ACT I: … in which our heroes meet the Fundamentals and Practicalities of Image Acquisition, Reconstruction, and Processing A medical imaging system is a device that transforms people into numbers. Jeff Siewerdsen, Ph.D. Department of Biomedical Engineering Johns Hopkins University M. Kessler Johns Hopkins University Schools of Medicine and Engineering Fundamentals and Practicalities Imaging Configurations • How do we get the numbers? - Source-object-detector configurations - Rad/Fluoro, CT, PET, US, and MR - Image acquisition - Image reconstruction Source Object Detector Processor Display Observer ? • What do the numbers mean? - Pixel values (“intensity”) - Mechanisms of contrast • What are their limitations? - Spatial resolution Noise Artifacts Geometric accuracy Quantitation (voxel value) Relevance to IGI: - Targeting - Localization - Segmentation - Registration - Therapy logistics • Source-Obj-Det configurations vary among modalities • Physical arrangement of source-object-detector • Physical nature of the source (x-rays, sound, radionuclide, B-field) • Type of detector [convert EM or Mech energy to a signal (typically e-)] • Proc-Disp-Obs configurations are comparatively similar Reconstruction, enhancement, display Segmentation, registration Interpretation (human or computer-assisted) Imaging Configurations: X-Ray Projection Radiography Source Object Detector Imaging Configurations: X-Ray Computed Tomography (CT) Imaging Configurations: X-Ray Computed Tomography (CT) Source Object Detector Imaging Configurations: Positron Emission Tomography (PET) Detector Detector Object Source Object Source Source Imaging Configurations: Ultrasound Imaging Source Imaging Configurations: Magnetic Resonance (MR) Imaging Source Object Detector Detector Object Source-Detector Transducer Imaging Configurations: Magnetic Resonance (MR) Imaging Multi-Modality Imaging Morphology Function Detector SPECT CT Gz Object Gy Gx Source B MR US PET Optical Pop-Quiz Multi-Modality Imaging: Review Which imaging modality has the most well defined source-detector geometry? D. W. Townsend, Multi-Modality Imaging of Structure and Function Physics in Medicine and Biology (Vol. 53(4): 2008) 58% 31% 2% 5% 4% Answer Which imaging modality has the most well defined source-detector geometry? (a)Radiography (b)CT Geometrically accurate. (c)PET (d)Ultrasound Source = detector (e)MRI Reference: “Medical Imaging Systems”, Prentice-Hall Inc, Albert Macovski 1. 2. 3. 4. 5. Radiography CT PET Ultrasound MRI Implications for Imaging in IGI • Configuration and Physical Basis • Compatibility with Tx environment • Open geometry • Patient access • Utility for guidance • Speed • Radiation Dose • Type of image data • Morphology • Function • Contrast, Image quality • Image artifacts • Geometric accuracy • Ability to segment structures • Ability to register to other images • Cost, workflow integration, … How to Get the Numbers (Signal) Computed Tomography For Example: Photon Detectors Photomultiplier Tube (PMT) X-ray Image Intensifier (XRII) Incident X-ray Incident X-ray X-ray Converter (Scintillator) X-ray Converter (Scintillator) Secondary Quanta (photons or e-) Secondary Quanta (photons or e-) Coupling Conversion Coupling Conversion Readout Readout Amplification Amplification Flat-panel Detector (FPD) Sir Godfrey Hounsfield Nobel Prize, 1979 Digitization How to Reconstruct the Numbers? Computed Tomography Hounsfield’s CT Scanner Projection radiography Detector p(ξ) I0 γ source The Sinogram: Line integral projection p(ξ) … measured at each