SR workshop Intro slide 1 SR Workshop Copyright OTech Inc. 2000 all rights reserved DICOM explained...

SR workshop Intro slide 1

SR Workshop

Copyright OTech Inc. 2000 all rights reserved

DICOM explained in the context of Structured Reporting

Herman Oosterwijk, OTech Inc.

[email protected]

NEMA workshop, Washington DC

March 29-30, 2000


SR Workshop


Objective:

• To get a basic understanding of DICOM services and objects in the context of Structured Reporting:• DICOM objects (IOD’s)• DICOM encoding: Data elements, VR,

sequences, Codes• DICOM exchange media


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Parts of the Standard:

1. Overview

2. Conformance

3. Information Objects

4. Services Class Specifications

5. Data Structures and Semantics

6. Data Dictionary

7. Message Exchange


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Parts of the Standard:

8. Network Support

9. Point to point

10. Media Storage and File format

11. Media Storage Application Profiles

12. Physical Media

13. Point to point Print mgt

14. Greyscale display function standard

xx. Supplements!!!


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Common Information Model Conformance claims to define functionality:

Matching is critical Roles: SCU/SCP Unique Identification of objects:

Each DICOM object is unique Documentation tools such as Macros

DICOM key parts:


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SOP Instance-------- C-Store Mrs. Smith SR

Key DICOM concept==SOP Class

(Service defn + Information Object Defn):

DIMSE -------------- C-Store

Service Elt.Info Object----------- SR Object

Defn (IOD)

SOP Class------------ C-Store SR


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Service ClassInformation Object

Definition(IOD)DIMSE Service

ElementsService Object Pair

(SOP) Class(=SOP Class)

IOD-->Module-->Attrib

C-StoreC-GetC-FindC-MoveC-Echo

N-CreateN-SetN-GetN-DeleteN-ActionN-Event-rep

DCM 3

DCM 7

DCM 4

Service Elements:

SVC Classes:

VerificationStorageStudy notf.Print MgtPatient MgtStudy MgtResults MgtStorage Commnt

Query/RetrieveBasicWlist Mgt

DCM 5,6

Relationship between:


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IOD Description; i.e. what is the real world object (Information Entities-IE) that is represented. Can be one or more IE’s (Composite, Normalized)

Examples:Image IOD: Patient, Study, Equipment,

Image ----> CompositePatient IOD: Patient info ---->Normalized

Information Object Definition (IOD):


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IOD Entity-Relationship model; provide the context (relationships) between the IE’s

Information Object Definition (IOD):

This information model is critical!

IOD Module table; which modules provide the attributes for the IOD

Modules are defined for “convenience reasons” (all patient info together, all image info together....)

Modules contain Attributes (Pat. name, etc.)


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Patient

Study

isthe subject

of

contains

spatiallydefines

creates

Equipment

ModalityLUT

VOI LUT

Frame of Reference

Image

Overlay

Curve

contains

Series

0,1 0,n

0,n0,n

0,n

1 1 11,n

0,n

1,n

1

1,n

1

StoredPrint

0,1

PresentationState

0,n

SRDocument

0,n

SR Information Model:


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IODs

ModulesBasic Text SR Enhanced SR Comprehensiv e

SR

Patient M M M

SpecimenIdentification

C C C

General Study M M M

Patient Study U U U

SR DocumentSeries

M M M

GeneralEquipment

M M M

SR DocumentGeneral

M M M

SR DocumentContent

M M M

SOP Common M M M


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Table A.35.1-1BASIC TEXT SR IOD MODULES

IE Module Reference Usage

Patient Patient C.7.1.1 M

Specimen Identification C.7.1.2 C - Required if the ObservationSubject is a Specimen

Study General Study C.7.2.1 M

Patient Study C.7.2.2 U

Series SR Document Series C.17.1 M

Equipment General Equipment C.7.5.1 M

Document SR Document General C.17.2 M

SR Document Content C.17.3 M

SOP Common C.12.1 M


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Table C.7.1.1 -- Patient Module AttributesAttribute Name Tag Type Attribute DescriptionPatient's Name (0010,0010) 2 Patient's full legal name.Patient ID (0010,0020) 2 Primary hospital

identification number orcode for the patient.

