TOPS IN NUMERICAL SCIENTIFIC COMPUT (SR)
TOPS IN NUMERICAL SCIENTIFIC COMPUT (SR) CS 689
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Computational Medical Imaging Analysis Chapter 2 Image Acquisition Systems Jun Zhang Laboratory for Computational Medical Imaging amp Data Analysis Department of Computer Science University of Kentucky Lexington KY 40506 Chapter 2 C8689 21a Introduction The goal of a biomedical image acquisition system is to capture and record localized information about the physical andor functional properties of tissues or components of tissues eg cells Faithfulness is the image realistically similar to the real object Efficiency how long will it take to acquire the image Most today s imaging systems are controlled by a computer and need computers to do some postprocess work especially to produce 3D images Chapter 2 C8689 21b Image Formation Some form of energy is measured after its passage through an interaction with a region of the body Mathematical estimates are computed and images produced of the 2D and 3D distribution of interactions of the energy with body tissue The interactions include absorption attenuation nuclear magnetic disturbances etc Many structures can be imaged simultaneously Many types of instrumentation may be used to measure the interactions between energy and ssues Chapter 2 C8689 21c Image Characteristics Image comparisons can be made based on some characteristics Inherent spatial resolution Contrast resolution Temporal resolution Other imaging system characteristics Images of structure Images of function Chapter 2 C8689 21d Spatial Resolution In discrete digital images each pixel 2D or voxel 3D has specific dimensions in the measurement space of the object The limits to spatial resolution in the final image are the smallest dimensions of the object differentiable by the total imaging system including image reconstruction The resolution and dimensions may differ for each orthogonal direction represented in a volume image anisotropic or they may be equal isotropic Chapter 2 C8689 216 Contrast Resolution In an image individual structures are recognized by localized differences in signal strength eg the amount of absorption reflection etc among immediately adjacent structures Contrast resolution is the ability of an imaging system to detect differences in signal intensity between two structures Contrast resolution is dependent on image acquisition the energy form used and the physical properties of the structures being imaged It usually specified as a percentage of the largest signal difference that can be detected and quantified Chapter 2 C8689 6 l 21f Temporal Resolution Two definitions the aperture time and the frame or repetition rate The aperture time is the amount of time the system takes to capture the signal information to form a single image key component in eliminating motion artifact The frame rate is the image repetition rate defined by the smallest interval of time required to produce successive images Both definitions do not include image reconstruction time or final image formation time Chapter 2 C8689 21 g More about Frame Rate The frame rate limits the ability of the system to acquire 4D data sets with the time line In most cases the frame rate of the imaging system is mechanically limited It may be triggered by physiological events to acquire gated images I Gated images are taken in accordance to the time intervals of certain repeated physiological events eg heart beat breath Chapter 2 C8689 2221 Biomedical Acquisition Systems Conventional radiography Conventional axial tomography Xray computed tomography CT Magnetic resonance imaging MRI Nuclear medicine imaging Ultrasound Biomagnetic imaging not covered Microscopy imaging not covered Chapter 2 C8689 22b Conventional Radiography Signal acquisition a beam of Xrays passing through the body is differentially absorbed and scattered by structures in the beam path physical density atomic composition of the structures energy of the Xray beam The differential absorption pattern is recorded by an Xray recorder radiographic film digital radiographs store process transport Chapter 2 C8689 10 22c Siemens X ray Machines Film based analogy multiX top machines Chapter 2 C5689 22d A Chest X ray Picture 226 Other Use of X ray Machines it 5 4 F 1 Chapter 2 C5689 22f X ray Image Characteristics Most Xray image is used for structural imaging the parameter recorded is the energy absorption Dimensionality is strictly 2D a projection of a 3D structure onto a 2D plane Spatial resolution is high from 10 to 05 mm2 Contrast resolution is on the order of 1 of full range Temporal resolution is about 10 milliseconds Digital radiographic images