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Three-dimensional multispectral stochastic image segmentation Johnston, Brian Gerard 1994

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THREE-DIMENSIONAL MULTISPECTRAL STOCHASTIC IMAGESEGMENTATIONByBrian Gerard JohnstonB. Sc. (Computer Science) Memorial University of Newfoundland 1990Ph. C. (Pharmacy) Cabot Institute of Technology 1982A THESIS SUBMITTED IN PARTIAL FULFILLMENT OFTHE REQUIREMENTS FOR THE DEGREE OFMASTER OF SCIENCEinTHE FACULTY OF GRADUATE STUDIESDEPARTMENT OF COMPUTER SCIENCEWe accept this thesis as conformingto the required standardJanuary 1994TUNIVERSIT BRITISH COLUMBIA© Brian Gerard Johnston, 1994In presenting this thesis in partial fulfillment of the requirements for an advanced degree at theUniversity of British Columbia, I agree that the Library shall make it freely available for reference and study. I further agree that permission for extensive copying of this thesis for scholarlypurposes may be granted by the head of my department or by his or her representatives. Itis understood that copying or publication of this thesis for financial gain shall not be allowedwithout my written permission.Department of Computer ScienceThe University of British Columbia2366 Main MallVancouver, CanadaV6T 1Z4Date:i/’(IAbstractCurrent methods of lesion localization and quantification from magnetic resonance imaging, andother methods of computed tomography fall short of what is needed by clinicians to accuratelydiagnose pathology and predict clinical outcome. We investigate a method of lesion aild tissuesegmentation which uses stochastic relaxation techniques in three dimensions, using images frommultiple image spectra, to assign partial tissue classification to individual voxels. The algorithmis an extension of the concept of Iterated Conditional Modes first used to restore noisy andcorrupted images. Our algorithm requires a minimal learning phase and may incorporate priororgan models to aid in the segmentatioll. The algorithm is based on local neighbourhoods andcan therefore be implemented in parallel to enhance its performance. Parallelism is achievedthrough the use of a datafiow image processing development package which allows multipleservers to execute in parallel.11Table of ContentsAbstract iiTable of Contents iiiList of Tables viiList of Figures viiiAcknowledgement x1 introduction 11.1 Overview of Segmentation Methods 31.2 Overview of the Thesis o1.2.1 Chapter Summary 62 Computerized Tomographic Imaging 82.1 Introduction 82.2 Computed Tomography(CT) 92.2.1 Physical Principles 102.2.2 Practical Aspects 142.2.3 Conclusion 152.3 Magnetic Resonance Imaging(MRI) 152.3.1 Introduction 152.3.2 Physical Principles 162.3.3 Practical Aspects 192.3.4 Conclusion. 201112.4 Emission Computed Tomography (PET and SPECT) 212.4.1 Introduction 212.4.2 Physical Principles 212.4.3 Practical Aspects 232.4.4 Conclusion 252.5 Combining Images 253 Basics of Image Segmentation 273.1 Introduction 273.2 Definitions 283.2.1 Techniques 303.3 Summary 334 Segmentation Applied to Medical Imaging 354.1 Difficulties with Medical Imaging 354.1.1 Partial Volume Effect 364.1.2 CT 364.1.3 MRI 374.1.4 PET/SPECT 384.2 Current Algorithms 394.2.1 Manual Tracing 394.2.2 Edge Detection 404.2.3 Thresholding and Cluster Analysis 404.2.4 Region Growing 424.3 Extensions to Fundamental Techniques 434.3.1 Mathematical Morphology 434.3.2 Pyramidal Techniques 454.4 Model-Based Approaches 46iv4.5 Markov Random Fields and the Gibbs Distribution 494.6 Iterated Conditional Modes 524.6.1 Segmentation Using Iterated Conditional Modes 535 3D Multispectral Stochastic Volume Segmentation 585.1 Returning to Basic Theory 585.2 Extensions to Iterated Conditional Modes 605.2.1 Neighbour Interaction Parameters 615.2.2 Neighbour Counts 625.2.3 Histogram Re-evaluation 625.2.4 Prior Organ Models 625.2.5 Convergence 635.2.6 Multispectral Approach 645.2.7 Parallelism 645.3 Implementation Platform 645.3.1 Dataflow Paradigm 655.3.2 WIT 665.3.3 Extensibility Using WIT 705.3.4 Parallelism Using Multiple Servers 715.3.5 Limitations of the Dataflow Approach 715.4 WIT Implementation of 1CM 746 Algorithm Testing and Results 816.1 Multiple Sclerosis 816.2 Results Analysis 836.2.1 Initial Histograms 856.2.2 Initial Neighbourhood Interaction Parameters 896.2.3 Recalculated Histograms 91V6.2.4 Recalculated Neighbourhood Interaction Parameters6.3 Segmentation Results6.3.1 Ti Segmentation6.3.2 T2 Segmentation6.3.3 Combining Ti and T2 Segmentations6.3.4 Post-Processing of the Segmentation6.3.5 Visualizing Partial Volumes6.4 Lesion Volume Analysis6.5 General Conclusions and Future Work6.5.1 Future Work949596969999101105108109AppendicesA 1CM Source Code KernelBibliography112112116viList of Tables6.1 Initial neighbourhood interaction parameters obtained from Ti image seqneuce. 896.2 Initial neighbourhood interaction parameters obtained from T2 image sequence. 896.3 Recalculated neighbourhood interaction parameters obtained from Ti image sequence 946.4 Recalculated neighbourhood interaction parameters obtained from T2 image sequence 95VIIList of Figures2.1 The 1-D projection g(8, ) of the 2-D function f(x, y) 122.2 The pulse sequence of a conventional MRI imaging system 182.3 Cross-sectional view of conventional Anger gamma camera 224.4 Examples of morphological operations 444.5 Pyramid representation of a one-dimensional signal 454.6 Neighbourhood systems in 2D 504.7 Neighbourhood systems in 3D 515.8 Sample WIT screen 675.9 Hierarchical igraph in WIT 69.5.10 Expanded hierarchical operator 695.11 Example of deadlock in a WIT Igraph 725.12 WIT igraph of 1CM algorithm 745.13 Expanded WIT igraph of icrnlnitialize operator 755.14 MRI Ti-Weighted data from which sample image is selected for ROl analysis. 765.15 Expanded WIT igraph of segmentation operator seg Volume 786.16 MS lesions on MRI 826.17 MRI series — Ti weighted 836.18 MRI series — T2 weighted 846.19 Histograms of Ti weighted MRI series 866.20 Histograms of T2 weighted MRI series 876.21 Recalculated histograms of Ti weighted MRI series 926.22 Recalculated histograms of T2 weighted MRI series 93viii6.23 Segmentation of Ti Echo Sequence 976.24 Segmentation of T2 Echo Sequence 986.25 Combined Segmentation of T1/T2 Echo Sequences 1006.26 Manual Segmentation overlaid on combined T1/T2 Segmentation 1016.27 Combined Lesion Segmentation of Ti/T2 Echo Sequences after post-processing. 1026.28 Illustration of partial volume assignment using colour images (No post-processinghas been applied.) i036.29 Illustration of partial volume assignment using colour images (Post-processinghas been applied.) 1036.30 Colour-map used to enhance partial volume characteristics of segmentation. . . . 1046.3i Graphs of lesion volumes determined at all stages of the segmentation, includingmanual segmentation 1066.32 Expanded graphs of lesion volumes of final segmentation and manual segmentation. 107ixAcknowledgementThe contributions, both physical and moral, of the following people are gratefully acknowledged:Dr. L.C.E. Phillips, my wife, without whose inspiration and support, this work could notpossibly have materialized;Dr. M.S. Atkins of Simon Fraser University and Dr. K.S. Booth of University of BritishColumbia, my co-supervisors in this project;Torre Zuk, my student reader, with whom I collaborated and, at times, conspired;Dr. James Little of University of British Columbia, the “third” reader of this thesis, whoseinput with respect to this work and otherwise, is greatly appreciated;The MS MRI Study Group at UBC Hospital, especially Andrew Riddehough and Dr. GuojunZhou, who supplied MRI scans and hand segmented the data for our analysis;Dr. K. Poskitt, of Children’s Hospital in Vancouver, who supplied both motivation and patientdata to the project;Terry Arden, the creator of WIT, the image processing platform on which the software portionof this thesis is based.Financial support for this project has been provided in part by the Natural Sciences and Engineering Research Council of Canada.xChapter 1IntroductionSince the advent of computer image processing, researchers have been seeking ways in whichto classify objects and the relationships between objects represented in these images. In thefield of medicine in particular, many attempts have been made to automatically classify andquantify tissues, organs, and disease states from images obtained by various medical imagingsources. It is the ease with which humans can so readily interpret these images that has beenthe impetus for attempting to force computers to do the same.Image segmentation is possibly the single most important area of image analysis researchbeing carried out today. Image segmentation can be considered the separation of an image intodifferent regions, each having a certain property, for example average gray level or texture. It isusually the first step in a process leading to description, classification and interpretation of animage by higher level processes. However, classificatioll and interpretation may form part of thesegmentation process itself. The applications of image segmentation are many and range frompattern recognition in robot vision systems to innumerable medical uses including aiding in thediagnosis, evaluation and treatment of disease. It is the application of image segmentation tomedical images which has motivated the development of this thesis.For many years physicians have been producing and analyzing medical images, from X-raysto ultrasound. Physicians usually employ computers and sophisticated hardware to producethe images and rely on their medical expertise and knowledge to analyze the images visually.There are many types of medical imaging techniques being employed in hospital settings today.We shall be concerned only with a subset of those techniques, however, this subset forms asubstantial concentration of the total amount of medical imaging being carried out today. The1Chapter 1. Introduction 2types of imaging which we shall encounter are each a category of what is termed tornographicimaging. That is, the images obtained from each of these modalities are pictures of cross-sectional slices of different areas of the human body. Multiple contiguous slices are combinedto provide a 3D volume represeuting selected organs of interest within the body.When analysing tomographic images, the physician is most often attempting to identify andquantify lesions, for example, cancerous tumours or cysts, which may be present in some organin the patient. Today the state of the art in quantifying lesions on medical scans is defined bythe manual outlining of the lesions on every slice in the scan, lesion by lesion, slice-by-slice. Theareas defined by the hand-drawn lesions are then summed slice-by-slice to determine the volumesof the lesions. The measurement of volumes aids the physician in determining a diagnosis anda prognosis with respect to the disease state of the patient. Lesions are also measured overtime, foliowing therapy, in order to assess the progress of the patient and determine the efficacyof the treatment being applied. Most often, in the course of imaging a patient over time,different medical personnel are responsible for the analysis of the medical scans obtained fromthe patient on any one occasion. This can lead to bias and inconsistencies in the identificationand measurement of lesions, and consequently in the diagnosis and evaluation of the patient.Accurate automatic lesion detection could provide a consistent, unbiased account of the diseaseprocess under investigation.Image segmentation, including medical image segmentation, has been studied extensivelyin the literature and many algorithms have been developed in an attempt to solve the problem.The efficacy and accuracy of many of these algorithms have not been clearly demonstrated. Asa result, the number of medical teams employing these algorithms in practise is quite small.The reasons for the difficulties encountered in general medical image segmentation are many.For example, the tremendous variation in the output of medical imaging devices makes it difficult to design a segmentation algorithm which will be effective in more than one imagingmodality, so most researchers carry out their studies using a single modality. Another problemis that no lighting or depth cues, generally available in other types of images, are observableChapter 1. Introduction 3in medical images. There are no shadows from light sources, and often no discernible foreground/background contrast to aid in the analysis. A third complicating factor in medicalimage segmentation is the fact that researchers involved in image segmentation work are generally computer scientists and engineers, while the people who produce and analyse medicalimages are physicians and medical technicians. It is difficult to merge the knowledge and expertise of both fields to acquire the composite knowledge that is essential to a valid solution tothe problem. The requisite multidisciplinary nature of this work is another motivating factor inthis thesis. We have endeavoured to maintain an ongoing liaison with several medical imagingcentres during the development of the research.One major obstacle which continues to complicate the segmentation of medical images is thepartial volume, or volume averaging problem. At surfaces between objects the correspondingimage elements (pixels in 2D or voxels in 3D) may be composed of more than one object,for example, gray matter and white matter in the brain. Most segmentation techniques try toclassify each pixel in an image as belonging to one type of structure. If volume averaging occursat a significant rate, which it does in medical images due to inherently poor spatial resolution,this will cause significant artifacts in the segmentation of these images.1.1 Overview of Segmentation MethodsIn general, image segmentation algorithms can be loosely categorized into thresholding methods,edge detection, and region oriented techniques.The simplest method of image segmentation involves thresholding. All pixels which have acertain property such as falling into a given intensity range are classified as belonging to thesame group. All pixels outside the given range are not included in the object. Most thresholdingtechniques involve a binarization of the image into foreground and background objects. Thislimits the application of these techniques to images having few objects. Another drawback tothresholdirig is the difficulty in the proper selection of the threshold value required to optimallyextract the desired objects. Many factors affect the observed intensity value of an object in anChapter 1. Introduction 4image. For example, the characteristics of the imaged material, the proximity of an object tonearby objects, and imaging conditions such as lighting and shadows ali combine to make itdifficult to obtain an optimal threshold value.Edge detection methods of image segmentation involve locating significant intensity changesin images which can most often be interpreted as edges between objects. Although manyimprovements in edge detection have been demonstrated in recent years, the methods are stilicomplicated by the difficulty of finding actual object boundaries as opposed to noise or artifacts.Foliowing edge detection it is often the case that many gaps exist along the detected contoursof an object. The complexity of properly linking the fragmented edges which most often resultfrom the application of these techniques further detracts from their general usefulness.The third general class of image segmentation techniques is defined by the region-orientedmethods. These techniques assume that objects are defined by individual, closed regions inspace. Region analysis techniques are further broken down into region growing methods andregion splitting and merging. In region growing, a pixel or pixels in the image are used as aseed and an analysis is performed of the neighbours of the seed to determine inclusion into theregion. This analysis is iteratively applied until the object ceases to grow further. The splitand merge methods of region analysis work by iteratively splitting the image into smalier andsmalier regions until it is determined that the resulting regions have some uniform property.The results of the image splitting are then merged with one another if it is determined thatthe merged regions also satisfy the desired property. The difficulty of defining the uniformityproperty and the complexity of applying these techniques detract from their general application.Recently the above general segmentation techniques have been augmented by the incorporation of mathematical morphology, pyramidal schemes, and model-based image segmentation. Ithas been observed that accurate segmentation of many images, especialiy medical images, wilirequire external knowledge about the object represented in the image. In order to incorporateexternal knowledge many organ and tissue models have been applied to the segmentation ofChapter 1. Introduction 5medical scans with limited success. Most of these model-based techniques involve the acquisition and analysis of many data sets in order to form the model. For this reason the success ofthese methods to date has been marginal.In this thesis we have extended a model-based approach which has been investigated inthe literature. The model used assumes the given image data represents a Markov randomfield (MRF). Using MRFs, we exploit the fact that pixels (or in 3D, voxels) in a given localneighbourhood of the image have similar intensity. The method we have implemented is iterativeand on each iteration an analysis is made of each voxel and its neighbours. Based on thisanalysis the voxel is classified. At each iteration every voxel in the volume is assigned a set ofprobabilities which represent the percentage of that voxel considered to be a particular tissuetype. In this manner, we present a solution to the partial volume problem. The classificationvalues for each voxel eventualiy converge if the MRF assumption is valid. The model usedrequires a minimum of user interaction in order to train the algorithm.The algorithm has been implemented in 3D using a visual datafiow programming environment. The use of this development environment has enabled us to paralielize the computation,which because of its 3D nature is relatively complex.1.2 Overview of the ThesisThis thesis has been designed to be readable and understandable by persons with a moderateComputer Science or Engineering background. Because of the extensive medical nature ofthe thesis, an attempt has been made to include as much background material as possible,relative to the medical aspects of the thesis. The segmentation solution presented, as weli asthe background literature leading up to the solution, employs a significant amount of statisticsand probability theory. However, readers with an introductory knowledge of these subjectsshould have no difficulty with the material presented here.This thesis, although essentialiy self-contained, is not meant to be read in isolation from thevast literatnre available concerning medical image segmentation. Interested readers are stronglyChapter 1. Introduction 6encouraged to explore the extensive bibliography at the end of the thesis.1.2.1 Chapter SummaryAs mentioned previously, the thesis has been written with the intent of applying its resultsto medical images. In light of this fact, we first introduce computerized medical imaging inChapter 2. Each of the commonly used methods of medical imaging including ComputedTomography (CT), Magnetic Resonance Imaging (MRI) and Emission Computed Tomography(ECT), is discussed in detail. For each imaging modality we present the physical principlesunderlying the technique, its main applications and its limitations. A small discussion of howresearchers have combined the various techniques in order to enhance their diagnostic potentialis also presented. This chapter has been included to provide the reader with informationnecessary to understand the medical terminology and references found in later chapters. Aswell, it provides an indication of the difficulty which arises in analysis of the images obtainedfrom these techniques.Chapter 3 introduces the problem of image segmentation. Some formal definitions andnotation are provided followed by a discussion of the fundamental techniques used to solve theproblem. The inherent advantages and disadvantages of each of these methods are also given.Each of the imaging methods discussed in Chapter 2 has unique features which complicatethe segmentation problem and detract from the discovery of a general solution which will workfor all modalities. In Chapter 4 these features are presented, followed by a discussion of howthe general segmentation techniques of Chapter 3 have been extended to medical images. Adetailed discussion of model-based segmentation methods is then given. Special consideration isgiven to the method of Iterated Conditional Modes, a model-based method employing Markovrandom fields. This technique provides the basis upon which our solution is built.We have extended and adapted the Iterated Conditional Modes method presented in Chapter 4 to incorporate 3D, partial volume features and this forms the bulk of the discussionChapter 1. Introduction 7contained in Chapter 5. A multispectral approach is presented which combines the segmentations obtained from independent image scans of the same organ. These scans are first aligned,or registered, so that corresponding voxels from each set represent the same structure. In thecase of MRI, registered independent scans can often be acquired simultaneously so that physicalalignment of the images is not necessary. A discussion of how the algorithm has been designedso that its implementation is easily parallelized is also included.The algorithm presented in Chapter 5 has been implemented using a visual datafiow programming environment specially designed for image processing. The environment allows rapiddevelopment of algorithms and provides explicit parallelism by distributing the computationto multiple workstations. The visual programming environment and the implementation of thealgorithm using the environment are also discussed in Chapter 5.The algorithm has been applied to multispectral MRI scans of the brains of Multiple Sclerosispatients. Multiple Sclerosis causes lesions in the brain which are visible on MRI scans. Thesegmentations obtained are evaluated visually and by a lesion volume comparison with handdrawn lesions obtained over the entire image volumes. The results obtained by our algorithmare presented in Chapter 6, and compare favourably with the hand drawn versions. Followinga discussion of the results of experiments using our algorithm, some future directions this workmay take in the coming months are also given. This will include further experimentation usingphantom or simulated data, improvements to the algorithm, and the development of an accuratemodel of brain tissue and lesions.Chapter 2Computerized Tomographic Imaging2.1 IntroductionA revolution has taken place over the last 20 years in diagnostic medical imaging, integratingadvances in the fields of medicine, physics, computer science and engineering. The result is avast array of tomographic medical imaging techniques designed to exploit the electro-magneticwave spectrum to the fullest. Tomographic imaging involves obtaining multiple projectionsthrough each of many planes or slices through the body. These multiple projections are usedto create images of consecutive cross-sections of interest. Together, these cross-sections ortornograrns form a 3D volume image of the organ(s) of interest. The manner in which theseprojections are obtained defines the types of computerized tomographic imaging currently available. The tomographic imaging repertoire now includes computed tomography (CT), magneticresonance imaging (MRI), and emission computed tomography (ECT) which is further brokendown into two classes, single photon emission computed tomography (SPECT) and positronemission tomography (PET).CT provides images of internal structures by measuring the attenuation of X-Ray beamspassed through body. Images are obtained with MRI using a combination of the inherentresonance characteristics of atomic nuclei and the application of a strong magnetic field to thepatient. Varying tissue characteristics can be determined and the spatial locations of the atomicnuclei can be discovered through gradient applications of further magnetic fields in orthogonaldirections.ECT yields images of slices through the body by measuring the gamma ray flux emittedby radiotracers, chemicals