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PACS: Picture Archiving and Communication System

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DICOM: Digital Imaging and COmmunications in Medicine ... 6 DATA DICTIONARY ... The 2003 Nobel Prize in Physiology or Medicine ... – PowerPoint PPT presentation

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Title: PACS: Picture Archiving and Communication System


1
PACS Picture Archiving and Communication System
  • Feipei Lai
  • National Taiwan University

2
PACS
  • A comprehensive computer system that is
    responsible for the electronic storage and
    distribution of medical images in the medical
    enterprise.
  • Reduce costs
  • Improve patient care

3
  • A PACS stores, retrieves, distributes, and
    presents digital medical images.
  • In a typical PACS, DICOM is used for image
    storage, retrieval, and data exchange.
  • DICOM also provides a framework for image
    information management such as Modality Worklist
    (MWL), Modality Performed Procedure Step (MPPS),
    and Storage Commitment (STC).
  • Furthermore, DICOM standardizes hard- and
    soft-copy display consistency and image
    import/export on rewritable media such as CDs or
    DVDs.

4
DICOM Digital Imaging and COmmunications in
Medicine
  • The goals of DICOM are to achieve
    interoperability and to improve workflow
    efficiency between imaging systems and other
    information systems in healthcare environments
    worldwide.

5
  • 1 Introduction and Overview
  • 2 Conformance
  • 3 Information Object Definitions
  • 4 Service Class Specifications
  • 5 Data Structures and Encoding
  • 6 Data Dictionary
  • 7 Message Exchange
  • 8 Network Communication Support for Message
    Exchange
  • 9 Retired
  • 10 Media Storage and File Format for Media
    Interchange
  • 11 Media Storage Application Profiles
  • 12 Formats and Physical Media
  • 13 Retired
  • 14 Grayscale Standard Display Function
  • 15 Security and System Management Profiles
  • 16 Content Mapping Resource
  • 17 Explanatory Information
  • 18 Web Access to DICOM Persistent Objects (WADO)

6
1 Introduction and Overview
  • provides an overview of the entire Digital
    Imaging and Communications in Medicine (DICOM)
    Standard.
  • It describes the history, scope, goals, and
    structure of the Standard.
  • In particular, it contains a brief description of
    the contents of each part of the Standard.

7
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8
2 Conformance
  • defines principles that implementations claiming
    conformance to the Standard shall follow
  • Conformance requirements. PS 3.2 specifies the
    general requirements which must be met by any
    implementation claiming conformance. It
    references the conformance sections of other
    parts of the Standard.
  • Conformance Statement. PS 3.2 defines the
    structure of a Conformance Statement. It
    specifies the information which must be present
    in a Conformance Statement. It references the
    Conformance Statement sections of other parts of
    the Standard.

9
CONSTRUCTION PROCESS FOR A NETWORK CONFORMANCE
CLAIM
10
CONSTRUCTION PROCESS FOR A MEDIA CONFORMANCE CLAIM
11
3 INFORMATION OBJECT DEFINITIONS
  • PS 3.3 of the DICOM Standard specifies a number
    of Information Object Classes which provide an
    abstract definition of real-world entities
    applicable to communication of digital medical
    images and related information (e.g., waveforms,
    structured reports, radiation therapy dose,
    etc.).
  • Each Information Object Class definition consists
    of a description of its purpose and the
    Attributes which define it.

12
4 SERVICE CLASS SPECIFICATIONS
  • PS 3.4 of the DICOM Standard defines a number of
    Service Classes.
  • A Service Class associates one or more
    Information Objects with one or more Commands to
    be performed upon these objects.
  • Service Class Specifications state requirements
    for Command Elements and how resulting Commands
    are applied to Information Objects.
  • Service Class Specifications state requirements
    for both providers and users of communications
    services.

13
5 DATA STRUCTURE AND SEMANTICS
  • PS 3.5 of the DICOM Standard specifies how DICOM
    applications construct and encode the Data Set
    information resulting from the use of the
    Information Objects and Services Classes defined
    in PS 3.3 and PS 3.4 of the DICOM Standard.
  • The support of a number of standard image
    compression techniques (e.g., JPEG lossless and
    lossy) is specified.

14
6 DATA DICTIONARY
  • PS 3.6 of the DICOM Standard is the centralized
    registry which defines the collection of all
    DICOM Data Elements available to represent
    information, along with elements utilized for
    interchangeable media encoding and a list of
    uniquely identified items that are assigned by
    DICOM.

15
7 MESSAGE EXCHANGE
  • PS 3.7 of the DICOM Standard specifies both the
    service and protocol used by an application in a
    medical imaging environment to exchange Messages
    over the communications support services defined
    in PS 3.8.
  • A Message is composed of a Command Stream defined
    in PS 3.7 followed by an optional Data Stream as
    defined in PS 3.5.

16
8 NETWORK COMMUNICATION SUPPORT FOR MESSAGE
EXCHANGE
  • PS 3.8 of the DICOM Standard specifies the
    communication services and the upper layer
    protocols necessary to support, in a networked
    environment, communication between DICOM
    applications as specified in PS 3.3, PS 3.4, PS
    3.5, PS 3.6, and PS 3.7.
  • These communication services and protocols ensure
    that communication between DICOM applications is
    performed in an efficient and coordinated manner
    across the network.

17
10 MEDIA STORAGE AND FILE FORMAT
  • PS 3.10 of the DICOM Standard specifies a general
    model for the storage of medical imaging
    information on removable media (see Figure
    6.10-1).
  • The purpose of this Part is to provide a
    framework allowing the interchange of various
    types of medical images and related information
    on a broad range of physical storage media.

18
DICOM Media Communication Model
19
11 MEDIA STORAGE APPLICATION PROFILES
  • PS 3.11 of the DICOM Standard specifies
    application specific subsets of the DICOM
    Standard to which an implementation may claim
    conformance.
  • These application specific subsets will be
    referred to as Application Profiles in this
    section.
  • Such a conformance statement applies to the
    interoperable interchange of medical images and
    related information on storage media for specific
    clinical uses.
  • It follows the framework, defined in PS 3.10, for
    the interhcange of various types of information
    on storage media.