are usually represented over a 12bit dynamic range from O to 4096 Chapter 2 C8689 14 22g 3D Superposition in Radiographs The attenuation is dependent on path length through an object as well as on the physical density and atomic composition of the object We cannot see from the film the different materials through which the beam passed The attenuation at different points along the beam path add up and are superimposed onto the same points on the detector I Regions where high density differences exist between structures can be seen clearly Chapter 2 C8689 15 22h More X ray Picture Lung and Heart Chapter 2 C5689 16 2321 Conventional Axial Tomography Conventional axial tomography was developed in an attempt to overcome the superposition problem The Xray source and photographic detector are moved in opposite directions parallel to the plane of the body to be imaged Distribution of densities of the focal plane will be sharply recorded outside of the focal plane will be blurred It cannot overcome the superposition problem entirely may blur the structure boundary Chapter 2 C8689 17 I 23b Illustration of Conventional Axial Tomography Motion of X ray Source Motion of Photographic Film Chapter 2 15689 18 24a X ray Computed Tomography CE CT collimates the beam to minimize scatter and eliminates superposition by scanning around a transaxial plane Recorded intensity differences can be less than 01 individual attenuation coefficients of structures in the beam path can be determined to within 05 accuracy I A full 3D representation can be obtained by reconstructing several cross sections of 2D slices stacking the cross section like a roll of coins Chapter 2 C8689 I 24b CT Machine for Body Chapter 2 C3689 20 24C IT Machine Scanning Chapter 2 C5689 21 24C A 3D Reconstructed CT View of Kidneys an Ureters j Chapter 2 C5689 22 I 2401 3D CT View of Vessels Chest Pulmonary Chapter 2 C8689 23 246 Signal Acquisition Conventional Xray CT scanners use a single Xray tube that rotates through a full 360 rotations while recording projections at fine angular increments during the rotation every 05 to 1 The projection images are processed in a computer and an image is formed through mathematical reconstruction techniques Xray beam forms a flat fanbeam geometry and the projects are coplanar the detector is a curvilinear array of solid state elements Chapter 2 C8689 24 I 24f Illustration of CT Systems a 1St generation translate rotate pencil beam geometry b 2nd generation translate rotate fan beam geometry 2 3rd generation rotate only geometry d 3rd generation off set mode geometn ChapterZ c5559 2 24g Spiral Helical CT The projection acquisition process traces out a spiral trajectory rather than a sequence of parallel flat projection fans This is achieved by a combination of continuous beamdetector rotation and continuous tabe movement causes the projection data to be acquired along a spiral path It is fast n It is the Xray CT imaging system of choice for acquiring 3D volume images of many structures Good for the application of 3D visualization and quantitative analysis techniques Chapter 2 C8689 26 24h Spiral CT Photo simulation of spiral CT Virtual reality 3D image of on abdomen lungs Chapter 2 C5689 27 241 Image Formation Reconstruction Tomography is the graphic representation of a cut or slice and implies the formation of 2D cross sectional images free of blurring from structures not in the planes of interest the tomograms Computed tomography CT is the formation of tomograms of Xray absorption coefficients by the method of reconstruction from recorded projections The term CT may be applicable to any techniques that requires computation in order to reconstruct an image with nonambiguous resolution in 3D Chapter 2 C8689 28 24j Computed Tomography All biomedical imaging systems that produce 3D volume images use computed tomography It is a computer implementation of an appropriate inversion formula to mathematically reconstruct adjacent cross sections of an object from measured fluctuations of some energy traversing the object from several different directions It reconstructs 3D images from a series of 2D projects or reconstructs 2D distribution of Xray attenuation coefficients in a plane slice from a number of 1D projections Chapter 2 C8689 29 24k CT Numbers The CT number produced by Xray scanner systems is an expression of the relationship of the linear attenuation of Xrays by a given material tissue to that by water for the same Xray energy it is CT Number k u uwuw where p is the attenuation coefficient of the material and uw is the attenuation coefficient of water The CT number is often called the Hounsfield unit H in honor of the inventor of the first