Magnetic Resonance Imaging Signal Processing - Coursework Example

MAGNETIC RESONANCE IMAGING SIGNAL PROCESSING Table of Contents MAGNETIC RESONANCE IMAGING SIGNAL PROCESSING 1 1.0 Executive Summary 4 2.0 Introduction 5 2.1 Historical Background of MRI 6 2.1.1 Tomographic Imaging 6 3.0 Problem Definition 7 4.0 Methodology 8 5.0 Objectives 8 6.0 Scope 8 7.0 Components of MRI Scanner 8 7.1 The Magnet 11 7.2 RF Coils (Radiofrequency Coils) 13 7.3 Gradient Coils 14 8.0 MRI Scanning Process 14 8.1 Image Acquisition 15 8.2 Tissue magnetization 16 8.2.1 Longitudinal Magnetization and Relaxation 17 8.1.2 Transverse Magnetization and Relaxation 18 8.2 Image Reconstruction 20 8.2.1 K Space 20 8.3 Fourier Transform 21 9.0 Factors affecting Image quality in MRI 22 9.1 Field of view 22 9.2 Slice Thickness 22 9.3 Number of Excitations 22 9.4 Image Acquisition Time 23 10.0 MRI Artifacts 23 10.1 Aliasing 23 10.2 Chemical shift artifacts 23 10.3 Truncation Artifact 23 11.0 Parallel Imaging 24 12.0 Conclusion 24 13.0 References 25 1.0 Executive Summary Magnetic Resonance Imaging has grown to be the primary technique throughout the body in the practice of performing diagnoses. It is fast replacing the once much hyped Computed Tomography (CT).This may be due to the perceived advantages of MRI being non-intrusive, using non-ionizing radiation with a high resolution of soft tissues. MRI also has the capability of providing images in both two and three dimensions. MRI is able to provide images containing morphological (surface information) and functional information. The obtained image is based on multiple parameters, any of which can modify tissue contrast. MRI can generate thin-section images when the body is exposed to an electronic field. It creates a strong magnetic field which magnetizes the hydrogen atoms contained in the body tissues of human beings. The MRI creates a steady state of magnetism in the body within the human body. It then stimulates the body with radio waves to change the induced magnetism of the body. MRI then stops the radio waves and registers the electromagnetic transmission of the body. Finally, the MRI concentrates the transmitted signal then uses it to reconstruct the images of the internal organs of the body by computerized axial tomography. The use of the MRI technology has not come without challenges. The machine produces a lot of noise once switched on and patients are encouraged to put on earmuffs to minimize the discomfort the noise can cause. Furthermore, the machine takes significant amount of time to produce a clear and easy to understand image. Research is currently underway to produce machines which can produce clear images and yet minimizing the time taken to produce such images. This factor is giving physicists and neuroscientists sleepless nights. The other area that requires research is the accurate scanning of the brain. Being a target in motion, it necessitates for the use of a more refined technique to sample and hence give a better understanding of what goes on in the brain. The MRI machine also requires the patient to remain still during the entire scanning period if a clear image is to be produced. Some patients may be nervous and unable to remain still, hence they may be injected with medicine which can help them relax. All these are simple rules that are to be taken into account in order for a scan to be carried out successfully. More importantly, efforts are being made to minimize the scan time and ensuring not to compromise on image quality. 2.0 Introduction The medical fraternity has witnessed immense technological changes as scientists strive to provide solutions to the never ending chain of diseases that face the human race. This has seen the invention of sophisticated machines from the primitive traditional methods of disease diagnosis to the more sophisticated, more accurate scanning techniques which can pin point any abnormality in the human body. This has revolutionized the health sector. One of the methods that have been to diagnose diseases in the human body without using surgery or x-ray is the Magnetic Resonance Imaging (MRI). To achieve this, MRI uses powerful magnets and radio waves to create pictures of the body. The scanned images can then be stored in a computer, with a single examination being able to produce several images. MRI has the significant advantage that the patient does not feel any pain during scanning and the patient does not need time to recover. The patient can continue with their normal routine immediately after scanning. 