– Ultrasound motion imaging – Simulating ultrasound images...– Ultrasound motion imaging –...

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– Ultrasound motion imaging –Simulating ultrasound images

a very brief introduction

byDamien Garcia

INSERM researcher, CREATIS, Lyon, France

[email protected]

April 22, 2019

Disclaimer: The views expressed in this course are those of the author and do not necessarily reflect the multiple positions of the ultrasound community. The examples may contain errors and can carry an implied judgement due to author’s preference for one side of an issue over another.Be critical and take a step back while reading this document!

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TOC

why using simulations? MUST: Matlab UltraSound Toolbox SIMUS: what’s inside?

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why doing simulations?

Before in vitro and in vivo, use computational ultrasound imaging to:

1. test your ultrasound sequences (PW, DW, MLT…)2. optimize your algorithms3. explore multiple configurations

4. compare with others (e.g. challenges)

Computational ultrasound imaging must ideally be:

1. easy to program2. realistic3. easy to parallelize in the 3-D era

The “optimal” methodology (if possible): in silico, in vitro & in vivo

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computational ultrasound imaging

• Computational ultrasound imaging is increasingly used

• Jørgen Jensen, “Field: A program for simulating ultrasound systems.” 1996

2000 2004 2008 2012 2016

50

100

150

200

2018

citations

source: Field II Simulation Program(http://field-ii.dk)

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mesh-based vs. mesh-free

Grid-based Mesh-free

k-Wave (www.k-wave.org) Field II (field-ii.dk)

Finite difference method Weakly backscattering particles

LAGRANGIAN

Each particle possesses and transports its physical properties

EULERIAN

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MUST: Matlab UltraSound Toolbox

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MUST & SIMUS

Matlab UltraSound Toolbox

1. a Matlab toolbox for ultrasound2. demodulation, beamforming3. color Doppler, vector Doppler

4. contains PFIELD and SIMUS

SIMulations for UltraSound

1. PFIELD: simulate acoustic pressure fields2. SIMUS: simulate transmit and receive in ultrasound imaging3. parallelizable

During the hands-on sessions, you will use SIMUS from the MUST

• MUST = Matlab UltraSound Toolbox• SIMUS = SIMulations for UltraSound

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acoustic far-field pattern

Far-field pattern

30

210

60

240

90o

270

120

300

150

330

180 0

0.2

0.4

0.6

0.8

1

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pressure fields with PFIELD

Focused Divergent MLT (“multi-line transmit”)

2 cm

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transmit focusing

*

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pressure fields with PFIELD

2 cm

MLT – Multi-Line Transmit3 simultaneous focused transmits

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source: doi:10.13140/RG.2.1.3563.2486

Specular scattering Diffuse (Rayleigh) scattering

scattering

ONLY the diffuse scattering is considered in SIMUS! (as in FieldII)

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Scatterers

Probe

basic principle in SIMUS

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1 cm 1 8 15 22 29 36 43 50 57 64element #

10

20

30

40

50

60

70

time

(μs) after

beamforming

RF signals with SIMUS

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B-mode with SIMUS

ww

w.yale.edu/im

aging/echo_atlas/views/apical_2c.htm

l

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color Doppler with SIMUS

1

2

3

plane wave

propagating downward

128 elements, 5 MHz

(cm

)

17 cm/s

24 cm/s

10 cm/s

source: Shahriari and Garcia.Phys Med Biol, 2018;63:205011.

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color Doppler with SIMUS

source: Shahriari and Garcia.Phys Med Biol, 2018;63:205011.

Doppler

0

17 cm/s

24 cm/s

0 0.5 10

0.2

0.4

(s)

(m/s)

vector Doppler reference (SPH)

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linear acoustic wave equation

Assumptions

1. no dissipative effects (no viscosity, no heat conduction)2. homogeneous, isotropic, elastic medium3. low-amplitude perturbations (small particle velocities, small

fluctuations of pressure and density)

4. ⇒ linearization

𝜕𝜕2𝑝𝑝𝜕𝜕𝑥𝑥2

+𝜕𝜕2𝑝𝑝𝜕𝜕𝑧𝑧2

−1𝑐𝑐2𝜕𝜕2𝑝𝑝𝜕𝜕𝑡𝑡2

= 0

�𝑃𝑃 = ℱ 𝑝𝑝 ⇒𝜕𝜕2 �𝑃𝑃𝜕𝜕𝑥𝑥2

+𝜕𝜕2 �𝑃𝑃𝜕𝜕𝑧𝑧2

+𝜔𝜔2

𝑐𝑐2�𝑃𝑃 = 0

2D acoustic wave equation:

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acoustic field of a 1-D element

1-D element model

1. linear piston in a rigid baffle2. piston vibrating with a uniform normal velocity3. high frequency; far field

4. ⇒ 𝑘𝑘𝑘𝑘 ≫ 1; 𝑘𝑘 ≫ ⁄𝜋𝜋𝑏𝑏2 𝜆𝜆

𝒑𝒑 𝒙𝒙, 𝒛𝒛,𝝎𝝎, 𝒕𝒕

= 𝝆𝝆𝝆𝝆𝒗𝒗𝟎𝟎 𝝎𝝎𝟐𝟐𝒊𝒊𝒊𝒊𝒌𝒌𝒌𝒌 𝑫𝑫𝒌𝒌 𝜽𝜽,𝒌𝒌

𝒆𝒆𝒊𝒊𝒌𝒌𝒊𝒊

𝒌𝒌𝒊𝒊𝒆𝒆−𝒊𝒊𝝎𝝎𝒕𝒕

2𝑏𝑏

𝜃𝜃

𝑘𝑘

𝑘𝑘: wavenumber𝜆𝜆: wavelength

𝑣𝑣0

𝐷𝐷𝑏𝑏 𝜃𝜃, 𝑘𝑘 = sinc 𝑘𝑘𝑏𝑏 sin𝜃𝜃directivity of the element:

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acoustic field of a 1-D array

1-D array

The acoustic field of a 1-D array is the sum of the acoustic fields generated by the single elements

(linear acoustics)

𝒑𝒑 𝒙𝒙, 𝒛𝒛,𝝎𝝎, 𝒕𝒕

= 𝝆𝝆𝝆𝝆𝒗𝒗𝟎𝟎 𝝎𝝎 �𝒏𝒏=𝟏𝟏

𝑵𝑵

𝑾𝑾𝒏𝒏𝒆𝒆𝒊𝒊𝝎𝝎∆𝝉𝝉𝒏𝒏𝟐𝟐𝒊𝒊𝒊𝒊𝒌𝒌𝒌𝒌 𝑫𝑫𝒌𝒌 𝜽𝜽𝒏𝒏,𝒌𝒌

𝒆𝒆𝒊𝒊𝒌𝒌𝒊𝒊𝒏𝒏

𝒌𝒌𝒊𝒊𝒏𝒏𝒆𝒆−𝒊𝒊𝝎𝝎𝒕𝒕

𝜃𝜃1𝑘𝑘1

𝜃𝜃𝑁𝑁𝑘𝑘𝑁𝑁

#1 #2 #3 #N

𝑊𝑊: apodizationΔ𝜏𝜏: delay

#n

𝑘𝑘𝑛𝑛

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receive signals

echo signals

1. The acoustic scatterers become individual monopole point sources when the incident wave reaches them (cylindrical waves in 2-D; spherical waves in 3-D)

2. The scatterers do not acoustically interact with each other (single scattering)

𝒑𝒑𝒒𝒒 𝝎𝝎, 𝒕𝒕

= 𝝆𝝆𝝆𝝆 𝒌𝒌𝒌𝒌𝒗𝒗𝟎𝟎 𝝎𝝎 �𝒎𝒎=𝟏𝟏

# 𝐨𝐨𝐨𝐨 𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩𝐩

𝐁𝐁𝐁𝐁𝐁𝐁𝒎𝒎 �𝒏𝒏=𝟏𝟏

𝑵𝑵

𝑾𝑾𝒏𝒏𝒆𝒆𝒊𝒊𝝎𝝎∆𝝉𝝉𝒏𝒏 𝑫𝑫𝒌𝒌 𝜽𝜽𝒏𝒏𝒎𝒎,𝒌𝒌𝒆𝒆𝒊𝒊𝒌𝒌𝒊𝒊𝒏𝒏𝒎𝒎

⁄𝒊𝒊𝒏𝒏𝒎𝒎 𝒌𝒌𝑫𝑫𝒌𝒌 𝜽𝜽𝒒𝒒𝒎𝒎,𝒌𝒌

𝒆𝒆𝒊𝒊𝒌𝒌𝒊𝒊𝒒𝒒𝒎𝒎

⁄𝒊𝒊𝒒𝒒𝒎𝒎 𝒌𝒌𝒆𝒆−𝒊𝒊𝝎𝝎𝒕𝒕

#q

Tx Rx

𝐵𝐵𝐵𝐵𝐵𝐵:backscattering coefficient

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Field II vs. SIMUS

Time-based frequency-based

Matlab m + mex files Matlab fully open codes

included in MUST

SIMUS

presently, only in 2-D

Field II

1

GENERATION OF REALISTIC SYNTHETIC ULTRASOUND IMAGES

A synthetic approach based on physical simulators

Olivier Bernard


University of Lyon, France

2

Cardiovascular diseases


Cardiac imaging for diagnosis

►Cardiac imaging

● Assessment of cardiac function (diagnosis / patient follow-up )

