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Image Processing for MRI. Tips and Pitfalls. Patient -> Image -> Beyond. signal reception FFT indices, coordinates File formats DICOM – 3D positions window levels. 16 bits are not enough precision. ~16 bit analogue to digital converter integers 0 – 65535.

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image processing for mri

Image Processing for MRI

Tips and Pitfalls

patient image beyond
Patient -> Image -> Beyond
  • signal reception
  • FFT
  • indices, coordinates
  • File formats
  • DICOM – 3D positions
  • window levels
16 bits are not enough precision
16 bits are not enough precision
  • ~16 bit analogue to digital converter
    • integers 0 – 65535.
  • True dynamic range is higher (variable attenuators in receiver chain).
  • Complex FFT and other processing.
  • Use “intensity” image (floating point values), rather than indexed or rgb.
    • avoid read/writing intermediate files in tiff, gif.
fft recipe
FFT Recipe

1 shift


3 unshift

fft other tips
FFT other tips
  • 1/N scaling between forward and reverse.
  • Lack of convention for forward/reverse.
  • Don’t 3D FFT multi-slice data.
  • Beware of indices and the location of DC.


N/2 + 1


vertical axis reflection
Vertical axis reflection
  • Care mapping:
  • spatial transformations
  • k-space frequencies
2d data in memory and files
2D data in memory and files

2D data stored sequentially in 1D memory/file

MATLAB matrix(row, column)

IDL matrix(column, row)

C array [ index1 ] [ index2 ]

index is written out most rapidly

Symptoms: rotated (transposed) images.

file formats
File Formats
  • See David Clunie’s Medical Image web site.
  • Files contain: Information and pixel values.
  • Information in either:
    • fixed length header (gipl)
    • fixed length separate file (Analyze)
    • tags (ACR/NEMA, tiff, DICOM, SPI)
endian not indian
Big endian

“big end first”


Motorola Mac

Little endian

“little end first”

Intel (Windows and Linux on a PC)

Endian (not indian)

Order in which multiple byte variables are stored

endian cont
Endian (cont)

Problems reading file previously written on a different system.

Most standard image file types and readers cope.

MATLAB – specify within fopen

IDL - byte swapping commands.

Do not just swap every pair of bytes blindly.

3d information in dicom
3D Information in DICOM

right-handed coordinate system

+z Head




centre of top-left pixel

+y Posterior



(rx, ry, rz, cx, cy, cz)

image row and column directions

+x Patient Left



  • restrict FOV
  • surf command
  • vertices specified
  • no edge color

!! relies on radiographer correctly entering supine/prone, head-foot !!

decoding a dicom directory
Decoding a DICOM directory
  • Thousands of files often with meaningless names.
    • Set up DICOM node to use sensible file names.
    • Examine the slice separations in 3D space using ImagePositionPatient.
    • for cardiac phases, use TriggerDelay?
  • Future standard: Multi-frame DICOM objects for MR. Also allow annotation for tractography, fMRI etc.





Tip: generate a 4x4 image, plot a point.

To find rotation centres, create a cross test object.

window levels
Window levels
  • Alarming differences in gamma
    • CRT, LCD
    • Sun, Mac, PC.
    • printer, toner level.
    • projector, room brightness.
  • Fix lower range at 0, adjust upper based on inspection (e.g. exclude fat). Guess gamma. Present with a colour bar.
  • Future: support for .png gamma correction.
  • In subtraction images, beware of negative values wrapping round the integer range.
  • signed vs. unsigned integers
  • MR data is complex: transpose, complex conjugate and Hermitian transpose are not the same.
    • software
    • test data (BrainWeb, Visible Human)
    • software links (Image Magick, MRIConvert).
misc cont
misc. (cont)
  • vtk good for surface visualisation.
  • Data is discrete, not continuous.
  • Voxels usually anisotropic.
  • Care: voxel sizes (distortion) and resolution (reduced phase encodes).
  • sinc interpolation is best on bandlimited data – but you may need the raw data, not a truncated image.
book recommendations
Book Recommendations
  • 3D coordinates, transformations, plane.

Computer Graphics

Foley, van Dam, Feiner, Hughes.

  • Numerical programming (not code itself)

Numerical Recipes in C

Press, Teukolsky, Flannery, Vetterling.

  • Eigenvalues, SVD, FFT, Google search!

Numerical Computing with MATLAB


book recommendations cont
Book Recommendations (cont)
  • Digital Image Processing

Digital Image Processing using MATLAB

Gonzalez, Woods and Eddins.

final remarks
Final Remarks
  • “Don’t image process unless the results can be validated.”
  • “Concentrate on acquisition not image processing.”