Xray CT scanner Chapter 2 C8689 30 241 Houns eld Unit I A Hounsfield unit H is given by H 1000L 1 u W To obtain the value of the attenuation coefficient relative to water 1H 1000 w Chapter 2 C8689 31 24m Image Characteristics The spatial resolution of voxels of CT data ranges from 01 to 1 mm2 in the plane of acquisition with the slice thickness ranging approximately from 1 to 10 mm With spiral CT the thickness can be reduced to 05mm The CT data is represented in a calibrated set of numbers the Hounsfield scale ranging in discrete value from 1000 to 1000 They are often shifted in positive range 0 t0 2048 stored as a 16bit computer value Chapter 2 C8689 32 25a Magnetic Resonance Imaging MRI MRI provides mechanism for intricate control of the signal being measured through modulation of the magnetic field and radiofrequency pulse sequences used to alter the spins of protons in the structure being imaged It is noninvasive does not use ionizing radiation as in the Xray MRI images the distribution of protons and is an excellent soft tissue imaging modality providing highly detailed structural images CT is better for higher density structures such as bones Chapter 2 C8689 33 l25b MRI Machines Chnptex 2 15689 34 25a Signal Acquisition Hydrogen nuclei protons are imaged due to their strong magnetic moment and prevalence in the soft tissues of the body water molecules I The externally applied magnetic field is called the BO field in MRI which makes the spin line up with the field I The full collection of spinning results in a net magnetic moment for all spins in the direction of the externally applied magnetic field Chapter 2 C8689 35 25d Radiofrequency Pulses amp MRI Signal The precessional frequency of a given atomic nucleus about the BO field axis is given by Larmor 730 F u where F is the precessional frequency BO is the strength of the externally applied magnetic field and y is a property of the magnetic moment for the specific type of nucleus under consideration For hydrogen y 4257 HzG and the common field of strength BO 15Tesla and F 63855 MHz Chapter 2 C8689 36 256 MRI Signal The radio frequency RF pulses distribute energy to the protons causing them to absorb energy when the RF pulses are on and dissipate that energy when off This is the resonance The RF frequency perpendicular to the BO external magnetic field is called the B1 field The net magnetic moment rotated about the BO field induces a current AC in a coil of wire located in the transverse plane The signal from the induced current is the source of signal for MR imaging Chapter 2 C8689 37 I 25f MRI Scan of Body Liver and Kidneys Chnptex 2 15689 I 25g MRI Scans of Head 25h Public Recognition The 2003 Nobel Prize in Physiology or Medicine was awarded to Paul C Laterbur at the University of Illinois at Urbana and Peter Mansfield at the University of Nottingham in England They are not doctors chemist and physicist Dr Raymond Damadian the MRI patent 1974 holder was not one of the recipients He published his first MRI paper in 1971 Chapter 2 C8689 40 251 Magnetic Moment Relaxation The RF energy can move the net magnetic moment away from the BO field axis by a flip angle Once the RF energy is turned off the spins will begin to realign themselves with the external BO field This process is called relaxation If a 90 RF pulse is used to rotate the net magnetic moment into the transverse plane and then turned offer the receiver coil oriented in the transverse plane will initially have a current proportional to the full magnetic moment but will diminish gradually The signal in the transverse plane has a characteristic exponential decay rate time constant called the T2 constant Chapter 2 C8689 41 25j T2 Relaxation Time The variation in precession rates of spins causes dephasing of the contribution of each individual proton s magnetic moment to the net magnetic moment causing it to decay The dephasing is related to the physical properties of the tissues being imaged The T2 constant or spinspin relaxation is measured as these spin decay and come back into alignment Chapter 2 C8689 42 25k Exponential Decay of Signal Strength Brain White Matter T2007S 1 xu u u uu39 huq Uv p A vv1w uau uvuu I l n39la muuuwnu 39I rAxIva 4I39tvl r i u u ruuuua u u ltquot439ll l 39 a u u u r su Jun wuu u vnnnr VIIv ua u v v wrn39tu39lhsv suns4 xu v v q 39 V v snauvu A v v wuIA39I s o w v lvtl vaw u qu aui wan s svs nonunionInnunun 4 v5 l 1 r a I I r s r s I I s I I s I r x I g r I 4 a r I t u m n I n s u u u Q39IquotIu u v1 4n p I 39 l m a 4 5 s w u In a u r Aw r a vlun a sns l l 439l 4 Ax lu39h as a Ivquot x n I In wax awn I an a lawn a u ru va 4 vahvdaw 1x nu z IAthns 1 xanxa o a a ve4vlsvatv tl l39s ll395 l39o