DeepReg Demo README Example

Note: Please read the DeepReg Demo Disclaimer.

Source Code

Author

DeepReg Development Team (optional corresponding Author Name) or Author Name for external contributor.

Application

Briefly describe the clinical application and the need for registration.

Data

Describe the source of the dataset. Dataset should be open-accessible.

Instruction

Installation

Please install DeepReg following the instructions and change the current directory to the root directory of DeepReg project, i.e. DeepReg/.

Download data

Please execute the following command to download/pre-process the data and download the pre-trained model.

python demos/name/demo_data.py

Launch demo training

Please execute the following command to launch a demo training. The training logs and model checkpoints will be saved under demos/name/logs_train.

python demos/name/demo_train.py

Here the training is launched using the GPU of index 0 with a limited number of steps and reduced size. Please add flag --full to use the original training configuration, such as

python demos/name/demo_train.py --full

Predict

Please execute the following command to run the prediction with pre-trained model. The prediction logs and visualization results will be saved under demos/name/logs_predict. Check the CLI documentation for more details about prediction output.

python demos/name/demo_predict.py

Optionally, the user-trained model can be used by changing the ckpt_path variable inside demo_predict.py. Note that the path should end with .ckpt and checkpoints are saved under logs_train as mentioned above.

Contact

Please raise an issue for any questions.

Reference

Related references in the form of [1] Reference.