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## Medical Image Analysis

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**Medical Image Analysis**Medical Imaging Modalities: Magnetic Resonance Imaging Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Magnetic Resonance Imaging**• Nuclear magnetic resonance • The selected nuclei of the matter of the object • Blood flow and oxygenation • Different parameters: weighted, weighted, Spin-density • Advance: MR Spectroscopy and Functional MRI • Fast signal acquisition of the order of a fraction of a second Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Figure comes from the Wikipedia, www.wikipedia.org.**Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Figure 4.12. MR images of a selected cross-section that are**obtained simultaneously using a specific imaging technique. The images show (from left to right), respectively, the T1-weighted, T-2 weighted and the Spin-Density property of the hydrogen protons present in the brain. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Magnetic Resonance Imaging**• 1H: high sensitivity and vast occurrence in organic compounds • 13C: the key component of all organic • 15N: a key component of proteins and DNA • 19F: high relative sensitivity • 31P: frequent occurrence in organic compounds and moderate relative sensitivity Adapted from the Wikipedia, www.wikipedia.org.**MR Spectroscopy**Figure comes from the Wikipedia, www.wikipedia.org. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MR Spectroscopy**Figure comes from the Wikipedia, www.wikipedia.org. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Functional MRI**Figure comes from the Wikipedia, www.wikipedia.org. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• : spin-lattice relaxation time • : spin-spin relaxation time • : the spin density Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• Great web sites • Simulations from BIGS - Lernhilfe für Physik und Technik • http://www.cis.rit.edu/class/schp730/bmri/bmri.htm Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• Spin • A fundamental property of nuclei with odd atomic weight and/or odd atomic numbers is the possession of angular moment • Magnetic moment • The charged protons create a magnetic field around them and thus act like tiny magnets Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• : the spin angular moment • : the magnetic moment • : a gyromagnetic ratio, MHz/T • A hydrogen atom • :42.58 MHz/T Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**m**N J J S Figure 4.13. Left: A tiny magnet representation of a charged proton with angular moment, J. Right: A symbolic representation of a charged proton with angular moment, J and a magnetic moment, μ. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• Precession of a spinning proton • The interaction between the magnetic moment of nuclei with the external magnetic field • Spin quantum number of a spinning proton: ½ • The energy level of nuclei aligning themselves along the external magnetic field is lower than the energy level of nuclei aligned against the external magnetic field Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Figure 4.14 (a) A symbolic representation of a proton with**precession that is experienced by the spinning proton when it is subjected to an external magnetic field. (b) The random orientation of protons in matter with the net zero vector in both longitudinal and transverse directions. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• Equation of motion for isolated spin • Solution: Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Longitudinal Vector OX at the transverseposition X**Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**S**S Lower Energy Lower Energy Level Level H H0 Higher Energy Higher Energy Level Level N N Figure 4.15 (a). Nuclei aligned under thermal equilibrium in the presence of an external magnetic field. (b). A non-zero net longitudinal vector and a zero transverse vector provided by the nuclei precessing in the presence of an external magnetic field. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**z**z H0 Net Zero Transverse Vector Non-zero Net Longitudinal Vector y y x x Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• The precession frequency • Depends on the type of nuclei with a specific gyromagnetic ratio and the intensity of the external magnetic field • This is the frequency on which the nuclei can receive the Radio Frequency (RF) energy to change their states for exhibiting nuclear magnetic resonance • The excited nuclei return to the thermal equilibrium through a process of relaxation emitting energy at the same precession frequency**MRI Principles**• 90-degree pulse • Upon receiving the energy at the Larmor frequency, the transverse vector also changes as nuclei start to precess in phase • Form a net non-zero transverse vector that rotates in the x-y plane perpendicular to the direction of the external magnetic field Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**S**S w w N N z y x Figure 4.16. The 90-degree pulse causing nuclei to precess in phase with the longitudinal vector shifted clockwise by 90-degrees as a result of the absorption of RF energy at the Larmor frequency. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• 180-degree pulse • If enough energy is supplied, the longitudinal vector can be completely flipped over with a 180-degree clockwise shidf in the direction against the external magnetic field Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**S**S z w w y x N N Figure 4.17. The 180-degree pulse causing nuclei to precess in phase with the longitudinal vector shifted clockwise by 180-degrees as a result of the absorption of RF energy at the Larmor frequency. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• Relaxation • The energy emitted during the relaxation process induces an electrical signal in a RF coil tuned at the Larmor frequency • The free induction decay of the electromagnetic signal in the PF coil is the basic signal that is used to create MR images • The nuclear excitation forces the net longitudinal and transverse magnetization vectors to move Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• A stationary magnetization vector • The total response of the spin system Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Figure 4.18. The transverse relaxation process of spinning**nuclei. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• The longitudinal and transverse magnetization vectors with respect to the relaxation times • where Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Mx,y (t)**t Mz (t) t Figure 4.19. (a) Transverse and (b) longitudinal magnetization relaxation after the RF pulse. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• The RF pulse causes nuclear excitation changing the longitudinal and transverse magnetization vectors • After the RF pulse is turned off, the excited nuclei go through the relaxation phase emitting the absorbed energy at the same Larmor frequency that can be detected as an electrical signal, called the Free Induction Decay (FID) Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MRI Principles**• The NMR spin-echo signal (FID signal) Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MR Instrumentation**• The stationary external magnetic field • Provided by a large superconducting magnet with a typical strength of 0.5 T to 1.5 T • Housing of gradient coils • Good field homogeneity, typically on the order of 10-50 parts per million • A set of shim coils to compensate for the field inhomogeneity Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Gradient**Coils Gradient Coils RF Coils Magnet Patient Platform Data-Acquisition System Monitor COMPUTER Figure 4.20. A general schematic diagram of a MR imaging system. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Figure comes from the Wikipedia, www.wikipedia.org.**Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Figure comes from the Wikipedia, www.wikipedia.org.**Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MR Instrumentation**• An RF coil • To transmit time-varying RF pulses • To receive the radio frequency emissions during the nuclear relaxation phase • Free Induction Decay (FID) in the RF coil Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MR Pulse Sequences**• NMR signal • The frequency and the phase • Spatial encoding in MR imaging • Frequency encoding and phase encoding Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Sagital**y z y Axial y z x x Coronal x z Figure 4.21 (a). Three-dimensional object coordinate system with axial, sagittal and coronal image views. (b): From top left to bottom right: Axial, coronal and sagittal MR images of a human brain. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Figures come from the textbook: Medical Image Analysis,**Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Z Gradient**90 RF Pulse (Slice Selection) X Gradient Phase-Encoding (x-scan selection) Z Gradient 180 RF Pulse (Slice Echo Formation) Y Gradient Frequency Encoding (Read-Out Pulse) MR Pulse Sequences Figure 4.22. (a): Three-dimensional spatial encoding for spin-echo MR pulse sequence. (b): A linear gradient field for frequency encoding. (c). A step function based gradient field for phase encoding. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**External Magnet**S S Phase -Encoding Gradient Step Linear Gradient Positive Phase Change Varying Spatially Dependent Larmor Frequency w w Negative Phase Change Precessing Nuclei N N Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MR Pulse Sequences**• Frequency encoding • A linear gradient is applied throughout the imaging space a long a selected direction • The effective Larmor frequency of spinning nuclei is also spatially encloded along the direction of the gradient • Slice selection for axial imaging Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**MR Pulse Sequences**• The phase-encoding gradient • Applied in steps with repeated cycles • If 256 steps are to be applied in the phase-encoding gradient, the readout cycle is repeated 256 times, each time with a specific amount of phase-encoding gradient Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Spin Echo Imaging**• : • Between the application of the 90 degree pulse and the formation of echo (rephasing of nuclei • : • Between the 90 degree pulse and 180 degree pulse Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**RF Energy: 90 Deg Pulse**RF Energy: 90 Deg Pulse In Phase Relaxation Zero Net Vector: Zero Net Vector: Dephasing Random Phase Random Phase RF Energy: 180 Deg Pulse Rephasing In Phase Echo Echo - - Formation Formation Figure 4.23. The transverse relaxation and echo formation of the spin echo MR pulse sequence. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Spin Echo Imaging**• K-space • The placement of raw frequency data collected through the pulse sequences in a multi-dimensional space • By taking the inverse Fourier transform of the k-space data, an image about the object can be reconstructed in the spatial domain • The NMR signals collected as frequency-encoded echoes can be placed as horizontal lines in the corresponding 2-D k-space Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Spin Echo Imaging**• K-space • As multiple frequency encoded echoes are collected with different phase-encoding gradients, they are placed as horizontal lines in the corresponding k-space with the vertical direction representing the phase-encoding gradient values Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Figure comes from the Wikipedia, www.wikipedia.org.**Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**Spin Echo Imaging**• : the cycle repetition time • weighted • A long and a long • weighted • A short and a short • Spin-density • A long and a short Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.**TE /2**180 deg RF pulse 90 deg RF pulse RF pulse Transmitter Gz: Slice Selection Frequency Encoding Gradient TE /2 Gx: Phase Encoding Gradient Gy: Readout Frequency Encoding Gradient TE NMR RF FID Signal Figure 4.24. A spin echo pulse sequence for MR imaging. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.