20
12 STORAGE FUNCTIONS AND MEDIA FORMATS FOR DATA
INTERCHANGE
  • This part of the DICOM Standard facilitates the
    interchange of information between applications
    in medical environments by specifying
  • a) A structure for describing the relationship
    between the media storage model and a specific
    physical media and media format.
  • b) Specific physical media characteristics and
    associated media formats.

21
14 GRAYSCALE STANDARD DISPLAY FUNCTION
  • PS 3.14 specifies a standardized display function
    for consistent display of grayscale images.
  • This function provides methods for calibrating a
    particular display system for the purpose of
    presenting images consistently on different
    display media (e.g. monitors and printers).

22
15 SECURITY AND SYSTEM MANAGEMENT PROFILES
  • PS 3.15 of the DICOM Standard specifies security
    and system management profiles to which
    implementations may claim conformance.
  • Security and system management profiles are
    defined by referencing externally developed
    standard protocols, such as DHCP, LDAP, TLS and
    ISCL.
  • Security protocols may use security techniques
    like public keys and smart cards.
  • Data encryption can use various standardized data
    encryption schemes.

23
16 CONTENT MAPPING RESOURCE
  • PS 3.16 of the DICOM Standard specifies
  • templates for structuring documents as DICOM
    Information Objects
  • sets of coded terms for use in Information
    Objects
  • a lexicon of terms defined and maintained by
    DICOM
  • country specific translations of coded terms

24
17 explanatory information
  • This part of the DICOM Standard contains
    explanatory information in the form of Normative
    and Informative Annexes.

25
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26
18 Web Access to DICOM Persistent Objects (WADO)
  • This standard specifies a web-based service for
    accessing and presenting DICOM (Digital Imaging
    and Communications in Medicine) persistent
    objects (e.g. images, medical imaging reports).
  • This is intended for distribution of results and
    images to healthcare professionals.
  • It provides a simple mechanism for accessing a
    DICOM persistent object from HTML pages or XML
    documents, through HTTP/HTTPs protocol, using
    DICOM UIDs (Unique Identifiers).
  • Data may be retrieved either in a
    presentation-ready form as specified by the
    requester (e.g. JPEG or GIF) or in a native DICOM
    format.
  • It does not support facilities for web searching
    of DICOM images.
  • This standard relates only to DICOM persistent
    objects (not to other DICOM objects or to
    non-DICOM objects).

27
1. Select patient information
  • When a patient is registered and a procedure is
    ordered, this is typically communicated to a
    Radiology Information System (RIS), which does
    the scheduling and creates information about the
    procedure, scheduling, and patient demographics
    available (using the DICOM Modality Worklist) to
    the technologist at the modality.
  • This info is then used to perform the
    acquisition, because the scheduled procedure
    information (such as CT-Abdomen) is available for
    the technologist.
  • In addition, the patient demographic information
    is copied automatically and used to identify the
    images that are sent out.

28
2. (Optional) retrieve prior images
  • In certain cases, prior images could be helpful
    to ensure that the acquisition uses the same
    techniques, and that those techniques can be
    easily compared with the previous study.
  • In such cases, a technologist might pull them
    over by using DICOM Query/Retrieve.

29
3. Start procedure
  • As soon as the acquisition starts, the PACS and
    Health Information System are notified using the
    DICOM Modality Performed Procedure Step.
  • The Image Manager in the PACS knows that images
    will be forthcoming and it could remove the
    procedure from the scheduling list so that other
    devices will not attempt to perform the same
    procedure.

30
4. Send images
  • Images are acquired and sent or pushed, using
    the DICOM Storage Service, to a PACS archive or
    QA station.

31
5. Update with exam complete status
  • When completed, the DICOM Modality Performed
    Procedure Step will communicate what the actual
    performed procedure was (should it have been
    changed from the originally scheduled procedure),
    and how many images were created.
  • The number of images is important for the Image
    Manager, which inventories them to make sure it
    has them all available in the PACS archive.
  • Knowing that the exam was completed is important
    for the PACS scheduler so that it can alert a
    radiologist to read the study. (It does this by
    adding it to the interpretation Worklist.)
  • The actual performed procedure information will
    be used by the RIS to ensure that the billing is
    done correctly.
  • Radiation dose information might be exchanged as
    well, in the case of an X-Ray exam.

32
6. Read study
  • A radiologist opens the to-be-read folder on a
    workstation, which was created using the DICOM
    General Purpose Worklist services.
  • Prior exams might be pulled over using the DICOM
    Query/Retrieve.
  • Depending on the system architecture, these prior
    images could have been pushed to the workstation
    prior to the reading in order to increase
    performance (by using the DICOM Storage).

33
7. Make images available for physician
  • The images could be made available for the
    Referring Physician as well.
  • They could access the images using a workstation
    in their office.
  • The DICOM grayscale standard display function is
    used to make sure that the images look almost
    identical on the radiologist workstation and the
    physician workstation.
  • In addition, any additional annotation and
    changes in the image appearance, such as window
    width and level, are exchanged between the
    radiologist workstation and the physician
    workstation.

34
8. Create hardcopy/softcopy
  • The patient might need an additional hardcopy,
    such as film or a CD to take to the physician or
    specialist.
  • A file room clerk can retrieve the images using
    DICOM Query/Retrieve and either print the
    significant images using DICOM Print or burn a
    DICOM-compatible disc (either CD or DVD).

35
9. Make images available for Primary Care
Physician
  • Using the Internet, the images could also be made
    available to the Primary Care Physician.
  • DICOM security will make sure that the
    information delivered over the Internet to the
    physician is encrypted and that the proper
    authorization has taken place prior to the image
    retrieval.
  • The DICOM Key Object Note identifies which images
    are significant so that the complete study will
    not have to be reviewed.

36
  • Wherever possible, DICOM utilizes relevant parts
    of other mature standards such as LOINC, SNOMED,
    JPEG, MPEG, BIRADS, TCP/IP and other Internet
    Standards.

37
  • BI-RADS is an acronym for Breast
    Imaging-Reporting and Data System, a quality
    assurance tool originally designed for use with
    mammography.

38
Modality Work List
  • DICOM Modality Work List (MWL), which allows for
    the scheduling, ordering and patient demographic
    information to be retrieved at a modality.

39
Modality Performed Procedure Step
  • Modality Performed Procedure Step (MPPS) allows a
    device to communicate what the exam performed
    actually was (vs. the exam that was scheduled) to
    allow changes in the procedure to be
    communicated.
  • In addition, it tells when a procedure has been
    started, indicating this on the scheduling list,
    and provides information about the number of
    images generated.

