sr workshop intro slide 1 sr workshop copyright otech inc. 2000 all rights reserved dicom explained...
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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.
NEMA workshop, Washington DC
March 29-30, 2000
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SR Workshop
Copyright OTech Inc. 2000 all rights reserved
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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SR Workshop
Copyright OTech Inc. 2000 all rights reserved
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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SR Workshop
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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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SR Workshop
Copyright OTech Inc. 2000 all rights reserved
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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SR Workshop
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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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SR Workshop
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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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SR Workshop
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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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SR Workshop
Copyright OTech Inc. 2000 all rights reserved
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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SR Workshop
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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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Copyright OTech Inc. 2000 all rights reserved
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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Copyright OTech Inc. 2000 all rights reserved
Human language is not exact, many variations are possible:
e.g. Exam type is:ChestThoraxChest PA/LATchest
Codes, Why?:
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SR Workshop
Copyright OTech Inc. 2000 all rights reserved
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
Query/Retrieve
Verification
Storage Commit
DICOM Services:
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SR Workshop
Copyright OTech Inc. 2000 all rights reserved
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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SR Workshop
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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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SR Workshop
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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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SR Workshop
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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