![Page 1: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/1.jpg)
Advanced Topics and Diffusion MRI
Modified by Mark Chiew ([email protected])
Slides available at:http://users.fmrib.ox.ac.uk/~mchiew/teaching/
Slides originally by Karla Miller, FMRIB Centre
![Page 2: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/2.jpg)
MRI Physics
★ Spin vs. gradient echo (T2 & T2*)★ Fast imaging & artefacts★ Diffusion MRI
✦ Diffusion weighting✦ Acquisition techniques✦ Tradeoffs & complications
![Page 3: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/3.jpg)
Phase
Magnitude (length or st
rength)
Phase (orientation or direction)
![Page 4: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/4.jpg)
Voxel Volume Net Magnetization (sum)
Net Magnetization (in-phase)
![Page 5: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/5.jpg)
B0
Precession (in-phase)
courtesy of William Overall
ω0 = γ(B0+ΔB)main field offset (gradients or errors)
rotational frequency
∆B+
![Page 6: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/6.jpg)
Magnetic field imperfections: T2* decay
Always some local imperfections in magnetic field = range of precession frequencies in a voxel
Over time, spins lose alignment (“dephase”)
![Page 7: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/7.jpg)
Voxel Volume Net Magnetization (sum)
Net Magnetization (in-phase)
![Page 8: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/8.jpg)
Net Magnetization (dephasing)Voxel Volume Net Magnetization (sum)
![Page 9: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/9.jpg)
Voxel Volume Net Magnetization (sum)
Net Magnetization (dephased)
![Page 10: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/10.jpg)
Simple Voxel Model Voxel Signal
Dephasing
![Page 11: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/11.jpg)
Refocusing (180o RF pulse) with no dephasing
90°180°
The 180º RF pulse complete “flips” the magnetisation around an axis
![Page 12: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/12.jpg)
Spin echo: The time at which the spins are re-aligned Refocusing pulse: 180o pulse that creates a spin echo
90°180°
Refocusing (180o RF pulse) with dephasing
![Page 13: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/13.jpg)
Simple Voxel Model Voxel Signal
Dephasing
![Page 14: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/14.jpg)
180º Refocusing Pulse!
![Page 15: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/15.jpg)
Rephasing After Spin Echo
Simple Voxel Model Voxel Signal
![Page 16: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/16.jpg)
Refocusing (180° pulse) spin echo
Spin echo: The time at which the spins are re-aligned Refocusing pulse: 180o pulse that creates a spin echo
time
sign
al
90°180°
![Page 17: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/17.jpg)
Gradient echo vs. spin echo
GRE signal(sometimes called a FreeInduction Decay = FID)
SE signal(signal decays, then
comes back as “echo”)
time
sign
al
90°
time
sign
al
90°180°
pure signal decay decay with partial recovery
(i.e. no spin-echo)
![Page 18: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/18.jpg)
T2 vs T2* Relaxation
Spin echo refocuses part of the signal decay– T2* includes parts that can be refocused– Without refocusing, signal will have T2* contrast
time
sign
al
SE signalT2* decay (imperfect field)T2 decay (perfect field)
Even spin echo signal experiences some decay– T2 refers to signal decay that cannot be refocused– With refocusing, signal will have T2 contrast
![Page 19: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/19.jpg)
GRE refers to a sequence with: excitation-delay-readoutAny kind of readout can be used (linescan, EPI, spiral…)Image signal depends on TE, but not on readout method!
time
sign
al
TE
ACQ
time
sign
al
TE
ACQ
What defines a gradient echo sequence?
![Page 20: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/20.jpg)
What defines a spin echo sequence?
SE refers to a sequence with: excitation-refocus-readoutThe key is the formation of an echo (signal peak)!Like GRE, any kind of readout can be used
time
sign
al
timesi
gnal
TE TE
`
ACQACQ
![Page 21: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/21.jpg)
MRI Physics
★ Spin vs. gradient echo★ Fast imaging & artefacts★ Diffusion MRI
✦ Diffusion weighting✦ Acquisition techniques✦ Tradeoffs & complications
![Page 22: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/22.jpg)
Echo-planar Imaging (EPI) Acquisition
Acquire all of k-space in a “single shot”Used for FMRI, diffusion imaging
![Page 23: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/23.jpg)
EPI gradients: Approximation
Gy
Gx
Gy
Gx
Gy
Gx
Gy
Gx
Simplify gradient sequence to understand source of image distortions...
readout/frequency encode axis
phase encode axis
![Page 24: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/24.jpg)
EPI gradients: Approximation
Gy
Gx
Gy
Gx
Gy
Gx
Gy
Gx
Simplify gradient sequence to understand source of image distortions...
readout/frequency encode axis : strong axis
phase encode axis : weak axis
![Page 25: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/25.jpg)
EPI gradients: Approximation
Gy
Gx
Gy
Gx
Gy
Gx
Gy
Gx
Simplify gradient sequence to understand source of image distortions...