I39ll v I 39 I39u myhuImIanIA uvIua l v olsosr3939tIrt44Ilsts39lvv sII r l39 39a s39I4sIso 39IIVIr39l l39lI39tt wnut agttt39aiav39l 1 IA 1 r I I vnza I 39I39I i rtnvr l l39l I39l I39 39I l r sunqAvaum 39I39IV39II39 N39Ip I vn I a u 39I39 Chapter 2 C5689 251 T1 Relaxation Time Immediately after a 90 pulse the net magnetic moment along the longitudinal plane is zero It will increase as the spins return to their alignment in this plane with BO This is the spinlattice relaxation process and is characterized by an exponential time constant T1 A coil in the longitudinal direction can measure the buildup of signal along the external field axis as spins return to equilibrium T1 relaxation time can be computed for different imaged tissues in the body Chapter 2 C8689 44 25m Exponential Nature of T1 Constant 63 spins return to its original position 3420 01quot Illgt20 3 g vnvruanvaa ovuvru x I 1391 yln v I I 39l 1x 1x 4 5 I xIn I 39I I u I x s a 4 I w I a A 39 r I I M I I h v E f39 u 5 I z r w w nunJul hw avu I u IIaIr 39I39 w u l r IJ 3939l I39In39l 39l 3939 Chapter 2 C5689 45 2511 T2 Relaxation Time and T2 Time 9 130 1RD RF ltgt A gt V TT Ida4515r T2decay Echo IM Mr 1391 139 I Chapter 2 C5689 46 250 Echo Time TE and Repetition Time TE The time between the original 90 pulse and the rephasing of the individual magnetic moments is called the echo time TE and is specified in the pulse sequence design The time needed for repeated excitation and echo formation is called repetition time TR The flip angle is the one that formed by the protons after the RF pulse moving the net magnetic moment away from the BO field These are the parameters used to design specific pulse sequence to image various structures in the body Chapter 2 C8689 47 25p Magnetic Field Gradients and Spatial Localization Position information can be encoded into the signal by adding a magnetic field gradient The resonance frequency of the protons will vary along the gradient axis as each will have a slightly different magnetic field 3D spatial position can be encoded by adding gradients along three orthogonal spatial axes Special coils are used to produce these spatially varying field gradients for encoding the spatial position of any voxel in MRI Chapter 2 C8689 48 25q Surface Coils and Paired Saddle Coils Image spines shoulders Image knees H H Failed Saddle Cdil Surface Jails 25r Helmholtz Pair Coil and Bird Cage Coil Image pelvis and cervical spines Image head 8 39 Hehnhulta 1 Pair Coil EN 5393 Coil Chapter 2 C5689 50 25s Signal Acquisition amp Reconstruction Signals are acquired as sums of all of the frequency components each with distinct amplitudes and relative phases in the frequency domain They must be transformed into the spatial representation of the image using a Fourier transform The frequency space kspace data can be processed in many ways to reduce artifacts noise or correct for any inhomogeneities in signal or spatial encoding Chapter 2 C8689 51 25t Image Characteristics The value at any given voxel in an MR image is a measure of the MR signal amplitude for the mobile protons contained within the discrete bounds of that 3D voxel A T2 weighted image is acquired with a long TR time and TE is prolonged to the range of tissue T2 values A T1weighted image is obtained by a short TR time in the range of the T1 values for tissues and very short TE This very short TE does not allow time for significant decay of the transverse relaxation ie no T2 difference Chapter 2 C8689 52 25u MRI Volume Images 2D to 5D 2D images are singleslice reconstruction from a single section of structure with a thickness 3D images can be reconstructed from either 2D multiple adjacent slice techniques or true 3D volume acquisitions Most MR images are reconstructed into 256x256 matrix interpolated from frequency and phase encodings ranging from 128 to 256 with 1 to 128 sections in a given volume image The inplane spatial resolution ranges from 05 to 1 mm with the slice thickness from 1 to 10 mm Chapter 2 C8689 53 25V Some De nitions The matrix size is the number of frequency encoding steps in one direction and the number of phase encoding steps in the other direction of the image plane I The frequency encoding depends on how rapidly the signal is sampled by the scanner Increasing the sampling rate has no time penalty The Fieldof View FOV is the total area that the matrix of phase and frequency encoding covers Dividing the FOV by the matrix size gives the voxel size Chapter 2 C8689 54 2621 Nuclear Medicine Imaging Nuclear medicine imaging systems image the distribution of radioisotopes distributed within the body preferably to a specific organ or structure of interest I It provides a direct