which are combined with radioactive nuclei and injected into the8Chapter 2. Computerized Tomographic Imaging 9patient. Different radiotracers have affinity for different tissues and locate selectively in theorgan of interest. Depending on the method of creation of the gamma ray photons, ECThas evolved into two separate imaging modalities; positron emission tomography (PET) andsingle photon emission computed tomography (SPECT). Both of these methods are capable ofquantitatively measuring metabolic and physiological processes.The results of each of the above imaging modalities can be used to develop 3D models of theorgans or tissues being imaged. Using advanced computer graphics techniques, the images canbe correlated and interpolated to compute the volumes and surfaces of the objects. These volumes can then be viewed from any desired angle and the usual post-processing techniques suchas thresholding, scaling, contrast enhancement, etc., previously applied to the two dimensionalviews, can be applied to the 3D image.The purpose of this chapter is to provide an introduction to each of the currently availabletomographic imaging techniques, to describe the fundamental aspects of the physics of each andto establish a framework for the remainder of the thesis. It is not intended to be an exhaustivesurvey. The interested reader is encouraged to explore the reference list at the end of the thesisfor further details on each technique.The images obtained from each of these methods can also be combined or registered to yielda composite view, consisting of both the structural information obtained from CT or MRI andthe functional information granted by SPECT and PET. The registration of multi-modalityimages serves to enhance the diagnostic potential of any single technique. The final section inthis chapter discusses some of the methods and difficulties associated with image registration.2.2 Computed Tomography(CT)Since its conception in 1971, computed tomography, or computerized axial tomography (CAT),has revolutionized the field of diagnostic imaging and provided the impetus for the developmentof more advanced imaging modalities such as magnetic resonance imaging. Known more familiarly as CAT scanning, this technique provides images of the internal structures of organs byChapter 2. Computerized Tomographic Imaging 10measuring the X-ray attenuation of underlying tissues in a slice through the body. A series of1-D projections is obtained, from which tomographic reconstruction methods are used to obtaina 2-D image of the slice. Because noise from over- and under-lying tissues, so detrimental iuordinary X-ray imaging, is substantialiy reduced, much better resolution and contrast betweentissues is obtained. A series of 2-D images of a given portion of the body under study can beused to obtain volumetric images using either volume rendering or surface rendering techniquesprovided by advanced computer graphics.2.2.1 Physical PrinciplesImaging of the body with computed tomography is accomplished by measuring the attenuationof X-ray beams lying entirely within successive planes of the section being imaged. In orderto obtain the 1-D projections necessary to reconstruct the image accurately, the attenuationsmust be measured at many different angles around the body. This results in a need for imagingequipment which can be rotated at an angle which is transverse to the long axis of the body.Hence, most of the images obtained in this manner are transaxial images.When Geoffrey Hounsefield of EMI in Great Britain first experimented with CT in 1972,the source/detector arrangement consisted of a single X-ray generator and a single detectormechanism which would exist at opposing sides of the area to be imaged [123]. By translatingboth the source and detector coincidentaliy, through the plane of interest, a single view wasobtained. The unit would then be rotated by 10 and the process repeated until 180 such viewswere obtained. Each view required 160 translations thus culminating in 28,800 ray sums beingobtained. Each such slice would take approximately 4 minutes, creating considerable difficulties,since many slices would have to be obtained to provide a worthwhile study.This first generation CT scanner has been succeeded by three major design modificationsculminating in the modern fourth generation scanners available to day. In the fourth generationdesign the X-ray is emanated in fan-beam fashion extending over the entire plane of interest.The detectors, of which there are as many as 1200, are arranged in a static ring around theChapter 2. Computerized Tomographic Imaging 11patient. Thus no translation of the source is necessary and a complete scan can be obtainedfrom a single rotation of the source/detector coupling through an arc of 180 degrees. Thedetectors are composed of scintigraphic crystals with short afterglow, coupled to solid statephoto-iodes sensitive to scintillation photons. A single scan now takes 1.5 to 18 seconds insteadof 4 minutes. Each detector makes approximately 1024 measurements resulting in over 1.2miffion samples per slice. Most modern third and fourth generation CT systems incorporatevariable scanning rates in order to accommodate the different requirements of imaging varioustissues and organs. As well, the diameter of the field of view can be adjusted to further reducethe imaging times where appropriate.Regardless of which generation scanning system is employed, the end result of any CT scanis a series of data in the form of g(8, .s), the line integral sum along angle of orientation 0 withoffset s from the center of the section. Figure 2.1 illustrates one such projection through animage f(x, y). The problem then is to transform the data into a 2-D distribution in the spatialdomain from the set of line integrals so obtained, that is, to determine f(x, y) from g(O, s).The function g(0, .s) is called the Radon transform of f(x, y), named after the mathematicianJ. Radon who determined, in the late 19th century, how the transform could be achieved.The basic property of X-ray absorption which is necessary for the evaluation is given inEquation 2.1:ln(j-) = —ctL (2.1)where a = the absorption coefficient for a uniform absorbing material of length L.I = transmitted intensity of the X-ray beam.I = the detected intensity of the X-ray beam.Human tissue is obviously not uniform along any given length so Equation 2.1 must bemodified to incorporate the integral of intensity along the length of the tissue. This is given byEquation 2.2 below:Iln(—)- I a(z)dz (2.2)10 ftChapter 2. Computerized Tomographic Imaging 12xFigure 2.1: The 1-D projection g(O, s) of the 2-D function f(x, y). The line integral along t atangle 9 and offset s from the center of the object are illustrated.g( 0,f(x,y)X-Ray sourceChapter 2. Computerized Tomographic Imaging 13Solving for I we obtain:I = Ioe1L (2.3)In order to reconstruct f(x, y), the original data, we need to determine a(z). Severalmethods of reconstruction have been developed to obtain the 2-D spatial intensity distributionfrom the line integrals. The first method to be developed, which has largely been displaced bythe filtered back-projection technique, was the Arithmetic Reconstruction Technique (ART).ART uses an iterative method to obtain successive approximations using a best fit strategy.The filtered back-projection method is used extensively in CT, PET, SPECT and otherimaging modalities with minor variations across the imaging spectrum. One view of a sectionof the body under consideration is defined as a set of parallel rays obtained at any given angle0. All values of ray sums are back-projected such that each point intensity in this intermediateimage is equal to the sum of all the views contributing to it. Each point in the unfiltered back-projection gives rise to artifactual densities proportional to 1/r, the distance from the pointdensity location. All points thus contribute to the blur of each other point. The transformation so obtained is the Radon transform of the image and the result is the original functionblurred by the point spread function 1/z2 + y2. The original function can be restored by anapproximation of the 2-D inverse filter whose frequency response is given by:F = + v2where mm and v are the frequency domain counterparts of the z and y spatial coordinates,respectively.A series of filters have been designed and used to obtain the reconstructed image, and theuse of any particular one is determined by the preference of the radiologist using the equipmentand the characteristics of the hardware used to obtain the projections. It is beyond the scopeof this chapter to further explore the difficulties encountered and the techniques used in imagereconstruction from projections. The interested reader is encouraged to explore Herman [44]and Jam [51].Chapter 2. Computerized Tomographic Imaging 14An enormous number of calculations is required to perform the reconstruction process andthus specialized hardware is necessary to obtain reasonable results in a reasonable amount oftime. To facilitate the process, array processors and other parallel processing hardware andsoftware are employed in the reconstruction process.Having obtained the approximation of the slice of the body under investigation, a greatmany post-processing techniques are available to further extract information from the resulting2-D image slices, using filtering, edge detection, thresholding, etc. As well, the 2-D imagescan be manipulated to obtain 3-D views using the volume rendering and surface reconstructiontechniques of modern computer graphics installations. The reader is referred to Kaufman [61]for an exhaustive survey and a comprehensive bibliography of volume visualization research.2.2.2 Practical AspectsAlmost all CT scanners available today use some variation of the aforementioned methods ofsignal generation, detection and image reconstruction from projections. Progress has been madein all these areas over the last twenty years, resulting in complete examinations requiring aslittle as 8-20 seconds. The actual display of the generated images can proceed in parallel, withthe 3-D reconstructions taking only seconds more. Thus a patient can be imaged in real-timeallowing maximum utilization of the available resources.Recent innovations in CT research have led to thin-section imaging techniques obtainingsection thicknesses in the range of 1-2mm with scan times of 1-23 seconds per slice. Theresolution obtained is quite remarkable. The ultra-fast CT scanner can produce an image in50msec and complete an examination of the heart in under a second [69].The use of CT does have some problems and limitations and is not a panacea for all imagingrequirements. For example, one advantage of CT is not requiring invasive procedures. Thisadvantage is lost when cardiovascular and bowel viewing is considered. It then becomes necessary to use a contrast medium since the differential across tissue demarcations is not sufficientlyChapter 2. Computerized Tomographic Imaging 15pronounced. Another major drawback of CT is its inability to fully characterize tissue, especially significant in distinguishing between malignant and benign lesions, a problem common toall currently available imaging modalities. The only way to differentiate malignant tumors isthrough multiple scans over a period of time sufficient to detect changes in the affected tissue.CT costs about half the price of MRI, both for installation and maintenance, but is more than10 times as expensive as readily available ultrasound imaging.2.2.3 ConclusionCT has revolutionized the diagnostic capabilities of modern medical science. Through thedevelopment of low cost, versatile hardware, this tomographic imaging method has become areality for even the smallest of general hospitals. Though it has its disadvantages, CT promisesto be one of the leading methods of organ and tissue visualization for the next several decades.2.3 Magnetic Resonance Imaging(MRI)2.3.1 IntroductionNo imaging modality has witnessed the explosion of growth and development that MagneticResonance Imaging has over the past 10 years. Once labeled NMR, for Nuclear Magnetic Resonance imaging, the “Nuclear” term has recently been replaced due to its negative connotationsamong the general public. Using a combination of the inherent magnetic resonance propertiesof tissue and application of radio frequency pulses, MRI obtains images by measuring varyingtissue characteristics. The resulting frequency information is converted, using Fourier Transform techniques, to spatial intensity information of slices through the body. As with CT theseslices can be integrated using advanced computer graphics techniques to produce 3-D views ofthe imaged tissues. Unlike CT, where the signal is generated by X-Ray beams, in MRI thepatient becomes the signal source.Chapter 2. Computerized Tomographic Imaging 162.3.2 Physical PrinciplesAtomic nuclei of odd number exhibit a magnetic moment, somewhat as if the nuclei werereplaced by tiny magnets. In the absence of an applied magnetic field these magnetic momentsare arbitrary and random. Following the application of a large magnetic field, B0, on theorder of 0.3 to 2.0 Tesla, the magnetic moments of all the atomic nuclei align themselves inthe direction of B0. This results in a net magnetic moment, M, the vector sum of all theindividual magnetic moments of the charged nuclei, in the direction of B0. Currently, the mostprevalent entity for which measurements are taken is the ‘H nucleus. Other nuclei in the bodyare suitable for measurement but the ‘H nucleus is the preferred entity, for two reasons. Firstly,J[ is abundant throughout body tissues in the form of H20, and secondly the ‘H proton yieldsthe highest detectable signal of all the available atomic nuclei. Other nuclei such as ‘3C, ‘9F,23Na, 31P, while less efficient, are finding increased use both in the research laboratory and inestablished MRI installations in a limited number of hospital settings. The use of these nucleioffers the advantage of exploring a large number of metabolic processes not possible using ‘H.For the remainder of this discussion, however, we will assume that ‘H is the nuclei of reference.When ‘H nuclei are placed in the magnetic field, B0, they precess or wobble at a characteristic frequency known as the Larmor frequency, proportional to the strength of B0, accordingto the following equation:= 7B1 (2.4)where w = the Larmor frequency.= the magnetogyric ratio of the atomic nuclei,for 1H,7 = 42.6MHz/TeslaB0 = the strength of the applied magnetic field in TeslaFollowing the application of the magnetic field, a radio frequency (RF) pulse is appliedperpendicular to B0 at the Larmor frequency, c. This causes the induced magnetic moment,M, to rotate or nutate away from B0. The extent of the nutation varies linearly with theChapter 2. Computerized Tomographic Imaging 17amplitude and the duration of the RF pulse. In this manner the operator controls what isimaged and how the imaging takes place. If we now cease the application of the RF pulse theinduced magnetic field, M, reverts to its original direction, namely that of B0. A signal isproduced in the RE coil wound around the inside of the magnet bore. Two relaxation timesare associated with the decay of the resonant signal; T,, which is a measure of the longitudinalrelaxation time, and T2, which is a measure of the transverse relaxation time.The information obtained thus far is only a measure related to the concentration of ‘Hprotons in the tissue being imaged. In order to spatially encode the frequency data received,pulsed magnetic gradients in the x, y and z directions are imposed concurrently with theprimary magnetic field B0. If no gradients are applied then all locations in the magneticfield precess at the same Larmor frequency. If a gradient is applied then the Larmor frequencydetected becomes a function of the position of the 1H proton which generated the signal. Thesegradients are applied in a timed sequence known as a pulse sequence. The pulse sequence ofa conventional MRI imager is shown in Figure 2.2. An RF pulse, modulated by a sinc-likefunction, is applied at the Larmor frequency, the amplitude of which determines the nutationangle. Simultaneously a z-gradient is applied inducing a z-dependency in the Larmor frequencyof the object. This determines the slice to be imaged within the object. The negative lobe inthe z-gradient wave form, following the RF pulse, is used to rephase the spins within the excitedslice. The spins within the slice can then be encoded spatially in the x and y directions.The first pulse in the x-gradient ensures that all spins in the resulting signal are in phase.The second pulse is applied when the signal is to be measured, causing the Larmor frequencyto vary in the x direction.The final gradient performs encoding in the y direction. It is applied such that the incremental phase accumulation corresponds to powers of complex exponential functions. The timefrom application of the RF pulse to the end of the y-gradient application is called the repetitiontime or TR of the cycle. The time from the centre of the RF pulse to the center of the signalis the echo time or TE time.Chapter 2. Computerized Tomographic Imaging 18Detected MR SignalRFZ-GradientY-GradientX-Gradient tFigure 2.2: The pulse sequence of a conventional MRI imaging system.Chapter 2. Computerized Tomographic Imaging 19The data acquisition phase is terminated when many cycles of the pulse sequences illustratedin Figure 2.2 have been applied. If the gradient fields are applied as shown in Figure 2.2 then atransaxial slice is produced. Interchanging z, y, and z yields coronal and sagittal slices. Takinglinear combinations of x, y, and z waveforms can produce oblique views from any desired anglein the section being imaged.The relaxation times T1 and T are produced differently and have varying effects on theresulting image [69]. If the TR and TE times are relatively short then T1 or spin-spin relaxationtimes result, and the images obtained contain more detail. If the TR and TE times are longthen T2 relaxation times are produced resulting in more contrast between different tissues. Theoperator has full control over the application of RF pulses and z, y, aud z gradients and thushas control over the T1 and T2 images which result.The ensuing frequency eucoded information can be decoded in several standard ways. Thefiltered back-projection methods discussed in Section 2.2 apply equally to the reconstructionof MRI data. This was the method of choice during the early development of MRI. Today,however, the back-projection methods have largely been replaced by faster and more accurate2-Dimensional Fourier Transform techniques [28]. Foliowing reconstruction, various geometricand other compensatory techniques are applied to reduce artifactual contamination caused byimperfections in the reconstruction process.2.3.3 Practical AspectsMagnetic resonance imaging has many advantages over computed tomography, but also suffersfrom some distracting difficulties. Clinically, MRI is superior to CT in detecting demyelinatiuglesions, such as those found in Multiple Sclerosis. Because MRI is relatively insensitive to bone(due to the lack of “20 in bone) it can image regions abutting bone, such as the cerebralcortex and the base of the brain, much more clearly. This imaging modality was previouslythe slowest of all imaging techniques, requiring up to 8 minutes per slice and up to 45 minutesfor a single examination of a desired section. Recent research has resulted in producing imagesChapter 2. Computerized Tomographic Imaging 20in breath-holding times by reducing the number of excitations required down to just one [28].Most present day systems still suffer from the long examination times, however, which resultin imaging artifacts. These artifacts arise from physiological motions originating from patientbreathing, peristalsis, and even pulse beats. Patients for whom remaining still for long periodsis a problem create a serious difficulty for MRI, as the measurements are quite sensitive to eventhe slightest motion. The MRI source/detector coupling is enclosed in a large doughnut shapedstructure which encloses the patient during examination. Many patients suffer claustrophobiafrom being placed in the imaging area and as many as 15 per cent of patients refuse theprocedure on these grounds.As well as patient-related difficulties, installation of MRI machines presents technical problems. The requirement for exclusion of external RF interference means that specialized roomsmust be designed to keep out secondary radio frequency waves. This adds to the cost of thealready high price of MRI imaging equipment. Although no health related disorders have beenattributed to the application of strong magnetic fields and radio frequency pulses to date, thelong-term safety of magnetic resonance imaging has yet to be determined. There are othersafety factors to consider as well such as ensuring that no metallic prostheses or implants arecontained within the patient, since these may lead to serious injury when placed inside the largemagnetic field. Radio frequency waves also may lead to disruption of implanted pace-makerswithin the heart.2.3.4 ConclusionMRI has provided a second revolution in medical imaging and is currently just in its infancy.Future developments in reducing the scanning times and the costs to the patient, high speedreconstruction methods, and the use of several other atomic nuclei will make MRI a leader indiagnostic radiology in years to come. Research involving post-processing of MRI images using3D graphics techniques is also ongoing, and offers broad opportunities for further developmentof the technology.Chapter 2. Computerized Tomographic Imaging 212.4 Emission Computed Tomography (PET and SPECT)2.4.1 IntroductionTomographic radiopharmaceutical imaging or emission computed tomography (ECT) is basedon the detection of gamma-rays emitted by radioisotopes such as 99mTc 1231, 15w, and ‘3C.The images acquired in this manner contain physiological information as opposed to CT orMRI which almost invariably yield structural or anatomical images. Organ and tissue specificpharmaceuticals are labeled with the gamma-ray emitting radioisotopes and injected into thepatient, producing a set of 2-D projectional images of the distribution of the isotopes within thetissue being investigated. These 2-D projections are used to obtain 3-D images of radionucidedistributions within the body. Reconstruction of these 2-D projections is accomplished usingthe same reconstruction techniques used with CT, with corrections being made for attenuationand scatter of gamma-rays within the affected organ or tissue.Emission computed tomography (ECT) has developed along two fundamentally different butcomplementary paths, the basic difference being how the direction of the emitted gamma-ray isdetermined and the type of radioisotope used. Positron emission tomography (PET) relies onthe coincident detection of two collinear annihilation photons resulting from the combinationof both a positive charged electron (positron) and a negatively charged electron. Single photonemission computed tomography (SPECT) determines the direction of the gamma-ray by thesingle and sequential detection of collimated photons emitted by the radionucides.2.4.2 Physical PrinciplesSPECT is achieved with the use of the traditional gamma camera first developed by 11.0 Angerin 1957 [123]. The camera is composed of a large diameter (30-45cm) sodium iodide (Na])scintillation crystal coupled to an array of photomultipier tubes. A cross-sectional view of thegamma camera is shown in Figure 2.3. Gamma-rays interact with the Nal scintillation crystaland the crystal in turn emits energy in the form of light. The photomultiplier tube in closestChapter 2. Computerized Tomographic Imaging 22proximity to the arriving gamma photon produces the largest output. The signals received fromall the photomultiplier tubes are converted to electrical impulses and combined to determinewhere the gamma-ray was absorbed by the crystal. The coffimator, which is composed of leadand is approximately 2-3 cm thick, is used to provide entry to oniy those gamma rays whichare nearly perpendicular to the face of the camera, thereby determining the directional rayalong which the photon was emitted. The coffimator yields a projectional image of the gammaray flux. Single and dual headed cameras are in current use. They are rotated around thepatient through 180° and 360° respectively, in 30 or 6° increments. Since each increment of thecamera acquires a 2-D projection, a single rotation of the