2.1 Historical Background of MRI It all began when Nikola Tesla discovered the Rotating Magnetic Field in1882 in Budapest, Hungary. This became a fundamental discovery and all MRI machines are today calibrated in Tesla Units. Nuclear Magnetic Resonance, a technique that the MRI is based, was first discovered by Raymond Damadian, a physician working at Brooklyn’s Downstate Medical Center. He discovered that hydrogen signal in cancerous tissue stays longer even after the MRI machine is switched off than signal from normal tissue. This he, explained, is because cancerous tumors contain more water hence more hydrogen atoms. The first NMR image was produced in 1973 by Paul Lauterbur, a Chemist at State University of New York. Although it did not have the clarity of the modern ones, it was a major breakthrough in the field of medical technology. It laid the foundation of research on the Magnetic Resonance Imaging machines. The first human scan was produced in 1977, as the first MRI prototype. Today, the MRI scanners can instantly map and analyze any part of the body with a lot of details and at the same time allowing for visual diagnosis of nearly all medical conditions from a strained heart to a cancerous tissue. 2.1.1 Tomographic Imaging This is a computer based teaching package used to provide clear understanding the principles of MRI from both microscopic, macroscopic, and imaging system. Magnetic resonance started as a tomographic imaging technique for producing NMR images of a slice through the human body. The magnetic resonance image is composed of several pictures called pixels, with an intensity proportional to the NMR signal intensity of the contents of the corresponding volume element of the object being imaged. Magnetic Resonance Imaging employs the principle of absorption and emission of energy in the radio frequency range of the electromagnetic spectrum. The misleading perception that imaging using radio waves was impossible made the development of non-ionizing imaging equipment. This myth was however broken by the invention of MRI which produces based on spatial variations in the phase and frequency of the radio frequency energy being absorbed and emitted by the imaged object. 3.0 Problem Definition MRI equipment are faced with a number of challenges that hinder their effectiveness. Among these are the challenge of scan time and the time it takes for a scanner to produce an image. This becomes a major hindrance to offering health care services since it takes longer to scan a single patient, making it hard to scan many patients as it would be if the machines would have been faster enough. This may make patients die as they wait for their disorders to be scanned. The other challenges are the noise produced by the scanner as it is in use, poor clarity when scanning moving objects, e.g. the brain, with the need of patients required to remain still during the entire scanning process. All these are challenges that prompted me to embark on the research to find ways to solve these problems. 4.0 Methodology Magnetic Resonance Imaging is a high research field and I had to get a full understanding of the latest developments in the field by reading widely. I consulted printed as well as online books, journals, magazines and newspapers. I also visited MRI research websites to ensure that I came up with a comprehensive and reliable report. 5.0 Objectives The aim of this project is to propose the improvements that can be done on the MRI machine to improve the speed while at the same time preserving the image quality, by use of two algorithms, i.e. SENSE and GRAPPA. 6.0 Scope This project is concerned with trying to providing a solution to the long scan times that are characteristic of MRI machines, and image artefacts. 7.0 Components of MRI Scanner Depending on the company that manufactured the equipment, MRI equipment may have varying arrangement of the components. The main components of MRI have undergone several improvements over the years to try and make them more efficient. Since the main issues with the MRI equipment are the time it takes to produce an image and image quality, most changes have been effected on the components of the equipment to achieve these. Figure 1.1:A picture of 1.5 Tesla GE Signa scanner. Installed at the University of Hull in 1992 and upgraded in 1996 and 2003.The second upgrade improved the gradient specifications to a maximum amplitude of 23 mT/t in a rise time of 190 µs. (Gary, P. 2014) Figure 1.2: A second scanner at Hull University. This is a 1.5 Tesla system (a Philips intera), installed in 2001. Maximum gradient amplitude improved to 30 mT/m, with rise times of 200 µs. Shown here is the RF head coil on the patient bed. (Gary, P. 2014) Generally, MRI equipment is made up of three major parts, namely: The Magnet RF Coils Gradients Coils Figure 1.3: A pictorial representation of MRI equipment indicating the patient position. (Kristen, C. 2014) Figure 1.4: A block diagram for MRI system 7.1 The Magnet Figure 1.5: MRI scanner gradient magnets. (Kristen, C. 2014) This