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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 - PowerPoint PPT Presentation
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Medical Image File Formats
Justin Senseney, DCB/CIT/NIHhttp://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• Part 4 – All together and everything
else– Practical: Use file formats
2
Imaging – Why?• NIH has 27 institutes and centers
– 14 are here• http://
www.idoimaging.com/index.shtml
3
Bits vs BytesBits 1 1 0 1 0 1 0 1
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Decimal Binary bits Hexadecimal
0 0000 0
1 0001 1
2 0010 2
3 0011 3
4 0100 4
5 0101 5
6 0110 6
7 0111 7
8 1000 8
9 1001 9
10 1010 A
11 1011 B
12 1100 C
13 1101 D
14 1110 E
15 1111 F
Byte = 8 bits:D5
CT image with HU = 213at position (4,9)
binary
Sign
• 2’s complement– Unsigned 213 = -43 signed, just fat
– Recognize sign bits
• Offset scaling– Discrete to decimal– Common in dicom
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Bits 1 1 0 1 0 1 0 1
Comp.
0 0 1 0 1 0 1 1
Sub 1 1 1 0 1 0 1 0 0
Endianness
• Big Endian – most sig. = lowest address
– In DICOM: Film destination
• Little Endian - least sig. = lowest address
– In DICOM: Image comments 9
Little (0020, 4000)
Big (2000, 0040)
Address
0 1 2 3
Bytes 20 00 00 40
Compression
• RLE – run length
• LZW - dictionary
• Huffman – variable length
• DCT - discrete cosine transform– lossy
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Data Types• Boolean – 1 bit
• Byte – 1 byte
• Short – 2 bytes– Dicom
• Int – 4 bytes
• Long – 8 bytes11
Part 1.B – Image Basics
• Resolution• Dimensions/Extents• Color• Orientation• Origin• Transformations• Encoding
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Encoding
• Encapsulating image – JPEG compression in DICOM, Tiff
• Embedding image– Thumbnail image
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DICOM
• NEMA standard– ftp://medical.nema.org/medical/dicom/2
011/
• Header– Communication– Storage
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Dicom properties
• Dimensions– (0028,0010) and (0028,0011)
• Image– (7FE0, 0010)
• Transfer syntax– (0002, 0010)
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Dicom – Pixel map
• (0028, 1052) is slope• (0028, 1053) is intercept
• Y (true value) = ax+b for x short
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DICOM Mosaic
• Matrix of image slices:
– Concatenate into 3D/4D volume
– Calculate relevant DICOM tags
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NIfTI
• Standard for ANALYZE by NIMH
• See : http://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h
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NIfTI - Orientation
• +x = right
• +y = anterior
• +z = superior
• Is default, but in Analyze 7.5, +x = left
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Afni
• Needed to use AFNI tools for fMRI
• Latest paper: http://dx.doi.org/10.1016/j.neuroimage.2011.08.056
• .BRIK with data, .HEAD header
• Allows PET, CT, SPECT
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Matlab
• *.mat files (not *.m)
• Array data as “raw” image
• No encoding of image information
• http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf
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Conclusion
• http://www.idoimaging.com/index.shtml
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Questions
• [email protected]• http://dcb.cit.nih.gov/~senseneyj• http://mipav.cit.nih.gov• http://imagej.nih.gov
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Contact Us
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