camera about the patient is all that isnecessary to obtain the 3-D distribution of radionudides. Conventional radionucides, such as99mTc, 1231, 1311, and 111n (Indium), available in most modern nuclear medicine departments,are used to provide the source gamma rays. The nudides used have relatively long half-lives(e.g. 6 hrs for 99mTc, 13 hrs for 1231) and thus require no special equipment to produce otherthan that already in place in the nuclear medicine department.Photomultiplier tubesNaT Crystal>CollimatorFigure 2.3: Cross-sectional view of conventional Anger gamma cameraPET utilizes radioisotopes which produce a positron (a positively charged electron) duringdecay, including ‘1C, 15w, ‘3N and 18F. The short half-lives of these radionucides, in the rangeof just a few minutes, necessitate the use of a cyclotron to produce. This, of course, creates anenormous expense and severely restricts the use of PET to well-equipped research hospitals.When one of these radionucides drops from an unstable to a stable state, a positron is emitted. This positron travels a short distance (2-3mm), losing its kinetic energy, before combiningChapter 2. Computerized Tornographic Imaging 23with a negatively charged electron. Both the positron and the electron are annihilated, sub—sequently producing two diametrically opposed photons, each of energy 511 KeV. Scintillationdetectors, usually composed of bismuth germanate (BGO), similarly coupled to photomultipliertubes as in SPECT, are placed in a ring around the patient and await the arrival of the photons.Once a photon reaches a detector, a time window of approximately l2ns is opened to await thedetection of the coincident photon immediately opposite the already detected gamma ray. Thedetection of single events, that is the detection of a unpaired gamma ray, is minimized by thehigh speed circuitry. The number of detectors is in the order of 4096 with approximately 1.5miffion coincident registrations being detected to produce the 3-D spatial distribution map [56].Coffimation of the arriving photons is no longer required as in SPECT, but coffimation in thetransverse direction is still necessary. PET thus achieves a superior spatial resolution.Following the acquisition of the 2-D projections, both PET and SPECT employ filteredback-projection reconstruction techniques similar to that of CT as described in Section 2.2.Further processing must be applied, however, in order to account for tissue attenuation, scatterand absorption of gamma rays. This processing can be performed on the raw projection dataor to the image itself. This further processing is applicable to both PET and SPECT, withminor changes in either case to account for geometric differences [52].2.4.3 Practical AspectsThe spatial resolution obtained from both PET and SPECT is inferior to that of CT due tocoffimation, attenuation and scatter of gamma rays within tissues. The resolution obtained withSPECT (918mm) is determined to a large extent by the precision of the coffimator, while PETresolution is limited by its ability to distinguish coincident photons, which is further determinedby the size of individual detector crystals. Since a collimator is not required with PET, itsspatial resolution is superior to SPECT, ranging from 6-12 mm, measured at full width halfmaximum (FWHM) of the point spread function. The resolution of both imaging modalities isalso determined by the count rates achieved by the detectors, which in turn is influenced by theChapter 2. Computerized Tornographic Imaging 24affinity of the radiopharmaceuticals for the target organ, the half-life of the radionucides, thedose given to the patient and the pharmacokinetics of the labeled pharmaceuticals. For all thesereasons it is usually necessary to calibrate the system using phantoms of known materials [52].Both imaging methods are fundamentally limited in the spatial resolution achievable, which isrestricted by attenuation, scatter, and limited count statistics [56].The applications of PET and SPECT are many and varied but are related by the commonability of both to measure metabolic and physiological changes as opposed to CT, which simplymeasures anatomical information. SPECT is used primarily in oncological investigations ofthe central nervous system and visceral organs. PET research is focused on the diagnosis andtreatment of central nervous system disorders such as Alzheimer’s disease, schizophrenia andParkinson’s disease. Development of 18F labeled deoxy-glucose has led to advanced researchinto glucose metabolism in the brain both in medical disorders and in normal individuals.The low cost of SPECT and its general availability will ensure its position in diagnosticradiology in the years to come. A SPECT installation costs roughly $300,000 compared to thecost of PET which can exceed $5 miffion dollars to install and over $800,000 per annum tomaintain [52].Current research in ECT is focused on increasing the spatial resolution and the developmentof new radiotracers which are more organ and tissue specific and which yield higher achievablecount rates in vivo. Recent advances in SPECT research include the development of multiple-head cameras which provide dynamic, real time, 3-dimensional views in rapid sequence. Thisis particularly useful in cardiac studies, where the motion of the heart can be monitored fordefects and disease [103]. Fan-beam collimators, which rotate in front of a stationary detectorring are also being investigated in order to decrease noise and increase resolution. Researchin PET imaging is focused 011 increasing the transverse resolution and increasing the signal tonoise ratio, by developing fast scintillators, and increasing the number of detectors. Attemptsare being made to increase the number of sections imaged simultaneously using continuous,position-sensitive cameras, thus reducing imaging time and the overall cost of PET.Chapter 2. Computerized Tomographic Imaging 252.4.4 ConclusionDramatic advancements in ECT in recent years, together with its unique characteristics andabilities, ensure its position in medical imaging for the foreseeable future. Increased resolutionand detection efficiency, together with continually new uses for the technology make ECT aninvaluable tool in diagnostic medicine.2.5 Combining ImagesImages from CT and MRI generally offer information related to structure and anatomy, whilethose from PET and SPECT yield functional information related to metabolic and physiologicalprocesses. The spatial resolution from CT and MRI far exceeds that of PET and SPECT. Itwould be of tremendous benefit if images obtained by the various methods could be combined toyield enhanced information content, thereby increasing their diagnostic potential. Comparisonof images obtained from the same imaging modality, obtained over a temporal sequence, isalso desirable, and has been carried out with partial success using all the imaging modalitiesdiscussed.Combining images from different modalities presents many difficult problems. To dateno method satisfactorily completes the task with limited operator interaction and efficientcomputing activity.In order to combine images it is necessary to ensure that the same imaging planes arecombined. This may be accomplished by simply matching visually recognizable features ineach image. Another method of image combination uses external skin markings and projectedlaser light beams to correlate planes of interest [32]. This requires that the patient be restrainedfirmly, but comfortably, and sometimes takes over two hours to complete.There are of course scaling and positional differences across imaging modalities which mustalso be overcome. Scaling differences are overcome by using the known physical characteristicsof the imaging equipment. Translational positioning is accomplished by eye or by exploiting thecenter of gravity of the image outline. Resolving rotational differences is extremely difficult toChapter 2. Computerized Tomographic Imaging 26automate, but attempts have been made to solve the problem. Both rotational and translationalpositioning can be achieved by physically attaching imaging markers to the patient’s bodywhich are sensitive to each of the imaging methods under investigation. This provides accuratedetection of the proper orientation of the patient during imaging and is adaptable to all areasof the patient’s body.Once corresponding imaging planes have been determined, comparison and registrationof the images presents further difficulties. Each imaging method possesses a different 2-Dspatial resolution, making comparison of small areas difficult. As well, the images have differenteffective thicknesses in the third dimension. This difficulty may be overcome by combiningmultiple slices of high resolution images such as CT or MRI to give the effective thickness of therelatively low spatial definition images of PET or SPECT. Images can also be compared simplyby placing them side by side and using a dual tracker, which is mouse driven, to investigatecoincident regions of interest.Current research has led to the development of several approaches to image registration [86].These include: (1) analytical approaches with respect to structure using Fourier analysis andwarping techniques; (2) analytical methods with respect to surfaces employing least squaressearch techniques, principal axis techniques, and moment-matching techniques; (3) proceduralmethods using stereotactic frames attached to the head of the patient; (4) the use of anatomicalatlases where the images in the atlas are transformed to fit the images under investigation,followed by overlaying of the anatomical image over the functional image; and (5) the use ofexternal markers as discussed earlier.The process of combining images from several imaging modalities has not yet been perfectedand is subject to two main drawbacks. Firstly, image registration requires the expertise of aradiologist, an anatomist and other operating personnel. Secondly, at the moment the amountof computer processing time required to perform the operations is extensive. Research is aimedtoward reducing the number of interactions between personnel, increasing the accuracy of themethods and reducing the processing time required to obtain the composite images.Chapter 3Basics of Image Segmentation3.1 IntroductionOne of the most difficult to solve problems and extensively researched areas in image analysisover the past fifteen years has been the problem of image segmentation. Image segmentation canbe considered the division of an image into different regions, each having a certain property, forexample average gray level. It is the first step in a process leading to description, classificationand interpretation of an image, usually by higher level processes.To date, no generalized segmentation algorithms exist which are suitable for all or evenmany different types of images. Most currently available algorithms are ad hoc in nature. Oneof the reasons for the difficulty encountered in segmenting images is the infinite number ofpossibilities that an image can represent. A truly general image segmentation algorithm wouldrequire the storage and retrieval of vast amounts of knowledge and data. Another problem arisesin the evaluation of segmentation algorithms. There is no adequate solution to the problem ofdetermining the validity or accuracy of a given segmentation algorithm. In many cases, variousmathematical and other assumptions are made with respect to the image under investigation.Given these assumptions verification of the segmentation technique is possible to some degree.However, it is generally the case that algorithms are validated for a specific and often smallnumber of images. Despite these difficulties, many hundreds of segmentation algorithms havebeen published in the literature.The applications of image segmentation are many and include but are not limited to suchareas as pattern recognition in computer vision systems and numerous biomedical uses includingautomated tumour volume determination and 3-dimensional visualization. Before discussing27Chapter 3. Basics of Image Segmentation 28any algorithms, it will be necessary to formally define image segmentation.3.2 DefinitionsThere have been several definitions put forward for image segmentation but the one that isgenerally accepted as the definition is as follows:A segrnerLtation [35] of a 2D image grid, X, over a predicate P is a partition of X into Nnon-empty, disjoint subsets X1,X2,. . . , Xj such that:NUX= (3.5)X, i = 1,2,. . . , N is connected (3.6)XflX=0,forallij (3.7)P(X)= TRUE,fori= 1,2,...,N (3.8)P(X U Xj) = FALSE, for i j where X and X3 are adjacent. (3.9)Equation 3.5 above states that every picture point must be in a region. That is, no pixelin the image can exist outside of some defined region Xi.’ Equation 3.6 says individual regionsmust be connected; each X is composed of contiguous lattice points.2 Equation 3.7 indicatesthat the intersection of two regions is empty; regions are disjoint.The predicate P in Equation 3.8 implies that the region X must satisfy some property,for example, uniform pixel intensity. Equation 3.9 states that if two regions X and Xj areadjacent and disjoint then the predicate P cannot be true for the region defined by the unionof X and X3. That is, properties are different for adjacent regions. The predicate P discussedin Equations 3.8 and 3.9 above is formally defined below:‘In later discussions this requirement wifi be adapted to include the possibility that a given pixel may becomposed of more than one object class.‘This condition can and is relaxed in many applications of image analysis, including medical image analysis,since it is quite possible to have disjoint regions of an image which belong to the same class. For example, incervical cancer smears, many nuclei may be affected but are disjoint, but all should be assigned to the same classlabeling.Chapter 3. Basics of Image Segmentation 29Let X denote the image sample points in the picture, i.e., the set of pairs(i,j) i = 1,2,...,M, j = 1,2,. ..,Nwhere M and N are the number of pixels in the x and y directions respectively. LetY be a non-empty subset of X consisting of contiguous picture points. A uniformitypredicate F(Y) is one which (i) assigns the value true or false to Y depending onlyon the properties related to the brightness matrix f(i, j) for the points of Y and (ii)has the property that if a region Z is a subset of Y and P(Y) is true, then P(Z) isalso true.The most basic form of uniformity predicate is based on the comparison of the mean pixelintensity in a given region and the standard deviation from the mean. In general, a region, R,is called uniform, i.e. P(R) = TRUE, if there exists a constant a such that:max,I(f(i,j))-aj <Tfor some threshold value T.Using the mean, ji and standard deviation, a, this means that:max,(f(i,j))— ILl <kafor some constant multiple, k, of a.Other features used to determine region uniformity are based on a variety of propertiesof the image including the co-occurrence matrix, texture, Fourier Transform and correlationfunctions. The co-occurrence matrix is composed of values C(i, j), the number of pairs of pixelshaving gray levels i and j which exist at a particular distance apart and at a fixed angle.Properties of the co-occurrence matrix such as entropy and correlation are used to determinetextures of regions [143].Chapter 3. Basics of Image Segmentation 303.2.1 TechniquesSegmeiltation methods can be loosely subdivided into three principal categories including (1)characteristic feature thresholding or clustering, (2) edge detection methods and (3) regionoriented techniques.ThresholdingThe simplest method of image segmentation involves thresholding. All pixels which have acertain property such as faffing into a given intensity range are classified as belonging to thesame group. In its most gelleral form thresholding can be described mathematically as:S(i,j) = kifTkl <f(i,j)<Tkforkz’1,2,...,mwhere (i,j) = the coordinates of a pixel in the x, y directions, respectively,S(i, j) = the segmentation function,f(i,j) = the characteristic feature (e.g. gray level) functionT0,. . . Tm the threshold values, andm = the number of distinct labels to be applied to the image,If rn = 1, the thresholding method is termed binary thresholding. If m> 1, these methodsare described as multi-modal thresholding techniques. Thresholding is best applied to imagesof relatively few homogeneous areas which are contrasted against a uniform background. Forexample, in the case of binary thresholding, a suitable applicatioll is extraction of text from aprinted page.Well known histogram modification and manipulation techniques are applied in imagethresholding [38]. From the survey papers by Lee et al. [76] and Sahoo et al. [112] it appears that a method of thresholding labeled moment preserving thresholding (MPT) [131] isChapter 3. Basics of Image Segmentation 31the most suitable of the commonly used methods tested by those authors. In MPT the objectis to preserve the k’th moments of an image and to find the threshold values which maintainthe moments in the segmentation. The k’th moment of an image, mk, is defined to,)mj=MNThus the zeroth moment of an image is 1, and the first moment is the average gray level presentin the image. These moments are also obtainable from the histogram of the image. Preservationof moments is motivated by the assumption that the original image is simply a blurred versionof the true segmentation. Tsai et al. [131] use a value of k 3 in order to obtain segmentationsusing 2, 3, and 4 different threshold levels. Extensions to higher dimensional thresholding arepossible but with substantial increases in computational load. The success of MPT methodsapplied to medical image segmentation has not been validated, and is not likely to succeed asmost medical images do not contain few homogeneous areas.The reader is encouraged to explore the survey papers by Lee et al. [76] and Sahoo etal. [112] for detailed descriptions of MPT and other classic thresholding methods.A multidimensional extension of thresholding, called feature clustering, segments the imagebased on pixels clustered in a feature space and the properties of these clusters. Clusters aregenerally formed using two or more characteristic features. The clusters need not be contiguousin space.Thresholding and clustering methods have the advantage of being fast and simple to implement. There are, however, inherent shortcomings present in all thresholding techniques.Primarily, there is the problem of threshold selection, which usually requires some a prioriknowledge of the image being segmented. As well, valleys and peaks in the histograms used tosegment the images are often not well defined and are difficult to differentiate.Edge DetectionEdge detection methods of image segmentation involve locating local discontinuities in pixelintensities, followed by some method of connecting these fragmented edges to form longer,Chapter 3. Basics of Image Segmentation 32hopefully significant and complete boundaries. Most methods of edge detection involve theapplication of a smoothing filter (e.g. Gaussian), followed by a first or second order gradientoperator. In the case of a first order gradient, local maxima signify the existence of an edge. Ifa second derivative operator is applied then zero crossings in the result indicate the presenceof an edge. A thresholding operator is usually applied to the result to filter out insignificantedges, or edges caused by noise which was not filtered in the smoothing process.The biggest drawback to edge detection methods of image segmentation is the sensitivity tothe size and type of smoothing and derivative convolution masks applied to the original image.In some cases these two masks are not parameterized and are therefore not under user control.This limits the applicability of these algorithms to different types of images.As well, most edge detection algorithms are very sensitive to noise and can yield edgeinformation that is not a boundary between regions in an image. Furthermore, edges that arecomputed are often not linked where contiguity exists in the image. These edges must be joinedto be useful in successfully segmenting the image. Algorithms for edge linking are often at leastas complex as the edge detection algorithms used in the first place.Region-oriented SegmentationRegioll based methods of image segmentation can be further subdivided into two main categoriesincluding (1) region growing and (2) region splitting and merging.While thresholding and edge detection methods involve determining the differences in pixelintensities or groups of intensities, region growing and region splitting and merging deal withthe similarities between pixels and groups of pixels.Region growing methods start with one or more pixels as a seed and then make an analysisof the neighbours of the seed pixel(s). If the neighbours of the seed have similar intensity orsome other property then those pixels become part of a region. This process continues with thenew region until no further expansion is possible.One advantage of region growing is that little a priori information is necessary to segmentChapter 3. Basics of Image Segmentation 33the image. As well, isolated areas with similar features can be successfully segmented by seedingthese regions independently. For example, muscle and brain have similar gray levels on magneticresonance images, but can be differentiated by seeding each region individually. Difficulties areencountered with choosing a seed point or region and with evaluation of inclusion criteria forneighbouring pixels. The latter usually involves a common problem with all techniques, thatof threshold selection.In contrast to the forms of image segmentation discussed so far, region splitting and mergingbegins with an image subdivided into smaller regions. These regions are grouped together if thepixel intensities meet some uniformity criteria, for example, similar average intensity level. Theregions are then examined for uniformity and are further split if they do not meet the uniformitycriterion. The order of splitting and merging is variable and dependent on the implementationand data structures used. Relatively complex data structures are required to perform split andmerge techniques with corresponding complexity in maintaining these structures. Again, theproblem exists of determining a valid uniformity criterion and of determining a threshold atwhich to assign the uniformity.3.3 SummaryImage segmentation has been studied extensively to date and many algorithms have been developed to solve the problem. These algorithms can be loosely categorized into characteristicfeature thresholding and cluster analysis, edge detection methods, and region oriented techniques.Thresholding methods, although simple and fast, are suited to images of low numbers ofregions with highly contrasting backgrounds.The problem with edge detection methods is that it is possible to detect an edge whichis not a boundary between regions. Detected edges often have gaps in them which involvecomputationally expensive methods to eliminate.Both thresholding and edge detection methods are sensitive to image noise. Again edgesChapter 3. Basics of Image Segmentation 34are detected which may not exist. Noise affects thresholding by altering the peaks and valleysof the histograms used to determine the thresholds.Region growing requires user input to determine a seed or seeds and requires thresholddetermination for pixel inclusion as well. Region splitting and merging is computationallycomplex and also requires threshold analysis.The choice of any segmentation technique is highly application dependent. This chapterhas only just begun to explore the many and varied algorithms currently applied to imagesegmentation. One point that general segmentation algorithms raise is the need for semanticand a priori information to be incorporated into the segmentation process. The segmentationof medical images is one area where semantic and a priori information is generally available.However, due to relatively low signal to noise ratios and inherent artifacts generally presentin medical images, their segmentation is particularly difficult. The next chapter details theintrinsic characteristics of medical imaging techniques, including CT, MRI, PET and SPECT,which further complicate the segmentation task. A more detailed discussion of segmentationmethods applied to medical imaging is also presented.Chapter 4Segmentation Applied to Medical ImagingThe basic segmentation techniques discussed in Chapter 3 are all currently employed withmodifications