40
Storage Commitment
  • Storage Commitment (STC), which transfers the
    responsibility for the images to the receiver, so
    they can be safely removed from the local disc.

41
LUT
  • In order to achieve this consistency, devices
    have to support the DICOM grayscale or color
    standard, potentially implementing a so-called
    presentation Look Up Table to map the values.

42
Presentation State
  • There is one other component of the presentation
    consistency, and that occurs when a physician
    does things like zoom an image, add annotation,
    or change the Window width and level. This
    information should be preserved in a standard
    manner.
  • This issue is addressed by the DICOM Presentation
    State.

43
imaging integration
  • to indicate information about the images, such as
    measurements, computer aided diagnostic data for
    significant images.
  • DICOM identifies the key images of a study so
    that a physician does not have to review every
    image in the study (which is especially important
    when the initial study contains thousands of
    images such as for CT and MR).
  • The measurements and findings, either by a human
    or computer, are generally encoded as a
    Structured Report (SR).

44
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46
PACS ?????
  • 1. Core Switch 6509 ????
  • ??????????,?????????????????
  • 2. Main PACS client ????
  • Client ??? Edge Switch ??? Core Switch?,??
    Edge Switch????????????? Core Switch??????
  • 3. ?? RAD PACS ???????????
  • ????????????????,??????????????????,??????????
    ????????????? RAD PACS?????????? PACS Core
    Switch?,?????????????????,?????????????? PACS???

47
  • 4. ?????????????
  • ?????????? 30?,?????? 3???????????????48?10/100
    /1000????,?????????24?10/100/1000
    ?????????????????? Core Switch?
  • 5. ???????? RAD PACS????
  • ????????????,???????
  • a.???????????,?? ACL (Access Control List)
    ???,?????????,??????? IP ???? RAD PACS ????
  • b.?????????

48
Various Network Technologies, Bandwidths and
Typical Transfer Times
49
  • 5MP?????????
  • ? 64MB(?)??RAM???,
  • ??? ? 25602048, Dual 8 /10 bit DVI 20(?)??TFT
    LCD?????
  • ?? ? 700 cd/M2,
  • ?????170?
  • Contrast Ratio ? 6001

50
  • 3MP?????????
  • ? 64MB(?)??RAM???,
  • ??? ? 15362048, Dual 8 /10 bit DVI 20(?)??TFT
    LCD?????,
  • ?? ? 700 cd/M2,
  • ???? ? 170?,
  • Contrast Ratio ? 9001

51
Medical images
  • Topographic imaging
  • Represents the surface of the body
  • Projection imaging
  • The interactions of radiation penetrating along a
    known path of the radiation through the body
  • Tomographic imaging
  • The spatial distribution of the local interaction
    of the radiation with tissue in a thin slice
    through the body.

52
Medical images
  • The quality of the images is represented by
    contrast and resolution.
  • The contrast is determined by the nature of the
    interaction of the radiation with the tissue
    material (e.g., via partial absorption) or its
    structure (e.g., via reflection) or the
    preferential accumulation of indicator materials
    (e.g., iodine for X-ray, gadolinium ? for
    Magnetic Resonance Imaging, microbubles in the
    Ultrasound or radionuclides for Scintigraphy
    ????? ).

53
Medical images
  • The resolution is expressed as spatial, temporal
    or contrast.
  • Temporal resolution involves the exposure time
    required to complete the scan of a single image
    and the frame rate of the sequential individual
    images.

54
Medical images
  • Plays a major role in medical research activities
    such as detection and quantitation of
    pathophysiological structure-to-function
    relationships, drug discovery and phenotyping.

55
phenotype
  • A phenotype describes any observed quality of an
    organism, such as its morphology, development, or
    behaviour, as opposed to its genotype - the
    inherited instructions it carries, which may or
    may not be expressed.

56
Imaging instrument
  • Components that generate the probing energy (such
    as electromagnetic radiation, ultrasound or
    electrical current)
  • The detector system
  • The tomographic image reconstructor (generally
    involves a mechanical or electronic scanning
    process and a variant of solving an inverse
    problem)
  • The image display (generally involves a computer
    terminal).

57
  • Novel ideas only survive if the environment for
    implementing the idea is present and/or the need
    is perceived.

58
PACS
  • Ultrasound
  • Magnetic Resonance Imaging
  • Computed Tomography

59
NMR
  • Lauterbur realized that the slight variation in
    magnet uniformity (the bane of spectroscopists)
    could be used to spatially localize the signal of
    interest and, hence, the controlled variation in
    magnetic field could form the basis of an imaging
    approach.

60
Ultrasound microbubbles
  • Intravascular microbubbles were developed as an
    ultrasound contrast agent, but the harmonic
    frequencies generated which contaminated the
    Doppler signal used to measure their velocity
    became the basis of a great increase in
    specificity and sensitivity of the microbubble
    use in ultrasound.

61
  • Specificity (true negative rate)
  • TN / (TN FP)
  • Sensitivity (true positive rate)
  • TP / (TP FN)
  • TP True Positive
  • TN True Negative
  • FP False Positive
  • FN False Negative

62
Chemical shift
  • The paramagnetic effect of oxygen in the blood
    could be used to generate highly specific images
    of cerebral oxygen use and spectroscopic
    evaluation of metabolic events in tissues such as
    in the brain and heart.

63
Positron Emission Tomography (PET)
  • Measures radioactive traces injected into the body

64
reference
  • Proceedings of the IEEE, Vol. 91, No. 10, October
    2003, pp. 1483-1491.

65
Basic concepts in Image Generation
  • Spatial resolution
  • The number of pixels per image area
  • Contrast resolution
  • The number of bit per pixel determines the
    contrast resolution
  • Temporal resolution
  • A measure of the time needed to create an image

66
Ultrasound
67
Principle of Echo Scanners
  • In echo scanners, sound pulses are generated with
    frequencies of about a few MHz.
  • These pulses are absorbed, scattered, or
    reflected in the patient.
  • The reflections give rise to relatively strong
    echoes.

68
  • Reflections occur at interfaces between media
    that are different with respect to density and/or
    the velocity of sound.
  • Sound is reflected at interfaces with different
    acoustic impedances the so-called acoustic
    impedance is equal to the product of sound
    velocity and density.

