Classical nonrigid registration for prostate MR images¶
Note: Please read the DeepReg Demo Disclaimer.
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.
Registering inter-subject prostate MR images may be useful to align different glands in a common space for investigating the spatial distribution of cancer.
Data is an example MR volumes with the prostate gland segmentation from MICCAI Grand Challenge: Prostate MR Image Segmentation 2012.
Please install DeepReg following the instructions and
change the current directory to the root directory of DeepReg project, i.e.
Please execute the following command to download and pre-process the data.
Please execute the following command to 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.
The following command can be executed to generate a plot of three image slices from the the moving image, warped image and fixed image (left to right) to visualise the registration. Please see the visualisation tool docs here for more visualisation options such as animated gifs.
deepreg_vis -m 2 -i 'demos/classical_mr_prostate_nonrigid/logs_reg/moving_image.nii.gz, demos/classical_mr_prostate_nonrigid/logs_reg/warped_moving_image.nii.gz, demos/classical_mr_prostate_nonrigid/logs_reg/fixed_image.nii.gz' --slice-inds '4,8,12' -s demos/classical_mr_prostate_nonrigid/logs_reg
Note: The registration script must be run before running the command to generate the visualisation.
Please raise an issue for any questions.
 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.