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Medical Image File Formats

Medical Image File Formats. Justin Senseney, DCB/CIT/NIH http://mipav.cit.nih.gov http ://dcb.cit.nih.gov/~senseneyj. Overview. Part 1 – Basics Data Image Part 2 – Medical File Formats Practical: See underlying data Part 3 – General File Formats

chandler-nelson
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Medical Image File Formats

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  1. Medical Image File Formats Justin Senseney, DCB/CIT/NIH http://mipav.cit.nih.gov http://dcb.cit.nih.gov/~senseneyj

  2. Overview • Part 1 – Basics • Data • Image • Part 2 – Medical File Formats • Practical: See underlying data • Part 3 – General File Formats • Part 4 – All together and everything else • Practical: Use file formats

  3. Imaging – Why? • NIH has 27 institutes and centers • 14 are here • http://www.idoimaging.com/index.shtml

  4. Imaging – How? • Data communication • Standards

  5. Part 1.A – Data Basics • Bits vs Bytes • Endianess • Sign • Compression • Data types

  6. Bits vs Bytes • Bit – a number system • Byte – a language

  7. Bits vs Bytes binary CT image with HU = 213 at position (4,9) Byte = 8 bits: D5

  8. Sign • 2’s complement • Unsigned 213 = -43 signed, just fat • Recognize sign bits • Offset scaling • Discrete to decimal • Common in dicom

  9. Endianness • Big Endian – most sig. = lowest address • In DICOM: Film destination • Little Endian - least sig. = lowest address • In DICOM: Image comments

  10. Compression • RLE – run length • LZW - dictionary • Huffman – variable length • DCT - discrete cosine transform • lossy

  11. Data Types • Boolean – 1 bit • Byte – 1 byte • Short – 2 bytes • Dicom • Int – 4 bytes • Long – 8 bytes

  12. Data Types (2) • Decimal – IEEE standard • Float – 4 bytes • Double – 8 bytes

  13. Raw Data Demo • Hex Editor NEO

  14. Part 1.B – Image Basics • Resolution • Dimensions/Extents • Color • Orientation • Origin • Transformations • Encoding

  15. Resolution • Level of detail • Width of dimension unit • Computing area, volume • Time in seconds

  16. Dimensions/Extents • 3D • As stacks • 4D • Multi-file • Complex • Multi-channel

  17. Color • Channels • RGB or HSV • CMYK • N-bit color is 2^n possible colors

  18. Orientation • Axial/Transverse • Sagittal • Coronal

  19. Origin • In n-dimensions • Scanner space vs image space

  20. Transformations • Image space to scanner space • Dicom • NIfTI

  21. Encoding • Encapsulating image • JPEG compression in DICOM, Tiff • Embedding image • Thumbnail image

  22. Header • Text based • Binary • XML

  23. Header Demo BrukerBioSpin format

  24. Part 2 – Medical File Formats • XML • DICOM • NIfTI

  25. XML - Basic • Instance is .xml file • Schema is .xsd file

  26. XML - Basic

  27. DICOM • NEMA standard • ftp://medical.nema.org/medical/dicom/2011/ • Header • Communication • Storage

  28. Dicom - Tags • Chapter 6 • Group – 2 bytes • Element – 2 bytes • Public vs private

  29. Dicom – Tag values • Chapter 5 • Value representation (VR) • Little endian, explicit VR default

  30. Dicom – Tag construction From 2011 standard • VR can be implicit for public tags

  31. Dicomv.3.0 - Standard • Chapter 3 From 2011 standard

  32. Dicom properties • Dimensions • (0028,0010)and (0028,0011) • Image • (7FE0, 0010) • Transfer syntax • (0002, 0010)

  33. Dicom – Pixel map • (0028, 1052) is slope • (0028, 1053) is intercept • Y (true value) = ax+b for x short

  34. DICOM Mosaic • Matrix of image slices: • Concatenate into 3D/4D volume • Calculate relevant DICOM tags

  35. Dicom Demo

  36. NIfTI • Standard for ANALYZE by NIMH • See : http://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h

  37. NIfTI - Data • Allows complex data, 64 bit integer • Provides patient-space coordinates

  38. NIfTI - Orientation • +x = right • +y = anterior • +z = superior • Is default, but in Analyze 7.5, +x = left

  39. NIfTI – q_form, s_form • Matrix of offsets • Codes for orientation

  40. NIfTI Demo

  41. Part 3 – Image File Formats • Vector Images • Graphics/Bitmap Images

  42. Vector Images • CAD applications • Lines/ROI/VOI

  43. Graphics Images • GIF • TIFF • BMP • PNG • JPEG

  44. GIF • LZW • Small (8 bit) color range • Little endian • Sequence of 2D possible

  45. TIFF • RLE, JPEG • Larger color range (to 24 bit) • Microscopy • Image File Directory

  46. BMP • RLE • Up to 32-bit

  47. PNG • 48 bit color range (outside of vision) • Best for large, lossless compression

  48. JPEG • DCT (lossy), Huffman • Down-sampling • Markers

  49. General Image Demo • ImageJ + batteriesn=Fiji

  50. Part 4 – All together • Afni • BrukerBioSpin • GESigna • LSM • Minc • MATLAB • Parrec • Raw

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