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Registration of functional PET and structural MR images. PVEOut satellite meeting Budapest, June 11 th 2004 Peter Willendrup & Claus Svarer Neurobiology Research Unit Copenhagen. Registration needed PVEOut.

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registration of functional pet and structural mr images

Registration of functional PET and structural MR images

PVEOut satellite meeting

Budapest, June 11th 2004

Peter Willendrup & Claus Svarer

Neurobiology Research Unit


registration needed pveout
Registration needed PVEOut
  • Structural MR and functional PET image has to be registered/aligned as the structural information is applied to each voxel in the functional image
  • As image are coming from same subject only a rigid 6 parameter transformation has to be estimated:
    • 3 translations (along X, Y and Z axis)
    • 3 rotations (around X, Y and Z axis)

NRU, 2004

what automatic methods are available
What automatic methods are available?
  • West J, Fitzpatrick JM, Dawant BM, et al.
  • Headmounted fiducials serves as ``Gold standard'' coregistration between the modalities (MR/CT/PET).
  • Coregistration parameters are kept for reference, and fiducials are removed from the datasets and replaced by artificial noise.
  • Methods are tested ``blindly'' - no knowledge of the Gold standard answer.



NRU, 2004

why are the automatic approaches not always a good idea
Why are the automatic approaches not always a good idea?
  • These methods are very well suited for registration of images where:
    • There in the PET image is an equal uptake in all brain regions
    • There is no inhomogenity variation in the MR images
  • This is not the case for all receptor PET images, e.g. 5-HT2A altanserin PET images where there are very limited uptake in Cerebellum



NRU, 2004

what manual methods have been proposed
What manual methods have been proposed?

Many different approches exist in the litterature

  • Landmark based: "Graphics applied to medical image registration", G. Q. Maguire, Jr., M. E. Noz, H. Rusinek, et al., Comput Graph Appl, 1991, vol. 11, pp. 20-29.
  • Surface based: "Accurate three-dimensional registration of CT, PET, and/or MR images of the brain", C. A. Pelizzari, G. T. Y. Chen, D.R. Spelbring, R. R. Wechselbaum, and C-T. Chen, J Comput AssistTomogr, 1989, vol. 13, pp. 20-26.
  • Image overlay: "Quantitative Comparison of Automatic and Interactive Methods for MRI-SPECT Image Registration of the Brain Based on 3-Dimensional Calculation of Error ”, Pfluger T, Vollmar C et al.: J Nucl Med 2000; 41:1823-1829
  • Voxel based: "MRI-PET registration with automated algorithm", R. P. Woods, J. C. Mazziotta, and S. R. Cherry, J Comput Assist Tomogr, 1993, vol. 17, pp. 536-546.

NRU, 2004

mars multiple algorithms for registration of scans
MARSMultiple Algorithms for Registration of Scans
  • Modular design
    • The problem of coregistration can be divided into subtasks
      • Data selection
      • Registration
      • Visualisation / Inspection
      • Parameter I/O
      • Reslicing / Re-Interpolation
    • All subtasks realised by ‘plugins’ - easy inclusion of alternative method
    • Different registration approaches benefit from shared code

NRU, 2004

Main programMARS
  • This is now included in pvelab

NRU, 2004

  • Subtask modules
    • Registration
      • Interface to Air 5.0 - Roger P. Woods
      • Interface to SPM 2 - J. Ashburner et. al.
      • IIO (Interactive Image Overlay) - NRU *
      • IPS (Interactive Point Selection) - NRU *
    • Visualisation
      • Inspect (NRU visualisation program) *
  • Asterisk-marked will be further explained

NRU, 2004

registration 1 interactive image overlay1
Registration 1: Interactive Image Overlay

Translation and rotation

of overlay image and surface

by keyboard commands

NRU, 2004

inspection of registration
Inspection of registration


Side by side

NRU, 2004

evaluation study setup
Evaluation study: Setup
  • Images (5 subjects)
    • T1 weighted MR images (MPRAGE)
    • 18F-Altanserin 5HT-2A receptor images
    • Simulated PET images
  • Evaluation by 7 volunteers
    • 3 rounds of MR / Altanserin registration
    • 1 round of MR / Simulated PET registration
    • Registration order randomised
    • Max. one ‘round’ of registrations pr. day
  • Images also registered using SPM99 and Air 3.0

NRU, 2004

evaluation study simulated pet
Evaluation study: Simulated PET
  • Simulated PET datasets
    • Good: known registration parameters
    • Bad: “easy” for cost fct. Based methods

NRU, 2004

evaluation study altanserin pet
Evaluation study: Altanserin PET
  • Altanserin PET images
    • Bad: Lack of gold standard registration method
    • Good: Real world ‘limited uptake’ images

NRU, 2004

evaluation study
Evaluation study
  • Error measure - Euclidean distance between transformation endpoints
  • Evaluated for 1% evenly distributed brain voxels.
  • Mean and std. dev. calculated
  • Mean transformation realized by 6-parameter estimation to mean of transformed voxels



NRU, 2004

evaluation study result
Evaluation study: Result



Mean manual

No Altanserin binding

should be seen in


Rotation problem?

Too little binding in

Altanserin image,

Translation problem?

NRU, 2004

registration conclusion
Two manual co-registration methods and the interface to two automatic methods have been implemented and incorporated in the PVEOut SW package (pvelab).

Four registration methods are included:

Interface to SPM 2 (J. Ashburner et. al.)

Interface to Air (R. Woods)



For FDG/flow type images, SPM and Air are preferred, with reported errors in the range 2-3 mm.

For neuroreceptor type images, with limited binding in areas of the brain, the manual methods can be used and possibly preferred.

Measured errors:

Registration: Conclusion

Simulated images

F18-Altanserin images

NRU, 2004