69
Principle of Echo Scanners
  • At an interface between soft tissue on one side
    and bone or air on the other side, a strong
    reflection is observed.
  • Scattering takes place if the dimension of the
    object is small (i.e., about the wavelength of
    the incident radiation).
  • The beam is then scattered in all directions, and
    therefore, the amplitude of the signal detected
    by the transducer is relatively small.

70
Principle of Echo Scanners
  • The resolution of an echo scan, that is, the
    degree with which details located close together
    can still be distinguished, is determined by both
    the wavelength of the sound waves and the
    duration of the emitted pulse.
  • The pulse is usually several wavelengths long. In
    practice, therefore, reflections from two points
    separated by a few wavelengths can be
    discriminated.
  • The smaller the wavelength the better the
    resolution. Since the wavelength is inversely
    proportional to the frequency, the resolution is
    proportional to the frequency.

71
Principle of Echo Scanners
  • The attenuation coefficient (which expresses how
    much the beam is attenuated per centimeter of
    tissue because of scatter and absorption) is
    proportional to the sound frequency for soft
    tissue and is even proportional to the square of
    the frequency for other types of tissues.
  • The depth of penetration of the sound waves is
    inversely proportional to the frequency. The more
    the beam is attenuated, the more difficult it is
    to measure the reflections of deeper structures,
    since the signal-to-noise ratio gradually becomes
    smaller.

72
Principle of Echo Scanners
  • Since resolution and penetration depth pose
    contradictory requirements
  • Deeper structures can only be visualized with
    relatively low frequencies, with a concomitant
    lower resolution.
  • The type of tissue influences the amount of
    absorption of the beam. Air and bone, for
    example, are strong absorbers, whereas muscle
    tissue and water hardly attenuate the beam.

73
Principle of Echo Scanners
  • At a frequency of 3 MHz (wavelength of 0.5 mm)
    depths of up to 10 cm are well visualized, with
    an axial resolution on the order of 1 mm.
  • For eye examinations a higher resolution is
    needed. In this case frequencies of between 5 and
    13 MHz (wavelengths of between 0.25 and 0.075 mm,
    respectively) are used.
  • For brain examinations the sound beam must first
    pass bone structures (e.g., the temporal).
    Because of the high absorption of bone,
    especially for high frequencies, only low
    frequencies can be used, implying a lower
    resolution.

74
Temporal ????,??
  • The space, on either side of the head, back of
    the eye and forehead, above the zygomatic arch
    and in front of the ear.

75
The 2003 Nobel Prize in Physiology or Medicine
  • The Nobel Assembly at Karolinska Institutet
    awarded The Nobel Prize in Physiology or Medicine
    for 2003jointly to
  • Paul C Lauterbur and Peter Mansfield for their
    discoveries concerning "magnetic resonance
    imaging"

76
Summary
  • Imaging of human internal organs with exact and
    non-invasive methods is very important for
    medical diagnosis, treatment and follow-up.
  • Seminal discoveries concerning the use of
    magnetic resonance to visualize different
    structures.
  • These discoveries have led to the development of
    modern magnetic resonance imaging, MRI, which
    represents a breakthrough in medical diagnostics
    and research.

77
  • Atomic nuclei in a strong magnetic field rotate
    with a frequency that is dependent on the
    strength of the magnetic field.
  • Their energy can be increased if they absorb
    radio waves with the same frequency (resonance).
  • When the atomic nuclei return to their previous
    energy level, radio waves are emitted.
  • These discoveries were awarded the Nobel Prize in
    Physics in 1952.

78
  • When the atom is placed in a magnetic field, the
    interaction energy -?B of the spin magnetic
    dipole moment with the field causes further
    splittings in energy levels and in the
    corresponding spectrum lines.

79
  • During the following decades, magnetic resonance
    was used mainly for studies of the chemical
    structure of substances.
  • In the beginning of the 1970s, this years Nobel
    Laureates made pioneering contributions, which
    later led to the applications of magnetic
    resonance in medical imaging.

80
  • Paul Lauterbur (born 1929), Urbana, Illinois,
    USA, discovered the possibility to create a
    two-dimensional picture by introducing gradients
    in the magnetic field.
  • By analysis of the characteristics of the emitted
    radio waves, he could determine their origin.
  • This made it possible to build up two-dimensional
    pictures of structures that could not be
    visualized with other methods.

81
  • Peter Mansfield (born 1933), Nottingham, England,
    further developed the utilization of gradients in
    the magnetic field.
  • He showed how the signals could be mathematically
    analysed, which made it possible to develop a
    useful imaging technique.
  • Mansfield also showed how extremely fast imaging
    could be achievable.
  • This became technically possible within medicine
    a decade later.

82
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83
Rapid development within medicine
  • A great advantage with MRI is that it is harmless
    according to all present knowledge.
  • The method does not use ionizing radiation, in
    contrast to ordinary X-ray (Nobel Prize in
    Physics in 1901) or computer tomography (Nobel
    Prize in Physiology or Medicine in 1979)
    examinations.
  • However, patients with magnetic metal in the body
    or a pacemaker cannot be examined with MRI due to
    the strong magnetic field, and patients with
    claustrophobia may have difficulties undergoing
    MRI.

84
Especially valuable for examination of the brain
and the spinal cord
  • Today, MRI is used to examine almost all organs
    of the body.
  • The technique is especially valuable for detailed
    imaging of the brain and the spinal cord.
  • Nearly all brain disorders lead to alterations in
    water content, which is reflected in the MRI
    picture.
  • A difference in water content of less than a
    percent is enough to detect a pathological change.

85
  • In multiple sclerosis ??? , examination with MRI
    is superior for diagnosis and follow-up of the
    disease.
  • The symptoms associated with multiple sclerosis
    are caused by local inflammation in the brain and
    the spinal cord.
  • With MRI, it is possible to see where in the
    nervous system the inflammation is localized, how
    intense it is, and also how it is influenced by
    treatment.

86
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87
  • Another example is prolonged lower back pain,
    leading to great suffering for the patient and to
    high costs for the society.
  • It is important to be able to differentiate
    between muscle pain and pain caused by pressure
    on a nerve or the spinal cord.
  • With MRI, it is possible to see if a disc
    herniation is pressing on a nerve and to
    determine if an operation is necessary.