representation of metabolism or function in the organ or structure being imaged Two main technologies single photon emission computed tomography SPECT and positron emission tomography PET Chapter 2 C8689 55 26b Single Photon Emission CTSPECT SPECT systems image the distribution of radiopharmaceuticals that emit photons upon decay using a gamma camera Image reconstruction is similar to Xray CT Patients will be injected or inhaled a small amount of physiologic radioisotopic tracers Its principal strength is its ability to provide functional information by the use of radiopharmaceuticals that are indicator of in vivo biochemical or hemodynamic functions Chapter 2 C8689 56 26c SPECT Illustration Callummr on a thmuMhplva rm Amy vmm um I m1m Baum Emu comma cmpmz cssag 26d Positron Emission Tomography ltPETgt PET produces transverse tomographic images of the distribution of positronemitting radionuclides systematically administered to the subject under study The image data is supplied by the detection of the annihilation radiation emitted as a result of the annihilation of positrons in matter Radionuclides commonly used are carbon11 nitrogen13 oxygen15 etc PET is very useful in the study of biochemical processes of fundamental importance in biology and medicine Chapter 2 C8689 58 I 26e Nuclear Medicine Machine Chapter 2 C5689 59 26f Nuclear Medicine Imaging Machine Chapter 2 C5689 60 26g Nuclear Medicine Machine Chapter 2 C5689 61 I 26h Images of PET Bones 132651 I Fall ir Chapter 2 C3689 62 26i PET and MRI Images Hanna39 Jrug a 39 rn I n Combined MRI u r quot Chapter 2 C8689 63 26j PET Hearts Exercised Rest 2721 Ultrasound Ultrasound is acoustical energy that contains frequencies higher than the upper audible limit In diagnostic imaging context longitudinal waves usually have frequencies between 05 and 15MHz The basis of ultrasonic imaging is to determine information about intrinsic tissue properties from observations of the way in which probing waves are perturbed or scattered by the tissues Bscan imaging records pulse echoes from a single transducer over time and shape and is tomographic Chapter 2 C8689 65 26b New Ultrasound Techniques New generation ultrasound techniques usually employ a computer to reconstruct images from raw or measured data Small ultrasound transducers can be made sufficiently small to be inserted into body for internal imaging The biggest advantages of ultrasound imaging is that the system is inexpensive and the procedure is safe Chapter 2 CS689 66 H 26C Ultrasound Machine Chapter 2 C5689 67 26c Ultrasound Image of Fetus SIEMENS svssvns oo n uu v 1quot v w r szwziiu Chapter 2 C5689 266 Ultrasound Image of Kidney Chapter 2 C8689 69 Computational Medical Imaging Analysis Chapter 7 Biomedical Applications Jun Zhang Laboratory for Computational Medical Imaging amp Data Analysis Department of Computer Science University of Kentucky Lexington KY 40506 Chapter 7 C8689 71a Neuronal Microanatomy and Function Rapid growth of 3D visualization of microscopic structures happens with the advent of Light and electron microscopy classical Confocal microscopy Atomic force microscopy Tunneling microscopy Chapter 7 C8689 71b Light and Electron Microscopy Light microscopy images digitized directly from the microscope can provide a 3D volume image by incrementally adjusting the focal plane It is usually followed by image processing to deconvolve the image to remove blurred outof focus structures Electron microscopy can generate multiple planes by controlling the depth of focus Further processing is necessary for selective focal plane reconstruction Chapter 7 C8689 3 71b Light Microscopes u E39i39EPIECES L HEAD msz EDIME mum LE wquot N SEPIECE om ECTWES STAGE CONDENSER Fm USING BASE 15mm ILLUMINATGR 515 mm A WEIGHT Micmsaup manly 3me 8kg Halli PUWER CDMSUMP I IDH 50w Chapter 7 C5689 4 71b Electron Microscope 69000 Chapter 7 C5689 71C Confocal Microscopy Confocal microscopy uses incoherent light or laser with precise optical control to selectively image specific parallel sections within the microscopic structure Multiple image planes can be selected providing direct volume image acquisition without the need of signal from structures outside of the plane of interest I These images are often acquired using specific fluorescent dyes to selectively image a particular component of the structure under study Chapter 7 C8689 6 I 71C Confocal Microscope Chapter 7 C5689 Idennmamn a mm mm mwlzs m Hum mammges 1mg cantata mlcmsmpy cmpmv csssg 71c Confocal Microscopy Images Chapter 7 C8689 i 71d Neuron Visualization The morphology and function of neurons from selected ganglia in the mammalian peripheral autonomic nervous system can be visualized