● Different modalities for different needs

Most common modality (safe, cheap, portable)

More advanced examination (better image contrast)

Gold standard for motion quantification

US Cine MR Tagged MR

3

Cardiovascular diseases


►Cardiac function analysis through

● Anatomical measurements Volumes / Ejection fraction

● Dynamic measurements Strain / Flow / Doppler

Color Doppler Myocardium strain Ejection Fraction


4


Strain imaging – echocardiography illustration

Apical 4 chambers

view

Short axis view


5


Longitudinal Radial Circumferential

L L L

𝒆 = ∆𝑳

𝑳

Normalized deformation

Strain imaging – echocardiography illustration


6

Echocardiography illustration


Longitudinal strain

Source: GE Healthcare web site


7



Radial strain



8



Circumferential strain



9


►Sensitive to change of systolic function

● Strong potential for detecting heart diseases at early stage

► Ischemic case: reduced motion of specific segments

Myocardial strain

LCX: Occlusion of Left Circumflex RCA: Occlusion of Right Coronary Artery LADdist: Distal occlusion of the Left Anterior Descending Artery LADprox: Proximal occlusion of the Left Anterior Descending Artery


10


Myocardial strain

► LCX example


11


Myocardial strain

►So everything is beautiful in a wonderful word ?

● Not really…

►Only global longitudinal strain (GLS) is used (in ultrasound)

►Regional strain NOT used (despite the clinical interests)

Strain measurements are not reproducible enough Needs for automatic and reproducible measurements

Solid quantitative validations are required


12


Validation of cardiac strain quantification

Manual tracking Physical

phantom

Animal experiments

Realistic synthetic images

Straightforward Real

acquisitions Measure strain

directly Dense strain Ground-truth

• Tedious • Inter and

intra-expert variability

• Realism (image quality/involved structures) not yet sufficient

• Image quality is too good

• Ethical question

• Let’s see what’s going on


13

Generation of realistic synthetic images

Motivations


14

Motivations


15

● Physical principle

● Physical simulator

● Proposed pipeline

Ultrasound modality


Ultrasound modality


16

Physical principle

1) Transmit focused beam 2) Receive backscattered echoes

𝒎𝒆𝒅𝒊𝒖𝒎 𝒎𝒆𝒅𝒊𝒖𝒎

beamforming

3) Reconstruct one part of the image

𝒎𝒆𝒅𝒊𝒖𝒎

4) Repeat for each part of the image

𝒎𝒆𝒅𝒊𝒖𝒎 𝒎𝒆𝒅𝒊𝒖𝒎

4) Repeat for each part of the image

𝒎𝒆𝒅𝒊𝒖𝒎

Typical frame rate: from 50 to 100 images / second

Ultrasound modality


17

Interaction between wave and medium

►When propagating, acoustic waves

● create expansion and contraction of the insonified medium

● interact with the medium in many different ways

Reflection

Refraction

Scattering

Attenuation

Ultrasound modality


18


►Specular

● Large reflector (dimensions > 𝝀)

● Smooth surface (e.g. bone)

Specular

Incident wave reflected

wave

Transmitted wave

Impedance Z1

Impedance Z2

Diffuse

Incident wave

Transmitted wave

Ultrasound modality


19


►Diffuse

● Rough surface (e.g. smooth tissue)

● Wave is reflected in several directions

Specular


wave

Transmitted wave

Impedance Z1

Impedance Z2

Diffuse

Incident wave

Transmitted wave

Ultrasound modality


20


Specular (spine)

Specular (skull)

Diffuse (brain)

Ultrasound modality


21


►Scattering

● Structures with dimensions < 𝝀

● Particularly true with blood (red cell dim ~8µm, 𝝀>0.1mm)

one scatterer few scatterers

Emmanuel Bossy, Institut Langevin, ESPCI Paris, France

Ultrasound modality


22


►Scattering

● Many scatterers => speckle phenomenon !