88
Improved diagnostics in cancer
  • MRI examinations are very important in diagnosis,
    treatment and follow-up of cancer.
  • The images can exactly reveal the limits of a
    tumour, which contributes to more precise surgery
    and radiation therapy.
  • Before surgery, it is important to know whether
    the tumour has infiltrated the surrounding
    tissue.
  • MRI can more exactly than other methods
    differentiate between tissues and thereby
    contribute to improved surgery.

89
  • MRI has also improved the possibilities to
    ascertain the stage of a tumour, and this is
    important for the choice of treatment.
  • For example, MRI can determine how deep in the
    tissue a colon cancer has infiltrated and whether
    regional lymph nodes have been affected.

90
Magnetic Resonance Imaging
  • The aim of MRI is to provide an image of the
    tissue distribution in a plane through the body,
    for example, by measuring the hydrogen density in
    that plane.
  • The idea is, once again, to obtain a
    two-dimensional image of a two-dimensional slice
    through the body.

91
Principle of Magnetic Resonance Imaging
  • How can the density of hydrogen nuclei at each
    location of interest in the body be obtained?
  • The hydrogen atoms at each location have their
    own specific Larmor resonance frequency,
    depending on the local strength of the external
    magnetic field.

92
Principle of Magnetic Resonance Imaging
  • By irradiating the body with EM radiation at a
    certain frequency in a direction perpendicular to
    the external magnetic field, only those hydrogen
    nuclei that have a Larmor frequency equal to the
    frequency of the RF excitation pulse will
    resonate.
  • The Larmor frequency depends on the strength of
    the magnetic field, so these nuclei are located
    in a small volume.

93
Principle of Magnetic Resonance Imaging
  • The RF excitation pulse has such a duration that
    after the pulse the magnetization vector will
    process perpendicularly to the external magnetic
    field (the 90o RF pulse).
  • A current is then induced in a coil perpendicular
    to the external magnetic field. This current has
    an amplitude proportional to the number of the
    resonating nuclei in that volume and a frequency
    equal to the Larmor frequency.

94
Principle of Magnetic Resonance Imaging
  • This frequency determines the position of the
    sampled volume. This procedure is repeated with
    other frequencies for all volumes with a specific
    Larmor frequency.
  • By this procedure the density of hydrogen nuclei
    can be obtained at all locations of interest.

95
Principle of Magnetic Resonance Imaging
  • The external magnetic field consists of two
    parts
  • a strong homogeneous field
  • a smaller magnetic field, of which the strength
    changes linearly in a certain direction. The
    linearly changing field can be applied in three
    directions by three orthogonally placed gradient
    coils. This changing magnetic field is also
    called the magnetic field gradient.

96
  • If the field gradient is directed, for instance,
    from head to toe, every transverse slice in the
    patient resonates at a different Larmor
    frequency.
  • RF coils may be used to detect the resultant
    magnetization changes, also called receiving
    coils.

97
Principle of Magnetic Resonance Imaging
  • All nuclei in a slice orthogonal to the gradient
    direction will experience the same external
    magnetic field strength and therefore will have
    the same Larmor frequency (this gradient is
    called the slice selection gradient).
  • The amplitude of the current in the receiving
    coil after the application of a 90o RF pulse will
    be proportional to the total number of hydrogen
    nuclei in this slice.

98
The phenomenon of spins aligning themselves to an
external magnetic field. At 0 K all spins are
aligned when an external magnetic field is
present (a) when no external magnetic field is
present the spins will point in all directions
(b) at room temperature only a small part of the
nuclei will align themselves 1 per million
(c) at a field strength of 0.1 tesla and 5 per
million (d) at a magnetic field strength of 0.5
tesla (after Philips). Figure 9.11
99
Tesla
  • The units of B is the same as the units of F/qv.
  • The SI unit of B is equivalent to 1 N.s/C.m
  • 1 tesla 1 T 1 N/A.m
  • Another unit of B, the gauss (1G 10-4 T)

100
Principle of Magnetic Resonance Imaging
  • more position selectivity is attained as follows.
  • after the 90o RF pulse, the slice selection
    gradient is switched off and another magnetic
    field gradient is applied orthogonally to the
    direction of the slice selection gradient (this
    additional gradient is called readout or
    measurement gradient, because it is applied after
    the 90o pulse and just before the induced current
    is measured in the receiving coil) the frequency
    of the resonating nuclei will change

101
  • nuclei in the slice located along different rows
    orthogonally to the readout gradient direction
    will experience a different external magnetic
    field strength (the sum of the first homogeneous
    field and the readout gradient field) and
    therefore will have different Larmor frequencies
    in the different rows.

102
Principle of Magnetic Resonance Imaging
  • This means that each row of hydrogen nuclei in
    the slice induces a current with a different
    frequency in the receiving coil. The amplitude of
    the component with a certain frequency, again, is
    proportional to the number of hydrogen atoms
    along the corresponding row, and the frequency
    now determines the position of the corresponding
    row.

103
Precession of magnetization under the influence
of an external magnetic field with strength Bo
and an oscillating field B1 (due to
electromagnetic radiation) during a 90? RF pulse
as seen from the observer (A) and as seen from
the standpoint of the rotating field (B)
(Philips). Figure 9.12
104
Principle of Magnetic Resonance Imaging
  • Since the sum of signals with all of these
    different resonance frequencies is detected
    simultaneously, a Fourier transformation needs to
    be conducted to obtain amplitude and position
    information in the specific frequency spectrum.
  • Each frequency corresponds to a row in the slice.
    The amplitude of each frequency component is
    proportional to the number of resonating nuclei
    in a certain row.

105
Principle of Magnetic Resonance Imaging
  • The frequency spectrum corresponds to a profile
    representing the number of hydrogen nuclei in
    each row as a function of the location along the
    direction of the readout gradient.
  • By measuring the profile for different directions
    of the readout gradient and using a
    back-projection technique, the distribution of
    the hydrogen nuclei over the slice can be
    obtained.
  • The procedure can be sped up by applying a second
    field gradient orthogonally to the readout
    gradient before the latter is applied and by
    using the resulting phase differences.

106
Principle of Magnetic Resonance Imaging
  • After termination of the 90o RF pulse, the
    magnetization gradually returns back to its
    equilibrium position, which is parallel to the
    external field. This phenomenon is called
    relaxation.