and adaptations in the analysis of medical images. Section 4.1 deals with theinherent difficulties encountered by each of the medical imaging modalities discussed in Chapter 2. Section 4.2 discusses the use of the basic methods of thresholding and clustering, edgedetection, and region analysis as applied to medical images. In addition, medical investigatorshave developed several new methods for the segmentation of medical images. These includethe manual tracing of structures of interest using a mouse or other drawing tool, statisticalrelaxation methods, morphological segmentation methods, and pyramidal techniques. Thesenew techniques are discussed in Section 4.3. Model-based or knowledge-guided techniques, discussed in Section 4.4, exploit the a priori knowledge of the characteristics of how human tissuesreact to the different imaging modalities. One such model-based technique called the methodof Iterated Conditional Modes [14] is described in detail beginning in Section 4.5. This method,first developed to restore noisy and corrupted images, is based on the theory of Markov randomfields and Gibbs distributions from probability theory. Because this work forms an integral partof the thesis a significant amount of this chapter is devoted to its discussion.4.1 Difficulties with Medical ImagingMedical images, including CT, MRI, PET and SPECT data, add new complications to theproblem of image segmentation. Each modality has particular characteristics that detract froma straightforward solution. These difficulties range from the partial volume effects common toall modalities to RF inhomogeneities experienced by MRI, beam hardening effects of CT and35Chapter 4. Segmentation Applied to Medical Imaging 36scatter and attenuation problems common to PET and SPECT imaging. The following sectionsdescribe in greater detail the characteristics of some of these inherent shortcomings.4.1.1 Partial Volume EffectAll medical imaging modalities suffer from the partial volume effect to some extent. Themeasured signal represents an average signal received through a section of tissue of specificthickness. Voxels may intersect more than one tissue type, depending on the area and the slicethickness realized. For example, a given voxel in a brain image obtained from a CT studymay represent the attenuation through a cubic volume of brain tissue measuring several cubicmiffimeters. This volume of tissue may contain 40% gray matter and 60% white matter. If graymatter usually yields a CT value of 50 and white matter a CT value of 100 then the measuredvalue will be an average attenuation measurement representing the combined composition, i.e.80, which is not an accurate representation of the underlying tissue. Spatial and tissue resolutionare thereby decreased.The problem is of lesser but still significant importance in MET scans because the obtainabletissue resolution of Mlii images is higher than that of CT. Since the spatial resolution in thefunctional modalities (PET and SPECT) is much less than CT or MET, the partial volumeeffect is especially pronounced in images obtained using these methods.4.1.2 CTBeam HardeningIn CT, a phenomenon known as beam hardening is another source of artifacts which reduces thespatial resolution in certain image areas and forms dark streaks in the image. Beam hardeningoccurs due to the polychromatic nature of the X-ray beam. Attenuation coefficients of individualtissues vary with the energy level of incident X-ray photons. Because X-ray beams are madeup of a distribution of varying photon energies, as the X-ray beam passes through the patient,low energy photons are more readily absorbed so that the average beam energy increases orChapter 4. Segmentation Applied to Medical Imaging 37hardens. As a result, a given voxel will yield a different attenuation value, depending on thepath of the incident X-Ray beam. The result is dark streaks, especially noticeable close todense bone, such as the area between the skull and the brain. As well, X-rays passing throughthe periphery are less hardened than those passing through the center of the imaged object.This phenomenon is also known as cupping. Reconstruction modifications have been developedwhich help to decrease the cupping effect, but these procedures are time consuming and arenot often employed.ScatterX-ray photon scatter leads to another artifact in CT studies. In areas around dense bone X-rayscatter leads to detection in surrounding tissues, which is higher than normally transmitted bythat tissue. As before this leads to streaks in the areas between high and low density tissues.Detector Non-linearitiesNon-linear detector response also leads to visible artifacts in CT images. This occurs in severalforms where detector response is not proportional to actual irradiation levels. Non-linearitiescan result from dark current, where there is indicated detection of photons but no radiationhas actually passed to the detectors. A second source of detector non-linearity is hysteresis,a phenomenon which leads to measured output after irradiation ceases. Thirdly, saturationoccurs where detector output is maximal but rncident energy is still increasing. Each of theseproblems may lead to streaks in the image.4.1.3 MRIRadio Frequency and Magnetic Field InhomogeneitiesSlight fluctuations in both the radio frequency (RF) signal and the applied magnetic field duringan MRI scan can result in what is termed the shading artifact. This artifact, which was muchmore pronounced in early MRI machines, causes a subtle change in average gray level in identicalChapter 4. Segmentation Applied to Medical Imaging 38tissues from image to image. Methods have been developed to reduce this difficulty and havebeen incorporated into both the pre- and post-reconstruction phases of image creation.Effect of Imaging SequenceAs discussed in Chapter 2, different pulse sequences applied during an MRI scan result invarying tissue discrimination capabilities. If a scan relies primarily on the Ti component ofthe MRI signal, it is termed an inversion recovery sequence. For brain imaging, Ti imageshighlight the contrast between gray and white matter. Sequences which rely most heavily onthe T2 component of the MRI signal are termed spin-echo sequences and produce images whichare less anatomically clear. However, differentiation of subtle tissue pathology is much easierwith T2 weighted images.Both types of sequences show tumours well, showing up as dark areas on Ti weighted imagesand bright areas on T2 weighted sequences.Normal tissues usually appear differently on different scan sequences, with fat showing asbright due to short Ti and long T2 time. On the other hand air, calcification and cortical boneare usually dark due to low hydrogen ion concentration. Rapid flow in healthy blood vesselsresults in no signal and thus dark image areas.Because of these differences in Ti and T2 scans, prior knowledge of the scan sequence typeis necessary in order to interpret the results properly. These decisions must be made prior toimaging, depending on what needs to be emphasized or visualized in the scan.4.1.4 PET/SPECTImages obtained from PET or SPECT studies are inherently difficult to interpret becausethe resulting gray levels represent physiological processes as opposed to structure as in CTand MRI. A thorough knowledge of the injected radionucide and the pharmacokinetics of thetagged pharmaceuticals is necessary in order to fully understand the process being representedby the images.Chapter 4. Segmentation Applied to Medical Imaging 39Other factors affecting analysis of functional images include decreased spatial resolution andincreased slice thickness, leading to an exaggerated partial volume effect [95].In both PET and SPECT, scatter of gamma rays occurs as in CT leading to reduced contrastand artifacts in the images. Attenuation of photons results in an underestimation of gamma rayactivity. Average attenuation is greatest at the center of the object being imaged and tapers offtowards the periphery. A gradual, increasing under-estimation of activity from the edge to thecenter of imaged object results. Many methods of reducing the effects of attenuation and scatterin PET and SPECT studies have been developed and are usually performed post-reconstruction[90].4.2 Current AlgorithmsOne of the goals of the segmentation of medical images by computer is to determine the volumesof organs, tissues and lesions present in a given patient. These volumes and the changes in thesevolumes over time aid in the diagnosis, prognosis and treatment planning of patients underinvestigation. Long et al. [80] compare a number of segmentation techniques used in SPECT,including manual methods, various thresholding methods and several edge detection techniques.Their results indicate that, for SPECT, 3D edge detection yields the most consistent, reliable,and reproducible results.4.2,1 Manual TracingManual tracing of structural and lesion boundaries is the most basic of all segmentation techniques and is still quite commonly used in clinical and research settings [4, 81, 85]. The operatormanually traces the border of structures of interest on the computer screen using a digitizingtablet or mouse. If the operator is skilled at recognizing tissue and lesion boundaries, thismethod is highly accurate. However, because demarcation of regions of interest (ROTs) is doneon an image-by-image basis, the process is time consuming. The investigator may wish to delineate several structures of interest per image while the structures may extend through multipleChapter 4. Segmentation Applied to Medical Imaging 40images. This process becomes labour intensive, especially for radiologists whose expertise couldbe better applied elsewhere. One of the main goals of automated segmentation techniques isto free the operator from the tedium of outlining hundreds of structures per study, sometimescosting hours per study to segment.4.2.2 Edge DetectionDespite the disadvantages of edge detection methods, including the computational complexityof defining incomplete edges and the inaccuracies of the technique when noise and artifactsare present in an image, many researchers have adapted common methods of edge detection tomedical image segmentation.Williams et al. [141] use a method based on detecting and linking local maximum gradientsin the image. First the images are smoothed using a Gaussian kernel and then a directionalderivative operator is applied to determine the gradient image. The gradient image is thenprocessed by an edge linking algorithm which sequentially links the edges locally, pixel bypixel.Udupa [132] uses dynamic programming to locate globally optimal boundary paths. Evenin two dimensions the algorithm is computationally complex and a clear, adequate definitionof optimal is not evident.Other authors employ 3D gradient operators with further increases in computational load.The 3D methods almost certainly are more accurate but at the cost of increased computationalcomplexity. Long et al. [79] compare the effectiveness of a 2D and a 3D edge operator applied tothe segmentation of SPECT images. The superiority of the 3D method is clearly demonstrated.4.2.3 Thresholding and Cluster AnalysisOne of the biggest difficulties encountered by the thresholding methods is the selection of aproper threshold or several thresholds if multi-modal thresholding is necessary. Suzuki andToriwaki [127] have proposed a technique which involves a goodness measure to aid in theChapter 4. Segmentation Applied to Medical Imaging 41selection of a threshold value. A priori knowledge of brain tissue densities and locations is usedto iteratively refine a threshold until the goodness measure is achieved.MacAuley, Haluk and Palcic [83] describe four bimodal thresholding algorithms which theysuccessfully applied to discrimination of nuclei and cytoplasm of cervical cancer cells. The firstmethod uses multiple modified gradient weighted histograms to find valleys between nucleus,cytoplasm, and background. The second method extends the work of Kittler and lllingworth tobimodal histogram analysis. The third method extends this technique by applying a Sobel-likegradient operator rendering the algorithm less susceptible to noise. Method four extends thealgorithms of the previous two techniques to local histogram selection. All of these methodsfail if the tissue to be segmented has four or more regions of interest, including background.Lachmann and Barillot [73] employ a texture analysis algorithm applied to the modifiedco-occurrence matrices obtained from the image data. Following a statistical analysis of theco-occurrence matrix for each image, a probability is assigned to each pixel indicating thelikelihood of that pixel being one of several tissues. These probabilities are determined througha clustering and classification process applied to the second order statistics of the co-occurrencematrices.The method requires the creation of a multi-parametric database consisting of six imagesfor each slice in the data volume. Each of these six images is determined by different measuresapplied to the co-occurrence matrix and by fractal analysis. For each image in the data volume,a set of n probability images results, one for each tissue type that needs to be segmented.Thus a space requirement of n + 6 times the original volume size is necessary to perform thesegmentation. The segmentation has been carried out in 2D and although Lachmann claimsthat extension to 3D is “direct”, it is likely that the computational aspects of the algorithmmay contradict this assumption.Several authors have used multiple echo MRI studies (e.g. Ti and T2) to create twodimensional histograms of image intensities [41, 68, 93]. For each image slice a 2D histogram iscomputed which represents the population densities from both the PD and T2 sequences. EachChapter 4. Segmentation Applied to Medical Imaging 42axis represents the distribution of pixel intensities for one of the two measured pulse sequences.The value at a given coordinate (x, y) in the histogram represents the number of pixels in theimage which yielded x in one sequence and y in another. The 2D histogram clearly showsclusters which hopefully represent individual tissue and lesion types. The resulting clustersof points are partitioned according to several commonly used methods of cluster analysis [68].These methods are clearly superior to one-dimensional histogram analysis.Handels and Tolxdorff [43] exploit the multispectral characteristics of the MRI signal tocreate an n-dimensional clustering method which assigns pixels to one of n clusters (in this casen = 6) interactively defined by the program. In this manner the operator can combine differentrelaxation times with proton density characteristics together with partial volume to measuredifferent biochemical properties of the tissues. A multi-cluster colour image is generated to aidin the visualization of different combinations of cluster membership. Extensive user interactionis required on a slice-by-slice basis. No results (other than visual) were presented by the authors.4.2.4 Region GrowingSandor, Metcalf and Kim [117] use a modified region growing technique together with corrections for beam hardening and partial volume effects in the analysis of CT images. Thecupping effect induced by the polychromatic nature of the X-Ray beam, discussed in Section4.1.2, is reduced by fitting the image surface with a bivariate spline function which resemblesthe cup artifact. Following the reduction of the beam hardening artifacts, the brain tissue isisolated from the skull contour. Seed pixels are then chosen using specific threshold values ofthe histogram. These values have a high probability of being accurately assigned a particulartissue/fluid classification. The remaining pixels are then classified using a nearest neighbourregion growing algorithm. Regions are grown from seed pixels depending on a combination ofpixel intensity, the number of surrounding pixels which have been classified as tissue or fluid,the sum and difference of already classified pixels, the number of already classified pixels anda polarization index calculated based on the histogram value for that particular pixel. ThisChapter 4. Segmentation Applied to Medical Imaging 43defines an initial segmentation of brain tissue.Lesions are segmented from the brain tissue by applying the algorithm to the result of theinitial segmentation. Again, extensive user interaction is required on a slice-by-slice basis andthe algorithm is highly specific to CT images of the head.4.3 Extensions to Fundamental TechniquesThe discussion of general segmentation algorithms discussed in Chapter 3 is by no means complete. Many other methods of image segmentation have been applied to medical images withvarying degrees of success. Some of the more widely publicized methods to be discussed further include mathematical morphology, pyramidal schemes, relaxation methods and techniqueswhich attempt to combine the best features of several methods.4.3.1 Mathematical MorphologyThe term morphology originally referred to the study of the form and structure of living organisms. In image processing, mathematical morphology means the study of the form and structureof objects from images of those objects. The process is based on the concept of hitting an objectwith a structuring element in order to reduce the object to a more recognizable and simplifiedshape.Two basic operations are applied in mathematical morphology, the processes of erosion anddilation [51]. Given an object 0 with origin x and a structuring element 5, erosion amounts toANDing each element of 0 with S yielding a new object, 0’. That is, 0’ is defined as the setof all points x such that S is included in 0. Dilation, an ORing operation, is defined similarlyas the set of all points x such that S hits 0, i.e. they have a non-empty intersection. Erosionamounts to a shrinking operation while dilation corresponds to an enlargement. Figure 4.4illustrates the application of erosion and dilation to a binary image of a black square on whitebackground with a square structuring element. The operations are carried out pixel by pixel bycentering the structuring element over each pixel and applying the operation. The applicationChapter 4. Segmentation Applied to Medical Imaging 44Object Structure Eroded ObjectElement000000 000000000000o....o •• oo...oo••••o •• oo•••oo••••o / oo•••o000000 origin 000000Dilated Object000000 000000o•••••o••••o •• o•••••o....o •• o.....o....o / o.....000000 origin o•••••Figure 4.4: Examples of the application of the morphological operations erosion and dilation.Each dot represents one pixel in the image. The reader is encouraged to apply the structuringelement pixel by pixel to the object on the left in order to verify the result (right).of each of these operations to 3D data sets is straightforward.Combinations of these of two fundamental operators in various guises yields an entire familyof morphological operators used in image processing. Two of these operators are opening, whichis an erosion followed by a dilation and amounts to a smoothing operator and closing, which isthe opposite of opening, a dilation followed by an erosion.The choice of structuring element is critical in any application of mathematical morphologyand this is the drawback to generalized use of this approach. Different image types require different structuring elements depending on the structures in the image which need to be isolated.Hohne and Hansen [46] use a selection of 3D morphological operators including erosionand dilation, in combination with thresholding and connected component labeling, to segmentMRI scans as part of a more generalized interactive 3D visualization package. Following theapplication of an arbitrary threshold selected by the user interactively, connected components(any regions containing pixels which are adjacent to others on at least one corner or side) areChapter 4. Segmentation Applied to Medical Imaging 45automatically determined by the algorithm. Morphological operations are performed on theconnected components to isolate individual objects. This process is repeated iteratively on eachimage until the operator is satisfied with the segmentation. The method requires extensive userinteraction and has not been validated except visually. One effect of the use of morphologicaloperators, iliustrated by Hohne, is that generalized opening and closing operations cause anon-measurable loss (and gain) in pixels at region boundaries.4.3.2 Pyramidal TechniquesPyramidal segmentation schemes [88, 91, 109] rely on the creation of representations of animage at progressively lower resolutions. These representations form a pyramid with the lowest resolution image being the top of the pyramid. Figure 4.5 represents progressively lowerresolutions of a one-dimensional signal, with the lowest resolution being at level 5.Level 5 LILevel4 LI LILevel3 LI LI LILevel2 U LI LI LILevell LI LI LI LI LILevelO LI LI LI LI LI LIFigure 4.5: Pyramid representation of a one-dimensional signal at progressively lower resolutionsas the pyramid reaches the apex. Each square represents a discrete value in the signal. Level 0represents the highest resolution and Level 5, the lowest.Each row in the pyramid represents the image at a different spatial scale, thus isolatingstructures of different size and shape. Pixels in lower levels of the pyramid are classified bylinking to pixels in higher levels. This linking is performed by comparison of pixels betweenany two levels with respect to nearest gray level and geometric proximity. Ultimately pixels inthe higher levels of the pyramid form roots of a tree. The roots of the tree are not linked toChapter 4. Segmentation Applied to Medical Imaging 46any pixels in higher levels of the pyramid. The resulting tree forms a specific segment for thatimage.Mathieu et al. [91] apply a graph theoretic approach to pyramidal segmentation by representing the pixels as nodes in a graph. The links of the graph represent a neighbourhoodrelationship between pixels. Through iterative application of graph contraction, using standard algorithms, successive graph representations form the levels of a pyramid. The resultingpyramid is called a stochastic pyramid because graph contraction is known to be a stochasticprocess. Nodes in the pyramid graphs are linked using a variation on the method discussedpreviously, ultimately forming a segmentation.Most pyramid segmentation techniques have been proven to be shift-, rotation-, and scale-variant [15] giving unreliable and unreproducible results. These methods have therefore notbeen investigated further by the author.4.4 Model-Based ApproachesA relatively recent development in medical image segmentation is the model-driven technique.The purpose of using model-based approaches to medical image segmentation is to transfer thelow-level pixel/voxel information into high level semantic information, for example anatomy,pathology, or physiology of tissues. Medical images lend themselves well to model-based methods since much more a priori information is available compared to general object recognition asapplied in the artificial intelligence (AT) approach to vision. Medical images already contain 3Ddata as opposed to a 2D projection of a 3D scene used in AT vision. In AT research perceptualprocesses are usually modeled and care must be taken to allow for different views, illumination,shadows, and hidden objects, etc.Applying a model-based approach first involves the creation of a parameterized model,allowing for modifications in shape, size, texture and other properties of objects. An attempt isthen made to match the available data to the computer model of the data. The model constrainsthe possible interpretations of the data. Inconsistent interpretations are never considered, thusChapter 4. Segmentation Applied to Medical Imaging 47drastically reducing the search space to valld, consistent solutions of the segmentation problem.We have incorporated a material percentage model as part of this thesis (See Chapter 5) inan attempt to assign a probabilistic classification to brain tissues. This method is an exampleof a model-based approach to medical image segmentation. A solution to the partial volumeproblem is offered, assigning a set of percentages to each voxel. These percentages can beconsidered the probability of a certain voxel containing a particular tissue.Arata et al. [8] use a composite image model to guide the segmentation of ventricles fromPD and T2 weighted MRT scans. The model provides ROT and boundary information, whilenew data provides gray level information used to