Plane wave Focus wave

Ultrasound modality


23


►Scattering

● Soft tissue behaves as a set of scattering points

● Ultrasound image is mainly an interference imaging technique

● Intrinsic speckle properties (local signature of the tissue)

Ultrasound modality


24




Ultrasound modality


Ultrasound modality


25

Ultrasound modality

Physical simulator

►Several existing physical simulators in the literature

● Field II (Cole)

● Creanuis

● Simus

● …

►Based on the same strategy

● Modeling of the emitted field (linear / non-linear propagation)

● Modeling of the insonified medium through points scatterers

https://field-ii.dk

https://creatis.insa-lyon.fr/site7/fr/CREANUIS

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https://field-ii.dk/






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26

Ultrasound modality

Physical simulator

Probe settings

Medium definition

Physical simulator


27

Cardiac probe

Properties Value

Nb. of elements 64

Pitch 0,28 mm

Height 13 mm

Elevation focus 60 mm

Center Frequency 2.7 MHz

Bandwidth 60 %

Linear phased-array

Ultrasound modality

Physical simulator – modeling of the emitted field

Ultrasound Probe design


28

Ultrasound modality

Physical simulator – modeling of insonified medium

► Scattering map 𝒙𝒊, 𝒚𝒊, 𝒛𝒊 , 𝒂𝒊 𝒊∈[𝟏,𝑵]

● positions 𝒙𝒊, 𝒚𝒊, 𝒛𝒊

● amplitude 𝒂𝒊

● number of scatterers N

► Specular reflection

● Strong amplitudes 𝒂𝒊

► Scattering

● Many scatterers per resolution cell


29

Realistic synthetic image

► How to choose N, 𝒙𝒊, 𝒚𝒊, 𝒛𝒊 and 𝒂𝒊 ?

Physical simulator

Ultrasound modality



30

Ultrasound modality


► Scatterers position and number

● From the chosen probe settings

Compute the corresponding resolution cell (≈ 𝟎, 𝟓𝒎𝒎𝟑)

● From the dimensions of the image to simulate

Choose 𝟐𝟎 scatterers per resolution cell

(fully developed speckle)

Compute the corresponding total number of scatterers N

The N scatterers are then uniformly distributed over the image dimensions to fill the image space


31

Ultrasound modality

► Scatterers amplitude

● Synthetic image-based approach

Compute the corresponding backscattered amplitude from a real image (template)

𝒂𝒊 = 𝟏𝟎𝒅𝑩𝒓𝒂𝒏𝒈𝒆

𝟐𝟎𝑰

𝑰𝒎𝒂𝒙−𝟏

Real image Synthetic image Scattering map

Cole


32

Ultrasound modality

Static image simulation examples


33




Ultrasound modality


Ultrasound modality


34

Ultrasound modality

Temporal sequence simulation

? ? ? 𝒌𝒔𝒊𝒎


35

Ultrasound modality

►How to extend the simulation to a full sequence with the corresponding ground-truth ?

A Pre-processing

3D dataset: image + mesh 1

B Cardiac motion

E/M ground truth motion 1

Measured motion 2

3

Spat

io-t

emp

ora

l re

gist

rati

on

C

Scat

teri

ng

map

s

1

Sim

ula

tor

2

Simulation


36

► Step A-1 Pre-processing

● Choose a given real sequence (template)

● Semi-automatic segmentation of the left-ventricle over the cardiac cycle

Ultrasound modality

𝒌𝒕𝒆𝒎𝒑𝒍


37

► Step B-1 Electromechanical ground-truth model

Ultrasound modality

Radial motion Long. motion

torsion Inverse rotation

● E/M model

Electrical activation

Mechanical contraction

● Biophysical parameters

Myocardial contractility

Stiffness

Conduction


38

► Step B-1 Electromechanical ground-truth model

Ultrasound modality

𝒌𝒔𝒊𝒎


39

► Step B-3 Spatio-temporal registration

Ultrasound modality


40

Myocardium scatterers

Backscattered amplitudes kept constant over the cardiac cycle

Speckle decorrelation is ensured thanks to the use of the physical simulator

Positions updated from the EM model

Motion reference

Ultrasound modality

► Step C-1 (Temporal) scattering maps


41

Surrounding (non-myocardium) structure scatterers

Backscattered amplitudes re-estimated at each frame of the simulated cardiac cycle

Ensure the realistic nature of the simulation

Positions updated from the EM model

Random positioning out of the myocardium region

Ultrasound modality

► Step C-1 (Temporal) scattering maps


42

Ultrasound modality

► Step C-2 Physical simulation

Pipeline designed for 3D simulations


43

► 2D simulations: need additional steps

A Pre-processing


B Cardiac motion

E/M ground truth motion 1

Measured motion 2

3

Spat

io-t

emp

ora

l re

gist

rati

on

C

US simulation

Scat

teri

ng

map

s

1

Sim

ula

tor

2

1

2D templates

3

Pre-alignment

Ultrasound modality

Simulation


44

Vendor 1

Vendor 4 Vendor 3

Vendor 2

Ultrasound modality

[Alessandrini et al. - TUFFC 2018]


45

Realistic synthetic 2D sequences

►Normal case

4CH 2CH

Ultrasound modality


46

► E/M model introduction of controlled pathologies

Simulated ischemic region

Longitudinal strain – A4C +10

-15

Ultrasound modality


47

Time to play together…

►Any diagnosis ?

