Unpaired prostate ultrasound registration

Note: Please read the DeepReg Demo Disclaimer.

Source Code

This DeepReg Demo is also an example of cross validation.

Author

DeepReg Development Team

Application

Transrectal ultrasound (TRUS) images are acquired from prostate cancer patients during image-guided procedures. Pairwise registration between these 3D images may be useful for intraoperative motion modelling and group-wise registration for population studies.

Data

The 3D ultrasound images used in this demo were derived from the Prostate-MRI-US-Biopsy dataset, hosted at the Cancer Imaging Archive (TCIA).

Instruction

  • Install DeepReg;

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

  • Run demo_data.py script to download 10 folds of unpaired 3D ultrasound images;

python demos/unpaired_us_prostate_cv/demo_data.py

  • Call deepreg_train from command line. The following example uses three GPUs and launches the first of the ten runs of a 9-fold cross-validation, as specified in the ``dataset` section <./unpaired_us_prostate_cv_run1.yaml>`_ and the ``train` section <./unpaired_us_prostate_cv_train.yaml>`_, which can be specified in separate yaml files. The 10th fold is reserved for testing;

deepreg_train --gpu "1, 2, 3" --config_path demos/unpaired_us_prostate_cv/unpaired_us_prostate_cv_run1.yaml demos/unpaired_us_prostate_cv/unpaired_us_prostate_cv_train.yaml --log_dir unpaired_us_prostate_cv

  • Call deepreg_predict from command line to use the saved ckpt file for testing on the 10th fold data. The following example uses a pre-trained model, on CPU. If not specified, the results will be saved at the created timestamp-named directories under /logs.

deepreg_predict --gpu "" --config_path demos/unpaired_us_prostate_cv/unpaired_us_prostate_cv_run1.yaml demos/unpaired_us_prostate_cv/unpaired_us_prostate_cv_train.yaml --ckpt_path demos/unpaired_us_prostate_cv/dataset/pre-trained/weights-epoch5000.ckpt --mode test

Pre-trained Model

A pre-trained model will be downloaded after running demo_data.py and unzipped at the dataset folder under the demo folder. This pre-trained model will be used by default with deepreg_predict. Run the user-trained model by specifying with --ckpt_path the location where the ckpt files will be saved, in this case (specified by deepreg_train as above), /logs/unpaired_us_prostate_cv/.

Tested DeepReg version

Last commit at which demo was tested: 7bec018b5e910f1589888f3f286e9f6a11060c31

Contact

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