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INRIA's Research Centers Statistical computing on manifolds and data assimilation: from medical images to anatomical and physiological models Centrale OMA/MA33 - MVA 2016-2017 X. Pennec Introduction to medical image acquisition and processing Asclepios team 2004, route des Lucioles B.P. 93 06902 Sophia Antipolis Cedex http://www-sop.inria.fr/asclepios 1 •4 INRIA’s Research Centers INRIA Lille Nord Europe INRIA Paris Rocquencourt •INRIA Nancy •Grand Est INRIA •INRIA Rennes Saclay •Bretagne Atlantique Île-de-France 2,800 scientists in INRIA Grenoble computer science Rhône-Alpes INRIA Bordeaux 1300 researchers and teaching- Sud-Ouest researchers •INRIA Sophia Antipolis 1000 Ph.D. students •Méditerranée 500 postdoctoral fellows Statistical computing on manifolds and data assimilation: from medical images to anatomical and physiological models Medical Imaging – Module 2 - MVA 2016-2017 Fri Jan 6: Introduction to Medical Image Analysis and Processing [XP] Fri Jan 13: Statistics on Riemannian manifolds and Lie groups [XP] Fri Jan 20: Biomechanical Modelling and Simulation [HD] Fri Jan 27: Diffeomorphic transformations for image registration [XP] Fri Feb 17: Statistics on deformations for computational anatomy [XP] Fri Feb 24: Manifold-valued image processing: the tensor example [XP] Fri Mar 3: Data assimilation methods for physiological modeling [HD] Fri Mar 10: Surgery Simulation [HD] Fri Mar 17: Exam [Hervé Delingette, Xavier Pennec] 3 1 Course overview The data of Computational Anatomy & Physiology Image acquisition Medical Image Analysis processing 4 1895 Roentgen First Nobel prize in Physics in 1901 5 Todays’s Medical Imaging modalities CT Scan MRI PET Ultrasound •Source :T. Peters 2 Dynamic Images (4-D) CT Scan MRI Bio-signals ECG Pressure Sensor Temperature Medical Imaging in clinical practice TEACHING Image DataBase PREVENTION DIAGNOSIS THERAPY Pre-operative Patient Patient Patient Post-operative robot •CT •US •X-Ray •MRI •X-Ray •US •US •Video •NM •iMRI Per-operative 3 Course overview The data of Computational Anatomy & Physiology Image acquisition Introduction Tomography Nuclear medicine MRI Medical Image Analysis processing 10 Today MRI X-Scan Density and X-ray structure of absorption protons density PET / SPECT Ultrasounds Density of Variations of Radioactive acoustic isotopes impedance 11 Different imaging modalities X-ray Magnetic resonance imaging anatomic, functional, angiographic, diffusion, spectroscopic, tagged Transmission Tomography (X Scan) Nuclear Medicine : Positron emission tomography (PET) Single photon emission tomography (SPECT) Ultrasonography Histological Imaging, confocal in-vivo microscopy, molecular imaging,… 12 4 Characteristics of medical images Intensity values are related to physical tissue characteristics which in turn may relate to a physiological phenomenon Anatomy Physics Physiology Volumetric medical images Very often medical images are volumetric Voxel Representation I (x,y,z) Example of volumetric images : CT-scan (Scanner) Size: 512 x 512 x 128 Resolution: 0.5 x 0.5 x 1 mm 5 Volumetric images T2 MRI 16 Course overview The data of Computational Anatomy & Physiology Image acquisition Introduction Tomography Nuclear medicine MRI Medical Image Analysis processing 17 Principle of CT Imaging (1) X-Ray X-Ray 18 6 Principle of CT Imaging (2) Input X-Ray intensity : Ni Measured Output X-Ray intensity : No Ni N0 Exponential attenuation : Objective : measure (x) = absorption coefficient of X-ray 19 Computed Tomography Principle : • Reconstruct n dimensional function (image) from projected data of (n–1) dimension Radon Transform (1917) • “Two dimension and three dimension object can be reconstructed from the infinite set of projection data”. Fourier Slice Theorem 1D Fourier Transform of Projected slice of 2D field (x,y) is equal to 1D slice in the same direction of the 2D Fourier Transform of (x,y) 21 7 Basic principle of CT -Reconstruction of 2 dimensional image- Projection Data curvilinear integral of absorption coefficient regarding Y y y object x x X-ray tube Data Acquisition field Reconstruction field Simple Backprojection Reconstruction Principle Backprojection based on inverse Radon Transform 1 , . 