is the main component of the MRI machine. Some low field magnets are permanent or resistive, but for MRI machines above 1.0 Tesla, the magnet is usually superconductive. It is wound from an alloy, for instance Nb-Ti, which has zero electrical resistance below a critical temperature. The magnet is enclosed and cooled by a cryogen containing liquid helium, which require monthly maintenance. Poor superconductive windings will make the scanner lose over 5g per year, which causes quench; a situation where the magnet suddenly loses its superconductivity and then begin to heat up. Vents are usually attached to ensure that the magnet loses any extra heat safely. The other type of magnet found in the MRI equipment is permanent magnet constructed from ferromagnetic material. It is larger than the superconductive magnet and can function even in the absence of electricity. It has the advantage that it provides for flexibility in the MRI design. Its size and weight however makes it less popular in addition to that its ability to generate a stable magnetic field is questionable. 7.2 RF Coils (Radiofrequency Coils) Figure 1.6: The three types of RF coils showing body, head and surface coils that are the antenna for transmitting pulses and receiving signals from the body of the patient. The RF system is used for transmitting radiofrequency radiation that causes the hydrogen atoms to emit signals. The RF system then recieves the signals that are emitted and amplifies the signals so that it can be at a state that can be manipulated by the computer. The RF coil is the most essential component of the RF system. The coils are created to produce an ascillating magnetic field, which then induces an atom at a designated area to absorb RF radiation which in turn emit a signal. The coils are made in such a way that they are capable of receiving the emitted signal and transmit it to the computer. RF coils may be either saddle RF coils or solenoid RF coils. The coil is aligned as much as possible with the patient to increase efficiency and minimize signal to noise ratio by focusing only on the point of interest. The transmitters and the recievers in the RF system are highly sensitive to signal. 7.3 Gradient Coils The fuctional role of the gradient coils is to produce linear changes in magnetic field in each of the x, y and z axes. Through combination of gradients in pairs, it is possible to produce oblique images. Gradient specifications are stated in terms of a slew rate which is equal to the maximum achievable amplitude divided by the rise in time. Typical modern slew rates are in the range of 150 T/m-s. the gardient coils are shielded in a similar manner to the main windings to reduce eddy currents induced in the cryogen which would otherwise degrade the image quality. 8.0 MRI Scanning Process 8.1 Image Acquisition This is the first step in Magnetic resonance imaging and forms the basis of successful image formation by MRI machine. The patient is made to lie on the table and the machine is switched on. A strong magnetic field is then applied on the patient. There are three methods to generate this field; fixed magnets, resistive magnets and super-conducting magnets. Fixed and resistive magnets are restricted to field strengths below 0.4T and thus cannot generate the higher magnetic strengths required for clear imaging. The magnetic field required must be strong and uniformly aligned in space and stable in time. The magnetic field thus applied causes hydrogen atoms in the body to be excited and thus align with the external magnetic field. A pulse of low energy radio waves is then sent to the body. The aligned hydrogen atoms then re-transmit the waves which are then received by the receiver of the RF system and transmitted to the computer for processing. The ability of MRI to distinguish between different types of tissues is based on the fact that different tissues , both normal and pathologic, become magnetized to different levels or will change their levels of magnetization (relax) at different rates. The time required to acquire images is determined by the duration of the imaging cycle or cycle repetition time (TR), and the number of cycles. The more the number of cycles, the better the image quality. 8.2 Tissue magnetization The placement of a tissue in the magnetic field makes the tissue reach its maximum magnetization within a few seconds and it can remain in that state of maximum magnetization unless there is a change in the magnetic field or if there are pulses of RF energy applied. The tissue to be scanned is cycled through changes in its magnetization during the imaging cycle. The direction of tissue magnetization is specified in reference to the direction of the applied magnetic field. The tissue can be subjected to either longitudinal magnetization (the direction parallel to the direction of the field), or transverse magnetization (tissue magnetized at 90⁰ with respect to the direction of the magnetic field) The direction of tissue magnetization can be changed (flipped) by applying a pulse of RF energy and this is done throughout the imaging process. The magnetization angle flip is determined by the duration and strength of the RF pulse. 