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Image Registration: John Ashburner
Image Registration: John Ashburner
Registration
John Ashburner
* Smooth
* Realign
* Normalise
* Segment
With slides by Chloe Hutton and Jesper Andersson
Overview of SPM Analysis
fMRI time-series Design matrix Statistical Parametric Map
Anatomical Reference
Contents
* Preliminaries
* Smooth
* Rigid-Body and Affine Transformations
* Optimisation and Objective Functions
* Transformations and Interpolation
* Intra-Subject Registration
* Inter-Subject Registration
Smooth
Smoothing is done by convolution.
Value of parameter
Objective Functions
* Intra-modal
* Mean squared difference (minimise)
* Normalised cross correlation (maximise)
* Entropy of difference (minimise)
* Inter-modal (or intra-modal)
* Mutual information (maximise)
* Normalised mutual information (maximise)
* Entropy correlation coefficient (maximise)
* AIR cost function (minimise)
Transformation
* Images are re-sampled. An example in 2D:
for y0=1..ny0 % loop over rows
for x0=1..nx0 % loop over pixels in row
x1 = tx(x0,y0,q) % transform according to q
y1 = ty(x0,y0,q)
if 1x1 nx1 & 1y1ny1 then % voxel in range
f1(x0,y0) = f0(x1,y1) % assign re-sampled value
end % voxel in range
end % loop over pixels in row
end % loop over rows
* What happens if x1 and y1 are not integers?
Simple Interpolation
* Nearest neighbour
* Take the value of the
closest voxel
* Tri-linear
* Just a weighted
average of the
neighbouring voxels
* f5 = f1 x2 + f2 x1
* f6 = f3 x2 + f4 x1
* f7 = f5 y2 + f6 y1
B-spline Interpolation
A continuous function is represented by 2D B-spline basis functions
a linear combination of basis functions of degrees 0, 1, 2 and 3
+
B0 B0
Andersson et al, 2001
Contents
* Preliminaries
* Intra-Subject Registration
* Realign
* Coregister
* Mutual Information objective function
* Inter-Subject Registration
Inter-modal registration
• Match images from same
subject but different
modalities:
– anatomical localisation of
single subject activations
– achieve more precise
spatial normalisation of
functional image using
anatomical image.
Mutual Information
* Inter-subject averaging
* Increase sensitivity with more subjects
* Fixed-effects analysis
* Extrapolate findings to the population as a whole
* Mixed-effects analysis
* Standard coordinate system
* e.g., Talairach & Tournoux space
Spatial Normalisation - Procedure
* Minimise mean squared difference from template
image(s)
EPI PD PET PD T2 SS
Belonging
probabilities
are assigned
by normalising
to one.
Mixing Proportions
* The mixing proportion gk represents the prior
probability of a voxel being drawn from class k -
irrespective of its intensity.
* So:
Non-Gaussian Intensity Distributions
* Multiple Gaussians per tissue class allow non-Gaussian
intensity distributions to be modelled.
* E.g. accounting for partial volume effects
Probability of Whole Dataset
* If the voxels are assumed to be independent, then
the probability of the whole image is the product of
the probabilities of each voxel:
y r(b) y r(b)
Tissue Probability Maps
* Tissue probability maps (TPMs) are used instead
of the proportion of voxels in each Gaussian as
the prior.
Optimum
Alternate between
optimising different groups
of parameters
Schematic of optimisation
Repeat until convergence…
Tissue
probability
maps of GM
and WM
Cocosco, Kollokian, Kwan & Evans. “BrainWeb: Online Interface to a 3D MRI Simulated Brain Database”. NeuroImage 5(4):S425 (1997)
References
* Friston et al. Spatial registration and normalisation of images.
Human Brain Mapping 3:165-189 (1995).
* Collignon et al. Automated multi-modality image registration based on
information theory. IPMI’95 pp 263-274 (1995).
* Ashburner et al. Incorporating prior knowledge into image registration.
NeuroImage 6:344-352 (1997).
* Ashburner & Friston. Nonlinear spatial normalisation using basis functions.
Human Brain Mapping 7:254-266 (1999).
* Thévenaz et al. Interpolation revisited.
IEEE Trans. Med. Imaging 19:739-758 (2000).
* Andersson et al. Modeling geometric deformations in EPI time series.
Neuroimage 13:903-919 (2001).
* Ashburner & Friston. Unified Segmentation.
NeuroImage in press (2005).