107
Computed Tomography
  • Consider a cross section through the body of a
    patient with a thickness of about 1 mm. Now,
    divide the cross-section into a large number of
    small squares, each with an area of about 1 mm2.
  • When a narrow X-ray beam, a so-called pencil
    beam, passes through the slice, each square
    through which the beam passes attenuates it to a
    certain extent.

108
Computed Tomography
  • The amount of attenuation is determined by the
    molecular composition and the density of the
    tissue present in the square.
  • The intensity of the eventually transmitted beam
    will be smaller than the intensity of the
    incident beam.
  • The intensity reduction is caused by all the
    squares through which the beam passes.
  • Each square may attenuate the beam differently
    because of the presence of different tissue.

109
Computed Tomography
  • To measure the attenuation of a beam, it is
    necessary to use a combination of an X-ray tube
    and a detector.
  • The absorbing tissue slice is located between
    them. The X-ray tube produces a pencil beam of
    known intensity and the detector measures the
    intensity of the transmitted beam.
  • the combination of X-ray tube and detector
    (mounted into the so-called gantry) can both be
    shifted along a line ("translated") and rotated
    (see Fig. 9.6).

110
Principle of computed tomography. The combination
of X-ray tube and detector is translated across
the patient, producing a density profile p(k,
f). By rotating the X-ray tube-detector
combination, a number of profiles will be
obtained. From these profiles the attenuation
coefficients of each pixel can be
determined. Figure 9.6
111
Computed Tomography
  • by displaying the attenuation coefficients (the
    values indicating the amount of absorption per
    millimeter) we can obtain an anatomical image, we
    must be able to determine the attenuation
    coefficients of each square separately.
  • From one measurement it is not possible to deduce
    how much each separate square attenuated the
    beam.
  • Yet, determination of the attenuation of each
    square in the cross-section is the purpose of the
    procedure.

112
Computed Tomography
  • Since one pencil beam covers only one row of
    squares, we must translate the beam over a
    distance equal to its width.
  • In this way we can take into account the
    attenuation coefficients of the squares located
    on a neighboring row.
  • After measuring the transmitted intensity, the
    procedure is repeated by translating the beam and
    measuring the transmitted intensity until we have
    covered the total cross section.

113
  • It is still not possible, however, to determine
    the individual attenuation coefficient of each
    square from these data for each position of the
    beam we obtain the total attenuation due to the
    attenuation caused by all squares that are passed
    by the pencil beam.

114
Computed Tomography
  • What we have obtained is an intensity profile
    (and, therefore, a measure of the total
    attenuation) of the transmitted beam as a
    function of the position of the beam.
  • Each point in the profile indicates how strongly
    the incident beam was attenuated by the row of
    squares that was passed by the beam in that
    position (Fig. 9.6).
  • we repeat the procedure outlined above for
    various angles of the beam.
  • It is possible to compute the attenuation per
    square from these data.

115
  • an X-ray beam is attenuated in an exponential
    way, depending on the length of the path and the
    attenuation coefficients of the squares, denoted
    here as pixels encountered along its path.
  • If we assume that the attenuation coefficient is
    constant over the whole pixel and if we represent
    the attenuation of pixel i by the attenuation
    coefficient mi, then the intensity of the
    transmitted beam (I) can be related to the
    intensity of the incident beam (I0) in the way
    represented in Fig. 9.7.

116
  • If we take the natural logarithm of the ratio of
    I and I0, we obtain the following relation for
    each pixel
  • In(I/I0) ?i1 N dimi

117
The intensity of the transmitted beam as a
function of the attenuation coefficient of the
pixels traversed. Upper part, the intensity after
crossing one volume element middle part, after
traversing n volume elements lower part, the
analog case. Figure 9.7
118
  • Here, di is the length of the path that the beam
    traversed through each pixel i, and mi is its
    attenuation coefficient.
  • We have obtained an equation with, to the left,
    the measured intensity ratio and, to the right, N
    unknown quantities the coefficients mi. Since
    the geometry of the beam and the cross-section
    are known, the length of the path di traversed
    through each pixel is also known.

119
  • The number of unknown quantities therefore only
    increases.
  • After the beam has covered the whole cross
    section, the equations contain as many unknowns
    as there are pixels in the cross section.
  • By turning the gantry over a small angle and
    repeating the earlier procedure we obtain another
    intensity profile.

120
  • The attenuation coefficients of the pixels remain
    the same, but the length of the paths traversed
    through each pixel has changed.
  • In this way we obtain new equations with the same
    number of unknowns.
  • By measuring the intensity profiles at enough
    angles we can, in principle, obtain as many
    equations as there are unknowns.

121
  • As can be seen from Fig. 9.8, a visualization of
    the values of the attenuation coefficients by way
    of grey values indeed produces an anatomical
    image.
  • The procedure of CT as explained here is not used
    in practice, because it would be too
    time-consuming, but it provides a good insight
    into the principles of CT.
  • In practice, back-projection algorithms are used,
    since these are more efficient.

122
Example of cross-sections through several parts
of the body skull, thorax, and abdomen, obtained
by computed tomography. Figure 9.8
123
  • Back projection is one of the techniques that is
    used in practice to obtain the attenuation
    coefficients mi.
  • This technique can be used when intensity
    profiles that cover the total cross section under
    various angles are available.
  • In an individual profile, each point represents
    the amount of attenuation by the pixels
    transmitted by the beam.

124
  • Figure 9.9 shows the intensity profiles that
    result from a single attenuating pixel. Each
    profile shows a dip at the location where the
    beam passed through this pixel.

125
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126
  • Upper left, density distribution of a point
    absorber along a line through the object lower
    left, the resulting intensity profiles lower
    right, the back-projection upper right,
    reconstructed density distribution on a line
    through the object (after Philips).

127
  • If we have only one intensity profile we cannot
    determine where on the path the pixel was
    located. We cannot even decide whether the
    absorption was due to a single pixel or was due
    to an attenuating medium that was present over
    the whole path.
  • The only inference that we can make is that the
    attenuating medium was present only along one
    line in the cross section, since the intensity
    profile showed a dip at only one point.