90⁰ and 180⁰ flip angles are the most common. A 90⁰ pulse applied to longitudinal magnetization flips the tissue to the transverse plane. This reduces the longitudinal magnetization to zero, a condition called saturation. It also produces transverse magnetization which is unstable or excited condition. A 90⁰ pulse applied to longitudinal magnetization produces both saturation of the longitudinal magnetization and a condition of saturation. The quality of the image obtained will depend on the following times of the scanning period: Longitudinal magnetization relaxation time (T1) Transverse magnetization relaxation time (T2) 8.2.1 Longitudinal Magnetization and Relaxation If magnetization is temporarily redirected by an RF pulse, the tissue will return to its original longitudinal position over a period of time. If the longitudinal magnetization is considered individually, it regrows after it has been saturated. This regrowth of longitudinal magnetization is the relaxation process, which occurs after saturation. All this is determined by the characteristics of the material and the strength of the magnetic field. Longitudinal magnetization grows exponentially. The brightness of the image formed in MR imaging is dependent on the level of magnetization. The brightness of the tissue changes during saturation to a dark image which recovers brightness during the relaxation period. Figure 1.7: The growth of longitudinal magnetization (and tissue brightness) during the relaxation process following the saturation (Sprawl Educational Foundation, 2011) The relaxation time is hard to predict because of its exponential nature. Conventionally, the time required to reach a magnetization of 63% is taken as the longitudinal relaxation time, T1. Factors that affect either the proton resonance frequency or the frequency associated with the molecular motions will most likely affect the values of T1. Small molecules will tend to have a relatively longer T1 values than larger molecules. Figure 1.8: T1 image showing the relationship of tissue brightness to T1 values and the level of magnetization during the longitudinal relaxation process. (Sprawl Educational Foundation, 2011) 8.1.2 Transverse Magnetization and Relaxation This is produced by applying a pulse of RF energy to the magnetization tissue. This is achieved by a 90⁰ pulse which converts longitudinal magnetization into transverse magnetization. This is an unstable or excited condition that quickly decays after termination of the termination of the excitation pulse. The decay of transverse magnetization is a relaxation process characterized by specific relaxation times, T2. Different tissues have different T2 values that are used to tell tissues apart and adjust the image contrast. Table 1.1: T1 and T2 values for various tissues T2 (msec) T1 (0.5T) (msec) T1 (1.5T) (msec) Adipose (fat) 80 210 260 Liver 42 350 500 Muscle 45 550 870 White Matter 90 500 780 Gray Matter 100 650 920 CSF 100 1800 2400 Transverse magnetization is used during tissue formation so as to develop the image contrast based on the differences in T2 values, and to generate the RF signals emitted by the tissue. Transverse magnetization is a spinning magnet condition that generates an RF signal. Figure 1.8: transverse magnetization decay during the relaxation process and the associated tissue brightness (Sprawl Educational Foundation, 2011) The T2 value is the time required for 63% of the initial magnetization to dissipate, leaving 37% of the initial magnetization. Tissues with shorter T2 values darken faster leaving tissues with longer T2 values. Figure 1.9: T2 image showing relationship between tissue brightness and signal intensity (SEF, 2011) 8.2 Image Reconstruction 8.2.1 K Space During the image acquisition process, the signals are collected, digitized and stored in the computer memory. This is a configuration process known as k space, and it is divided into lines of data that are filled one at a time. The k space must be completely filled before the image reconstruction process can be terminated. The size of the k space (number of lines) is determined by the necessity for good image quality. Figure 2.0: Imaging process illustrating the k space The image reconstruction process is usually fast compared to the acquisition process and do not require any adjustments by the machine operator. The relationship between k space data and the image data is Fourier transformation. In 2-D Fourier transform imaging, a line data correspond to the digitized MR signal at a particular encoding level. 