Interpolation of deformation field for brain-shift compensation using Gaussian Process

Type: BA thesis

Status: finished

Date: September 1, 2019 - November 15, 2019

Supervisors: Siming Bayer, Andreas Maier, Jie Luo (Harvard Medical School)

Brain shift is the change of the position and shape of the brain during a neurosurgical procedure due to more space after opening the skull. This intraoperative soft tissue deformation limits the use of neuroanatomical overlays that were produced prior to the surgery. Consequently, intraoperative image updates are necessary to compensate for brain shift.

Comprehensive reviews concerning different aspects of intraoperative brain shift compensation can be found in [1][2]. Recently, feature based registration frameworks using SIFT features [3] or vessel centerlines [4] has been proposed to update the preoperative image in a deformable fashion, whereas point matching algorithm such as coherent point drift [5] or hybrid mixture model [4] are used to establish point correspondences between source and target feature point set. In order to estimate a dense deformation field according to the point correspondence, B-spline [6] and Thin-plate-spline [7] interpolation techniques are commonly used.

Gaussian process [8] (GP) is a powerful machine learning tool, which has been applied for image denoising, interpolation and segmentation. In this work, we are aiming at the application of different GP kernels for brain shift compensation. Furthermore, GP-based interpolation of deformation field is compared with the state-of-the-art methods.

In detail, this thesis includes the following aspects:

  • Literature review of state-of-the-art method for brain shift compensation using feature-based algorithms
  • Literature review of state-of-the-art method for the interpolation of deformation field/vector field
  • Introduction of Gaussian Process (GP)
  • Integrate GP-based interpolation technique into feature based brain shift compensation framework
    • Estimate dense deformation field from a sparse deformation field using GP
    • Implementation of at least three different GP kernels
    • Compare the performance of GP and state-of-the-art image interpolation techniques on various dataset, including synthetic data, phantom data and clinical data, with respect to accuracy, usability and run time.

[1] Bayer, S., Maier, A., Ostermeier, M., & Fahrig, R. (2017). Intraoperative Imaging Modalities and Compensation for Brain Shift in Tumor Resection Surgery. International Journal of Biomedical Imaging, 2017 .

[2] I. J. Gerard, M. Kersten-Oertel, K. Petrecca, D. Sirhan, J. A. Hall, and D. L. Collins, “Brain shift in neuronavigation of brain tumors: a review,” Medical Image Analysis, vol. 35, pp. 403–420, 2017.

[3] Luo J. et al. (2018) A Feature-Driven Active Framework for Ultrasound-Based Brain Shift Compensation. In: Frangi A., Schnabel J., Davatzikos C., Alberola-López C., Fichtinger G. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. MICCAI 2018. Lecture Notes in Computer Science, vol 11073. Springer, Cham

[4] Bayer S, Zhai Z, Strumia M, Tong.  XG, Gao Y, Staring M, Stoe B, Fahrig R, Arya N, Meier. A, Ravikumar N. Registration of vascular structures using a hybrid mixture model in: International Journal of Computer Assisted Radiology and Surgery, Juni 2019

[5] Myronenko, A., Song, X.: Point set registration: Coherent point drift. IEEE Trans.Pattern. Anal. Mach. Intell.32 (12), 2262-2275 (2010)

[6] D. Rueckert, L. I. Sonoda, C. Hayes, D. L. G. Hill, M. O. Leach and D. J. Hawkes, “Nonrigid registration using free-form deformations: application to breast MR images,” in IEEE Transactions on Medical Imaging, vol. 18, no. 8, pp. 712-721, Aug. 1999.

[7] F. L. Bookstein, “Principal warps: thin-plate splines and the decomposition of deformations,” in IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 11, no. 6, pp. 567-585, June 1989.

[8] C. E. Rasmussen & C. K. I. Williams, Gaussian Processes for Machine Learning, the MIT Press, 2006