128
  • The back-projection method starts with the
    assumption that the absorbing medium is uniformly
    distributed over the line. Of course, this may be
    incorrect, but it will be demonstrated that the
    errors resulting from this assumption can be
    corrected.
  • If we have several intensity profiles obtained at
    different angles, we get a reconstructed image,
    as shown in Fig. 9.9.
  • The reconstruction has a star-like distribution.
    By increasing the number of angles, the intensity
    in the center will increase much faster than the
    intensity at the periphery.

129
  • With the use of more angles, the back-projected
    image becomes more similar to the actual one,
    only it is less sharp instead of an image
    showing one attenuating pixel, the neighboring
    pixels are visible in the reconstructed image as
    well.
  • This blurring effect can be corrected to a
    certain extent by using appropriate filtering
    techniques, resulting in a sharper image.

130
  • Since a real cross section can be considered a
    union of cross sections, with each one containing
    only one attenuating pixel, the back-projection
    technique can also be applied to real patient
    cross sections.
  • The back-projection technique can also be used in
    MRI (magnetic resonance imaging) and SPECT
    (single photon emission computed tomography).

131
  • It appears that the attenuation coefficient is
    characteristic for the type of tissue (or more
    correctly, the chemical composition of the
    tissue), as is apparent from Fig. 9.10.
  • When the values of the attenuation coefficients
    of the pixels are displayed on a monitor in the
    form of grey values, the result consists of
    anatomical images that can be directly
    interpreted.

132
Attenuation coefficients of several tissues
expressed in Hounsfield units.
133
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134
Medical image modeling tools and applications
135
Hepatic surgery simulation
  • Creating a simulator for training physicians to
    perform minimally invasive surgical procedures

136
Figure 1a. The different generations of surgical
simulators.
137
Figure 1b. The different technological components
of a second-generation simulator.
138
Figure 2. Extraction of the hepatic parenchyma ??
(parts a and b), the vascular trees and hepatic
lesions (parts c and d) from a CT scan image.
139
Figure 3a. Liver deformation using a linear
combination of precomputed elementary
deformations.
140
Figure 3b. Sequence of a simulated liver
resection that includes the clipping and cutting
of the portal vein.
141
Virtual colonoscopy
142
Figure 1. A user interface for the virtual
colonoscopy system (courtesy of Viatronix, Inc.).
143
Figure 2. Endoscopic view of painted information
after an antegrade flythrough (left) and an
example of a missed patch after both antegrade
and retrograde flythroughs (right). The green
areas were visualized, while the reddish areas
were missed.
144
Figure 3. A volume-rendered surface view (left)
and an electronic biopsy (right) of a polyp.
145
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146
Volumetric Heart Modeling and Analysis
147
SPAMM SPAtial Modulation of Magnetization
  • A magnetically tagged MRI technique
  • Advantage a number of material points within the
    myocardium walls can be marked noninvasively and
    tracked, providing the true 3D motion of the
    heart muscle over time.

148
Figure 1. The essential data needed (boundaries
and tag lines) from each MRI-SPAMM short-axis
image (left) End-diastole short-axis view
(right) Mid-contraction short-axis view.
149
Figure 2. Sample results from the automated
boundary detection algorithm for the LV and RV
and inflow and outflow tracts of the RV.
150
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151
  • Figure 3. The top row shows the estimation of the
    LV-RV endocardium ??? and the epicardium ??? on
    the MRI-tagged slices for a normal heart.
  • The second row shows a normal and an abnormal
    heart at end-diastole ???? .
  • The RV endocardium of the RV hypertrophy ??
    patient is significantly larger than that of
    normal heart
  • (a) Normal heart
  • (b) RV hypertrophy heart.
  • The third row shows the heart model's motion
    during systole ????.
  • Finally, the fourth row shows a finite element
    model of the ventricles?? derived from MRI, with
    local fiber angles (blue) derived from in vitro
    ???? data superimposed at corresponding locations
    in (left) subendocardium and (right)
    subepicardium.

152
Incorporating 3D Virtual Anatomy into the Medical
Curriculum
153
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154
  • Figure 1. a) Automated segmentation of temporalis
    muscle (1) color VH Male slice, (2) a fuzzy
    connected component, (35) iterations of the
    VD-based algorithm, (6) an outline of the
    boundary
  • b) 3D segmentation of the left kidney (1) input
    data, (2) fuzzy connectedness, (3, 4) VD
    classification (5) deformable model, (6) hand
    segmentation.
  • c) 3D segmented and visualized left kidney
    derived from the Visible Human Male data set3D
    models of (1) fuzzy connectedness, (2) Voronoi
    Diagram classification, (3) deformable model, (4)
    hand segmentation.

155
Figure 2. Foot anatomy a) flexor muscles
(oblique ?? view), b) all the structures (oblique
view), c) a "reference" 3D model (plantar view),
d) corresponding medical illustration based on
the model in c).
156
Figure 3. Issues in biomedical imaging
informatics.
157
Open source software for Medical Image Processing
and Visualization
158
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159
  • Figure. Examples of medical image segmentation
    and registration algorithms available in ITK
  • a) Functional MRI fused with MR angiography using
    landmark initialized mutual information
    registration (courtesy of UNC)
  • b) 2D to 3D registration of angiography data
    (courtesy of the Imperial College of London)
  • c) Inner-ear segmentation of the cochlea ?? and
    vestibular (??)??? system using fast-marching
    level-set methods (courtesy of Kitware)
  • d) Eyes, muscles, and optic nerves of the Visible
    Human Project data using interactive color
    watershed segmentation (courtesy of the
    University of Utah).

160
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161
The Visible Humans Project
  • The goal of the Visible Humans project, sponsored
    by the U.S. National Library of Medicine, is to
    provide image data sets of the human body for use
    in the study of anatomy, for use in conducting
    imaging research, and for use in a wide range of
    educational, diagnostic and treatment planning
    and simulation applications.

162
The Visible Humans Project
  • The first phase of the project has resulted in
    CT, MRI, and cryosection image sets for a human
    male and a human female.
  • The complete male data set consisting of scans
    taken at 1 mm resolution is 15 gigabytes in size.
  • The complete female data set consists of scans
    taken at 0.33 mm intervals and is 40 gigabytes in
    size.
  • Both datasets may be downloaded over the Internet
    by interested individuals for research and
    experimentation.