grow ventricular regions following registrationof the images with those of the model.To create the model, four MRI data sets are first hand segmented and interpolated to giveuniform voxel dimensions of approximately T mm3. The segmented sets are then registered to astandard position, orientation and size using centroids and principal axes. New scan data usesa composite model to guide the segmentation of ventricles. The model slice which most closelyresembles the scan slice is “easily” identified [8]. The algorithm then uses a region growingtechnique with ventricle regions seeded according to pixels that have been labeled ventricles inthe model.Problems with this model are evident and iliustrate the difficulty in applying the model-based technique. Firstly, the limited number of patients used to standardize the scans is inadequate. Patients whose scans will be used in the model must therefore match the model withrespect to age, sex, gender and health, since there is tremendous variability in these parameters in different patient groups. As well, the accuracy of the registration method used willgreatly affect the accuracy of the segmentation. Since no accurate, automatic method of imageregistration exists to date, this can only adversely affect the results.Kamber et al. [57] use a similar approach to segment multiple sclerosis (MS) lesions frommulti-dimensional MRT data. They developed a probabilistic model using MRT scans of twelvehealthy volunteers. Each of the original scans is mapped to a standardized 3D rectangularChapter 4. Segmentation Applied to Medical Imaging 48coordinate space which they call Talairach space. The mapping is based on the 3D spatiallocation of landmark anatomical features of the brain. Homomorphic filtering is then used toreduce the RF inhomogeneity effect. Ventricular cerebrospinal fluid (CSF) is then manuallysegmented from each study. A supervised Bayesian classifier is used to segment gray matter,white matter and external CSF. The 12 scans are subsequently averaged to form the compositeprobabilistic model. At each point in the Talairach space, five probability values are stored. Thevalues indicated the probability of gray, white, ventricular CSF, external CSF and backgroundat each point in the standardized space.The model is used to provide geometric features using the probabilities assigned to thevoxels. It is also used to confine the search space for MS lesions to white matter areas of thebrain since 95% of MS lesions occur in white matter. The model is combined with a decisiontree classifier using 300 tissue samples to train the classifier. The nodes in the decision treerepresent some kind of test on a feature of a particular tissue, until ultimately reaching theleaves of the tree which represented specific tissue classes.The results obtained with the probabilistic model are compared to a manual segmentationof the same patient data. The results obtained from experiments that confined the searchspace using the model increased the accuracy of the segmentation by 3-5% relative to the non-model-based approach. False positive lesions, indicating MS pathology where none existed,were reduced by 50%.Although the results reported are significant, the method illustrates again the inherentproblems of model-based segmentation, that of limited numbers of patients with which to formthe model and the registration of patient data to a standardized space. As well as requiring vastamounts of patient data with which to form the model, training of the decision tree classifieralso requires excessive amounts of data storage, user and computational time.Having converted the test data to the Talairach space and performed the segmentation,the results are displayed in Talairach space as well. It is not evident from the paper thatthe transformation process is invertible, so that the results can be converted back to “real”Chapter 4. Segmentation Applied to Medical Imaging 49space. Many radiologists, having been trained to analyze tomographic scans using real data,will perhaps not be willing or able to extract from these images the information that wouldotherwise be quite apparent.4.5 Markov Random Fields and the Gibbs DistributionA modeling method which has previously been applied to the restoration of corrupted images [14, 37] has recently been adapted, with varying degrees of success, to the segmentationproblem [18, 23, 59, 122, 125]. Using this model, an image is assumed to represent a locallydependent Markov Random Field (MRF), exploiting the assumption that pixels in a given local neighbourhood of the image have similar intensity. Before discussing this model, it will benecessary to first define the notation to be used in the remainder of this section and later inthe thesis.Consider the 3D cubic lattice of the image space as a set, S, of n voxels indexed in somemanner from i = 1,2,. . ., n. Let the observed data y represent one set of data values ona particular realization of a random vector Y. The value y, denotes the observed record atposition i. A segmentation of y will be represented by a set z, a particular realization of arandom vector X. The value x denotes the segmentation value at pixel i. Let x* represent thetrue segmentation of y. Throughout the remainder of this discussion two assumptions will bemade with respect to the observed record of intensities [14].• Assumption 1: Each ‘r has the same known conditional density function, p(yjxj), whichis dependent oniy on x. So the conditional probability of the observed record y, given x,is determined by:p(yx)=1h9(yIx)• Assumption 2: The true segmentation x is a realization of a locally dependent MRF withdistribution p(x).Chapter 4. Segmentation Applied to Medical Imaging 50A probability distribution p(x) is a MRF if the following condition holds:P(XiI{Xk\}) = p(xIxN)where = {xkk i}, N indexes a neighbourhood system around pixel i, but not includingindex i, and XN1 {xIi NJ.A neighbourhood system is described by its order, q = maxj(j)2 I j e N, where 5jj is theEucidean distance between the centres of pixels (voxels) i and j, assuming uniform pixel (voxel)dimensions. Figure 4.6 illustrates first (q = 1) and second (q = 2) order neighbourhood systemsin 2D. We shall be mostly concerned with second order neighbourhood systems in 2D and third__I__a.1b.Figure 4.6: Neighbourhood systems in 2D; (a) first order (b) second order.order neighbourhood systems in 3D. In 3D a second order neighbourhood system coilsists of the18 nearest neighbours of voxel i, 8 co-planar neighbours and 5 neighbours in each of two adjacentslice planes. A third order neighbourhood system in 3D extends the second order neighbourhoodto include the 26 nearest neighbours of pixel i. Figure 4.7 illustrates first (q = 1), second (q = 2)and third (q = 3) order neighbourhood systems in 3D. Of all the possible interactions betweenthese neighbourhood systems and pixel i we shall be concerned with pairwise interactions only.It has been shown that these limitations on neighbourhood interactions do not significantlyaffect the application of MRF’s to image restoration or segmentation [14, 37]. As a consequenceof these limitations, the computational load is substantially decreased.Given the assumption that the image can be modeled by a MRF, the distribution, p(x), isChapter 4. Segmentation Applied to Medical Imaging 51a.b.c.Figure 4.7: Neighbourhood systems in 3D; (a) first order (b) second order (c) third order.a Gibbs distribution with respect to x [37]. That is, the probability that the system is in aparticular state, x, is given by:e_(x)=(4.10)where i is a parameter, U(x) is an energy function and Z is a normalization factor, or partitioning function. U(x) is a sum of functions, one for each pixel in x, which describes theinteraction of each pixel with its neighbours. There are many possibilities for describing neighbour interactions, for example, the Eucidean distance between a pixel and its neighbours. Thenormalization factor, Z, is the summation of e(2) over all possible x, i.e.,Z = (4.11)where w defines the set of all possible configurations of x.The probability given in Equation 4.10 is the a priori probability, that is, the probabilityin the absence of the data, y. Maximizing this probability gives us the state that is mostlikely, given the interaction model defined by U(x) and given that the values of each x areindependent of all other x3, where j 0 N. Unfortunately, finding the state that maximizes p(x)is an enormous task, given the size of w.We need to fluid the a posteriori probability, that is, the probability given the observeddata, y. Let be the state that maximizes this probability. According to Bayes Theorem,Chapter 4. Segmentation Applied to Medical Imaging 52maximizing this probability is equivalent to maximizingp(xly) oc p(yIx)p(x) (4.12)The state is the maximum a posteriori (MAP) estimate of the true segmentation x and isthe mode of the posterior distribution of x.Given Assumptions 1 and 2 previously, maximizing p(xly) is equivalent to maximizing theconditional probability of each x, given the record at i, y, and the current estimate of theneighbours of x. That is, it is equivalent to maximizing, with respect to x,p(xIy,N) (4.13)at every pixel site, i, in the image. Through application of Bayes Theorem and simplifying,this is equivalent to maximizingp(yiIxi)p(xiIN) (4.14)It turns out that this distribution is also Gibbs distributed with the U(X) term of Equation 4.10expanded into a sum of two terms, one, as before, pertaining to the neighbourhood interactionpotential and one term describing the differences between the observed and predicted data.4.6 Iterated Conditional ModesApplication of Equation 4.14 to each pixel in an image constitutes a single iteration of whatBesag has coined Iterated Conditional Modes (1CM) [14]. Convergence to a local maximumof p(xjy) is achieved after approximately 6 to 10 iterations of 1CM. However, this depends onthe model used for the prior distribution of x and that used for the conditional distribution ofthe record given the current estimation of x, i.e. p(yx). Besag originally used the method torestore noisy and corrupted images, however, if we consider the true segmentation xK to be theoriginal image we wish to recover, the method is readily applied to the segmentation problem.Chapter 4. Segmentation Applied to Medical Imaging 534.6.1 Segmentation Using Iterated Conditional ModesVarious simplifying assumptions have been proposed in order to reduce the computation necessary in the evaluation of the partition function Z. Choi et al. [23] have developed an algorithmusing a variation of Besag’s Iterated Conditional Modes to segment multichannel MRI imagesof the brain. Choi uses a partial volume model of tissue segmentation and models the posterior distribution of y given x by an rn-dimensional Gaussian, where m is the number of MRIchannels present. In order to reduce the computational demands of determining the partitionfunction Z, it is assumed that the probability distribution of the energy function U(x) is alsoGaussian. This also aided in the determination of an optimal j3. Although the results reportedin [23] were encouraging, we believe the algorithm suffered from some important drawbacks.Firstly, an assumption was made that the variance for pixels of pure tissue type is negligible,ignoring the natural variations which exist due to biological inconsistencies throughout a tissue(e.g. anatomy, physiology, metabolism). This will be especially pronounced in various tissuepathologies, due to the variation in extent of disease in individual tissues. Another difficultythat was raised in the paper was the following: in order to solve the matrix of equations thatresulted from the model used, the number of distinct tissues differentiable in the scan had tobe at most one less than the number of image channels available. Given that it is extremelydifficult to obtain more than two perfectly registered MRI data sets from a single scan [68],this restriction raises doubts about the robustness of the method. Choi uses heuristics and arule based approach which must be adapted according to the number and types of tissues beingsegmented in order to circumvent this restriction. As well as these deficiencies, the algorithmis applied on a slice-by-slice basis, in 2D, and does not incorporate any 3D information.Besag has shown [14] that given only pairwise neighbour interactions, and two estimates ofthe segmentation that differ only at index i, the most general form of the probability that pixeli belongs to class k, given the the neighbours of pixel i in the previous estimate, isp(xj = kIN) o (4.15)Chapter 4. Segmentation Applied to Medical Imaging 54where (i) ce(k) is an external field parameter representing prior knowledge of the spatial distribution of class k, (ii) 13k1 = 13k, which, when positive, gives a prize for neighbouring pixelsbelonging to the same class, and (iii) u(l) counts the number of neighbours of pixel i belongingto class 1. Since we are attempting to maximize 4.15, the normalization constant, Z, is notnecessary and has been dropped from the equation. It is also worth noting that the symmetryof the /3 parameters is a necessary condition to conform to the MRF assumption [14, 60].Karssemeijer [59] has adopted this approach in order to segment abdominal CT scans, exploiting some important assumptions. In order to make an initial estimate of the segmentation,Karssemeijer initializes all /3k1 to zero and thereby models the external field as 1n(p(x =the prior log likelihood that pixel i belongs to class k. This maintains Bayes Theorem in Equation 4.15. Considering these assumptions and combining Equations 4.14 and 4.15, the initialsegmentation estimate was reduced to the productp(yjxj = lc)p(x = k) (4.16)The prior probabilities, p(Xj), were obtained by “normalizing” a series of 18 CT scans of theabdominal area and registering the new scans to the normalized data. The conditional probabilities p(yjjxj) were obtained by combining the record with the prior distributions.In subsequent iterations of 1CM the interaction parameters were determined by trial anderror, with small values for tissue pairs which often occur together and a value of infinityfor tissue types which are never adjacent. Adjacent scan planes were also used to estimateinteraction with a single orthogonal neighbour in 3D. The o?s were maintained as 1n(p(x = k))even though, as Karssemeijer pointed out, this no longer holds when /3k1 # 0.Karssemeijer obtained good results for the data which was used in his experiments, however, general application of the algorithm will require significant amounts of new training datadepending on the imaging technique and equipment used. As well, accuracy and extensibilityof the registration technique used to obtain the prior distributions has not been validated.In an effort to more fully automate the method of Karssemeijer, Broekhuijsen et al. [18]adapted the previous approach and applied it to the segmentation of myocardial CT scans.Chapter 4. Segmentation Applied to Medical Imaging 55Prior and conditional probabilities were obtained in a similar manner to that of Karssemeijer.The interaction parameters were estimated from training data and calculated as = thepercentage of the total number of pixels labeled Ic which lie on the border of regions labeled 1.As a result, the range of values of /3k1 are adjusted to 0.0 < [3ia K 1.0. However, the symmetrycondition is violated by allowing 13k1 !3lk The neighbour counts u(l), from Equation 4.15,are further replaced by percentages of neighbouring pixels labeled 1. In order to normalize theresulting expression to yield a value between zero and one, Broekhuijseu replaced the summationterm of Equation 4.15 with its reciprocal, yielding the new productp(yjxj = k)p(x = k)e+ (4.17)wherez= Z!3kluiQ) (4.18)lkSince both the /3’s and the neighbour counts u(l) range from zero to unity, it is clear that0.0 K Z K t, where t is the number of discrete possibilities for labeling voxels, resulting inprobability measures ranging from 0.0 to e ?. Broekhuijsen uses a heuristic to overcome thissignificant inconsistency by arbitrarily assigning 0.5 to the highest resulting probability, 0.25to the next highest, and so on, in an effort to normalize the resulting distributions. Thisdrawback, combined with the violation of not conforming to the symmetry condition imposedby the assumed MRF nature of the data, precludes the use of this algorithm in a general setting.Stringham, Barrett and Taylor [125] have extended the work of Broekhuijsen [18] and Karssemeijer [59] by including region growing and edge information into the MRF context. Stringhamadds an edge probability term to the product of Equation 4.17 and eliminates the prior probability measure altogether. The segmentation is initialized by seeding a series of representativetissue samples from a single slice in the scan to be segmented. From these regions, normalized,low pass filtered histograms are obtained representing the conditional probabilities. The neighbourhood interaction parameters are either obtained empiricaliy or initialized to 1 for the initialsegmentation. A gradient image is also obtained and is used to generate edge probabilities to beChapter 4. Segmentation Applied to Medical Imaging 56incorporated into the 1CM equation. Following calculation of the conditional probabilities the1CM equation is applied only to those pixels which border the seed regions obtained previously.In this manner, region growing is incorporated into the algorithm. Following convergence ofthe algorithm on the initial slice, the resulting segmentation is used as the seed segmentationfor adjacent slices. If necessary, neighbour interaction parameters and conditional probabilitiesmay be recalculated based on the final segmentation. The process continues until the entirevolume is segmented.This approach suffers from some major drawbacks. The edge probability measure is usedto coerce region boundaries towards points of high gradient magnitude in the edge image. Thiswill only happen, however, if the region boundary and the detected edge in the gradient imageoccur within the pixel width of the edge filter used to obtain the gradient image. As such, edgeinformation is utilized only after regions have grown sufficiently (and possibly erroneously) tofall within the range of the edge filter used. This problem is alleviated somewhat (at leastfor the initial segmentation) by seeding multiple disjoint regions according to the histogramsobtained during initial training, yielding a much more accurate initial segmentation than thatobtained by simply using the seed regions themselves. Since adjacent slices may contain newstructures and/or lose structures present in the previous slice, the problem is again presentwhen proceeding to adjacent image planes.Secondly, the edge probability measure included in Stringham, Barrett and Taylor’s paperdepends heavily on the scale of the gradient magnitude image. For example, given discrete pixelvalues of 0-255 in the image scans, the gradient magnitude image will have values in the samerange, 0-255. The edge probability associated with pixel x is calculated by the expressionE(x) = 0.5 + f * m (4.19)where f is a proportionality factor (0.1 was used in Stringham [125]) and m is a minimum(maximum) difference measure on the gradient magnitudes of pixel i and its neighbours, depending on the edge classes that have been assigned to pixel i and its neighbours. Thus—255 m 255, and it follows that the edge probability measure will have values in the rangeChapter 4. Segmentation Applied to Medical Imaging 57—25,0 < E(x) <26.0 for the value f = 0.1 used in the paper. The edge probability term willalmost certainly dominate the probability product.These inherent difficulties draw into question the robustness of this algorithm. Little in theway of results was given in the paper, making verification difficult as well. It is interesting to notethat no mention of MRF’s or Gibbs distributions is made in the Broekhuijsen or Stringhampapers. This in turn is likely the reason that the methods stray so significantly from thetheory and produce questionable results. In the next chapter we attempt to maintain theMRF assumption, while almost eliminating the need for prior organ models. We examine a3D, multichannel, partial volume solution to the segmentation problem based on MRF theorywhich requires a minimum of user input. Our method also provides a high level of parallelismto speed the computation.Chapter 53D Multispectral Stochastic Volume SegmentationIn this chapter we describe a quasi-automatic solution to the segmentation problem using thetheory of MRF’s in 3D, resulting in partial membership of voxels in several tissue types. Themethod is simple, requiring a minimum of user input and allowing a high degree of parallelism.In Section 5.1 we revisit the theoretical basis for our solution. Section 5.2 describes the extensions we have made to the Iterated Conditional Modes algorithm in order to incorporatethe available 3D information. In Sections 5.3 and 5.4 we describe the implementation of thealgorithm using a datafiow image processing environment, WIT. The benefits and limitationsof adopting the dataflow paradigm will also be presented.5.1 Returning to Basic TheoryAs is evident from the preceding discussion, the variations made to 1CM by Karssemeijer [59],Broekhuijsen [18], and Stringham [125] are not always consistent with the theory of MRF’s andmay require extensive training and user interaction in order to perform properly. As well, noneof the authors exploits the 3D nature of the data to any appreciable extent. In the followingsections we describe how we perform the segmentation while at the same time maintaining theMRF property. User intervention is kept at a minimum by training the algorithm using aninitial region of interest (ROl) selection on a single image from the volume to be segmented.The ROT selection yields conditional probability profiles for each tissue to be segmented. Wefully utilize the third dimension by incorporating a 3rd order neighbourhood system in 3D. Wemake the solution tractable by allowing extensive parallelism.As the partial volume problem is still one of the major difficulties encountered in medical58Chapter 5. 3D Multispectral Stochastic Volume Segmentation 59image segmentation, we have endeavoured to provide a solution which yields a probabilityclassification for each voxel, indicating the percentage composition of different tissues in thatvoxel. Each x will now be considered a vector of values indexed from k = 1,2,. . . , t, wheret is the number of tissue types present in the data volume. The kth value of element x,which we call its labeling, represents the probability that voxel i is of tissue type k. Theseprobabilities can be viewed as the partial volume contribution from each tissue type to voxelx. As such, p(Xjk) = 1.0 must hold at each iteration of the algorithm. The basicassumption introduced by Karssemeijer [59] is maintained here. That is, the external field, owill still be modeled by ln(p(x = k)) in order to simplify the general form of the 1CM equation.Now, on each iteration of 1CM, the probability that x belongs to a particular tissue type,k, is given byp(Xjk) = p(yiIxk) * p(ik)e_Z (5.20)whereZ = /3iu(l)and ( I xj) is the conditional probability of the record, given its labeling, obtained from theinitial histograms, p(ik) is the provisional estimate of the probability of pixel i belonging totissue type k, 13k1 is a measure of the interaction between tissues labeled k and 1, and is obtainedusing partial memberships of voxels in a particular tissue class.The energy term u(l), in Equation 5.20, is the number of neighbours of voxel x, havinglabel 1. It is likewise determined from partial volume memberships weighted by inter-voxeldistances. The total number of tissues considered to be present in the image volume, t, isobtained implicitly from the initial regions of interest selected by the user.A minimum of user intervention is required to train the algorithm by requiring the manualoutlining of regions of interest in a single image selected from the volume. Each of these possiblydisjoint regions represents the user’s belief that the voxels contained within the circumscribedregions are pure voxels. Normalized, low pass-filtered histograms are obtained from each ofChapter 5. 