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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 l.jpg

Image Processing for MRI

Tips and Pitfalls

Patient image beyond l.jpg
Patient -> Image -> Beyond

  • signal reception

  • FFT

  • indices, coordinates

  • File formats

  • DICOM – 3D positions

  • window levels

16 bits are not enough precision l.jpg
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 on 2d k space l.jpg
FFT on 2D k-space



Fft recipe l.jpg
FFT Recipe

1 shift


3 unshift

Fft other tips l.jpg
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 l.jpg
Vertical axis reflection

  • Care mapping:

  • spatial transformations

  • k-space frequencies

2d data in memory and files l.jpg
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 l.jpg
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 l.jpg

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 l.jpg
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 l.jpg
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

Example l.jpg



  • restrict FOV

  • surf command

  • vertices specified

  • no edge color

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

Decoding a dicom directory l.jpg
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.

Coordinates l.jpg





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

To find rotation centres, create a cross test object.

Image presentation l.jpg
Image Presentation

same image

Window levels l.jpg
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.

Slide19 l.jpg

  • 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 l.jpg
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 l.jpg
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 l.jpg
Book Recommendations (cont)

  • Digital Image Processing

    Digital Image Processing using MATLAB

    Gonzalez, Woods and Eddins.

Final remarks l.jpg
Final Remarks

  • “Don’t image process unless the results can be validated.”

  • “Concentrate on acquisition not image processing.”