angle θ p(ξ;θ) “Sinogram” p(x;θ) Turntable and linear track 9-day acquisition 2.5-hr recon Circa 1895 θ I = I 0e P( x ) = ln I0 − µ ( x , y )dy d I = µ ( x, y )dy 0 Digitization ξ Filtered Backprojection p(ξ;θ) Simple Backprojection: Trace projection data p(x;θ) through the reconstruction matrix from the detector (x) to the source Filtered Backprojection The Filtered Sinogram: Convolve with RampKernel(ξ) p(ξ)*RampKernel(ξ) Equivalent to Fourier product P(f)|f| p(ξ;θ) p(ξ;θ)*RampKernel(ξ) p(ξ;θ) Simple backprojection yields radial density (1/r) θ Therefore, a point-object is reconstructed as (1/r) Solution: “Filter” the projection data by a “ramp filter” |r| X-ray source Filtered Backprojection: Implementation Loop over all views (all θ) Filtered Backprojection p(ξ, θ) p(ξ) µ(x,y) X-ray source ξ Projection at angle θ p(ξ,θ) Filtered Projection g(ξ,θ) Backproject g(ξ,θ). Add to image µ(x,y) µ(x,y) Third-Generation CT Dual-Source CT “Third Generation” CT Scanner Helical Acquisition Fan-Beam X-ray Source 1-D Detector Array Multiple Projections, P( ξ,θ) Typical rotation time: 0.3 sec (3 rotations / sec) Typical couch speed: ~5-30 mm/s Siemens Medical Solutions – Somatom Definition From “Fan” to “Cone” Conventional CT: Fan-Beam 1-D Detector Rows Slice Reconstruction Multiple Rotations Two complete x-ray and data acquisition systems on one gantry. 330 ms rotation time (effective 83 ms scan time) Cone-Beam CT: Cone-Beam Collimation Large-Area Detector 3-D Volume Images Single Rotation Cone-Beam CT Projection data Multiple projections over ~180o Volume reconstruction Sub-mm spatial resolution + soft tissue visibility Cone-Beam Filtered Backprojection Geometry 2D Interpolation Filter Weight Pixel Values (“Intensity”) and Contrast Reconstruction Volume # of voxels Repeat × # of projections Some Fundamentals Some Fundamentals (really fundamental) (really fundamental) This is not a pipe. It is: 1. 2. 3. 4. 7% 76% whatever you believe it is. an image of a pipe. in French, so I don’t know. too early in the morning for 16% philosophy. 1% 1 2 3 4 This is not a pipe. It is: (a)whatever you believe it is. (b)an image of a pipe. (c)in French, so I don’t know. (d)too early in the morning for philosophy. Pixel Values: X-Ray Projections 256 Displayed Pixel Values The CT image pixel values have units of the attenuation coefficient, µ (cm-1 or mm-1) 0 In X-ray Projection Images level Window / level adjustment Displayed Pixel Value window • Pixel value can be anything you want! Pixel Values: CT Commonly converted to a convenient scale: Hounsfield Units (HU) HU’ = 1000 Actual Pixel Value 0 • Raw pixel values are line integrals 10,000 µ’ - µwater µwater Fat (-100) Liver (+85) • Depend on the intensity of the beam (kVp and mAs) • Subject to considerable processing (“tone scaling”) Polyeth (-60) Water (0) • For example: conversion to “Log-Exposure Space” • Range 0-4000 (12-bit) representative of exposure to detector 100 mR, Pixval 3000 10 mR, etc. • Pixval 4000 • Changes in pixel value corresponds to consistent change in EA Brain (8) Breast (-50) See also: AAPM Task Group #116 and IEC International Standard 62494-1 (“Exposure Index…”) Hounsfield Units (HU) Contrast Pop-Quiz A “large-area transfer characteristic” Defined: • As an absolute difference in mean pixel values: C = µ1 − µ 2 For example: C = |0.18 cm-1 – 0.20 cm-1| = 0.02 cm-2 or C = |-100 HU – 0 HU| = 100 HU ROI #1 ROI #2 • As a relative difference in mean pixel values: C= µ1 − µ 2 (µ 1 ) + µ2 2 For example: C = |0.18 cm-1 – 0.20 cm-1| 0.19 cm-1 ~ 