Medical Image Processing Basics of medical imaging Prof
Medical Image Processing Basics of medical imaging Prof. Leo Joskowicz School of Engineering and Computer Science The Hebrew University of Jerusalem, ISRAEL Copyright L. Joskowicz, 2011
First Medical Image: Xrays Copyright L. Joskowicz, 2011 Roentgen, 1895
Characteristics of medical images Intensity values are related to physical tissue characteristics which in turn relate to a physiological phenomenon Anatomy Physics Physiology Copyright L. Joskowicz, 2011
Imaging devices spectrum Copyright L. Joskowicz, 2011
Physics of imaging modalities MRI CT-Scanner Density and structure of protons Density of X-Ray absorption Ultrasound Variations of Acoustic Impedance Copyright L. Joskowicz, 2011 Scintigraphy Density of injected isotopes
Most common imaging modalities • X-rays: film, digital, fluoroscopy, Digital Substraction Angiography (DSA) • Ultrasound: 2 D and 2. 5 D (stack of slices) • Video: laparoscopes and endoscopes • CT: Computed Tomography • MRI: Magnetic Resonance Imaging • NM: Nuclear Medicine – PET -- Positron Emission Tomography – SPECT -- Single Photon Emission Tomography • Many specialized modalities: DSA, heart, etc. Copyright L. Joskowicz, 2011
Medical images: characteristics (1) • Preoperative or intraoperative use – depends on the size and location of imaging machine • Dimensionality: 2 D, 2. 5 D, 3 D, 4 D, 5 D – projection, cross section, stack of projections, time 3 D reconstructions, sequences, evolution over time • Image quality – pixel intensity and spatial resolution – amount of noise; signal/noise ratio – spatial distortions and intensity bias Copyright L. Joskowicz, 2011
Medical images: characteristics (2) • Field of view • Radiation to patient and to surgeon • Functional or anatomical imaging – neurological activity, blood flow, cardiac activity • What it’s best for – bone, soft tissue, fetus, surface/deep tumors, etc • Clinical use – diagnosis, surgical, navigation Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
X-ray images Film or Digital X-ray Copyright L. Joskowicz, 2011 X-ray Fluoroscopy
X-ray imaging Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
Fundamentals of X-ray Physics X-ray is an electromagnetic waveform. The energy: The wavelength and the energy of diagnostic x rays:
X-ray imaging: principle • Measure absorption of X-ray radiation from source to receptors • Film X-ray has very high resolution Io z μ = linear attenuation coefficient [cm-1] Id Id = Io exp[−∫ μ dz] Gray value proportional to radiation energy Copyright L. Joskowicz, 2011
Record the x-ray flux impinging on the x-ray detector after attenuation by a patient
Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
X-ray fluoroscopy Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
Xray imaging with contrast agent Copyright L. Joskowicz, 2011
Xray mammography Copyright L. Joskowicz, 2011
Angiography – continuous fluoroscopy Copyright L. Joskowicz, 2011 Use of injected contrast agent
3 D X-ray fluoroscopy (Iso 3 D C-arm) Copyright L. Joskowicz, 2011
X-ray image properties • Traditional, cheap, widely available • 2 D projections (at least two required) • High resolution, low noise (more fluoroscope) – film size, 64 K gray levels – fluoroscopic images: TV quality, 20 cm field of view • • Relatively low radiation Bone and metal images very well Fluoroscopy used for intraoperative navigation Also dynamic (angiography), bi-planar. Copyright L. Joskowicz, 2011
Ultrasound imaging Copyright L. Joskowicz, 2011
Ultrasound: principle • Probe sends high-frequency (1 – 5 Mhz) sound waves into body • Sound waves travel into tissue and get reflected by boundaries • Reflected waves recorded by probe • Time of flight gives spatial info of the boundaries • Frequency of signal depends on a tradeoff resolution versus attenuation Copyright L. Joskowicz, 2011
Reflection, Diffraction, Refraction of US Waves Reflection of sound waves off surfaces can lead to the phenomenon of an echo. Diffraction of Sound Waves Diffraction involves a change in direction of waves as they pass through an opening or around a barrier in their path. The amount of diffraction (the sharpness of the bending) increases with increasing wavelength and decreases with decreasing wavelength. Refraction of Sound Waves Refraction of waves involves a change in the direction of waves as they pass from one medium to another. Refraction, or bending of the path of the waves, is accompanied by a change in speed and wavelength of the waves. Copyright L. Joskowicz, 2011 30
Ultrasound imaging: characteristics • No radiation • Poor resolution (1 mm) nonuniform, distortion, noise • Low penetration properties • One 2 D slice or several slices (2. 5 D) • Relatively cheap and easy to use • Preoperative and intraoperative use Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
Examples of US images -- tumors Copyright L. Joskowicz, 2011
3 D ultrasound • Reconstruct 3 D data from 2 D slices • Acquisition methods: linear, rotation, fanlike, freee-hand Copyright L. Joskowicz, 2011
3 D ultrasound images Copyright L. Joskowicz, 2011
Computed Tomography (CT) Copyright L. Joskowicz, 2011
Development of Computed Tomography Copyright L. Joskowicz, 2011
CT image quality 1970’s Copyright L. Joskowicz, 2011 2001
