DICOM Structure

Introduction to

shijupk@gmail.com

History• 1985-1988 :

• Joint effort between Radiologist and Manufacturers to specify ACR-NEMA 1.0 and 2.0• ACR : American College of Radiology• NEMA : National Electrical Manufacturer Association

• 1993 :• 9 parts of DICOM (3.0)

• 2007 :• 18 parts of DICOM - 126 Supplements

• DICOM is developed under joint efforts of• ACR (American College of Radiology) • NEMA (National Electrical Manufacturers Assoc.) …… also more than 25 vendors…

IntroductionDigital Imaging and COmmunication in Medicine

is a standard for handling, storing, printing, and transmitting information in medical imaging. It includes a file format definition and a network communications protocol. The communication protocol is an application protocol that uses TCP/IP to communicate between systems. DICOM files can be exchanged between two entities that are capable of receiving image and patient data in DICOM format. 

DICOM File Format

DICOM File Meta Info

DICOM Dataset

File Preamble

PrefixData ElementData ElementData ElementData Element

Data Element

***

128 Bytes (Set to 00H by default)DICMAttribute Name Tag Typ

eGroup Length (0002,

0000)1

File Meta Info Version (0002, 0001)

1

Media Storage SOP Class UID (0002, 0002)

1

Media Storage SOP Instance (0002, 0003)

1

Transfer Syntax UID (0002, 0010)

1

Implementation Class UID (0002, 0012)

1

Implementation Version Name (0002, 0013)

3

Source Application Entity Title (0002, 0016)

3

Private Info Creator UID (0002, 0100)

3

Private Info (0002, 00102)

1C

Group 0002H elements are always encoded in Explicit VR Little Endian

DICOM File Format

Data ElementData ElementData ElementData Element

Data Element

***

PrefixPreamble

Explicit V R other than above

Element Number

Group Number

Value Length Value Field

2 bytes2 bytes 4bytes Value Length bytes

Implicit V R

Element Number

Group Number

Value Representat

ionValue

Length Value Field

2 bytes2 bytes 2 bytes 2 bytes Value Length bytes

Explicit V R of OB, OW, OF, OD, SQ, UC, UR, UT or UNElement Number

Group Number

Value Representat

ionValue Field

2 bytes2 bytes 2 bytes Value Length bytes

Reserved

2 bytes

Value Length4 bytes

Value Representation (V R)• Clinical data comes in a wide variety of formats.

• Ex. Distances measured in millimeters, time in seconds, • patient names are typically written in alphabetic characters,

and so on. • The DICOM standard defines 27 basic data types, known as

value representations (VRs), • which are designed to encapsulate all possible clinical data

types. • Each VR has its own abbreviated two-letter name, a definition

of what it represents, a description of what characters are allowed in its data, and a pre-scribed data length.

Value Representation•Free Form Text VR:• SH: Short String• LO: Long String• ST: Short Text• LT: Long Text• UT: Unlimited Text

•Math VR:• IS: Integer String• DS: Decimal String• US: Unsigned Short• SS: Signed Short• UL: Unsigned Long• SL: Signed Long• FL: Floating Point Single• FD: Floating Point Double

• Fixed Format VR:• DA: Date• TM: Time• DT: DateTime• PN: Person Name

• Other VR:• OB: Other Byte• OW: Other Word• OF: Other Float • SQ: Sequence• AE: Application Entity• AS: Age String• AT: Attribute Tag

• Other VR•CS: Code String•UI: Unique Identifier•UN: Unknown

Unique IDentifier• UIDs are internal DICOM mechanism to identify

Studies, Series, Images, SOP classes, etc.• A UID is a string up to 64 characters including digits

and “.”• example SOP Instance UID 1.2.840.113619.2.65.3.200583648570.2428.1178103577.1

• No Leading zeroes in UID components are not allowed.• This string is MUST be UNIQUE around the world.