10% Contrast is higher in CT than in xray projections, because: 20% 10% 71% 1. CT uses a higher dose 2. Because you inject a contrast agent 3. Because µ 1 − µ 2 > µ (x, y, z )dy − µ ( x, y , z )dy x1 x2 Contrast Pop-Quiz Contrast is higher in CT than in xray projections, because: Why CCT >> Crad? CT Radiograph 1. CT uses a higher dose 2. (b) Because you inject a contrast agent 3. (c) Because µ 1 − µ 2 > µ (x, y, z )dy − µ ( x, y , z )dy x1 19 22 40 17 30 21 25 63 25 20 282 x2 Contrast = I1 – I2 (I1 + I2)/2 Reference: Pixel Values: PET ACTIVITY Relating to Biological Process: 18F FDG Glucose metabolism 11C Methionine (MET) Amino-acid transport and metabolism 18F Fluoroethyltyrosine Amino-acid transport 18F Fluoromethyltyrosine Amino-acid transport 18F Fluorothymidine DNA synthesis (thymidine phosphorylation) 11C Thymidine DNA synthesis 18F Fluoromisonidazole (FMISO) Hypoxia 62Cu 15O ATSM water Perfusion gas Oxygen extraction rate 11C Choline Choline metabolism 99mTc annexin V Apoptosis 99mTc hydrazine nicotinamide Apoptosis 99mTc anti-EGF antibody Epidermal growth factor receptor (EGFR) 123I mAb 425 / 111In mAb 425 237 63–25 =86% (63+25)/2 282–237 =17% (282+237)/2 Pixel Values: PET Standard Uptake Value (SUV) • Ratio of tissue radioactivity concentration at time t: CPET(t) … to the injected dose (MBq), normalized to body weight: C (t) SUV = DPET •W Units: (g/ml) • SUVmax often used as a metric of tumor response. • Threshold in SUV often used for tumor volume measurement (region-growing segmentation with PixelValue V SUVthresh) SUVmean = average SUV within the segmented volume • Important to measure SUV at a common, late time point for purposes of comparison Hypoxia 15O CCT = Crad = “Medical Imaging Systems”, Prentice-Hall Inc, Albert Macovski Radiopharmaceutical 20 19 25 19 22 18 24 25 25 40 Major Drawbacks to Quantitation EGFR Y. Cao, University of Michigan • Variability associated with noise, resolution, and ROI defintition • SUV as a quantitative metric is discouraged MR Image Acquisition MR Image Acquisition LBNL 0.5 T MRI (circa 1988) T1 Magnetic Resonance (MR) Images: • Tissue Contrast • Physiology / Function • Metabolites • Acquisition in Arbitrary Planes Alignment and Precession Magnetic Dipoles DWI T2 Acquisition by means of various MR Pulse Sequences: Nuclei (e.g., protons) behave like magnetic dipoles (Magnetic Moment) Gd In the absence of an external magnetic field, the orientation of the dipoles is random. In the presence of an external magnetic field the dipoles align with direction of the applied B0 field. Flair In the same manner that a spinning top precesses around a gravitational field, the dipoles precess around the external B0 field ω = γ B0 Larmor Frequency MR Image Acquisition Net Longitudinal Magnetization Transverse Magnetization Mo=Mz MR Image Acquisition Measure the increase in Longitudinal Magnetization (Mz) Spin Flip + Phase Coherence … and the decrease in Transverse Magnetization (Mxy) Mx y Bo 0.63 Mxy Mz Apply RF pulse (B1 field) at Larmor frequency in transverse plane Flip Angle α = γB1τ 0.37 1 2 T1 Spin-Lattice Relaxation Time 3 1 2 3 T2 Spin-Spin Relaxation Time MR Image Signal and Contrast Tissue Contrast Ti Long T1 Long T2 Short T1 Long T2 Reduces T1 Reduces T2 Pixel Values: MR T2 Weighting Artifacts Process / Tissue Type / Metabolite FLAIR T2 Tumor, edema, … Post Gd T1 Vascular leakage, … ADC (diffusion coefficient) Water diffusion, intra- and extra-cellular structure Diffusion tensor imaging H20 anisotropy diffusion, axonal injury, muscular fiber Perfusion imaging Micro-circulation in normal tissue and tumor Blood volume imaging CBV fraction, tumor vascular density (functional) Permeability imaging BBB, vascular leakage Dynamic contrast enhancement Gd uptake, neovascularity 1H CSI Choline, Creatine, NAA, Lactate !! 