163
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164
  • Reconstruction of a sagittal cross section and a
    few horizontal cross sections through one of the
    visible humans

165
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166
  • Example of 3-D presentation of the chest after
    boundary detection, labeling, shadowing and
    coloring of organs

167
Volume rendering
  • The process of creating a 2D image directly from
    the 3D volumetric dataset of voxels.
  • Voxel Short for volume pixel, the smallest
    distinguishable box-shaped part of a
    three-dimensional image.

168
Reference
  • Communications of the ACM, February 2005, Vol.
    48, No. 2.

169
DICOM
170
Application data flow diagram
171
  • The Storage Application Entity sends images and
    Presentation States to a remote AE.
  • It is associated with the local real-world
    activity Send Images GSPS.
  • Send Images GSPS is performed upon user
    request for each study completed or for specific
    images selected.
  • When activated by users settings (auto-send),
    each marked set of images and associated
    Presentation States can be immediately stored to
    a preferred destination whenever a Patient/Study
    is closed by the user.

172
  • If the remote AE is configured as an archive
    device the Storage AE will request Storage
    Commitment and if a commitment is successfully
    obtained will record this information in the
    local database.

173
SEQUENCING CONSTRAINTS
174
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175
SEQUENCING OF ACTIVITY SEND IMAGES
176
Service-Object Pair (SOP) Class
177
SEQUENCING OF ACTIVITY ACQUIRE IMAGES
178
  • 1. The Worklist AE opens an association with the
    Departmental Scheduler
  • 2. The Worklist AE sends an N-CREATE request to
    the Departmental Scheduler to create an MPPS
    instance with status of IN PROGRESS and create
    all necessary attributes. The Departmental
    Scheduler acknowledges the MPPS creation with an
    N-CREATE response (status success).
  • 3. The Worklist AE closes the association with
    the Departmental Scheduler.
  • 4. All images are acquired and stored in the
    local database.

179
  • 5. The Worklist AE opens an association with the
    Departmental Scheduler.
  • 6. The Worklist AE sends an N-SET request to the
    Departmental Scheduler to update the MPPS
    instance with status of COMPLETED and set all
    necessary attributes. The Departmental Scheduler
    acknowledges the MPPS update with an N-SET
    response (status success).
  • 7. The Worklist AE closes the association with
    the Departmental Scheduler.

180
SEQUENCING OF ACTIVITY FILM IMAGES
181
  • 1. Hardcopy AE opens an association with the
    Printer
  • 2. N-GET on the Printer SOP Class is used to
    obtain current printer status information. If
    the Printer reports a status of FAILURE, the
    print-job is switched to a failed state and the
    user informed.
  • 3. N-CREATE on the Film Session SOP Class creates
    a Film Session.
  • 4. N-CREATE on the Presentation LUT SOP Class
    creates a Presentation LUT (if supported by the
    printer).

182
  • 5. N-CREATE on the Film Box SOP Class creates a
    Film Box linked to the Film Session. A single
    Image Box will be created as the result of this
    operation (Hardcopy AE only uses the format
    STANDARD\1,1)
  • 6. N-SET on the Image Box SOP Class transfers the
    contents of the film sheet to the printer. If
    the printer does not support the Presentation LUT
    SOP Class, the image data will be passed through
    a printer-specific correction LUT before being
    sent.
  • 7. N-ACTION on the Film Box SOP Class instructs
    the printer to print the Film Box
  • 8. The printer prints the requested number of
    film sheets

183
  • 9. The Printer asynchronously reports its status
    via N-EVENT-REPORT notification (Printer SOP
    Class). The printer can send this message at any
    time. Hardcopy AE does not require the
    N-EVENT-REPORT to be sent. Hardcopy AE is
    capable of receiving an N-EVENT-REPORT
    notification at any time during an association.
    If the Printer reports a status of FAILURE, the
    print-job is switched to a failed state and the
    user informed.
  • 10. N-DELETE on the Film Session SOP Class
    deletes the complete Film Session SOP Instance
    hierarchy.
  • 11. Hardcopy AE closes the association with the
    Printer

184
Network interfaces
  • Physical network interface
  • Ethernet 100baseT
  • Ethernet 10baseT

185
  • DICOMSRV DICOM MWL and MPPS application
  • MWL Modality Worklist
  • MPPS Modality Performed Procedure Step

186
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187
  • DICOMSRV accepts associations for Verification
    from Verification SCUs and responds automatically
    with Success status
  • DICOMSRV accepts Association Requests for
    Modality Worklist from MWL SCUs and responds to
    queries from these SCUs. When a query is received
    DICOMSRV engages in local real-world activity
    Scheduled Procedure Queries. This results in a
    set of matching responses that DICOMSRV returns
    to the MWL SCU.

188
  • DICOMSRV accepts Association Requests for
    Modality Performed Procedure Step from MPPS SCUs
    and responds to N-CREATE and N-SET Requests from
    these SCUs. When an N-CREATE or N-SET is received
    DICOMSRV engages in local real-world activity
    Update Procedure. This results in updates to the
    DICOMRis Database per the contents of the
    received message. DICOMSRV then returns N-SET or
    N-CREATE status to the MPPS SCU.

189
  • SCU Service Class User
  • SCP Service Class Provider
  • SOP DICOM Service-Object Pair
  • GSDF Grayscale Standard Display Function
  • IOD Information Object Definition
  • LUT Look-up Table
  • UID Unique Identifier

190
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191
  • 1. The Modality queries for a worklist of
    Scheduled Procedure Steps
  • 2. DICOMSRV searches its database and returns
    matches to the query
  • 3. The Modality begins performance of a Procedure
    Step and sends the MPPS N-CREATE
  • 4. The Modality completes or discontinues the
    procedure and sends the MPPS N-SET with status of
    COMPLETED or DISCONTINUED

192
SEQUENCING DIAGRAM FOR ACTIVITY CONFIGURED AE
REQUESTS MWL QUERY
193
  • 1. The Modality opens an Association with
    DICOMSRV for the purpose of querying for a
    Modality Worklist
  • 2. The Modality sends an MWL C-FIND query to
    DICOMSRV
  • 3. DICOMSRV queries its database using the
    attributes from the C-FIND Request and returns 0
    to N C-FIND responses depending on matches
    returned from the database. DICOMSRV checks for a
    C-FIND Cancel Request after a configured number
    of responses are sent. If a Cancel is received
    then no further Pending responses are sent.
  • 4. DICOMSRV sends the final C-FIND response
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