Frequencies

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

choosing a slice
Choosing a Slice

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

changing slice thickness
Changing Slice Thickness

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

changing slice location
Changing Slice Location

(Note: manipulating gradient is simpler than changing slice bandwidth.)

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

interleaved slice acquisition

13

12

Interleaved Slice Acquisition

3

2

1

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

slide22
FMRI – Week 3 – Image Formation Scott Huettel, Duke University
spatial encoding
Spatial Encoding

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

how not to do spatial encoding
How not to do spatial encoding…

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

a better approach
… a better approach

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

temporal signal combination of frequencies
Temporal Signal = Combination of Frequencies

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

effects of gradients on phase
Effects of Gradients on Phase

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

core concept k space coordinate integral of gradient waveform
Core Concept:k-space coordinate = Integral of Gradient Waveform

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

slide29

k-space

Image space

ky

y

kx

x

Acquired Data

Final Image

Fourier Transform

Inverse Fourier Transform

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

spatial image combination of spatial frequencies
Spatial Image = Combination of Spatial Frequencies

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

k space
k Space

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

image space and k space
Image space and k space

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

parts of k space
Parts of k space

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

slide34

So, we know that two gradients are necessary for encoding information in a two-dimensional image?

What would happen if we turned on both gradients simultaneously?

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

frequency encoding
Frequency Encoding
  • During readout (or data acquisition, DAQ)
  • Uses gradient perpendicular to slice-selection gradient
  • Signal is sampled & digitized about once every few microseconds
    • Readout window ranges from 5–100 milliseconds
    • Why not longer than this?
  • Fourier transform converts signal S(t) into frequency components S(f)

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

phase encoding
Phase Encoding
  • Apply a gradient perpendicular to both slice and frequency gradients
  • The phase of Mxy (its angle in the xy-plane) signal depends on that gradient
  • Fourier transform measures phase  of each S(f) component of S(t)
  • By collecting data with many different amounts of phase encoding strength, we can assign each S(f) to spatial locations in 3D

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

slide37
FMRI – Week 3 – Image Formation Scott Huettel, Duke University
slide38

Echo-Planar Imaging (EPI)

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

slide39

Sampling in k-space

K

Dk

FOV

FOV = 1/Dk, Dx = 1/K

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

problems in image formation
Problems in Image Formation

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

magnetic field inhomogeneity
Magnetic Field Inhomogeneity

FMRI – Week 3 – Image Formation Scott Huettel, Duke University

gradient problems
Gradient Problems

FMRI – Week 3 – Image Formation Scott Huettel, Duke University