31P CSI Phospho - choline, - creatine, - ethanolamine, pH BOLD contrast, T2* Tissue / blood oxygenation change, ion deposition BOLD contrast w carbogen & O2 Functionality of vasculature O2 extraction and consumption Tissue oxygen consumption 19F-MRI Hypoxia Molecular targeted contrasts Enhanced T1 sig Reduced T2 sig Time T1 Weighting perfluoro-15-crown-5-ether Bright T1 signal Gray T2 signal Gd Contrast ∆Mxy Time Acquisition Method Dark T1 signal Bright T2 signal Fat A ss ue B ∆ Mo Water B T2 (ms) Transverse Magnetization T2 Contrast Spin-Spin sue Tis Ti ss ue A T1 Contrast Spin-Lattice ue ss Ti T1 (sec) Longitudinal Magnetization Intrinsic Tissue Properties Contrast Weighting e.g., Anti-angiogensis Y. Cao, University of Michigan www.e-mri.org Pixel Values and Contrast: Implications for IGI Image 0 Image Registration Image Quality: Beyond Contrast Image 0 Proj • Intensity-based registration • For example: - Mean-square difference - Demons algorithm • Non-intensity based registration • For example: - Mutual information (MI) - Finite element models (FEM) CT Resolution-Limited PET US Contrast-to-Noise Limited MR Spatial Resolution al 1 mm ideal Spleen “128” Spine 1975 2000 “256” “512” Image Size “1024” Voxel size: 0.12 mm voxels Full-width at half-max: ~0.42 mm Hanning reconstruction filter 0.4 mm “512” 0.8 mm “256” Ram-Lak Liver tu Full-Width Half-Max (µm) AO ac blur Pancreas Voxel “Image Size” Size 0.2 mm “1024” 0.2 sampling GB FWHM (mm) Axial image of steel wire Voxel Size (mm) 0.8 0.6 0.4 Hanning CT Image Quality Reconstruction Filter Coeff. hwin Modulation Transfer Function (MTF) Reconstruction Filter “Smooth” “Sharp” 127 µm Wire in H2O 1.0 J J JJ J J J Steel Wire J J Signal (mm-1) 0.8 J J J J J 0.6 J J J J Improved Spatial Resolution Higher Noise Reduced SNR Reduced Soft-Tissue Visibility www.impactscan.org Image Noise ) m y( 0.0 J J J J 0.5 1.0 J J J J JJ J JJ J J JJ JJ JJJ JJ J JJ JJJJ 1.5 Spatial Frequency (mm -1 ) Reconstruction Filter k E 1 K xy Do η a 3xy a z 1 1 1 ∝ ∝ Do az a 3xy Barrett, Gordon, and Hershel (1976) Sharp σ2 = 0 σ∝ J MTF ( f x , f y ) = FT [LSF (x , y )] Smooth c J 0.0 η 2 Kxy ∝ df MTFrecon J Noise / Resolution Tradeoff • CT image noise depends on – Dose Do – Detector efficiency – Voxel size Axial axy Slice thickness az – Reconstruction filter f x (m m m) J Measured 0.2 Reduced Spatial Resolution Lower Noise Improved SNR Improved Soft-Tissue Visibility System MTF J 0.4 2.0 Pop-Quiz Artifacts The main image quality advantage of CT over radiography is: 2% Rings Shading Streaks Motion 29% 65% 2% 2% Metal Lag Truncation 1. 2. 3. 4. 5. Energy resolution Spatial resolution Contrast resolution Temporal resolution Speed of acquisition “Cone-Beam” Answer Pop-Quiz In CT and cone-beam CT, image noise exhibits which of the following dependencies: The main image quality advantage of CT over radiography is: (a)Energy resolution (b)Spatial resolution (c)Contrast resolution (d)Temporal resolution (e)Speed of acquisition 33% 35% 8% 23% 1% Reference: “Computed Tomography”, McGraw-Hill, Stuart Bushong 1. 2. 3. 4. 