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PET DICOM Format

PET DICOM Format. Chunlei Han Turku PET Centre Sep. 14, 2005, Turku, Finland. Content. 1. General Introduction 1.1 Short History 1.2 Overview 1.3 Documentation 2. Encoding 2.1 Attribute Structure 2.2 Group and Element 2.3 Value Represention and Value Length 2.4 Value Field

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PET DICOM Format

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  1. PET DICOM Format Chunlei Han Turku PET Centre Sep. 14, 2005, Turku, Finland

  2. Content • 1. General Introduction • 1.1 Short History • 1.2 Overview • 1.3 Documentation • 2. Encoding • 2.1 Attribute Structure • 2.2 Group and Element • 2.3 Value Represention and Value Length • 2.4 Value Field • 2.5 Encoding Rule • 3. My Plan on DICOM

  3. 1.1 Short History of DICOM • 1970, first CT(computerised tomography) was introduced. Digital medical imaging format emerged. • 1985, ACR-NEMA standard was published. • 1993, DICOM standard was published and is continuously being extended ever since • In 1995, DICOM was accepted as a formal standard in Europe (MEDICOM, ENV 12052). ACR:American Colleg of Radiology NEMA: National Electrical Manufacturers Association DICOM: Digital Imaging and COmmunications in Medicine

  4. 1.2 Overview of DICOM DICOM provides • Data structure for medical images and related data • Network oriented services: image transmission, query of an image archive, pring, modality integration • formats for storage media exchange. • It is widely accepted as a standard in medical imaging technics. • It has become an indispensable component for the integration of digital medical imaging systems • It covers almost all the medical imaging devices: such as CT, Ultrosound, X-ray (conventionel, angiographical, dental ect), MRI, PET and even Non-imaging data, such ECG, cardiac electrophysiology and hemodynamic information.

  5. 1.3 DICOM Standard Documentation • DICOM Part 1: Introduction and Overview • DICOM Part 2: Conformance • DICOM Part 3: Information Object Definitions • DICOM Part 4: Service Class Specifications • DICOM Part 5: Data Structures and Encoding • DICOM Part 6: Data Dictionary • DICOM Part 7: Message Exchange • DICOM Part 8: Network Communication Support for Message Exchange • DICOM Part 10: Media Storage and File Format for Media Interchange • DICOM Part 11: Media Storage Application Profiles • DICOM Part 12: Media Formats and Physical Media for Media Interchange • DICOM Part 14: Grayscale Standard Display Function • DICOM Part 15: Security and System Management Profiles • DICOM Part 16: Content Mapping Resource • DICOM Part 17: Explanatory Information • DICOM Part 18: Web Access to DICOM Persistent Objects (WADO) http://medical.nema.org/

  6. 2.1 Attribute Structure 128 bytes 4 bytes (four characters: ”DICM”) Data Set Element Tag 4 bytes VR 2/4 bytes ValueLength (VL) 2/4 bytes Value Field (VF) defined by VL optional field - dependent on negotiated Transfer Syntax Data Element Tag: 4 bytes, hexadecimal, group (2 bytes), elements(2 bytes) Value Represention (VR): optional, 2 or 4 bytes, character, depends on transfer syntax Value Length (VL): 2or 4 bytes, long integer, defines value field length, dependent on VR Value Field (VF): length is defined by VL, format is defined explicitly by VR or implicitly.

  7. 2.2 Group and Element Tag 4 bytes VR 2/4 bytes ValueLength (VL) 2/4 bytes Value Field (VF) defined by VL group number 2 bytes element number 2 bytes • Two parts:group (2 bytes) and element (2 bytes), 16-bit unsigned integer, hexadecimal • Even number groups (such as 0002, 0008) are called public, definitions are same for all DICOM • Odd number groups (such as 0009) are called private, defined by user, but must follow DICOM standard • Currently defined public groups 0002, 0004,0008, 0010, 0012, 0018, 0020, 0022, 0028, 0032, 0038, 003A,0040,0050,0054,0060,0070,0088,0100,0400,2000,2010,2020,2030,2040,2050,2100,2110,2120,2130,2200, 3002,3004,3006, 3008, 300A, 300C,300E,4000,4008,4FFE,50xx, 5200, 5400, 60xx,7FE0,FFFA,FFFC,FFFE • Private group examples: GE Discovery conformance defines 0009, 0011, 0013 groups. • Special groups • 0002 is registry of DICOM file meta elements • 0004 is registry of DCOM directory structing elements • Special element • gggg 0000 defines group length in bytes for all group.

  8. 2. 3. Value Representation and Value Length Defined VR: • AE: application entiy • AS: age string • AT: attribute tag • CS: code string • DA: date • DS: decimal string • DT: date time • FL: floating point single • FD: floating point double • IS: integer string • LO: long string • LT: long text • OB: other byte string • OF: other float string • OW: owther word string • PN: person name • SH: short string • SL: signed long • SQ: sequence of items • SS: signed short • ST: short text • TM: time • UI: unique identifier • UL: unsigned long • UN: unknown • US: unsigned short • UT: unlimited text VR 2/4 bytes ValueLength (VL) 2/4 bytes Value Field (VF) defined by VL Tag 4 bytes A, Explicit VR with reserved. VR is OB, OW, OF, WQ UT or UN reserved bytes=00000000H VR 2 byte Reseved 2 byte VL 4 bytes B, Explicit VR without reserved, VR is others. VL 2 bytes VR 2 byte B, Implicit VR (No VR !! ), therefore data set element becomes as Tag 4 bytes ValueLength (VL) 4 bytes Value Field (VF) defined by VL

  9. 2.4 Value Field and Others Value Field (VF) defined by VL VR 2/4 bytes ValueLength (VL) 4 bytes Tag 4 bytes Value Field • Length is defined by VL. • Content format is defined by VR or implicitly. (0002), (0010) is transfer syntax UID • 1.2.840.10008.1.2: implicit VR with little endian • 1.2.840.10008.1.2.1: explicit VR with little endian • 1.2.840.10008.1.2.2: explicit VR with big endian Pixel data is (7FE0), (0010)

  10. 2.5 Encoding Rules • Skip first 128 bytes for preamble • Skip 4 byts for ”DICM” • Start to read group and element number • first part is always group 0002 • find (0002), (0010), if transfer syntax UID is 1.2.840.10008.1.2: implict VR with little endian, No VR!!, VL is 4 bytes, little endian ValueLength (VL) 4 bytes Value Field (VF) defined by VL Tag 4 bytes 1.2.840.10008.1.2.1/1.2.840.10008.1.2.2: explict VR with little/big endian if VR is OB, OW, OF, WQ UT or UN: No VR!!, VR 2 bytes, reserved is 2 with 00000000H, VL is 4 bytes, and little endian ValueLength (VL) 4 bytes Value Field (VF) defined by VL Tag 4 bytes VR 2 bytes reserved 2 bytes if VR is SQ: go to encode by rule of sequence if VR is, others: VR is 2 bytes and VL is also 2 bytes ValueLength (VL) 2 bytes Tag 4 bytes VR 2 bytes Value Field (VF) defined by VL

  11. 3. My Plane on DICOM • DICOMReader (finished) for general and specific modality, such as GE Advance PET, GET Discovery PETCT and Philips MRI • DICOM2ECAT7(almost finished) • PETCT Viewer(finished) • DICOMModifer, rename and anonymyous • DICOMWriter and ECAT7toDICOM • DICOM Viewer and ROI tookit

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