3D Multispectral Stochastic Volume Segmentation 60these regions and used as input into the relaxation algorithm. These histograms provide theinitial estimate of the segmentation, which in turn provides the initial neighbour interactionparameters and energy term of Equation 5.20. In order to obtain an initial estimate of thesegmentation which represents our prior knowledge of the tissue distribution, the probabilitythat voxel Ij is of tissue type k is initialized to-‘ p(yiIxik)p(Xjk)=(5.21)p(yIx)which is simply a set of normalized probabilities based on the conditional probabilities obtainedfrom the histograms. In subsequent iterations of the algorithm, the i’s are assigned the valuewhich was obtained in the previous iteration.Application of Equation 5.20 to each voxel in 3D constitutes one iteration of the algorithm.After each iteration or a predetermined number of iterations, the histograms and neighbourhood interaction parameters may be recalculated. Relaxation of the segmentation occurs afterapproximately six to eight iterations. Following convergence, a partial volume estimation isproduced, indicating the probability that each candidate voxel is of a particular tissue type.Segmentations obtained from multiple echo sequences may be determined independentlyand then combined by forming the product of the probabilities of each tissue type for eachimaging spectrum. This combination is possible because the data sets are independent.5.2 Extensions to Iterated Conditional ModesIn order to accommodate a partial volume solution some modifications have been adoptedto automatically calculate neighbour interactions and neighbour counts in 3D. In light of thefact that voxels are rarely cubic, the neighbour interactions and neighbour counts are furtherweighted by the intervoxel distances between pixel i and its 26 neighbours in 3D. That is, we usea 3rd order neighbourhood system in 3D, believing that this is the minimum neighbourhood,in 3D, having a significant influence on the central voxel.Chapter 5. 3D Multispectral Stochastic Volume Segmentation 615.2.1 Neighbour Interaction ParametersOne of the difficulties encountered by previous authors was determination of neighbour interaction parameters. The parameters were estimated heuristically by Karssemeijer [59] and,although automatically calculated by Broekjhuisen [18] and Stringham [125], resulted in a non-symmetric matrix, contradicting a fundamental assumption of the theory of MRF’s. Broekjhuisen’scalculation required a modification to the 1CM equation which introduced inconsistencies in theresulting probabilities (see Section 4.6).A simple, intuitive notion of tissue interaction may be used to solve this difficulty, withoutrequiring a priori information about the tissues which must be segmented. We have defined theneighbour interaction parameters, 13k1, to be the inverse of the probability that tissues k and1 are adjacent, as opposed to the notion of the probability that tissue k is adjacent to tissue1. These adjacencies are weighted by the partial volume consistencies of each voxel and by therelative distance from each voxel to its neighbours in 3-space.The probabilities are determined from the tallied adjacencies for each tissue pair (k,l) inthe provisional estimate of the segmentation, . Let Tlkl represent the total number of weightedadjacencies involving both tissues k and 1. Let Tlk and represent the number of weightedadjacencies involving tissue k and 1 respectively. /3k1 is therefore defined as:kl= ( k1 (5.22)71k + 7lwherek1 = lk =i=1 jeNwhere n is the number of voxels in the image volume, N defines the neighbourhood systemsurrounding voxel i, and is the distance measure from the centre of voxel i to the centre ofits neighbour voxel j. The accumulated adjacencies for each tissue type, r, may be defined as:]kZ77kjChapter 5. 3D Multispectral Stochastic Volume Segmentation 62where t is the number of tissues present in the segmentation. Matrix is therefore symmetricwith (1.0 < /3, < cc) for all 1 and k (lim,7ko/31 = cc). These neighbourhood interactionparameters are determined from the initial segmentation estimate and may be updated after apredetermined number of iterations, thereby refining the accuracy of the segmentation.5.2.2 Neighbour CountsThe energy term u(l), in Equation 5.20, is the number of neighbours of voxel j, in the provisional estimate of the segmentation, having label 1. It is again determined from partial volumememberships weighted by inter-voxel distances. The neighbour counts for tissue 1 in voxel xare thus defined as:u(l) =jEN5.2.3 Histogram Re-evaluationAs the segmentation proceeds the accuracy of assigned probabilities increases. Since the histograms used to initialize the segmentation were based on a limited number of voxels from thevolume, we have allowed for the re-calculation of histograms to be used in further iterations.Thus histograms representing updated tissue profiles are computed as follows. The histogramentry Hkg, associated with each tissue class k and each possible discrete gray level value g isgiven by= p(jk) V {i I 1(y3) = g} (5.23)where I(y) is the intensity value of voxel y in the observed record. These histograms are ofcourse normalized and smoothed, as before, in order to eliminate sharp peaks which are likelythe result of noise in the observed record.5.2.4 Prior Organ ModelsThe prior probabilities defined in Equation 5.21 may also be obtained as by other authors,that. is, by analyzing multiple sets of image data, when available. The reality is, however, thatChapter 5. 3D Multispectral Stochastic Volume Segmentation 63construction of prior models is subject to the enormous variability between specific imagingmachines and imaging variables. For example, depending on the sequence of application ofRE pulses in the acquisition of MRI studies, significantly different tissue profiles will result.The normalization of such scans is not a straightforward task, and is complicated by imageregistration difficulties, not to mention the extra time and effort required to form the model.Although the priors obtained here may not be as accurate as those obtained through modelcreation, they do allow an accurate segmentation to be performed. The automatically generatedpriors may be accumulated and used to form a more suitable model over time. This is one focusof future work in the area.5.2.5 ConvergenceIt has been discussed that the segmentation continues until convergence is achieved, usuallyfollowing six to eight iterations of the algorithm. A measure of convergence has not beenspecified up to this point. There are a number of methods of measuring convergence of thealgorithm, usually done by placing a limit on the number of voxels which change from oneiteration to the next. With a partial volume solution to the problem, the number of voxelswhich change between iterations is not readily measurable. However we have adopted a methodwhich tracks the change in p(Ijj) between iterations, resulting in a vector of values for each j,indicating the change in each tissue. A scalar measure of the change in voxel i, on iteration m,denoted kjmI is obtained by calculating the 2-Norm of this vector such that:kjml (P(ik)m) P(ik) (rn_i))The user may then assess changes between successive iterations and apply suitable thresholdcriteria on the number of changes required per iteration, in order to allow convergence to beachieved within six to eight iterations. This is a significant computational burden to bear oneach iteration, but is partially offset by the inherent parallelism borne by the algorithm.Chapter 5. 3D Multispectral Stochastic Volume Segmentation 645.2.6 Multispectral ApproachWhen available, two or more independent sets of data may be used to drive the segmentationalgorithm. We have performed the segmentation on multiple echo MRI sequences, but othercombinations of data are just as valid, provided the data sets are independent and spatiallyregistered. For example, patient scans from PET analysis may be combined with MRI orCT. Since the data sets are independently acquired, the resulting probabilities calculated bythe 1CM algorithm may be combined by multiplying corresponding values. The result of themultiplication is again normalized such that p(Xjk) = 1.0. We have found that the resultsobtained from using two or more data sets are consistently more accurate than those obtainedfrom using either of the data sets alone.5.2.7 ParallelismIt is the elegance and simplicity of the MRF assumption that allows for high levels of parallelismin the implementation of 1CM in 3D. Since, at each iteration, the new segmentation estimates areentirely neighbourhood based, we could conceivably allow updating of each voxel to be carriedout by a separate processor. This would require the use of highly specialized hardware, such asa transputer network. The parallelism that we have achieved is provided by the image processdevelopment environment that we adopted as part of the implementation of this algorithm.This is described in the next section.5.3 Implementation PlatformIn this section we introduce the image processing development platform used to implement the3D 1CM algorithm on standard Sun Sparc workstations.Following extensive evaluation of several imaging platforms and visualization tools, it wasdecided that the implementation of 1CM would be developed using WIT®’, a state of the‘The word WIT is derived from pronunciation of the acronym OOIT which stands for Object Oriented ImagingTechnology.Chapter 5. 3D Multispectral Stochastic Volume Segmentation 65art image processing development package based on the data flow paradigm of software development. WIT is highly interactive and allows the rapid prototyping of algorithms underdevelopment.5.3.1 Dataflow ParadigmThe concept of dataflow is based on the notion of processing data while it is in motion. Adataflow network consists of a collection of nodes, or processing stations, linked together byarcs, to allow the flow of data through the network. Each of these processing stations may havemultiple inputs and outputs. Loops may be formed from the arcs and nodes to allow repeatedprocessing of dynamically changing data. Thus, data processing is not sequential as it is withtraditional von Neumann architectures.The notion of dataflow as described above is rather vague, and so we will concern ourselvesonly with one particular type of dataflow, namely pipeline dataflow. Using the pipeline approachimplies that it is not possible for data on an arc of the network to overtake other data travelingin the network. There are two basic principles associated with pipeline dataflow which provideinherent parallelism. The first principle is that of asynchrony which allows a node to be executedonly when all inputs to that node are present. The second principle of execution of a pipelinedataflow network is that of functionality. Each node in the network represents an atomicfunctional unit, which accepts inputs and produces unique outputs based on those inputs.There are no side effects, and therefore no global variables. These functional operations maythus be carried out in any order or in parallel, provided the inputs to the node are present.Parallelism is implicit in such a dataflow network, and therefore requires the existence of anexternal scheduling mechanism which tracks the arrival and exit of all inputs and outputs. Itis the need to establish and maintain a scheduling conflict resolution mechanism which makesdataflow programming difficult to implement, and not always appropriate.Chapter 5. 3D Multispectral Stochastic Volume Segmentation 665.3.2 WITThe image processing development environment adopted for implementation of this thesis,WIT, employs the pipeline dataflow approach to programming. Interfacing with WIT is asimple matter of selecting graphical icons from the multiple libraries of operators which areavailable, and joining these icons together by simple mouse point and click operations. Theoperators form the nodes of a dataflow network, which in WIT is termed an interactive graph,or igraph. The inherent parallelism of the dataflow approach is exploited by the use of a Unixclient/server model of computation to distribute execution of operators across a network ofresources.Along with the operator libraries which accompany WIT, the developer can easily incorporate new operators when more functionality is required. These operators may be added tocustom designed libraries created by the developer or added to already existing libraries andused in an equivalent manner to the operators already available. One of the advantages whichWIT enjoys over similar software products is its extensive control flow library which grants theuser significant powers of sequencing, iteration, and synchronization of operators in an igraph.The package was written in the C language, running under OpenWindows® on the SIInTMfamily of workstations and is currently being ported to other software and hardware platforms.WIT is pseudo-object oriented in that it provides encapsulation of both data and functionality. Polymorphism is achieved to some degree, by requiring all WIT data types to be someform of Object. It is up to the developer of new operators in WIT to assure that any new functionality introduced is applicable to multiple data types. There is no concept of inheritance inWIT and so it is not truly object oriented. WIT could have incorporated significantly moreobject oriented features, with some loss of efficiency, if it had been written in C++.The highly interactive nature of igraph formulation and editing can be exploited in order toaccurately trace execution of developed algorithms and to more readily analyze an algorithmunder investigation. Figure 5.8 is an example of a small WIT session, illustrating an elementaryigraph, together with the results of executing the igraph. We have used this igraph to simplyChapter 5. 3D Multispectral Stochastic Volume Segmentation 67Figure 5.8: A sample WIT session showing a small igraph and the results of executing theigraph. Note the spy-glass probes allowing visualization of data as it flows along the network.Chapter 5. 3D Multispectral Stochastic Volume Segmentation 68read in an MRI image and overlay a series of regions of interest (ROIs), which have beenpreviously obtained, indicating the presence of Multiple Sclerosis lesions in this area of thebrain.The WIT Status window updates operator, igraph, and server status as the igraph executes.The Operator property panel pops up when the user gives a mouse click over an operator iconof interest. In Figure 5.8 the rdObj or read Object operator panel is shown. The rdObj operatorreads in any of the WIT Object data types from disk. The property panel allows the user toedit the options pertaining to the operator, such as enabling or disabling its execution, and itsorientation or Flip mode on the igraph screen. As well, any parameters which are required to bemanually input to the operator can be modified through the property panel. These parameterscan be converted to inputs and thus provided to the operator by linkage from other operators.There are two copies of the rdObj operator in the igraph, one labeled readlmage and theother readROl. The readlrnage operator reads an image, in WIT format, while the readROloperator reads a region of interest description, also in WIT format. The operator is able todifferentiate the type of Object which it reads. Data flows from these two operators down thepipes (or links, as they are termed in WIT) and illto the next operator called overlayData.Data flows in the direction of the arrows seen on the links. The overlayData operator is alsosupplied in WIT and accepts the region of interest description and the WIT image as input andoverlays the ROI onto the image. The result of this overlay is displayed in the image labeledMS Lesions.Note the spy-glass shaped probes in Figure 5.8 which are visible on the links of the igraph.These probes can be interactively placed on any link in an igraph in order to observe the dataas it flows through the network. The image slice labeled MRI Slice and the ROIs object aredisplayed as a result of placement of these probes on the links.Following the display of any image in WIT, the user may interactively examine the image byaltering its scale, zooming, panning, adapting the colour map used in display of the image, andso on. In this example, an X-Profile, showing the profile of values across a selected horizontalChapter 5. 3D Multispectral Stochastic Volume Segmentation 69line in the image, has been acquired in order to more closely analyze tissue symmetry in thisparticular area of the brain.Fassname: dispIaFigure 5.9: An example of a hierarchical igraph in WIT. The derivedHipass operator is composedof a subgraph containing other operators, hidden to reduce igrapli size and add modularity.outFigure 5.10: The derivedHipass operator of Figure 5.9 expanded to show its sub-nodes. (Thevalues for the width and height parameters given here are different from Figure 5.9. They arethe default parameters which were input when the operator was created.)As igraphs become larger during development, it is possible and necessary to be able toencapsulate sets of operators and links into smaller, more manageable units. This is achievedin WIT through the use of hierarchical operators, networks which have been reduced to a singlenew operator in order to save space on the screen and to preserve modularity in the softwaredevelopment process. Figure 5.9 illustrates the use of a hierarchical operator supplied withWIT, called derivedHipass, which has been formed from a combination of a lowpass filteringfilename: saturn width: 3height: 3Chapter 5. 3D Multispectral Stochastic Volume Segmentation 70operator and an ALU operator. The expanded operator is shown in Figure 5.10. The ALUoperator’s parameters have been assigned such that the original image is subtracted from thelow pass filtered version in order to obtain the equivalent high pass filtered image. Note thatthe width and height parameters of the lopass2d operator are displayed in reverse video. Thisindicates that these parameters have been promoted to the hierarchical operator to which thisoperator belongs. This allows the user to enter the parameters directly via the derivedHipassoperator without having to expand it. A hierarchical operator is identified in an igraph by thedot in the upper right corner of the operator icon.In order to allow for accurate tracing of execution of these igraplis, WIT has incorporated avariable speed animation feature, highlighting operators and links which are currently active inthe igraph. This enables the developer to detect inconsistencies and possible deadlock situationswhich may occur during igraph execution, and to accurately pinpoint the location of programbugs.The foregoing introduction to WIT is not meant to be an exhaustive tutorial, as that is wellbeyond the scope of this thesis. It is meant to serve as a background for the description of morecomplicated igraphs to be encountered in later sections. The interested reader is encouraged toexplore the WIT User’s Guide [9] in order to obtain more information.5.3.3 Extensibility Using WITDue to the highly interactive nature of igraph development applied in the dataflow environmentof WIT, algorithms are easily extended and adapted, reducing development time and allowingthe sharing and reuse of software modules. As a parallel effort in solving some of the difficultiesin qualifying and quantifying brain tissues and lesions, Zuk has developed a series of imageregistration algorithms using WIT [145]. In order to accommodate the 3D nature of his work andours we mutually developed a set of operators which extend the 2D capabilities of WIT. Theseoperators consist of input/output functions and display functions which we found necessary inorder to develop our algorithms, but which are not currently available in WIT. The functionalityChapter 5. 3D Multispectral Stochastic Volume Segmentation 71of these operators encompasses reading a 3D raw data file and creating a Vector of WIT imagesfrom the raw data, displaying the resulting volume as a single image consisting of multiple slices,and applying a maximum projection function to the set of WIT images in order to obtain asimple volume visualization tool, to name just a few. These operators have formed an integral,reusable, common basis for dealing with 3D images in a 2D environment.On a higher level, the extensibility of the dataflow approach, WIT in particular, has allowedus to rapidly develop and extend our segmentation and registratioll algorithms without havingto rewrite code to an appreciable extent. Changes to igraphs usually involve no more than afew simple drag, drop and connect operations, while the effects of such changes are instantlyobservable by simply re-running the network following these changes.5.3.4 Parallelism Using Multiple ServersOne factor which influenced our decision to adopt WIT as our imaging platform is the explicitparallelism which can be achieved by assigning execution of specific operators to specific servers.When multiple servers are specified in WIT, the operator property panel for each operatorincludes, as a parameter, the particular server on which to execute the operator. The userthus has ultimate control over which functions are executed by which machines. Scheduling ofoperator execution is handled exclusively by WIT, so the programmer need not be concernedabout conflict resolution.5.3.5 Limitations of the Dataflow ApproachWe have found the datafiow environment of WIT to be subject to several limitations, some ofwhich are inherent in the dataflow paradigm itself. First, for a new user, one whose experiencehas been with the traditional von Neumann style of program execution, the concept of datafiowis bound to be a little foreign. The notion of datafiow, vis-a-vis control flow, demands anentirely different mindset when programming. This drawback is amplified when the operators(network nodes) are written in a von Neumann style programming language (e.g. C) such asChapter 5. 3D Multispectral Stochastic Volume Segmentation 72is the case with WIT. As a result of this relatively steep adjustment curve, it may take sometime before a user can exploit the dataflow environment to its fullest extent.filename:Figure 5.11: An example of deadlock in a WIT igraph illustrating an improperly formed ioop.The castOp operator is waiting for input from aizzOp #1 which is in turn waiting for input fromthe castOp operator.The risk of network deadlock is an ever present reality when executing an igraph, and thedeveloper must be diligent to ensure that such events are avoided during igraph execution.Deadlock occurs when execution of an igraph stops before all desired outputs are obtained,usually the result of improperly formed loops in the network.Figure 5.11 shows an example of deadlock in a WIT igraph indicating an improperly formedloop. The purpose of the igraph is simply to sum two images and then sum the result withanother image. The castOp operator casts the image received to whatever type is specified inthe cast Type parameter. The alnOp operator applies the operation given in its input parameter,in this case addition, to its two input images. Deadlock occurs because the castOp operator iswaiting for input from al’aOp #1 which is in turn waiting for input from the castOp operator.Thus neither of the aluOp operators will ever execute. This is a contrived example of deadlockaluop: +luOp 11aIiAOp: +castopca5tType: 8—bit unsignedChapter 5. 3D Multispectral Stochastic Volume Segmentation 73which would probably never occur in practise. However, when igraphs get more complicatedand more hierarchical, identification of the operators causing deadlock will not be as apparentas it is in this case.Cases of deadlock may occur in more subtle ways than that illustrated in Figure 5.11and depending on the pattern of execution of an igraph, may only show up under certaincombinations of inputs, and input sequences. With the complication of multiple servers, therisk of deadlock is increased, and it is possible that an igraph which executes properly with asingle server, may not execute properly when run under multiple machines. This anomaly isdue to the fact that the order of operator execution is usually static when a single server isemployed. The order of execution when using multiple servers is unpredictable, as the WITscheduler makes adjustments according to the availability of resources.It should be noted that igraph animation provided by WIT serves to enhance the user’sability to detect and correct deadlock in most situations. It should also be noted that withincreased igraph complexity and expansion in igraph hierarchy, the ability to detect deadlockand other program bugs becomes increasingly difficult.Another drawback with WIT is associated with the manner by which WIT achieves itsparallelism. WIT has no provision for sharing memory, such that any program or data whichmay be used in parallel by multiple servers must be copied to all the servers. This difficulty isinherent in the use of the standard Unix sockets and pipes employed in the WIT environment.WIT has many features not available in competing software, however, it suffers from fundamental problems, as discussed above. As well, we have found initial versions of WIT (we haveabsorbed several updates since the beginning of the project) to be plagued with memory andinput/output problems mostly resulting in frequent, unexplained program crashes. Althoughthese events do still occur to some degree in the current version (Version 3.23) they have beenminimized through an ongoing liaison with Logical Vision Ltd., the creators of WIT.The following section describes the implementation of our version of 1CM developed usingWIT.Chapter 5. 