8.3 Fourier Transform This is an operation which transforms functions from time to domain. After the k space is completely filled up, it undergoes Fourier transform. There are several reconstruction methods, but the most common for clinical applications is the 2-D Fourier transform. It is generally a mathematical procedure that sorts composite signals into individual frequency and phase components. Since each voxel in a row emits a unique signal frequency, and each voxel in a column a unique phase, the Fourier transformation is able to determine the location of each signal component and direct it to its respective pixel. Figure 2.1: The concept of signal encoding and image reconstruction 9.0 Factors affecting Image quality in MRI There are several factors that the MRI operator should be aware of when and before performing a scan as the can affect the quality of the image obtained. 9.1 Field of view An image consists of field of view that related to the region of interest to be covered. Most MRI equipment have field of view ranging between 10 to 50cm. this mean for instance, if the entire spinal cord is to be scanned in the sagittal plane, its upper and lower parts need complementary series of pulse sequence. The other uncovered parts would transmit signals which will be detected as noise by the scanner and this will lead to the formation of a distorted image. 9.2 Slice Thickness Giving each slice a thickness needs the excitation of a band of nuclei by an excitation pulse. Increasing the thickness of slices increases the SNR. As the thickness of a slice increases, the resolution decreases and SNR also increases. A thin slice produces an image with high resolution. 9.3 Number of Excitations Each signal contributing to the formation of an image in MRI can be received once or collected several times using repeated excitations. The average signal values can then be used to generate the image. This increases precision of the image. 9.4 Image Acquisition Time The longer the acquisition time, the more chances that the patient moves and the more chances of generation of artifacts that prevent interpretation of the images. The optimum scanning time should thus be maintained so as to produce appreciable image quality free from artifacts. 10.0 MRI Artifacts Imaging in MRI has come with its own score of challenges. These are as discussed below: 10.1 Aliasing This usually appears when the diameter of scanned area is greater than the dimensions of the scanned area. 10.2 Chemical shift artifacts These appear at the interfaces of water and fat since the processional frequency of protons is slightly different in the substances. The system displays them as dark regions of signal void on one side of the water containing tissue and a region of bright signal at the other end of the water fat interface. 10.3 Truncation Artifact These are bright and dark lines that are seen parallel and adjacent to boarders of abrupt intensity. These artifacts are commonly seen in phase encoding direction. 11.0 Parallel Imaging Parallel acquisition combines the signals of several coil elements in a phased array to reconstruct the image. The objectives of parallel imaging are either to improve the SNR or to increase the image acquisition and reduce scan time. Parallel acquisition algorithms can be divided into two main groups: Those that reconstruct the global image from the images produced by each coil (reconstruction in the image domain, after Fourier transform: Sensitivity Encoding (SENSE) Those that reconstruct the Fourier plane pf the image from frequency signals of each coil (reconstruction in the frequency domain, before Fourier transform): Generalized Auto-calibrating Partially Parallel Acquisition (GRAPPA) 12.0 Conclusion The use of MRI has revolutionized the world of medicine as the methods that were earlier used to view the internal human organs were accompanied by a score of side effect, some more lethal than the disease being scanned. The use of MRI for scanning is totally harmless and the images produced are easier to understand. Although the images would occasionally be distorted due to some factors, the development of SENSE and GRAPPA has enhanced the quality of output image. 13.0 References 1. R. Gonzales, R. WoodsDigital Image Processing, Addison-Wesley Publishing Company, 1992, pp 81 - 125. 2. B. HornRobot Vision, MIT Press, 1986, Chaps 6, 7. 3. NessAiver. All you really need to know about MRI physics. 1997. 4. Kastler. Comprendre l'IRM. 2006. 5. Korin, Felmlee. Adaptive technique for three-dimensional MR imaging of moving structures. Radiology. 1990 Oct;177(1):217-21. 6. Hood, Ho. Chemical shift: the artifact and clinical tool revisited. Radiographics. 