Embed Size (px)
Citation preview
National Alliance for Medical Image Computing http://na-mic.org
Registration in Slicer3
Julien JomierKitware Inc.
National Alliance for Medical Image Computing http://na-mic.org
Registration
• Coordinate System conversion
• Not only image-to-image: model-to-model, model-to-image
• Involves resampling and therefore interpolation
• Linear: Rigid, Similarity, Affine
• Deformable: TPS, EBS, B-Spline
National Alliance for Medical Image Computing http://na-mic.org
Fixed Image Grid
j
i
y
x
Fixed ImagePhysical Coordinates
y’
x’Moving Image
Physical Coordinates
Moving Image Grid
j
i
Space Transform
Coordinate System Conversion
National Alliance for Medical Image Computing http://na-mic.org
Images provided as part of the project: “Retrospective Image Registration Evaluation”, NIH, Project No. 8R01EB002124-03, Principal Investigator, J. Michael Fitzpatrick, Vanderbilt University, Nashville,
TN.
Images from the same patient
256 x 256 pixels
MRI-T2
Scaling Transform
128 x 128 pixels
PET
Scaling Factor
National Alliance for Medical Image Computing http://na-mic.org
I will not register images in pixel space
I will not register images in pixel space
I will not register images in pixel space
I will not register images in pixel space
I will not register images in pixel space
I will not register images in pix
Things I will not do
National Alliance for Medical Image Computing http://na-mic.org
FixedImage
MovingImage
Metric
Transform
Interpolator
Optimizer
Registration Method
Registration Framework
National Alliance for Medical Image Computing http://na-mic.org
In principle the denomination of
Fixed Image & Moving Image
is arbitrary
In practice the moving image
is the one that will be resampled
into the fixed image
coordinate system
Selecting Moving & Fixed Images
National Alliance for Medical Image Computing http://na-mic.org
Registration Initialization
• Coarse-to-fine approach
• Center of mass
• High order moments (principal axes)
• RealignVolume
National Alliance for Medical Image Computing http://na-mic.org
Mutual Information
• Mutual dependence between pixel values of images
• Based on histograms
National Alliance for Medical Image Computing http://na-mic.org
Joint Histograms: Mono-modality
Images Aligned Translated by 0 to 20 pixels
White = zero valueBlack = highest value
Misalignment causesdispersion
National Alliance for Medical Image Computing http://na-mic.org
Translated by 0 to 20 pixels
Misalignment causesdispersion
Joint Histograms: Multi-modality
Images Aligned
White = zero valueBlack = highest value
National Alliance for Medical Image Computing http://na-mic.org
Affine Registration
• Mattes Mutual Information
• Histogram Bin
• Spatial Samples
• Translation scaling- Rotation and translation are not in the same units
National Alliance for Medical Image Computing http://na-mic.org
Deformable Transform
y
Fixed Image
Transform
x
y
Moving Image
x
National Alliance for Medical Image Computing http://na-mic.org
Deformable transform
y
Fixed Image
Transform
x
y
Moving Image
x
National Alliance for Medical Image Computing http://na-mic.org
Deformable Transformation
y
x
National Alliance for Medical Image Computing http://na-mic.org
BSpline Grid
y
x
BSplineGrid
ResamplingGrid
National Alliance for Medical Image Computing http://na-mic.org
BSplines Grid & Image Grid
National Alliance for Medical Image Computing http://na-mic.org
BSplines Grid & Image Grid
BSplineGrid
National Alliance for Medical Image Computing http://na-mic.org
BSplines Grid & Image Grid
BSplineGrid
ValidRegion
National Alliance for Medical Image Computing http://na-mic.org
BSplines Grid & Image Grid
BSplineGrid
National Alliance for Medical Image Computing http://na-mic.org
BSplines Grid & Image Grid
BSplineGrid
ValidRegion
National Alliance for Medical Image Computing http://na-mic.org
BSpline Registration
• Mutual Information (Mattes)
• LBFGSBOptimizer
• Constrain Deformation: constrain the optimizer by bounds
National Alliance for Medical Image Computing http://na-mic.org
Slicer Demo
• Open Slicer
• Load Datasets
• Affine Registration
• BSpline Deformable Registration
• Transfer Functions Visualization
National Alliance for Medical Image Computing http://na-mic.org
Loading Datasets
National Alliance for Medical Image Computing http://na-mic.org
Affine Registration
National Alliance for Medical Image Computing http://na-mic.org
Affine Registration
National Alliance for Medical Image Computing http://na-mic.org
Deformable Registration
National Alliance for Medical Image Computing http://na-mic.org
Deformable Registration
National Alliance for Medical Image Computing http://na-mic.org
Adjusting Transfer Functions