Information about a neuron s shape and dimensions is needed to integrate and localize multiple synaptic inputs The number and location of selective neurotransmitter receptor sites provides valuable information about the potential response of a neuron to a specific transmitter Such visualization applications are termed as spatial physiology in which the function of microstructures are studies Chapter 7 C8689 10 I 71d Neuron Illustration Sums mu body Nucleus Myehn mam uznnmmnvmuya w w cmpmv 5659 l 71d Single Neuron Chapter 7 C8689 71f Imaging Neuron Architecture Visualization of the architectural relationships between neurons is less well advanced Nerve plexes where millions of sensory nerve cells are packed into a few cubic millimeters of tissue offer an opportunity to image a tractable number of cells in situ This difficulty underscores the need for computer assisted techniques to reconstruct neuronal architectures in vivo They may not be visible directly from the images but they can be visualized with assisting techniques Chapter 7 C8689 13 71f Rat Neuron Chapter 7 C8689 7221 Corneal Cell Analysis The density and arrangement of corneal cells is an indicator of the general health of the cornea These factors are routinely evaluated to determine suitability for transplant The corneal confocal microscope is a reflectedlight scanning aperture microscope fitted for direct contact with a living human cornea The image is a 3D tomographic optical image of the cornea Algorithms are developed for automated measurement of local keratocyte nuclear density in the cornea Chapter 7 C8689 15 72b Human Cornea Ennimc va 25 came Fianna Cor wnea Chapter 7 C5689 72c Local Keratocyte Density The sectional images represent a section about 15 microns think and at 1 micron intervals through the entire depth of the cornea Both global and local automated density counts in rabbit corneas correlate well to those obtained from conventional histologic evaluation of cornea tissue A decrease in keratocyte density toward the posterior of the cornea was found Chapter 7 C8689 17 72d Keratocyte Density Images Left Corneal confocal image Right Nuclei counting Chapter 7 C5689 18 726 In Vivo Stud of Cornea Density Day I g III11 1 2 In vivo confocal 39 microscopy images show the presence of densely packed ovoid or elliptical cell bodies decreasing after birth for a neonate Day 3339 Chapter 7 C5689 19 72f Cornea Density of Neonate chipmv csssg Laser scanning micrographs of neonatal corneas show decreasing cell density after birth confirming the in vivo confocal microscopy images 73a Trabecular Tissue Analysis in Glaucoma The trabecular tissue of the eye is a ring of spongy fluidfilled tissue situated at the junction of cornea iris and sclera This tissue lies in the only outflow path for aqueous humor it has long been implicated in the eye disease glaucoma The architecture of the trabecular tissue is so complex that most studies have focused on the arcitecture of the connected fluid space Chapter 7 C8689 21 U 7321 Trabecular Tissue Image a Chapter 7 C8689 73b Connected Fluid Space Analysis The fluid space is generally continuous from the anterior chamber through the trabecular tissue into Schlemm s canal l Morphometric analysis in which small chambers were successively closed revealed that the interconnection is maintained by very small chambers There are a large number of these narrowings and they occur at all regions of the tissue Chapter 7 C8689 23 I 73c Connected Fluid Space in Human Trabecular Tissue Before left and after rig ht morphological opening cmm cssm u 7421 Prostate Microvessels It is common practice to surgically remove cancerous prostates even though subsequent pathological examination of excised tissues suggest that some surgeries could have been avoided There is a great need for improved noninvasive preoperative techniques that can more accurately measure tumor volume and extent I The measures of prostate tumor size and microvessel density are useful indicators of the metastatic potential of tumor Chapter 7 C8689 25 7421 Prostate Cancer Narmal primate Pmstate cancer Chapter 7 C5689 26 74b 3D Visualization of Microvcssels 3D image analyses show that the ratio of gland volume to vessel length exhibits a twofold increase between benign and malignant tumors The normal tissue shows a characteristic circumferential pattern of the microvessels relative to the glandular tissue I In region with adenocarcinoma the pattern of microvessels is tortuous and radically diffused throughout the glandular volume Chapter 7 C8689 27 Chapter 7 C5689 28 I 74b Frog Microesel A Chapter 7 C86 89 74C Measurements of Microvessels Neovasculature exhibits a statistically significantly