Classical nonrigid registration for prostate MR images

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Source Code

This is a special demo that uses the DeepReg package for classical nonrigid image registration, which iteratively solves an optimisation problem. Gradient descent is used to minimise the image dissimilarity function of a given pair of moving and fixed images, often regularised by a deformation smoothness function.

Author

DeepReg Development Team

Application

Registering inter-subject prostate MR images may be useful to align different glands in a common space for investigating the spatial distribution of cancer.

Instruction

  • Change current directory to the root directory of DeepReg project;

  • Run demo_data.py script to download an example MR volumes with the prostate gland segmentation;

python demos/classical_mr_prostate_nonrigid/demo_data.py

  • Run demo_register.py script. This script will register two images. The optimised transformation will be applied to the moving images, as well as the moving labels. The results, saved in a timestamped folder under the project directory, will compare the warped image/labels with the ground-truth image/labels.

python demos/classical_mr_prostate_nonrigid/demo_register.py

Tested DeepReg version

0.1.0

Contact

Please raise an issue.

Reference

[1] Litjens, G., Toth, R., van de Ven, W., Hoeks, C., Kerkstra, S., van Ginneken, B., Vincent, G., Guillard, G., Birbeck, N., Zhang, J. and Strand, R., 2014. Evaluation of prostate segmentation algorithms for MRI: the PROMISE12 challenge. Medical image analysis, 18(2), pp.359-373.