5. proportional to (1/Dose) proportional to 1/sqrt(Slice Thickness) proportional to # projections proportional to scatter-to-primary ratio independent of reconstruction filter Answer Image Quality: Implications for IGI In CT and cone-beam CT, image noise exhibits which of the following dependencies: Localization / Targeting • Soft-tissue visibility • Spatial resolution • Geometric accuracy σ proportional to (1/Dose) (b) σ proportional to 1/sqrt(Slice Thickness) (c) σ proportional to # projections (d) σ proportional to scatter-to-primary ratio (e) σ independent of reconstruction filter (a) Segmentation • For example: intensity-based thresholding • Contrast-to-noise ratio • Artifacts (shading and streaks) Registration • Pixel value / contrast • Intensity- or Non-intensity-based • Consistent image information References: “Computed Tomography”, McGraw-Hill Co., Steward Bushong Barrett HH et al., “Statistical limitations in transaxial tomography,” Comput. Biol. Med. 6: 307-323 (1976). Therapy Logistics Pop-Quiz Geometry • • • • When Neil Armstrong and Buzz Aldrin re-entered the Lunar Module, the circuit breaker that arms the ascent engine was broken. What did they use to activate the switch? Patient access Field of view Portability Compatibility 40% Time • Speed of acquisition • Speed of reconstruction Oops! 8% 8% Cost • Relative to other aspects of Tx • “Comparative effectiveness” Radiation Dose • For IGRT, low in comparison to Tx dose • In general, quantifiable benefit to therapeutic outcome 25% 19% 1. A piece of wire 2. A moon rock 3. A piece of the American flag 4. A felt-tip pen 5. Spit Answer When Neil Armstrong and Buzz Aldrin reentered the Lunar Module, the circuit breaker that arms the ascent engine was broken. What did they use to activate the switch? (a) A piece of wire (b) A shard of moon rock (c) A piece of the American flag (d) A felt-tip pen (e) Saliva Thank you! What about CT? Integrated (Hybrid) MMI Multiple modalities integrated within a single exam: - Integrated hardware: hybrid scanners Modern: Scintillator / Semiconductor Conventionally: Gas (Xenon) • Natural history of CT scanners “Generations” of CT Advanced scanner technologies • Fundamentals of CT reconstruction Fourier slice theorem Filtered backprojection • Image quality / artifacts Physical factors Performance metrics Well-suited to Multiple Detector Rows Single-slice CT only • Radiation dose (MDCT) Magnitude and risk (in context) K. Kanal, University of Wisconsin OR Active areas of technology development - PET-CT… SPECT-CT - MR-PET… MR-Ultrasound… MR-Optical Simultaneous (or near-simultaneous) acquisition - Improves accuracy of co-registration / co-localization - Synergy of information (e.g., attenuation correction) - Improves clinical space, time, and workflow requirements Pop-Quiz Image Acquisition This is an image of: (a)A leaf (b) A starfish (c) A liver met (d) An apple Output Input q0(x) For Example: Digital Radiography Active Matrix Sensor (Photodiodes and TFTs) cm2 Area: ~(20x20) – (41x41) Pixel size: ~150µm – 400 µm q1(x) For Example: Digital Radiography Incident Fluence X-ray Converter (Scintillator or Photoconductor) System Beam energy (kVp) Tube current (mA) Exposure time (tx) Dose (mGy) For Example: Digital Radiography Incident Fluence Quantum Detection For Example: Digital Radiography Incident Fluence Quantum Detection Conversion to Secondary Quanta Fraction of x-rays interacting / depositing energy Beam energy (kVp) Thickness of converter Fundamental limit to SNR Maximum DQE = Optical photons (scintillator) e-h pairs (photoconductor) “Gain” depends on converter: η Nquanta ~ Eo / W(E) Swank conversion “noise” Fundamental limit to DQE: max DQE ~ ηI Spatial Spreading Blur For scintillators: depends on