3D Multispectral Stochastic Volume Segmentation 745.4 WIT Implementation of 1CMHaving had considerable experience using WIT prior to implementation of our algorithm, construction of the igraphs necessary to perform the segmentation was relatively straightforward.However, the igraphs may not appear so simple to the naive user.Figure 5.12: WIT igraph of the 1CM implementation. Note the null operator which acceptsoutputs which are available but not necessary for this igraph. The use of the null operatorensures proper memory management of data structures which are not needed.Figure 5.12 is the main igraph constructed to perform the segmentation. We have used dualecho MRI images of brain tumour patients and Multiple Sclerosis patients for our experiments.Following an initialization phase, each image spectrum, together with histograms of tissuesselected in the initialization phase and the total number of tissues present in the volume arepassed to the segmentation routine. Following individual segmentations, the results are thencombined to form the true classification for this data set. The results, together with finalhistograms and neighbourhood interaction parameters are written to disk as WIT objects.Note the probe on the link following the combinePVolSpectra operator in Figure 5.12, allowingnuflSegrn out SpectrurnliurrIutrIiwrHistlspectruml HistsrBj 1spectruml Bijr5ernentathmIILI,corn bi nedsegme ntationicmlter: 3neglter: 1minvoeelChange: ionSlice_Thick000s: 13Slice_ Gap: 0FieILof_Vie: 385spectrumzHistepectrum2nijChapter 5. 3D Multispectral Stochastic Volume Segmentation 75visualization of the result.We have expanded the operator icmlnitialize (Figure 5.13) in order to more fully explainthe pre-segmentation functions. As a first step, both image spectra are read in to the programby the ReadSpectrum operators, which are copies of a custom-made operator created to converta raw data volume into a vector of WIT images. The user then has the opportunity to maskoff an area around the volume in order to reduce the computation necessary to perform thesegmentation. The ExtractBoundary operators are actually just if control mechanisms, passingthe input to the top or bottom output port depending on whether the lower input is true (not0) or false (0). The get VolBo’undary and extractBndry Vol operators are therefore bypassed ifno masking is required. Otherwise, the user is asked to outline, on a maximum projectionimage obtained from the volume, the area to which the segmentation should be applied. ThisFigure 5.13: Expanded WIT igraph of icmlnitialize operator.Chapter 5. 3D Multispectral Stochastic Volume Segmentation 76is achieved through the application of the get VolBonndary operator. The extractBndry Voloperator masks off this area in each of the images in the volume.MRI (T1)Figure 5.14: MRI dataset from which the user selects the image for obtaining tissue profiles.(Ti weighted data)The user can then select the image which will best yield the tissue profiles necessary toperform 1CM. The images are displayed simultaneously on the screen as shown in Figure 5.14and the user interactively selects the desired image from this set. This task is performedby the hierarchical selectlmg operator. The imgNFrm Vec operator selects the correspondingimage from the second image spectrum. This starting image is then passed to the rnultRoioperator to allow the user to interactively select multiple ROTs for each tissue type present inthe image. If necessary, the user may use more than one image from which to obtain desiredROTs. Histograms and other statistical parameters (e.g. mean) are obtained from the regionsChapter 5. 3D Multispectral Stochastic Volume Segmentation 77of interest by the statsFrRois operator, which also normalizes and smoothes the histograms soobtained.As an optional output the rasterizeROls operators colour the ROTs with the mean gray levelin each region for possible later viewing. The histograms, coloured ROTs and image spectra(possibly masked) are then output to be processed by the segmentation operators.Some points worth noting from the expanded igraph of Figure 5.13 are (i) the use of hierarchical operators, some of which extend the hierarchy to even more levels; (ii) the potential forparallelism in execution of this igraph; (iii) the input parameters seen in some operators suchas the constant (K) operators, which have been promoted to the next level in the hierarchy sothat they can be entered in the main igraph without ever having to expand the icmlnitializeoperator; and (iv) the rapid increase in the complexity of the igraphs which occurs duringdevelopment.We can now move on to the segmentSpectr’um operators, one of which has been expandedand is shown in Figure 5.15. This hierarchical operator forms the core of the segmentationalgorithm. The image volume and histograms obtained from the initialization phase are inputto the operator, as well as the number of tissues determined to be present in the volume. Fromthe histograms an initial segmentation is obtained, as explained in Section 4.14. The crcateP Vol(create partial volume) operator is responsible for the computation of this initial segmentation.The memory operator (brain icon) holds the image vector until the input is required by otheroperators. Release of an input supplied to the top input port of the memory operator occurswhen any object is received at its bottom input port. This is necessary in order to allowrepeated access to this input, since all operators in WIT destroy their inputs upon releasingtheir outputs.In order to ensure that the creatPvol operator is bypassed in future iterations of the algorithm, the oneshot operator is used, shutting down further inputs once a single input haspassed. The initial segmentation output from the createPvol operator is passed to the icmSegoperator. The for and if operators allow the user to control the exact number of iterations ofChapter 5. 3D Multispectral Stochastic Volume Segmentation 78Figure 5.15: Expanded WIT igraph of segmentation operator seg VolumeChapter 5. 3D Multispectral Stochastic Volume Segmentation 791CM to be applied before recalculation of the neighbourhood interaction parameters and newhistograms.The icrnSeg operator accepts the image vector, the initial segmentation, a collection of histograms describing tissue profiles, and a set of neighbourhood interaction parameters (the /3k1),as inputs. From the input number of tissues, and the input parameters for slice thickness, slicegap and field of view, we are able to compute the neighbourhood interaction parameter matrix,as described by Equation 5.22 in Section 5.2.1. Operator icmGetBij is responsible for thiscomputation. Note how the input parameters are maintained in memory operators for futureiterations of the algorithm. The icrnSeg operator repeatedly applies the 1CM equation to eachvoxel in the input volume until convergence is achieved or until the number of iterations ofthe algorithm reaches the input parameter maximum, icrnlter. Convergence is determined tohave occurred when the number of voxels changing in a given iteration is less than the inputparameter minVoxelChange. (See Section 5.2.5 for a more detailed description of convergence.)When convergence has occurred or the number of iterations of 1CM reaches icrnlter, the outputsegmentation is passed to the if operator. If the number of segmentation iterations specifiedby the seglter parameter of the for operator has been reached, the segmentation is output asp VolSeg. Otherwise, a recalculation of neighbourhood interaction parameters and histogramsis performed by looping the output back to the icmGetBij and histFrom Vol operators. Thisrecalculation increases the accuracy of the segmentation. Equation 5.23 in Section 5.2.3 describes how the histograms are recalculated. Following execution of these operators, the newparameters are shunted back to the icmSeg operator, and the algorithm is repeated. Note howthe looping of the segmentation output to the memory operators triggers the release of theparameters necessary to repeat execution of the segmentation.The operator icmSeg forms the core of the segmentation algorithm. Although the algorithmis fully described in Section 5.1 we have included the source code of the kernel of this algorithmin Appendix A. We have duplicated the source code in the appendix in order to better conveythe complexity of dealing with 3D data in WIT and give some intuition for the significant timeChapter 5. 3D Multispectral Stochastic Volume Segmentation 80and space requirements of the operator.Chapter 6Algorithm Testing and ResultsWe have applied our version of the 1CM algorithm in 3D to MRI scans of the head obtained fromMultiple Sclerosis patients. In this chapter we first offer a short description of Multiple Sclerosisin order to motivate the application of our algorithm in this area of research. The results ofapplying our algorithm to the MS images in order to quantify the extent of Multiple Sclerosislesions are then discussed. The results are encouraging and serve to illustrate the difficultiesin solving the segmentation problem. The chapter concludes with some general observationsregarding the 1CM algorithm as implemented in this thesis followed by a description of futurework to be completed in the area.6.1 Multiple SclerosisMultiple Sclerosis (MS) is a disease of the central nervous system (CNS), i.e. the braill andspinal cord [110]. It is a debilitating and progressive disease which may result in a variety ofsymptoms from blurred vision to severe muscle weakness and degradation, depending on thearea of the CNS which is affected. Multiple Sclerosis is caused by a breakdown in the myelinsheath, a soft, white, fatty material which insulates the neurons of the CNS and provides forthe rapid transmission of nerve impulses along the nerve fibres of the brain and spinal cord. Asthe myelin breaks down, it is replaced by scar tissue, and the speed and frequency of impulsetransmission along the nerve fibre is reduced and in some cases eliminated. The scar tissueformed from demyelination results in the formation of characteristic plaques in the affectedarea. These plaques can be readily observed by post-mortem dissection and by MRI scanningof live patients.81Chapter 6. Algorithm Testing and Results 82Figure 6.16: MRI image (left) with MS lesions manually outlined by radiologist (right).Figure 6.16 shows MS plaques in a slice selected from the image volume analysed in ourtests. The left hand side shows the image itself while the image on the right has been overlaidwith hand drawn ROTs indicating the presence of MS lesions. Note how the lesions occur almostinvariably in the white matter of the brain. 1 Statistically it has been shown that approximately95% of MS lesions occur in the white matter [57].Observation of the characteristic plaques over time in MS patients shows how the demyelination of nerves is a reversible and recurrent process in these patients. Over time, with andwithout treatment, MS lesions grow, shrink, converge and diverge in a majority of patients.One of the goals of our research is to automate the quantitation of MS lesions in the brain toallow physicians to accurately track the progress of MS patients undergoing drug therapy [101].‘Gray matter forms the outer cortical regions of the brain surface with white matter occurring just under andadjacent to gray matter. Paradoxically, white matter shows up dark and gray matter light on Ti weighted MRIimages.Chapter 6. Algorithm Testing and Results 836.2 Results AnalysisFor our analysis, we have used dual echo MRI sequences, each consisting of 256x256x27 slicesacquired in the axial plane on a General Electric 1.5 Tesla MRI scanner. The images weresupplied by the UBC MS MRI Study Group. The slices are contiguous (no interslice gap) witheach voxel measuring 0.781mm x 0.781mm x 5.0mm in the x, y, and z planes respectively. Theimage volume has been scaled from 16 bit data to 8 bit data, with minimal reduction in imageresolution, in order to reduce both computation and storage requirements.MRlSeries(T1)Figure 6.17: MRI series of Ti weighted images of the brain of a Multiple Sclerosis patient.The first sequence shown in Figure 6.17 has been acquired so as to more heavily weightTi relaxation times, and will be described hereafter as the Ti sequence. The second sequence,Chapter 6. Algorithm Testing and Results 84MIII Series(T2)Figure 6.18: MRI series of T2 weighted images of the brain of a Multiple Sclerosis patient.Chapter 6. Algorithm Testing and Results 85shown in Figure 6.18, was acquired using an echo sequence designed to give more weight toT2 relaxation times and will be referred to as the T2 sequence. Note how the two sequencescontrast different tissue types with MS lesions showing up brightest on both.We have attempted to segment four different tissues from the scans: white matter, graymatter, cerebrospinal fluid and MS lesions. This results in an output of 108 images in thefinal segmentation, four for each slice in the volume, as well as 108 images for each of theT1/T2 segmentations alone. For this analysis, we have elected to recalculate histograms andneighbourhood interaction parameters just once, following convergence of the first segmentation which occurred after approximately 8 iterations. Convergence of the second run of thesegmentation occurred following approximately 6 iterations of the algorithm.In order to reduce bias introduced by the experimenter, and to obtain a more accurate tissueanalysis, the initial regions of interest required by the algorithm have been manually outlinedon selected images by a radiologist from the UBC MS MRI Study Group. This was performedat UBC Hospital, independent of our research and software development platform. The ROTsso obtained were then converted to WIT ROTs and applied to the corresponding images inorder to obtain characteristic histograms for each of the tissue types under consideration. Acomplete manual segmentation of just the MS lesions in the image volume was also obtained.This allowed us to compare the segmentation resulting from the application of our version ofIterated Conditional Modes to that obtained by an expert.6.2.1 Initial HistogramsThe initial histograms obtained by ROT analysis of the Ti and T2 images are shown in Figure 6.19 and Figure 6.20 respectively. The x axis represents the intensity of voxels in the chosenROIs while the y axis denotes the probability or frequency of voxels in the ROT at a particularintensity. These histograms have been smoothed to reduce noise in the distributions and havebeen normalized in order to give probabilities as opposed to actual numbers of voxels at particular intensities. As such, the area under each histogram is equal to one. These histograms showChapter 6. Algorithm Testing and Results 86p(x) 6.19: Co1ourcoded histograms of Ti weighted MRI series based on manually drawnROTs over a single image. Black = White Matter, Blue = Gray Matter, Red = CSF, Green =MS Lesion.0 20 40 60 80 100 120 140 160 180 200 220 240 260Chapter 6. Algorithm Testing and Results 87p(x)0.080.080, 20 40 80 80 100 120 140 180 180 200 220 240 280Intensity(x)Figure 6.20:drawn ROTsGreen = MSCo1ourcoded histograms of 12 weighted MRI series based on same manuallyas for Figure 6.19. Black = White Matter, Blue = Gray Matter, Red = CSF,Lesion.Chapter 6. Algorithm Testing and Results 88the distributions of each of the four tissue types to be segmented in each echo sequence. TheROTs were applied over corresponding images in both MRI series in order to obtain histogramsfor each spectrum.There are several observations that can be made by visual inspection of these histograms.First, note that the histogram for white matter is somewhat isolated from that of the other threetissues. This suggests that white matter is most easily segmented from brain MRI images. Thisis in fact the case, as will be demonstrated in later sections. The second factor to note is thatthe histograms for the MS lesions are broad and relatively low, indicating the non-homogeneityof these lesions. As well, the lesion histograms illustrate a tendency to be noisier than thepure tissues, indicated by the many small sharp spikes present in the lesion histograms. Thisnon-homogeneity is characteristic of many pathological conditions of the brain which result inlesions, including tumours and other neurological disorders. This non-homogeneity is also whatmagnifies the degree of difficulty in automatically segmenting brain lesions by computer.Another complicating factor is the amount of overlap exhibited by the lesion histograms.Any segmentation algorithm will, as a result of this extensive overlap, have significant problemsdifferentiating lesions from the remaining tissue types in the volume. As well as the lesionhistograms being broad and fiat it can be seen from the graphs that the other tissues alsooverlap, to a significant degree, in intensity profiles. The shoulders of each histogram overlapwith its neighbours in the graph, sharing intensity distributions.Finally, another not so obvious factor is illustrated by the histograms. The dynamic rangeof the data is rather small, for example, the Ti data shows a minimum intensity value of 93 anda maximum of 162. The dynamic range is actually significantly larger for both image spectrasince not all tissue types are represented in the histograms (e.g. skin, bone, fat, vessels, etc.).However, the narrow range of the data serves to further complicate the segmentation process.Since our algorithm relies heavily on these initial histograms, the accuracy of the segmentation which results is subject to the limitations imposed by these histograms. The first estimateof the segmentation, on which all further iterations of the algorithm rely, is solely based on theChapter 6. Algorithm Testing and Results 89Table 6.1: Initial neighbourhood interaction parameters obtained from Ti image sequence.Tissue Gray White CSF LesionGray 12.77 14.26 7.76 7.66White 14.26 4.47 4.51 35.64CSF 7.76 4.51 9.59 10.09Lesion 7.66 35.64 10.09 18.28Table 6.2: Initial neighbourhood interaction parameters obtained from T2 image sequence.Tissue Gray White CSF LesionGray 9.02 5.05 35.74 5.90White 5.05 4.03 8866.84 9.18CSF 35.74 8866.84 12.84 23.95Lesion 5.90 9.18 23.95 10.57conditional probabilities which are obtained directly from the initial histograms. The neighbourhood interaction parameters, computed as described by Equation 5.22 in Section 5.2.1, arein turn based on this initial segmentation which results from analysis of the initial histograms.6.2.2 Initial Neighbourhood Interaction ParametersThe neighbourhood interaction parameters calculated from the initial histograms of the Ti andT2 image volumes are shown in Tables 6.1 and 6.2 respectively.As described previously, relatively low numbers indicate high probabilities of tissues occurring adjacent to each other, while high numbers illustrate tissues which rarely occur adjacentto each other. For the most part, the entries in the Ti and T2 neighbourhood interactiontables are consistent with known neuro-anatomy, with some notable exceptions. As has beenmentioned previously, these numbers are subject to the accuracy of the initial segmentation,which in turn relies on the initial histograms. Because of this, some numbers in the tablesappear to be somewhat inaccurate, in terms of known neuroanatomical features. For example,Chapter 6. Algorithm Testing and Results 90we have mentioned that MS lesions occur almost exclusively in the white matter of the brain.However, the (white matter:lesion) adjacency measure given in Table 6.1 would suggest otherwise. But, if we keep in mind that the relative numbers of white matter (and other non-lesion)voxels far exceeds the numbers of lesion voxels, then this number seems more realistic. In factthe (white matter:lesion) interaction parameter actually increases when these parameters arerecalculated following the first convergence of the algorithm (See Table 6.3). Another reasonfor the apparent contradiction in the (white matter:lesion) interaction probability is the natureof the MS lesion itself. Although occurring in white matter almost exclusively, the lesions donot have sharp transitions from lesion to white matter. It can be seen on analysis that theintensity of MS lesions declines when measured from the centres of the lesions to the edges.Because the decline is gradual and because white matter is dark and lesion is brightest on bothTi and T2 images, the intensity proffle of the MS lesions passes through an area shared withgray matter.2 This phenomenon is borne out by the histograms of Figures 6.19 and 6.20. Thisresults in a higher than expected value in the interaction table for the (white matter:lesion)adjacency measure, and a lower than expected value for (gray:lesion).Consider the diagonal elements of Table 6.1. These numbers can be considered self-adjacencies,yielding measures of the relative quantities of different tissues and a measure of the convolutedness of the tissue structure. White matter, for example, which constitutes most of the brainmatter, yields a very low number, while lesion, which occurs infrequently, and thus must share alarger percentage of its total voxels with other tissues, exhibits a relatively large self adjacencynumber. This pattern is repeated in Table 6.2.When Table 6.1 is compared with Table 6.2, the corresponding entries are relatively consistent, but for a few notable exceptions. These differences are due to differences in the characteristics of the Ti and T2 imaging sequences of MRI, as well as the complex nature of tissueinteraction as measured by our algorithm. In particular the (CSF:white matter) interaction2Because of the reduced reproduction capabilities from raster to laser printer this phenomenon cannot beadequately ifiustrated in the thesis.Chapter 6. Algorithm Testing and Results91parameter is highly contrasted between the two tables. This results from the poor differentiability of CSF in the Ti image volume, due to the nature of the nature of the imaging sequence.The high value given in Table 6.2 is more plausible than the low value of Table 6.1, as CSF andwhite matter do not occur adjacently in healthy brain tissue.Following initial convergence of the 1CM algorithm, the histograms and neighbourhoodinteraction parameters are recalculated and used as input to the algorithm a second time. Thisrecalculation of parameters is performed in order to refine the segmentation, assuming thenew parameters are more accurate than those used initially. Since we are using intensity andsegmentation values from the entire volume in the second run of the algorithm, as opposed tojust a single slice, this assumption is realistic.6.2.3 Recalculated HistogramsThe new histograms are calculated as per Equation 5.23 in Section 5.2.3, using partial volumecontributions from each tissue to each voxel. Thus, the manner in which the histograms areobtained is fundamentally different than that which was used to obtain the initial histograms,i.e. manual segmentation. We would expect, theoretically, that the new histograms will be quitesimilar to the initial versions, and this expectation is fulfilled, despite the dramatically differentmanner in which the two sets of histograms are obtained. Figures 6.21 and 6.22 show theresults of reassessment of tissue profiles in the intermediate segmentation of the Ti and T2image sequences respectively. Note the similarities between these and the original histogramsof Figures 6.19 and 6.20. Again we notice the overlap in tissue distributions. Most notably, itis shown that the lesion intensity profiles are shared by several other tissues, especially graymatter and CSF. The white matter histogram is, again, less affected by other