1999 Mar-Apr; 19(2):357-71. 7. Bydder, Rahal. The magic angle effect: a source of artifact, determinant of image contrast, and technique for imaging. J Magn Reson Imaging. 2007 Feb;25(2):290-300. 8. Certaines and Cathelineau. Safety aspects and quality assessment in MRI and MRS: a challenge for health care systems in Europe. J Magn Reson Imaging. 2001 Apr;13(4):632-8. 9. Ihalainen, Sipila. MRI quality control: six imagers studied using eleven unified image quality parameters. European radiology. 2004 Oct;14(10):1859-65 A. JainFundamentals of Digital Image Processing, Prentice-Hall, 1989, pp 15 - 20. 10. MarionAn Introduction to Image Processing, Chapman and Hall, 1991, Chap. 9. Read More

2.0 Introduction The medical fraternity has witnessed immense technological changes as scientists strive to provide solutions to the never ending chain of diseases that face the human race. This has seen the invention of sophisticated machines from the primitive traditional methods of disease diagnosis to the more sophisticated, more accurate scanning techniques which can pin point any abnormality in the human body. This has revolutionized the health sector. One of the methods that have been to diagnose diseases in the human body without using surgery or x-ray is the Magnetic Resonance Imaging (MRI).

To achieve this, MRI uses powerful magnets and radio waves to create pictures of the body. The scanned images can then be stored in a computer, with a single examination being able to produce several images. MRI has the significant advantage that the patient does not feel any pain during scanning and the patient does not need time to recover. The patient can continue with their normal routine immediately after scanning. 2.1 Historical Background of MRI It all began when Nikola Tesla discovered the Rotating Magnetic Field in1882 in Budapest, Hungary.

This became a fundamental discovery and all MRI machines are today calibrated in Tesla Units. Nuclear Magnetic Resonance, a technique that the MRI is based, was first discovered by Raymond Damadian, a physician working at Brooklyn’s Downstate Medical Center. He discovered that hydrogen signal in cancerous tissue stays longer even after the MRI machine is switched off than signal from normal tissue. This he, explained, is because cancerous tumors contain more water hence more hydrogen atoms.

The first NMR image was produced in 1973 by Paul Lauterbur, a Chemist at State University of New York. Although it did not have the clarity of the modern ones, it was a major breakthrough in the field of medical technology. It laid the foundation of research on the Magnetic Resonance Imaging machines. The first human scan was produced in 1977, as the first MRI prototype. Today, the MRI scanners can instantly map and analyze any part of the body with a lot of details and at the same time allowing for visual diagnosis of nearly all medical conditions from a strained heart to a cancerous tissue. 2.1.

1 Tomographic Imaging This is a computer based teaching package used to provide clear understanding the principles of MRI from both microscopic, macroscopic, and imaging system. Magnetic resonance started as a tomographic imaging technique for producing NMR images of a slice through the human body. The magnetic resonance image is composed of several pictures called pixels, with an intensity proportional to the NMR signal intensity of the contents of the corresponding volume element of the object being imaged.

Magnetic Resonance Imaging employs the principle of absorption and emission of energy in the radio frequency range of the electromagnetic spectrum. The misleading perception that imaging using radio waves was impossible made the development of non-ionizing imaging equipment. This myth was however broken by the invention of MRI which produces based on spatial variations in the phase and frequency of the radio frequency energy being absorbed and emitted by the imaged object. 3.0 Problem Definition MRI equipment are faced with a number of challenges that hinder their effectiveness.

Among these are the challenge of scan time and the time it takes for a scanner to produce an image. This becomes a major hindrance to offering health care services since it takes longer to scan a single patient, making it hard to scan many patients as it would be if the machines would have been faster enough. This may make patients die as they wait for their disorders to be scanned. The other challenges are the noise produced by the scanner as it is in use, poor clarity when scanning moving objects, e.g. the brain, with the need of patients required to remain still during the entire scanning process.

All these are challenges that prompted me to embark on the research to find ways to solve these problems. 4.

Read More