structure and thickness For photoconductors: almost negligible “Modulation transfer function” x MTFconverter ~ FT [LSF] For Example: Digital Radiography Incident Fluence Quantum Detection Conversion to Secondary Quanta Spatial Spreading Coupling Incident Fluence Quantum Detection Conversion to Secondary Quanta Spatial Spreading Coupling Integration Sampling Conversion to e-h pairs Integration Integration by pixel aperture MTFaperture ~ sinc[ax] System spatial resolution MTFsystem ~ MTFconverter x MTFaperture For Example: Digital Radiography ax Signal at discrete pixel locations Potential for signal and noise “aliasing” Electronic Readout Additive electronic noise Pixel components (TFT and PD) TFT Capacitive readout lines Amplifier Digitizer Imparts exposure dependence on DQE Degrades imaging performance at low dose ADC Amp Cone-Beam CT Fully 3-D Volumetric CT CT Image Reconstruction Conventional CT: Fan-Beam 1-D Detector Rows Slice Reconstruction Multiple Rotations Cone-Beam CT: Cone-Beam Collimation Large-Area Detector 3-D Volume Images Single Rotation CT Image Reconstruction Fourier Slice Theorem The Fourier Transform of a projection of an object at a given angle yields a slice of the Fourier Transform of the object at the corresponding angle in the Fourier domain. y Fourier Slice Theorem p(ξ ξ,θ) ,θ v F [p(ξξ,θ)] ,θ y f(x,y) θ u x F(u,v) v ξ FT x θ u F(u,v) f(x,y) X-rays CT Image Reconstruction CT Image Reconstruction Fourier Slice Theorem Fourier Slice Theorem F [p(ξξ,θ)] ,θ y ) p(ξ,θ v ξ θ θ u x F(u,v) f(x,y) F [p(ξξ,θ)] ,θ y , θ) p(ξ v ξ θ F(u,v) f(x,y) X-rays θ u x X-rays CT Image Reconstruction Image Quality: A Very Quick Overview y F -1[F(u,v)] v x f(x,y) u p(ξ ξ,θ) ,θ F(u,v) • What are the pertinent IMAGE QUALITY METRICS? - Contrast resolution - Spatial resolution - Noise - Other… • What are the ACQUISITION and RECONSTRUCTION parameters? - kVp, mAs Reconstruction filter - Time, pulse sequence Voxel size - Pharmaceutical agent Slice thickness • What are the IMPLICATIONS TO IG PROCEDURES? - Visualization and Targeting - Image Segmentation - Image Registration Helical CT Noise-Power Spectrum • Noise-power spectrum (NPS) FT [∆d (x, y )] NPS ≡ • Note: + Nyq σ = 2 Slip ring gantry Continuous gantry rotation Continuous couch translation fyfy00 2 Pitch <1 : Overlap Higher z-resolution Higher patient dose f2 -f-fCC -f-fCC NPS ( f )df Rothko fCfC • Want to quantify: – Magnitude of fluctuations – Spatial correlations f1 − Nyq 00 Seurat ffxx ffCC Pitch = Table increment / rotation (mm) Beam collimation width (mm) Pitch >1: Non-overlap Lower z-resolution Lower patient dose WA Kalender, Computed Tomography, 2nd Edition (2005) Multi-Detector CT Cone-Beam CT • Multiple slices acquired in each revolution • Higher speed • Reduced slice thickness (Improved axial resolution) 4x 1.25 mm 4x 4x 2.5 mm 3.75 mm 4x 5.0 mm Projection data P(u,v,θ) 200 – 2000 projections in a single rotation GE Light Speed multi-row CT detector Volume reconstruction µ(x,y,z) Sub-mm spatial resolution + soft tissue visibility Spatial Resolution Factors affecting spatial resolution Focal spot size System geometry •X-ray focal spot size •Magnification (SDD/SAD) Detector configuration •X-ray converter •Pixel pitch Recon parameters •Recon filter •Slice thickness •Voxel size Patient motion Metrics of spatial resolution: Minimum resolvable line-pair Minimum resolvable Point-spread function (psf) line-pair group Modulation transfer function (MTF) Noise-Power Spectrum: in CT Axial Plane (x,y) S(fx, fy) Sagittal Plane (x,z) S(fx, fz)