Ultrasound modality

A4C A4C


48

Realistic synthetic 2D sequences

►Normal VS LCX

A4C A4C

A4C

Ultrasound modality


49

Many thanks

Together, we’re stronger !


50

Appendices

Appendices


51

Icing on the cake – MR simulation…

MULTIMODAL GENERATION OF REALISTIC SYNTHETIC IMAGES

52





MR modality


Magnetic resonance modality

53


MR modality

Physical principle

Play with intrinsic magnetization of protons present in the human body

54





MR modality



55


MR modality

Physical simulator - ODIN

MR sequence (e.g. bSSFP)

T1 / T2 / PD definition

Physical simulator

http://od1n.sourceforge.net/ [Jochimsen et al., (2006)]

http://od1n.sourceforge.net/



56


MR modality

Physical simulator - ODIN

MR sequence (e.g. EPI)

T1 / T2 / PD definition

Physical simulator

http://od1n.sourceforge.net/ [Jochimsen et al., (2006)]




57





MR modality



58


MR modality

Proposed pipeline

B Cardiac motion

E/M motion 1

Measured motion 2

3

Spat

io-t

emp

ora

l re

gist

rati

on

A Pre-processing


C

T1/ T2/ PD maps 1

Simulation 2

Simulation

59

► Step C-1 T1 / T2 relaxation time (𝒎𝒔)


MR modality

Gaussian distribution 𝝁 and 𝝈 from literature

Tissue labels

T1 map T2 map

60

► Step C-1 Proton density


MR modality

US simulation

Backscattered amplitude Bmode image

MR simulation

Proton density MR image intensity

Using analytic MR formulas

𝑷𝑫 = 𝒇(𝑰, 𝑻𝟏, 𝑻𝟐)

𝒂𝒊 = 𝟏𝟎𝒅𝑩𝒓𝒂𝒏𝒈𝒆

𝟐𝟎𝑰

𝑰𝒎𝒂𝒙−𝟏

61

► Step C-2 Simulations


MR modality

62


MR modality

3D cine MR sequence

63


MR modality

3D tagged MR sequence

(channel 1)

64




65



Strain computation

Longitudinal Radial Circumferential

𝒆 = ∆𝑳

𝑳

Normalized deformation

L L L

66

MODELING OF ULTRASOUND WAVES AND IMAGE RECONSTRUCTION

Ultrasound for medical imaging

Ultrasound and other diagnostic imaging modalities

Thomas L. Szabo. 2014

Diagnostic Ultrasound Imaging: Inside Out

Imaging Modalities

67


Physical principle of echography


►Reflection

● Due to a change of impedance between two media

● The interface should be smooth with dimensions higher than 𝝀

𝑹 =𝒁𝟏 − 𝒁𝟐

𝒁𝟏 + 𝒁𝟐

𝟐

𝑻 =𝟐 𝒁𝟏 𝒁𝟐

𝒁𝟏 + 𝒁𝟐𝟐

𝑹 + 𝑻 = 𝟏


68




►Reflection

Medium Z (kg/m2/s) x 106

air 0.0004

skin 2 1

0.999 0.001

Zair = 400 Zskin = 2106

● No transmission between air and skin !

● Need to use ultrasound transmission gel

69




►Refraction

● Oblique incidence between wave and interface

● The interface should be smooth with dimensions higher than 𝝀

𝒔𝒊𝒏 𝜽𝒊

𝒄𝒊= 𝒄𝒐𝒏𝒔𝒕


70




►Specular

● Large reflector (dimensions > 𝝀)

● Smooth surface (e.g. bone)

Specular


wave

Transmitted wave

Impedance Z1

Impedance Z2

Diffuse

Incident wave

Transmitted wave

71




►Diffuse

● Rough surface (e.g. smooth tissue)

● Wave is reflected in several directions

Specular


wave

Transmitted wave

Impedance Z1

Impedance Z2

Diffuse

Incident wave

Transmitted wave

72


Ultrasound image formation

IQ

RF

RF = radio-frequency signal IQ = in-phase/quadrature

York et al.

Annu Rev Biomed Eng 1999

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