readout/frequency encode axis : fast axis
phase encode axis : slow axis
![Page 26: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/26.jpg)
kslow
kfast
slowfast
field map fast gradient net (fast)
EPI undistorted along “fast” direction (frequency encode)
+ =
Field map errors have negligible effect on fast gradient
![Page 27: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/27.jpg)
kslow
kfast
slowfast
field map slow gradient net (fast)
EPI distorted along “slow” direction (phase encode)
+ =
Field map errors dominate slow gradient, signal is misplaced
![Page 28: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/28.jpg)
EPI distortion
Echo spacing: time between acquisition of adjacent lines (“speed” along slow axis”)Long echo spacing = worse distortion
EPI trajectoryLong inter-echospacing
Short inter-echospacing
![Page 29: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/29.jpg)
Coil sensitivity encodes spatial information Skip lines in k-space, reconstruction fills in missing lines based on coil sensitivityAllows “acceleration” of k-space acquisition
Parallel imaging (SENSE, GRAPPA, etc)
![Page 30: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/30.jpg)
Parallel imaging
EPI trajectory
Parallel imaging (SENSE, GRAPPA, etc) can reconstruct complete image from subset of k-space lines
No ParallelImaging
ParallelImaging (2x)
Current vendor coils enable 2-4x acceleration
Enables “accelerated” acquisition with lower distortion
![Page 31: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/31.jpg)
Many possible trajectories through k-space…
![Page 32: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/32.jpg)
EPIdistortion
& ghosting
Spiralblurring
& streaking
Cartesian vs Non-Cartesian: Image artifacts
![Page 33: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/33.jpg)
time
tissue 1
Single-shot acquisition takes 30-40 ms, so T2/T2* contrast varies during acquisition... what is contrast of image?
Rule of thumb: contrast of image reflects time at which central k-space was acquired (“effective” TE)
tissue 2
Cartesian vs Non-Cartesian: Contrast
![Page 34: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/34.jpg)
MRI Physics
★ Spin vs. gradient echo★ Fast imaging & artefacts★ Diffusion MRI
✦ Diffusion weighting✦ Acquisition techniques✦ Tradeoffs & complications
![Page 35: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/35.jpg)
What is diffusion?
![Page 36: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/36.jpg)
What is diffusion?
Random motion of particles due to thermal energyWater molecules collide and experience net displacement
Displacement described by diffusion coefficient (D)Normally, diffusion is isotropic (equal in all directions)
√2DT
![Page 37: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/37.jpg)
Why is diffusion interesting?
Diffusion is restricted by tissue boundaries, membranes, etcMarker for tissue microstructure (healthy and pathology)
Unrestricted Tissue boundaries
![Page 38: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/38.jpg)
Diffusion anisotropy in white matter
Water can diffuse more freely along white matter fibres than across them
![Page 39: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/39.jpg)
Diffusion anisotropy in white matter
Directionality of diffusion tells us about fibre integrity/structure and orientation
Diffusion in white matter fibres is “anisotropic”
![Page 40: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/40.jpg)
The diffusion tensor
Displacement due to diffusion is approximately ellipsoidalEigenvectors = axes of ellipsoid (direction of fibres)Eigenvalues = size of axes (strength of diffusion)
![Page 41: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/41.jpg)
The diffusion tensor: Useful quantities
Principal diffusion direction (PDD): what direction is greatest diffusion along? Info about fibre orientationFractional anisotropy (FA): how elongated is the ellipsoid? Info about fibre integrityMean diffusivity (MD): Info about tissue integrity
![Page 42: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/42.jpg)
Diffusion tensor imaging
Principal diffusion
direction (PDD)Fractional
anisotropy (FA)Mean
diffusivity (MD)
At each voxel, fit the diffusion tensor modelCan then calculate MD, FA, PDD from fitted parameters
![Page 43: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/43.jpg)
Mean diffusivity (MD)
Mean diffusion coefficient across all directionsCorrelate of tissue integrity (white and gray matter)Example: MD is altered in acute and chronic stroke
Control MD Acute Stroke
![Page 44: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/44.jpg)
Fractional Anisotropy (FA)
Inequality of diffusion coefficient across different directionsHigh in regions where diffusion is most directionalRelates to integrity of white matter fibre bundles
FA=0.8
FA=0
![Page 45: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/45.jpg)
Principal diffusion direction (PDD)
Direction along which greatest diffusion occursRelates to direction of fibre orientationsTypically, will use this as starting point for fibre tracking
![Page 46: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/46.jpg)
Diffusion tractography
Jones et al
Follow PDD to trace white matter fibers (“tractography”)
![Page 47: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/47.jpg)
MRI Physics
★ Spin vs. gradient echo★ Fast imaging & artefacts★ Diffusion MRI
✦ Diffusion weighting✦ Acquisition techniques✦ Tradeoffs & complications
![Page 48: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/48.jpg)
Spin Echo
90°180°
![Page 49: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/49.jpg)
Diffusion-weighted spin echo
![Page 50: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/50.jpg)
Case 1:No diffusion
![Page 51: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/51.jpg)
Case 2:Diffusion
![Page 52: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/52.jpg)
+5
-3
No motion (diffusion)No net dephasingNo contrast!