tissue profiles,though not to the same extent as with the original distributions.What is different about these histograms is that the lesion profiles have become less distributed, that is taller and thinner, perhaps indicating the attempt of the first run of thesegmentation to isolate the lesions from the other tissues. As well as the difference in the shapeChapter 6. Algorithm Testing and Results 92 1—'—f f 1 1 1 1 1 100 120 140 160 180 200 220 240 2G0 Intensity(x) Figure 6.21: Colour-coded histograms of T l weighted MRI series based on recalculation from intermediate segmentation. Black = White Matter, Blue = Gray Matter, Red = CSF, Green = MS Lesion Chapter 6. Algorithm Testing and Results 93ptx),0100 20 40 60 60 100 120 140 160 180 200 220 240 260Intensity(x)Figure 6.22: Colour-coded histograms of T2 weighted MRI series based on recalculation fromintermediate segmentation. Black White Matter, Blue Gray Matter, Red = CSF, Green= MS LesionChapter 6. Algorithm Testing and Results 94Table 6.3: Recalculated neighbourhood interaction parameters obtained from Ti image sequence.Tissue Gray White CSF LesionGray 15.42 26.14 6.47 5.72White 26.14 4.54 4.10 i42.i4CSF 6.47 4.10 7.14 54.04Lesion 5.72 142.i4 54.04 29.76of the lesion profiles, another interesting observation is that these sets of histograms, especiallythe lesion histogram are less noisy than the originals. Both these factors should improve thesecond run of the segmentation.One characteristic of the new histograms which is of particular note is the spike in thelow intensity end of the Ti gray matter profile of Figure 6.21. This spike occurs a significantdistance away from the main gray matter histogram and may be a result of other tissues inthe volume which were not specified in the original histograms, but which have been partiallyclassified in the intermediate segmentation.Overall it would appear that by recalculating the histograms, we have refined the conditionalprobabilities such that differentiation of the lesions may be significantly clarified.6.2.4 Recalculated Neighbourhood Interaction ParametersAs well as recalculating the new histograms, the intermediate segmentation is used to recalculate neighbourhood interactioll parameters. This re-evaluation allows us to seed the subsequentsegmentation with a more accurate description of how tissues interact. Table 6.3 and Table 6.4 contain the recalculated neighbourhood interaction parameters for the Ti and T2 imagesequences respectively. The tables differ from the original tables in some significant respects.The most notable differences occur, as suggested by the new histograms, in the (lesion:othertissue) columns of both Table 6.3 and Table 6.4. The (lesion:gray) interaction has remainedrelatively stable in both image sequences but the (lesion:white matter) measure has significantlyChapter 6. Algorithm Testing and Results 95Table 6.4: Recalculated neighbourhood interaction parameters obtained from T2 image sequence.Tissue Gray White CSF LesionGray 7.46 4.12 93.22 6.28White 4.12 3.89 oo 42.36CSF 93.22 00 10.17 9.98Lesion 6.28 42.36 9.98 36.43increased. This phenomenon has been addressed in Section 6.2.2. The value of the (CSF:lesion)interaction parameter has significantly increased in the Ti image sequence but decreased in theT2 sequence. We believe the Ti increase occurs due to the poor CSF differentiation in Tiimages. The decrease in the parameter in the T2 sequence is a reflection of improved detectioncapability in the T2 volume. Note that the (CSF:white matter) measure has increased to infinity in the T2 table, reflective of the non-overlapping of CSF and white matter in brain tissue,as mentioned previously.These neighbourhood interaction parameters are affected by a number of complex factors,including (i) the response of tissues to the applied echo sequence, (ii) the relative volumes oftissues in the organ being imaged, (iii) the relative amollnts of adjoining surface area in differenttissues, and of course, (iv) the accuracy of the segmentation which has been used to calculate theparameters. The complexity of these factors interacting together makes it extremely difficultto offer accurate analysis of the neighbourhood interaction tables without extensive applicationof the 1CM algorithm on many data sets. The use of phantom data would make it possibleto accurately measure the actual relative numbers of tissue adjacencies. Phantom analysis isanother aim of future research into validation and improvement of our algorithm.6.3 Segmentation ResultsWe have applied the 1CM algorithm using the aforementioned histograms and neighbourhoodinteraction parameters to each of the Ti and T2 weighted MRI series and then combined theChapter 6. Algorithm Testing and Results 96results by multiplying and normalizing the respective probabilities for each tissue type. We areable to do this because the two series have been acquired independently.6.3.1 Ti SegmentationWe have selected from the segmentation results a single slice from the volume to iliustrate theperformance of the 1CM algorithm. Figure 6.23 shows the result of the segmentation on slicenumber 18 (of 27) from the Ti weighted volume. The top four images show the segmentation ofCSF, gray matter, white matter and lesion, as labeled in the figure. The actual slice data, withand without the manually segmented lesions overlaid on the slice, are given in the bottom twoimages. The gray scale intensity of each of the four segmentation images is in direct proportionto the probability obtained for that tissue in the image.As anticipated, the results for white matter are by far the most impressive, whlie the algorithm had difficulty differentiating gray matter and CSF and gray matter and lesion. However,the results for lesion segmentation are accurate when compared to the manual segmentationand, when combined with the segmentation obtained from the T2 weighted sequence, producesatisfactory results.It is interesting to note that, as discussed in the Section 6.2.2, the edges of some MS lesionswhose intensities pass through the intensity distribution dominated by gray matter, have infact been incorrectly classified as gray matter in the Ti segmentation.6.3.2 T2 SegmentationFigure 6.24 shows the segmentation of the corresponding slice in the T2 weighted data set.Again, the white matter segmentation is the most accurate of all the tissues due to the relativeisolation of its intensity profile in the histograms. There is considerable improvement in thedifferentiation of CSF and gray matter, but again, the lesion/gray matter separation is burdened. As well, some CSF has been incorrectly classified as lesion. On the whole, however, thesegmentation is reasonably accurate.Chapter 6; Algorithm Testing and Results 97Figure 6.23: Segmentation of a single slice from the Ti Echo sequence by 1CM. The bottomimages show the original Ti data with (right) and without (left) overlaid hand drawn lesionsegmentations.Chapter 6. Algorithm Testing and Results 98Figure 6.24: Segmentation of a single slice from the T2 Echo sequence by 1CM. The bottomimages show the original T2 data with (right) and without (left) overlaid hand drawn lesionsegmentations.Chapter 6. Algorithm Testing and Results 996.3.3 Combining Ti and T2 SegmentationsWe combined the two previously illustrated segmentations and the result is given in Figure 6.25,together with the original image (from the T2 sequence) with lesions manually outlined. Considerable improvement is noticeable on all four tissue segmentations with the most noticeableerror still seen in the gray matter/lesion separability. Some lesions have been incorrectly classified as gray matter and some gray matter incorrectly classified as lesion. However, for the mostpart we have successfully isolated most lesions in the image. They are clearly differentiable inthe lesion segmentation image as the most intense regions of the image.Figure 6.26 shows further how the 1CM results match the manual segmentation. Here wehave overlaid the hand drawn ROTs over both segmentations to give a direct visual comparison.It can be seen that most lesions have been correctly classified, with some outlying lesionsmissed as described above. The complexity of lesion identification is illustrated here. It is quitedifficult to ascertain with the human eye which areas in the image are lesions and which are not.Note again that an experienced radiologist has identified the lesions which have been manuallyoutlined on the right.6.3.4 Post-Processing of the SegmentationFollowing the combined segmentation it was decided to apply some further post processing tothe lesion segmentations in order to more fully extract them from the volume. A morphologicalopening was applied to the combined result to reduce the number of isolated voxels in theresult. The result of this opening is given in Figure 6.27 (top right). The top left image inthe figure is the lesion segmentation resulting from combination of the results from the Tiand T2 segmentations, as given in Figure 6.25. The opening has clearly removed a numberof island voxels without significantly affecting the lesion segmentation. The result is a muchbetter segmentation but there is still room for improvement.Since the intensities given represent probabilities that a given voxel is a lesion voxel, wedecided to threshold the probability and only consider probabilities which were over a particularChapter 6. Algorithm Testing and Results 100Figure 6.25: Segmentation of a single slice obtained by combining the T1/T2 SegmentationsThe bottom images show the original T2 data with (right) and without (left) overlaid handdrawn lesion segmentations.Chapter 6. Algorithm Testing and Results 101Figure 6.26: Manual segmentation overlaid on combined T1/T2 Segmentation (left) and alsooverlaid on raw T2 image (right).measure, in this case 0.4. This thresholding operation was applied to the morphologicallyopened result obtained previously. Visually, this threshold gave the best result when comparedwith the manual segmentation. The thresholded final segmentation is given in the bottom rightof Figure Visualizing Partial VolumesPartial volume considerations are most significant near the borders of different tissue types,but this has not been clearly demonstrated to this point. In order to more fully appreciatethe partial volume solution that we have given, the segmentations of white matter and lesion(before and after post-processing) have been given in Figures 6.28 and 6.29 respectively.The gray scales in the previous images have been mapped to particular colours accordingto the colour map given in Figure 6.30, with bright red indicating the highest intensity, anddark blue the lowest. These figures illustrate that voxels in the central areas of tissues havemuch more definite composition, while there is less certainty about voxels nearer the bordersof tissue. This could not be properly appreciated in the grayscale versions of the segmentation.Chapter 6. Algorithm Testing and Results 102Figure 6.27: Lesion segmentation of a single slice obtained by applying a morphological opening(upper right) and subsequent thresholding (lower right) to the results of Figure 6.25. (Thebottom left image is the original data.)Chapter 6. Algorithm Testing and Results 103Figure 6.28: Colourized segmentation of white matter (left) and lesion (right) illustrating partialvolume voxels near the borders of tissues. (No post-processing has been applied.)Figure 6.29: Colourized segmeiltation of white matter (left) and lesion (right) illustrating partialvolume voxels near the borders of tissues. (Post-processing has been applied.)IrlbChapter 6. Algorithm Testing and Results 104Figure 6.30: WIT colour-map used to euhance partial volume characteristics of segmentationas sliowu iii Figures 6.28 and 6.29.Chapter 6. Algorithm Testing and Results 1056.4 Lesion Volume AnalysisWe have endeavoured to further examine our extensions to 1CM by measuring the lesion volumesgiven by our segmentations. Lesions have been manually outlined on every slice in the volumeby a radiologist from the MS MRI Study Group of UBC Hospital, as described previously. Wehave analysed the ROTs outlining the lesions in order to measure the lesion volume in eachslice. Any voxel which lay within the borders of the manual lesions was considered a completelesion voxel for our tests. The volumes so obtained can be considered a gold-standard by whichwe can measure the efficacy of our segmentation algorithm. However, lesion identification anddelineation, as admitted by our experts, is an extremely complex and subjective task, requiringyears of training and practise. It is with this in mind that we are able to make preliminaryjudgements regarding the accuracy of our algorithm.Following our segmentation and the analysis of the manual lesion ROTs, we determinedthe volumes produced by our own results. We used the partial volume quantity for eachvoxel in summing the volumes obtained by our segmentations. The volumes of each slice weremeasured for (i) the Ti segmentation, (ii) the T2 segmentation, (iii) the combined T1/T2segmentation, (iv) the combined segmentation following morphological opening, and (v) thefinal results obtained from thresholding the opened segmentation. The results have been plottedand are given in Figure 6.31. Note how, as the results are first combined, then post-processed,the ensuing volumes tend to more closely match the actual volumes determined from manualsegmentation, also presented in Figure 6.3i.The graphs for the final segmentation and the hand drawn lesions have been expanded andare shown in Figure 6.32. Note that, for the most part, the volumes obtained by the 1CMsegmentation are consistently and proportionately less than those measured from the manualsegmentation. This is especially true of the middle slices in the volume. We believe this is due toseveral factors: (i) the manual segmentation uses full values for each voxel included in the lesionROTs, while our segmentation measures partial volumes, (ii) errors by the radiologist in lesiondetection, and (iii) errors in the segmentation. The first factor is, in itself, not to be consideredChapter 6. Algorithm Testing and Results 106volume(voxels) (x ‘iO)7.6-5.4.s’ice numberj:fl ‘.;;(:Furfle—-lS)fl .urn-—3Ie. c)ri.,.:::I_1 rri—5Figure 6.31: Graphs of lesion volumes determined at all stages of the segmentation, includingmanual segmentation. Black (upper) = Ti, Red = T2, Green = T1/T2 Combined, morphologically opened, Brown = Ti/T2 combined, opened and thresholded, Black (lower) = ManualSegmentation.Chapter 6. Algorithm Testing and Results 1071000400200esi.::ri VC:hrflP—1Figure 6.32: Graphs of lesion volumes of final segmentation and manual segmentation, expandedfrom Figure 6.31. Black = T1/T2 combined and post-processed, Red = Manual Segmentationvolu me(voxels)120080080000 2 4 8 8 10 12 14 16 18 20 22 24 26silce numberChapter 6. Algorithm Testing and Results 108an error but perhaps an adjustment made by our program that is not possibly (or at leastnot easily) accomplished by manual outlining of regions. The second factor is usually due to atendency by clinicians to consistently classify an area as lesion when in fact there is considerableuncertainty as to the region’s composition. The third factor, errors in the segmentation, resultfrom inconsistencies in the histograms and neighbourhood interaction parameters as discussedpreviously, and will be addressed in future work to be completed in this area.6.5 General Conclusions and Future WorkWe have seen that the problem of accurate segmentation of MRI and other medical images isa complex, as yet unsolved problem in medical image analysis. We have endeavoured to offer areasonable, model-based solution using neighbourhood and histogram analysis. In so doing, anattempt was made to build a model of the image on a case-by-case basis, and use this modelas a foundation on which to refine the segmentation. We have developed this algorithm in3D using a datafiow-based visual programming environment which lends itself well to parallelimplementation. We have maintained a local neighbourhood analysis scheme throughout thealgorithm in order to preserve the potential for parallel computation.Some conclusions emanating from this work arise out of the previous discussion on theresults of our preliminary experiments. It is evident that a more accurate model of brain tissuecharacteristics may be necessary in order to more accurately obtain prior probabilities of thetissue composition of voxels in the volume. This model can be used as the external field term inthe 1CM equation. The model should be developed from not just conditional tissue probabilities,but must include spatial information as well. It is clear that the amount of knowledge requiredfor a human being, even an expert in the field, to identify tissues, structures, and pathology ina medical image scan is enormous. As has been mentioned, models developed to date by otherresearchers require vast amounts of data and accurate image registration techniques which havenot yet been validated.In the absence of an accurate tissue model, the current algorithm may be improved in otherChapter 6. Algorithm Testing and Results 109ways. First, a general masking of tissues outside the area of interest (in this case, the brain)would improve the results significantly. We have performed a trivial masking over the entirevolume but this does not accurately compensate for all non-interesting tissues. This maskingcould be acquired through the development of a user friendly, 3D, interactive ROT analysis tool.Second, an incremental compilation of tissue histograms and neighbourhood interactionparameters, as more data is analyzed, should provide a more accurate solution. As the accuracyof the segmentation relies ultimately on the accuracy of these histograms and neighbourhoodinteraction parameters, improvement in this area is imperative.Third, the T1/T2 sequences obtained for this study were not accurately matched to theparticular tissues which were under consideration. Further consultation with the MS MRIStudy Group and others is necessary in order to determine optimum echo sequences to beapplied to best contrast the tissues under study. Tt will also be of help to compensate forMRI RF inhomogeneity prior to attempting a segmentation. This was not performed for ouranalysis.Another concern which arises from this work is the issue of time and space requirements.Although a partial volume solution is vital to an accurate solution to lesion and tissue quailtitation, it does exact a heavy toll. The space required to store the resulting segmentation isup to m x n times the original data size, where m is the number of image channels used (inthis case just 2) and n is the number of tissues being investigated. This is reduced to at leastn times the data size if only the final segmentation will be stored. As well, in order to incorporate 3D information into the algorithm, the time required to perform the segmentation will beprohibitive unless there are multiple workstations with which to parallelize the computation.This is one of the reasons we have developed the algorithm using the datafiow environment ofWTT.6.5.1 Future WorkThe previous paragraphs identify innumerable areas for future development of our work.Chapter 6. Algorithm Testing and Results 110Phantom studies, whether obtained by imaging a manufactured phantom or by simulationof phantom data, should be carried out immediately. A better understanding of these neighbourhood interaction parameters will be obtained by the application of our algorithm to knownphantoms. This will allow us to assign the parameters in future segmentations according toexpert knowledge about the imaging modality used, the organs and tissues under investigation,and the pathology of the lesions being quantified. Phantom studies should also provide a moreaccurate analysis of our algorithm and indicate further areas of improvement.Assuming we can accurately register multiple imaging modalities, either by manual or automatic registration techniques, it will be worthwhile to perform the segmentation using bothstructural and functional images. In this manner we can determine the optimum combinationof techniques which yields the most accurate segmentation.The manner in which the segmentations are combined can be improved as well. Instead ofdoing independent segmentations based on histogram analysis and combing the segmentationslater, we can perform a cluster analysis on the combined histograms, and determine a singlesegmentation based on these clusters. The neighbourhood analysis could also be performed onthe vector of neighbours present from multiple data sets, as opposed to just single neighbouranalysis performed independently. This may, however, result in increases in computationalcomplexity.In cooperation with various imaging centres, an effort should be made to develop an accuratemodel of tissue distribution which can be used as the external field in the 1CM equation. The MSMRI Study Group is evaluating the efficacy of a new drug, interferon beta-ib, in the treatmentof Multiple Sclerosis. The group does not require an absolute quantitation of MS lesions in thebrain, but just what they describe as a “measure” of MS in these patients. We believe thatwith some improvements the algorithm we have implemented can provide that “measure”. Oneavenue of future work involves co-operating with the MS group and the developers of interferonbeta-lb in evaluating the drug’s efficacy in reducing and eliminating MS lesions over time.The problem of accurately and automatically segmenting medical images using computersChapter 6. Algorithm Testing and Results 111is an extremely complex and difficult task. It is hoped that through this thesis we may haveidentified aspects of the problem that will aid in its solution. Through future research, maybesufficient knowledge can be obtained that will lead to a general solution. Perhaps, just perhaps,no such solution exists.Appendix A1CM Source Code KernelThe following source code forms the kernel of the 1CM algorithm. One iteration of the do ioopconstitutes one iteration of 1CM through the image {nChanges = 0; /* initialize and track voxel ‘‘changes’’ *//* for each image */for (z0; z<nlmages; z++) {/* set pointer to first image voxel */srcp[z] = (u_Pix8 *) (sI->data[z].data[O]);/* for each voxel */for (y = 0; y < xsize; y-’-+) {for (x = 0; x < ysize; x++) {/* initialize statistics vectors to zerofor (k=0; k < nTissues; k++) {Pix[k] = 0.0;/* condition probability pixel i istissue k given record,obtained from histograms */Nxrtk] = 0.0; /* the e term in the icm equation *1Pxr[kJ = 0.0; /* prior probability */delta[k] = 0.0; /* measure of voxel change */}112Appendix A. 1CM Source Code Kernel 113/* count the neighbours *1icmGetGx(currentSeg, xsize, ysize, nlmages,x, y, z, ortho_xy, ortho_z,oblique_xy, oblique_z, oblique_xyz,nTissues, g);1* for each region */for (k0; k < nTissues; k++) {hist = histV[kJ .data; 1* get histogram for tissue k *1klndex = z*nTissues + k; 1* determine slice index */Pix[k] = hist[*(srcp[z])];1* get conditional for this pixel/tissue *1if (Pix[k] 0) { 1* ignore zero probabilities *//* compute neighbour interaction probability */Nxr[kJ = icmGetNxrknx(g, Bjk, k, nTissues);1* determine prior probability */1* set to previous seg value */Pxr[k] (float)*rpSegl[klndexj / MAXPIX8;1* compute 1CM partial volume probability *1Pxr [k] = Pix [k] * Pxr [k] * Nxr [k];}}/* sum all probabilities for this voxel *1/* for normalization *1sPxrk = 0.0;for (k0; k < nTissues; k++)sPxrk += Pxr[k];Appendix A. 1CM Source Code Kernel 114/* assign probabilites to segmentation and normalize *1for (k0; k < nTissues; k++) {klndex = z*nTissues + k; /* determine slice index *//* assign to segmentation *1if (sPxrk 0.0) {/* normalize Pxrk */Pxr [k] = Pxr [k] / sPxrk;*rpSeglplusl[klndex] = (u_Pix8) (MAXPIX8 * PxrLkJ);} else*rpSeglplusl[klndex] = 0;/*measure change in tissue composition[k] for this voxel*/delta[k] = (float) *rpSeglplusl [klndex]- (float)*rpSegl[klndex];1* advance segmentation pointers to next xy position *1rpSegl [klndex] ++;rpSeglplus 1 [klndex] ++;}1* assess changes in this voxel *1norm = getVNorm(delta, nTissues);if (norm > (O.1*MAXPIX8))nChanges++;Appendix A. 1CM Source Code Kernel 1151* advance pointer in source image to next xy pos *1srcp [z] ++;}}}nIt erat ions++;/* ‘copy’ new segmentation to currentSeg segmentation *1/* code omitted *//* adjust current pointers to ‘new’ segmentation *//* code omitted */} while ( (nlterations < maxlterations) &&(nChanges > minChanges) );Bibliography[1] A.S. 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