Transfer Syntax• A transfer syntax is the encoding methodology used to

send data over network, or to write data to a physical medium. 01001000

01100101 01101100 01101100 01101111 00100000 01000100 01001001 01000011 01001111 01001101 00001010

Hello DICOM

Transfer Syntax• Big Endian

• Store the most significant byte in the smallest address• Little Endian

• store the least significant byte in the smallest address

Address Value

1000 901001 AB1002 121003 cd

Address Value

1000 CD1001 121002 AB1003 90

Transfer SyntaxTransfer Syntax UID Transfer Syntax Name

1.2.840.10008.1.2 Implicit VR Endian: Default Transfer Syntax for DICOM1.2.840.10008.1.2.1 Explicit VR Little Endian1.2.840.10008.1.2.1.99 Deflated Explicit VR Little Endian1.2.840.10008.1.2.2 Explicit VR Big Endian

Transfer Syntax UID Transfer Syntax Name1.2.840.10008.1.2.4.50 JPEG Baseline (Process 1):

Default Transfer Syntax for Lossy JPEG 8-bit Image Compression1.2.840.10008.1.2.4.51 JPEG Baseline (Processes 2 & 4):

Default Transfer Syntax for Lossy JPEG 12-bit Image Compression1.2.840.10008.1.2.4.57 JPEG Lossless, Nonhierarchical (Processes 14)1.2.840.10008.1.2.4.70 JPEG Lossless, Nonhierarchical, First- Order Prediction

Default Transfer Syntax for Lossless JPEG Image Compression1.2.840.10008.1.2.4.80 JPEG-LS Lossless Image Compression1.2.840.10008.1.2.4.81 JPEG-LS Lossy (Near- Lossless) Image Compression1.2.840.10008.1.2.4.90 JPEG 2000 Image Compression (Lossless Only)1.2.840.10008.1.2.4.91 JPEG 2000 Image Compression1.2.840.10008.1.2.4.92 JPEG 2000 Part 2 Multicomponent Image Compression (Lossless Only)1.2.840.10008.1.2.4.93 JPEG 2000 Part 2 Multicomponent Image Compression1.2.840.10008.1.2.5 RLE Lossless1.2.840.10008.1.2.4.94 JPIP Referenced1.2.840.10008.1.2.4.95 JPIP Referenced Deflate1.2.840.10008.1.2.6.1 RFC 2557 MIME Encapsulation1.2.840.10008.1.2.4.100 MPEG2 Main Profile Main Level1.2.840.10008.1.2.4.103 MPEG-4 AVC/H.264 BD-compatible High Profile / Level 4.11.2.840.10008.1.2.4.102 MPEG-4 AVC/H.264 High Profile / Level 4.1

SOP Class UIDSOP Instance UID

Patient NamePatient IDPatient Birth DatePatient SexStudy UIDStudy DateStudy IDReferring PhysicianAccession NumberSeries UIDSeries NumberModality TypeManufacturerInstitution Name

Image UIDImage NumberImage TypeImage Pixel AttributesWindow width Window Center

Patient

Study

Series Series Series

ImageImageImageImageImageImage

ImageImageImage

Other Studies

Information Object Definition

Patient EntityStudy EntitySeries EntityImage Entity

General Image

AttributesImage Pixel Attributes

Samples per PixelPhotometric Interpretation

RowsColumns

Bits AllocatedBits Stored

Pixel RepresentationPixel Data

Planar Configuration

Image DisplaySamples per Pixel

Photometric InterpretationRows

ColumnsBits Allocated

Bits Stored

Pixel RepresentationPixel Data

Planar Configuration

Un used

Bits AllocatedPixel Cell

High Bit

High Bit

Un used Pixel Cell Un

used Pixel Cell

Pixel Data Stream

Pixel Sample0111215

Bits Allocated = 16Bits Stored = 12High bit = 11

Image DisplayPixel Cell

Pixel sample value

Pixel sample value

Pixel sample value

Pixel sample value

Pixel sample value

Pixel sample value

….. …. …. …..

…. …. …. … ……. …. …. ……. …. …. … ……. …. …. … …

Rows

Columns

Image displayPixel data Apply LUT Render

Window Width / Window Centerwhere x is the input value, y is an output value with a range from y min to y max 

c is Window Center (0028,1050) and w is Window Width (0028,1051):

If (x <= c - 0.5 - (w-1)/2), then y = y minelse if (x > c - 0.5 + (w-1)/2), then y = y max ,else y = ((x - (c - 0.5)) / (w-1) + 0.5) * (y max - y min )+ y min

VOILUT FunctionSIGMOID DescriptorIf the value of VOI LUT Function (0028,1056) is SIGMOID, the function to be used to convert the output of the (conceptual) Modality LUT values to the input of the (conceptual) Presentation LUT is given byOUT =whereIN is the input value of the LUT (i.e., the output of the (conceptual) Modality LUT).WC (resp. WW) is the Window Center (resp. Window Width) defined interactively by the useror by using the values provided in (0028,1050) (resp. 0028,1051).Output_range is the maximum output value

Questions are the answers!