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
Tips and Pitfalls
FAST Fourier Transform Convention
N/2 + 1
2D data stored sequentially in 1D memory/file
C array [ index1 ] [ index2 ]
index is written out most rapidly
Symptoms: rotated (transposed) images.
“big end first”
“little end first”
Intel (Windows and Linux on a PC)
Order in which multiple byte variables are stored
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.
right-handed coordinate system
centre of top-left pixel
(rx, ry, rz, cx, cy, cz)
image row and column directions
+x Patient Left
!! relies on radiographer correctly entering supine/prone, head-foot !!
Tip: generate a 4x4 image, plot a point.
To find rotation centres, create a cross test object.
Foley, van Dam, Feiner, Hughes.
Numerical Recipes in C www.nr.com
Press, Teukolsky, Flannery, Vetterling.
Numerical Computing with MATLAB
Digital Image Processing using MATLAB
Gonzalez, Woods and Eddins.