Patient's Birth Date (0010,0030) 2 Birth date of the patient.Patient's Sex (0010,0040) 2 Sex of the named patient.

Enumerated Values are:M = maleF = femaleO = other

Referenced PatientSequence

(0008,1120) 3 A sequence which providesreference to a Patient SOPClass/Instance pair. Only asingle reference is allowed.Encoded as sequence ofitems: (0008,1150) and(0008,1155)

Module Definition: Attribute Name, Tag, Type, Description


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Defined Terms:Can be extended (e.g. Modality: CT,MR,

ES, SR, etc.)Enumerated values:

No extensions, additions (e.g. Patient Sex: M, F, O)

Value of data elements can belong to a Set:

Value Multiplicity:More than one value, requires separator

(e.g. Other Patient Names)


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1: Required (e.g. pixel spacing)1C: Required when condition met (e.g.

pixel aspect ratio)2: Required, can be “0” if unknown (e.g.

Patient Name, Accession number)2C: Conditional (e.g. patient positioning)3: Optional (e.g. Other Patient Name)

Type Designation:


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Data Element Tag, Optional Value Representation, Length, Value Field

Tag VR Value

Length

Value Field

Data

Elem

Data

Elem

Data

ElemData

Elem

DICOM Part 5-6 Data set and structures:


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Tag: Identifies Attribute Value representation (VR): Groups similar

attributes for identification and definition purposes, e.g.:Patient name, Physician name, Other

Patient names, etc.: VR is “PN”Birth date, Exam date, etc.: VR is “DA” VR

syntaxes specified in part 5

Data set and structures (ctd):


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Implicit VR: Assumed based on tag Explicit VR: Explicitly specified

Note: VR is negotiated during association! Explicit VR: 0010,0010 PN 10 Smith^John

Implicit VR: 0010,0010 10 Smith^John

Data set and structures (ctd):


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Example of a DICOM Message:

SRTree

Depth

Nesting

Attribute Tag VR VL(hex)

Value

SOP Class UID (0008,0016) UI 001e 1.2.840.10008.5.1.4.1.1.88.33

SOP Instance UID (0008,0018) UI 0012 1.2.3.4.5.6.7.300

Study Date (0008,0020) DA 0008 19991029

Content Date (0008,0023) DA 0008 19991029

Study Time (0008,0030) TM 0006 154500

Content Time (0008,0033) TM 0006 154510

Accession Number (0008,0050) SH 0006 123456

Modality (0008,0060) CS 0002 SR

Manufacturer (0008,0070) LO 0004 WG6

Referring Physician's Name (0008,0090) PN 0014 Luke^Will^^Dr.^M.D.


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Sequences:

VR =“SQ” Sequence contains zero or more items, which

contains a set of Data Elements Used to encode repeating sets Accommodates multilevel nesting (recursion) Explicit length SQ: value of bytes in length

field Undefined length SQ: requires flag in length

field and SQ and item delimiters (sppt rqd)


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Document Root Node CONTAINER"Chest X-ray" (Document Title)

Has obs context

Content Node PNAME"Recording Observer =

Smith^John^^Dr^"* Relationship Modes = By-value = By-reference

contains

contains contains

inferred from

Content Node CODE"finding = mass"

Heading NodeCONTAINER"Conclusions"

Heading NodeCONTAINER "Specific

Image Findings"

Content Node CODE"conclusion = probable

malignancy"

Content node SCOORD"best illustration of

findings"

Leaf Node IMAGE "Baseline"

contains contains contains

Leaf Node NUM"diameter = 1.3 cm" margination infiltrative"

has properties

Leaf Node CODE" =

has properties

inferred from

Leaf Node IMAGE

selected from

Has obs context

Content Node UIDREF"Study Instance UID of

Evidence Directly Examinedby RO = 1.2.3.4.5.6.7.100"

Has obs context

Content Node PNAME"Patient-Data-Acquisition

Subject = Homer^Jane^^^"

has concept modLeaf Node CODE

"Views = PA and Lateral"SR Example:


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margination infiltrative"

has properties

Leaf Node CODE

SR Example:1.4.2 %item

1.4.2 >> Relationship Type (0040,a010) CS 000e HASPROPERTIES

1.4.2 >> Value Type (0040,a040) CS 0004 CODE

1.4.2 >> Concept Name Code Sequence (0040,a043) SQ ffffffff

1.4.2 %item

1.4.2 >>> Code Value (0008,0100) SH 0006 111000

1.4.2 >>> Coding Scheme Designator (0008,0102) SH 0008 SNMdemo

1.4.2 >>> Code Meaning (0008,0104) SH 000c Margination

1.4.2 %enditem

1.4.2 %endseq

1.4.2 >> Concept Code Sequence (0040,a168) SQ ffffffff

1.4.2 %item

1.4.2 >>> Code Value (0008,0100) SH 0006 222000

1.4.2 >>> Coding Scheme Designator (0008,0102) SH 0008 SNMdemo

1.4.2 >>> Code Meaning (0008,0104) SH 000c Infiltrative

1.4.2 %enditem

1.4.2 %endseq

1.4.2 %enditem


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SNOMED: Systematized Nomenclature for Human and Veterinary Medicine; maintained by College of American Pathologists (CAP); anatomic identifiers, observations, etc.Requires license fee

LOINC: Logical Observation Identifiers, Names and Codes (LOINC); measurementsNo license (free)

CPT, ICD9: Procedure Codes BI-RADS: Mammography 99SDM, SDM, DTMR

Codes:


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Human language is not exact, many variations are possible:

e.g. Exam type is:ChestThoraxChest PA/LATchest

Codes, Why?:


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From CAP, DUKE website, in supplements, eventually in new DICOM Supplement 53.

Encoding:Coding SchemeVersion #CodeMeaning

Optional Extended coding for context information

Codes, where, how to encode:


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Example from Digital X-Ray (DX) IOD:

Makes extensive use of Coded data entries using standard vocabulary:

Instead of specifying “sagittal” for View Code, one specifies:Code Value : R-112300Coding Scheme : SNOMEDScheme Version: Version 1.0Meaning : Sagittal


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MR

Information SystemModality Worklist Management

Performed Procedure Step

Storage

Print

Query/Retrieve

Verification

Storage Commit

DICOM Services:


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SCP level of conformance:Level 0 (local): user defined subset will be

stored onlyLevel 1 (base): Type 1 and 2 attributes will be

stored, others may be discarded. SCP is not required to validate the Attributes

Level 2 (full): Type 1,2,3 will be stored SCP is not required to validate Attributes

Patient ID, Study Instance UID and Series Instance UID may be coerced (negotiated)

Storage Service class (ctd):


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Why yet another way of encapsulating waveforms ?

Current mechanisms are proprietary; timing seems ripe for standardizationRelationship between images and waveforms is keyExisting Curve specification in DICOM was not sufficient

Waveforms:


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R-wave peak at 10:03.296)

10:03.4010:03.36

10:03.3210:03.28

10:03.2410:03.20

10:03.1610:03.12

10:03.0810:03.04

10:03.00

10:03.00 10:03.50

Multi-frame (cine)pixel data Waveform data

Waveforms: Relate Images


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DICOM Media Specifications:

DICOM Application Entity

Medical Imaging Application

OSI Upper layer svc boundary DICOM File svc boundary

50 pin OSI

TCP/IP

A B CMedia

Format

Media

Format

Media

Format

Phys.

Medium

Phys.

Medium

Phys.

Medium

DCM

Presn.


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DICOM Media Specifications (ctd):

DICOM Application Entity

Service / Object PairsBasic Dir.

DICOM File Format

Media Formats: e.g. File data structures

Physical Media: e.g. CD-R; 90 mm MOD, etc.

part

10

part

11

part

12


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DICOM SOP

Instance

DCM

File

Meta

Info

DICOM

Data

Set

DICOM SOP

Instance

DCM

File

Meta

Info

DICOM

Data

Set

FILE SET

SR workshop Intro slide 1 SR Workshop Copyright OTech Inc. 2000 all rights reserved DICOM explained...

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