2 cos , sin In practice use filtered back-projection to remove blur Model Image Simple Filtered Backprojection Backprojection 23 Spiral (3D) CT X-ray tube and detectors rotate 360 deg Patient table is continuously moving Produce an helix of image projections 3D reconstruction 26 8 CT Scan Imaging Measure absorption coefficient of X-ray related to density of tissue Invasive image modality (ionizing rays) Absolute Hounsfield Unit water 1024 water HU(water)=0, HU(air)= -1024, HU(Bone)=175 to 3000 Coded on signed 12 bits 27 Tomotensitometrie (Scanner X) 28 Course overview Introduction Image acquisition Tomography Nuclear medicine MRI Image processing 29 9 Principle of nuclear imaging Introduction into the patient body of a couple (radio-isotope / vector molecule) Vector Molecule Targets organ (drug, protein, blood cells…) Radio-isotope Detection of the molecule Emission imaging : the targeted organ emits radioactivity Reflect the metabolic function of the organ Metabolic or functional imaging Local relative concentration (relative) Concentration evolution during time 30 Nuclear Medicine / radioactivity Nucleus (Rutherford) A= nucleon number Isobars A = constant Z = proton number Isotopes Z = constant N = neutron number Isotones N = constant Radioactivity (Curie) Alpha: Helium nucleus Beta: 1/ electron - 2/ positron + 2 photons (511 kev) Gamma: Photon 31 Nuclear Medicine Density of radioactive tracers 32 10 Single photon gamma imaging Radio-isotopes Single photon emitters Technetium Tc 99m 6 h 140 kev Portative generator Iodine I 131 8 j 360 kev Reacteur (fission) Iodine I 123 13 h 159 kev Cyclotron (industry) Thallium Tl 201 73 h 80 kev Cyclotron (industry) Krypton (Kr 81 m), Gallium (Ga 67), Indium (In 111), Xenon (Xe 133, gaz) 33 Single photon gamma imaging Heart (myocardium perfusion) Stress/rest exam perfusion / perfusion Healthy area perfusion / (hypo/non-)perfusion Zone at risk (ischemia) (hypo/non-)perfusion / (hypo/non-)perfusion Infarcted Area 34 Positron emission tomography (PET) Radio-isotopes Emission : positron (+) Annihilation 2 photons of 511 kev at 180º Positron emitters Carbon 11C 20 mn cyclotron (medical) Nitrogen 13N 10 mn cyclotron (medical) Oxygen 15O 2 mn cyclotron (medical) Fluor 18F 112 mn cyclotron (medical) Physiological molecules 15 water H2O glucose fluoro-deoxyglucose (F18DG) 35 11 Positron emission tomography (PET) 36 PET Scan https://www.youtube.com/watch?v=GHLBcCv4rqk 37 Course overview Introduction Image acquisition Tomography Nuclear medicine MRI Image processing 38 12 Magnetic resonance imaging Density and structure of protons 39 Magnetic resonance imaging Sagittal Coronal or Frontal Axial or Transverse dimension: 256 x 256 x 128 résolution: 1x1x1.5 mm 40 MRI: a few dates • 1946: MR phenomenon - Bloch et Purcell • 1952: Nobel prize - Bloch et Purcell • 1950-1970: development but no imaging • 1980: MRI feasibility • 1986 - …: real development 41 13 MRI: One modality with multiple sequences • Anatomic MRI: T1, T2, DP weighted images • Angiographic MR • Functional MR: cognitive studies • Diffusion MR: brain connectivity • MR Spectroscopy No absolute quantification 42 Magnetism at the molecular level Electric charges in motion • magnetic momentum • Precession motion in a magnetic field 44 Bloch’s Equations Link between spin and magnetic momentum μ Nuclear magnetic momentum Gyromagnetic ratio Fundamental motion equation S: Angular speed (spin) m: Momentum (mechanic) In a magnetic field ∧ 45 14 Bloch’s Equations d Thus ∧ 0 t cos (Lt ) sin ( t ) B0 0 t L B0 z0 Larmor’s frequency L B0 46 Magnetism at the macroscopic level P+1/2=0.5000049 B0=1.5 T P-1/2=0.4999951 49 Magnetism at the macroscopic level 1023 spins 50 15 Resonance 51 Magnetic Resonance / excitation • Electro-magnetic field at Larmor’s frequency L B0 • Hydrogen protons enter into resonance Flip of the macroscopic momentum M 52 Magnetic Resonance / excitation 53 16 Magnetic Resonance / relaxation • Return to equilibrium / B0: time constant T1 dM z M z M B z dt T1 • Spin dephasing: Time constant T2 dM x, y M x, y M B x, y dt T2 54 Magnetic Resonance / relaxation T1 (ms) TISSUE T2(ms) 0.5 T 1.5 T Muscle 550 870 45 Heart 580 865 55 Liver 325 490 50 Kidney 495 650 60 Spleen 495 650 58 Fat 215 262 85 Brain, grey matter 655 920 100 Brain, white matter 540 785 90 540 55 MRI basics in video https://www.youtube.com/watch?v=djAxjtN_7VE 56 17 MRI / frequency selection X encoding by frequency Y encoding by phase Several measures are necessary 57 Anatomical MRI Proton density T1 T2 58 Angiographic MRI •INFLOW • Phases Maximum intensity projection (MIP) 59 18 Angiographic MRI X-Scan / radiology Selective injection of a contrast agent in one artery 60 Tagged MRI 61 Tagged MRI 62 19 Avantages of MRI • Non-Invasive: MRI does not depend on potentially harmful ionizing radiation, as do standard x-ray and CT scans. • MRI scans are not obstructed by bone, gas, or body waste, which can hinder other imaging techniques • Can see through bone (the skull) and deliver high quality pictures of the brain's delicate soft tissue structures • Images of organs and soft tissues 66 Drawbacks of MRI • Pacemakers not allowed • Not suitable for claustrophobic persons • Tremendous amount of noise during a scan • MRI scans require patients to hold
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