0
0
contrast
-5
+3
Posi
tion
![Page 53: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/53.jpg)
+5
-3
+ motion (diffusion)+ net dephasing+ diffusion contrast!
-2
-1
contrastPo
sitio
n
-3
+4
![Page 54: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/54.jpg)
No diffusion
Diffusion
If diffusion is present, gradients cause a drop in signal.
Greater Diffusion = Less Signal
Diffusion contrast
![Page 55: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/55.jpg)
Δ
+A+A
If diffusion is present, gradients cause a drop in signal.
Greater Diffusion = Less Signal
Diffusion contrast
b ∝ A2∆
S = S0e−bD
diffusioncoefficient
diffusionweighting
![Page 56: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/56.jpg)
If diffusion is present, gradients cause a drop in signal.
Greater Diffusion = Less Signal
Diffusion contrast
![Page 57: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/57.jpg)
Diffusion-weighted imaging
Directional encodingb=0
⊕
Fittedparameter
maps
![Page 58: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/58.jpg)
Spin Echo
Most commonly used sequence in diffusion imaging• Spin echo reduces image artefacts• Efficient diffusion preparation• Long TE ⇒ strong T2 decay
TE
![Page 59: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/59.jpg)
Gradient Echo
Spin Echo
Stimulated Echo
Hyper Echo
Steady State
![Page 60: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/60.jpg)
MRI Physics
★ Spin vs. gradient echo★ Fast imaging & artefacts★ Diffusion MRI
✦ Diffusion weighting✦ Acquisition techniques✦ Tradeoffs & complications
![Page 61: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/61.jpg)
Acquiring the image
Theoretically, any acquisition can be used• linescan • rapid scan (EPI)• etc...
In practice, motion sensitivity dictates what is possible
![Page 62: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/62.jpg)
Motion in DWI
Diffusion gradients encode tiny displacementSubject motion is also accidentally encodedImage artefacts if we try to combine data from multiple excitations (different motion)
Linescan diffusion image
![Page 63: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/63.jpg)
Can motion be avoided?
Subject restraints can reduce bulk motion, but......in the brain, there is significant non-rigid motion from cardiac pulsatilitycardiac gating helps, but brain is never very still!
blood
tissue
![Page 64: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/64.jpg)
b=1000 s/mm2
Single-shot echo-planar imaging (EPI)
Single-shot imaging freezes motion
magnetization k-spaceEPI acquisition
Most common method is echo-planar imaging (EPI)
Images have serious distortion and limited resolution
![Page 65: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/65.jpg)
Typical* Diffusion Imaging Parameters
Parameter Value Relevant points
TE(echo time) 100 ms Limited by b-value
Matrix size / Resolution
128x128 / 2 mm
Limited by distortion, SNR
Number of directions 6-60 Lower limit: tensor model
Upper limit: scan time
b-value 1000 s/mm2 Larger b = more contrast Smaller b = more signal
* Typical, not fixed!!
![Page 66: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/66.jpg)
MRI Physics
★ Spin vs. gradient echo★ Fast imaging & artefacts★ Diffusion MRI
✦ Diffusion weighting✦ Acquisition techniques✦ Tradeoffs & complications
![Page 67: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/67.jpg)
signal
Tradeoff: diffusion weighting vs TE
time
long TE = low signal
TE
![Page 68: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/68.jpg)
Eddy Currents
Diffusion gradients create large eddy currents, which persist into acquisition windowDistort the k-space trajectory, casing shears/scaling of images
effective gradient fields
Eddy currents “resist” gradient field changes
![Page 69: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/69.jpg)
Eddy Currents
Fractional Anisotropy(“variance”)
Diffusion-weighteddirections
![Page 70: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/70.jpg)
Twice Refocused Spin Echo
90o
length TE
180o 180o
EPI Readout
time
+ve
-ve
Eddy Currents
Reese MRM 2003
![Page 71: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/71.jpg)
Signal dependence: b-value
Signal is not a mono-exponential decay with b-value!“Apparent diffusion coefficient” (ADC)
Theory Measurement
S = S0e−bD
Beaulieu 2002
![Page 72: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/72.jpg)
Signal dependence: Orientation
b=100b=2500
Signal DisplacementEllipsoid
![Page 73: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/73.jpg)
More complicated models: Crossing fiber populations
![Page 74: Advanced Topics and Diffusion MRIfsl.fmrib.ox.ac.uk/fslcourse/physics+apps/2018/fsl_diffusion.pdf · MRI Physics ★ Spin vs. gradient ... • Efficient diffusion preparation •](https://reader034.vdocuments.site/reader034/viewer/2022052006/6019de70ca74a274ee33a32e/html5/thumbnails/74.jpg)
More complicated models: Crossing fiber populations