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Slicer Registration Use Case Exampe #8: Intra-subject whole-body PET-CT

this is the fixed reference image. All images are aligned into this space this is also a fixed reference image. All images are aligned into this space lleft this is the moving image. The transform is calculated by matching this to the reference image this is a passivley (tag) image. The calculated transforms are applied to this image LEGEND

lleft this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution
lleft this indicates the moving image that determines the registration transform.
lleft this indicates a passivley moving image.

lleft whole body CT baseline lleft whole body PET baseline lleft whole body CT follow-up lleft whole body PET follow-up
CT: 512 x 512 x 267
0.97 x 0.97 x 3.27 mm
PET: 128 x 128 x 267
4.7 x 4.7 x 3.3 mm
CT: 512 x 512 x 195
0.98 x 0.98 x 5.0 mm
PET: 168 x 168 x 195
4.1 x 4.1 x 5 mm

Objective / Background

Change assessment.

Keywords

PET-CT, whole-body, change assessment

Input Data

  • Button red fixed white.jpgreference/fixed : baseline CT: 0.97 x 0.97 x 3.27 mm , PET: 4.7 x 4.7 x 3.3 mm
  • Button green moving white.jpg moving: CT: 0.98 x 0.98 x 5
  • Button blue tag white.jpg moving: PET: 4.1 x 4.1 x 5 mm

Registration Results

Download


Link to User Guide: How to Load/Save Registration Parameter Presets


Discussion: Registration Challenges

  • accuracy is the critical criterion here. We need the registration error (residual misalignment) to be smaller than the change we want to measure/detect. Agreement on what constitutes good alignment can therefore vary greatly.
  • the two series have different voxel sizes
  • because of the large FOV we have strong non-rigid deformations from differences in patient/limb positions etc.
  • images are large volumes (>100 MB total)
  • image content reaches border of image on two sides
  • 2 images pairs have to be aligned, i.e. the calculated transform must be applied to the second (PET) image.

Discussion: Key Strategies

  • to calculate the transform, we use the images with the most accurate geometric representation and the smallest expected change, i.e. we align the follow-up CT to the baseline CT and then apply the transforms to the PET image.
  • because of the non-rigid differences due to posture and breathing we will need to apply a 2-step registration with an affine alignment followed by a BSpline.
  • the strong differences in head position is likely to distract the registration and lead to suboptimal results. Hence we produce a cropped version of the two CT images to calculate the BSpline transform.
  • the two images are far apart initially, we will need some form of initialization. We will try an automated alignment first. If this fails, we do a 2-step process with manual initial alignment, followed by automated affine.
  • because accuracy is more important than speed here, we increase the iterations and sampling rates. Note however the large image size, which makes comparable sampling % still large compared to other datasets.
  • the two images have identical contrast, hence we could consider "sharper" cost functions, such as NormCorr or MeanSqrd. However, since these are not (yet) available for the BSpline registration.