larger standard deviation of curvature than the normal vessels These measurements can be done with the images Volume of tissue required for the histologic analysis is similar to that obtained via needle biospy 3D image with biospy sample provides a marker for presurgical stage and outcome improve patient population stratification and eliminate unnecessary surgeries Chapter 7 C8689 30 74c Stages of Prostate Cancer The Stages of Prostate Cancer Stage T11 he mour Can39t be felt by DRE Smge T23 Tumour involves one lo a Stage T2h Tu our invulves both lobes Stage T3T4 Chapter 77 C5689 31 7521 Prostate Surgery Planning Radical prostatectomy is the most commonly performed surgical procedure The procedure has significant morbidity Minimizing these negative affects needs a careful balance between completely removal of all cancerous prostate tissue and sparing neural and vascular structures Routine surgical rehearsal using patient specific data could have significant effect on procedural success Chapter 7 C8689 32 l 75b Prostate Cancer Surgery Chapter 7 C5689 33 l 75c Presurgical Rehearsal Presurgical MR volume images of patients scanned with a rectal coil can be segmented to identify and locate the prostate bladder and other tissues The segmented images can be constructed into faithful patientspecific models and reviewed by surgeons interactively before the surgery The approach margins and critical tradeoffs can be evaluated and determined upon seeing the pathology localized relative to normal anatomy Rendered views of patientspecific models of prostate cancer can be used to accurately assess the tumor size and location relative to sensitive structures Chapter 7 C8689 34 75d Prostate Surgical Planning Chapter 7 C5689 35 76a Craniofacial Surgery Planning and Evaluation Craniofacial surgery CFS involves surgery of the facial and cranial skeleton and soft tissues Preoperative information is most often acquired using Xray CT scanning for the bony structures with MRI used for imaging the soft internal tissues 3D visualization facilitates accurate measurement of structures of interest allowing precise design of surgical procedures It also minimizes the duration of surgery reducing the risk of postoperative complication and cost Chapter 7 C8689 36 V 76b Craniofacial Surgery 1 I 76c Craniofacial Surgery 11 Chapter 7 C5689 76d Craniofacial Surgery Planning Gupta 7 15689 l 766 Craniofacial Reconstruction I in Fixation adamcarn Chapter 7 C5689 40 I 76f Craniofacial Reconstruction II Heated bane adamcum Chapter 7 C5689 41 i 7721 Neurosurgery Planning Neurosurgery needs extended knowledge and understanding of intricate relationships between normal anatomy and pathology Multimodality scans are coregistered to help neurosurgeon understand anatomy of interest Specific anatomical objects may be identified and segmented creating object maps within the digital volumeric data set The diagnostic information is used to determine the margins of pathology to avoid critical structures eg cerebral vasculature and eloquent cortical ssue Chapter 7 C8689 42 7721 Virtual Surgery Planning Virtual Reality Assisted Suigery Program VRASP Chapter 7 C5689 77b Neurosurgery Planning in Epilepsy Chapter 7 C5689 44 77cz Neurosurgery Planning in Tumor Resection Chapter 7 C8689 77d Neurosurgery I Chapter 7 C8689 46 776 Neurosurgery II Chapter 7 C8689 47 77f Neurosurgery HI Chapter 7 C8689 48 77g Intraoperative Guidance Interactive computation of lineof sight oblique planar images for planning neurosurgical approach to large tumor Neurosurgeon will have direct visualization of image planes along the path of surgical approach T1weighted MRI prior to contrast enhancement 2nd row T1wieghted MRI with gadolinium to define tumor size 3rcl row MR angiogram to localize position of important vessels 4th row Chapter 7 C8689 49 77g Neurosurgery IV Chapter 7 C8689 7821 Intraoperative Imaging Brain changes position during the neurosurgical intervention shifting as skull and dura are opened Use of preoperative images for navigation needs to be carefully calibrated against the brain shift Accurate segmented brain models can be provided by optical tracking or global positioning system A heads up display system can allow the surgeon to view 3D models transparently through the surface of the cerebra cortex Chapter 7 C8689 51 H 78b Intraoperative ultrasound images combined with MR If r 7 Chapier 7 C8689 52 79a Epilepsy Imaging Epilepsy is a prevalent disease 1020 caused by abnormal electrical activity in the brain This abnormal electrical signal usually originates at a specific location in the brain and spreads from a central focus to other regions I The location of the abnormal signal focus