Computed Tomography: images cuts Copyright L. Joskowicz, 2011 d= 5 mm d = 15 mm d = 25 mm d = 35 mm
Computed Tomography: images Series of parallel slices 2 mm apart Single slice Copyright L. Joskowicz, 2011
CT-scan views Size: 512 x 128 Resolution: 0. 5 x 1 mm 3 Copyright L. Joskowicz, 2011
Planes Copyright L. Joskowicz, 2011
Common structure of 3 D images Voxel representation M(i, j, k) = I(x, y, z) measures the physical properties of a volume element centered around (x, y, z). Copyright L. Joskowicz, 2011
Computed Tomography: principle X-rays intensity angle Copyright L. Joskowicz, 2011
What is Tomography? X-Ray Computed Tomography Copyright L. Joskowicz, 2011 47
Computed Tomography: types • • • Planar, parallel or fan (cone)-beam Spiral (helical) Single slice or multi-slice Takes about 1 sec/acquisition Current spiral units can take 4– 32 and even 64 slices simultaneously! • Reconstruction using variations of Fast Fourier Transforms (FFT). • Mostly preoperative, some intraoperative units Copyright L. Joskowicz, 2011
Helical CT – Principle Copyright L. Joskowicz, 2011
Helical CT - Image Reconstruction (1) Helical scan mode and reconstruction plane Copyright L. Joskowicz, 2011
Helical CT - Image Reconstruction (2) • Object inside scanning plane is changed during data acquisition. • Only one projection is acquired properly for any reconstruction plane. Helical correction is necessary: (a) without, and (b) with helical correction Copyright L. Joskowicz, 2011
Helical CT - Image Reconstruction (3) • Data acquired at range of positions • Scanner estimates data at slice position by linear interpolation Copyright L. Joskowicz, 2011
Helical CT - Image Reconstruction (4) Linear interpolation (simple and stable): Projections from two 360 o sets used to estimate one set of projections at a constant location Copyright L. Joskowicz, 2011
Computed Tomography: properties • Specifications: – 512 x 512 12 bit gray level images; pixel size 0. 5 mm – slice interval 1 -10 mm depending on anatomy – 50 -1, 000 slices per study – noise in the presence of metal (blooming) – Grey levels: Hounsfield Units (HU). Air is 1000 HU, Water is 0 HU, Fat is 100 to 300 HU, Water Muscle 10 -70 HU, Bone > 200 HU • All digital, printed on X-ray film • Costs about $400 -1, 000, each study $500 Copyright L. Joskowicz, 2011
Visual examination Copyright L. Joskowicz, 2011
Views reconstruction Axial ORIGINAL Copyright L. Joskowicz, 2011 Sagittal Coronal RECONSTRUCTED
Cine CT of the heart Copyright L. Joskowicz, 2011
Ionizing radiation Copyright L. Joskowicz, 2011
Magnetic Resonance Imaging • Similar principle and construction of CT machine, but works on magnetic properties of matter • Magnetic fields of 0. 3 to 7 Teslas (typical 1. 5, 3) • Similar image quality characteristics as CT • Excellent resolution for soft tissue • Costs $1– 3 M , each study $1, 000. • Open MR: intraoperative device • Odin’s “portable” intraoperative MR (0. 3 Teslas) • Functional MRI: Diffusion Tensor Imaging (DTI) Copyright L. Joskowicz, 2011
Magnetic Resonance Images Copyright L. Joskowicz, 2011
Types of MRI – Protocols Gradient Echo T 1 W-post Gd Copyright L. Joskowicz, 2011 T 1 W FLAIR T 2 W 3 D-fspgr-post Gd
MRI principle 1. Put anatomy in large magnetic field 2. Transmit radio waves into anatomy [2~10 ms] 3. Turn off radio wave transmitter 4. Receive radio waves re-transmitted by subject 5. Convert measured radio frequency data to image Important factors – – – Quantum properties of nuclear spins Radio frequency (RF) excitation properties Tissue relaxation properties Magnetic field strength and gradients Timing of gradients and RF pulse Copyright L. Joskowicz, 2011
Open MR Copyright L. Joskowicz, 2011
Odin MR system Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
Odin MR images Copyright L. Joskowicz, 2011
Nuclear Medicine Imaging (NMI) • Same slices principle • Source of photons or positrons is injected in the body. Shortly after, radiation of metabolism is measured. • Poor spatial resolution • Expensive machine AND installation ($4 -5 M) • Expensive and time-consuming • Provides functional info no other source does Copyright L. Joskowicz, 2011
Nuclear medicine images Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
Copyright L. Joskowicz, 2011
Image Fusion: MRI and NMI MRI (anatomy) Copyright L. Joskowicz, 2011 NMI (functional)
Video images from within the body Used in laparoscopic and endoscopic surgery Copyright L. Joskowicz, 2011
Laparoscopy Copyright L. Joskowicz, 2011
References • Principles of Medical Imaging Shung et al, Academic Press, NY, 1992 • Foundations of Medical Imaging Cho et al, Wiley, NY, 1993 • Medical Imaging Systems, Macovski, Prentice Hall, NJ, 1983 Copyright L. Joskowicz, 2011
Main medical imaging modalities X-ray Fluoro US US Film Digital 2 D 2. 5 D Pre/Intraop 2 D/2. 5 D Resolution Radiation Anatomy Procedure Copyright L. Joskowicz, 2011 Video CT MRI NMR Open MR
Medical imaging: summary • Many types of images, both anatomical and functional • Trend towards stacks of parallel slices • Experts: Radiologists • Need: software to visualize and process them! Copyright L. Joskowicz, 2011
Ionizing radiation Copyright L. Joskowicz, 2011
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