determines the characteristics of the seizure activity exhibited by the patient Typicals are abnormal motor activity or other unusual sensory behavior Chapter 7 C8689 53 79b Abnormal Epilepsy Behaviors 79c Epilepsy Brain Signal Activities hx qunyal v A xAet1v1tu 39 i xquot 2 K 3941 a L x 4 Kerrquot xx Eequre 393 Aehv u jquot l39139 I it link x 3 x seizure a discharge focus ng u F Wzs partial selzure Chapter 7 C5689 55 79d Dif culty to Locate Focus Abnormal electrical activities does not always correspond to any identifiable discrete pathology eg a tumor Electrical signal sampling with standard electroencephalogram EEG recording may give an overall picture of the pattern of electrical activity causing the seizure It will not allow point out accurate location to a specific part of the brain Even subdurally implanted electrodes on the cortical surface of the brain do not allow precise identification of regional brain tissue causing the seizure focus Chapter 7 C8689 56 7962 Monitoring Brain Electrical Activities Chapter 7 C5689 57 79f Epilepsy Imaging Using SISCOM A combination of SPECT and MR imaging for improved diagnosis of areas of regional activation in the brain during seizure Subtraction icta SPECT coregistered to MRI SISCOM takes advantages of the transient focal increase in cerebral blood flow in the region of seizure focus It images and statistically identifies the part of the brain involved in the seizure activity SPECT has demonstrated ability to map icta during seizure and interictal resting between seizures blood flow patterns provides potential for using these in combination to localize the seizure focus Chapter 7 C8689 58 79g SISCOM Images A MRI B PET C PET and MRI D 2nol MRI from SISCOM E Difference SPECT F SISCOM Chapter 7 C8689 59 79h Axial Images of Mesial Temporal Lobe Epilepsy MRI composite SISCOM I E Jquot E v quotquot 39 1 Y i z a if It Chapter 7 C5689 60 79i Coronal Images of MTLE 39m l y 3911 MRI composite SISCOM composite subtraction SPECT and rainbow color scales for anterior top and posterior Temporal bottom regions of left MTLE group Chapter 7 C5689 61 79j Sagittal Images of left MTLE group MRI composite SISCOM composite SPECT rainbow color Scale for left MTLE group Chapter 7 C5689 62 Computational Medical Imaging Analysis Chapter 1 Introduction to Imaging Science Jun Zhang Laboratory for Computational Medical Imaging amp Data Analysis Department of Computer Science University of Kentucky Lexington KY 40506 Chapter 1 C8689 11a Introduction Biological organisms including humans depend on the continuous movements of fluids to supply nutrition and carry away waste Fluid movements are actuated and controlled by voluntary or involuntary musculature Function of muscle cells is determined by their atomic constituency biochemical nature metabolic characteristics and geometric arrangements There is a need for improved understanding of the normal and pathophysiological processes by using visualizing and measuring these anatomic structures and functional variables Chapter 1 C8689 2 11b Means for Visualization It is desirable that visualization and measurements of bodily organs and tissues do not affect their working environment ie to be noninvasive They should involve minimum possible degree of morphological and physiological disturbance Transmission of radiant energy eg Xrays gamma ray radio waves or ultrasound waves etc through body produces images without subjective sensation and does not directly affect the function of bodily tissues at some dose levels for useful images Images are produced by differential absorption and scatter pattern of radiant energy by different tissues in all body parts Chapter 1 C8689 3 1 221 X ray In 1895 Wilhelm Conrad Rontgen a German physicist at the University of Wurzburgm made the great discovery of the invisible ray First radiograph of hand made with ray from fluorescence using cathode ray tubes Xray made it possible to see into the body in a painless nondestructive way n This discovery was quickly recognized and accepted as a new medical diagnostic technique Modest but acceptable risks are incurred due to the ionizing effect of the Xrays Chapter 1 C8689 4 12b Wilhelm Conrad Rontgen 1901 Nobel Prize in Physics Chapter 1 C5689 12C Developments Following X ray The discovery of Xray spurred a succession of evolutionary improvements in radiographic instrumentation and photographic procedures In 1940 introduction of fluoroscopic imaging with an image intensifier with a television dynamic Xray imaging systems n1950 nuclear medicine tomographic imaging In 1960 ultrasonography The basic radiographic process used by Rontgen had not changed very much for more than 75 years Chapter 1 C8689