DDMR was developed by SINTEF Health Research. The corresponding manuscript describing the framework has been submitted to PLOS ONE and the preprint is openly available on arXiv.
- Setup virtual environment:
virtualenv -ppython3 venv --clear
source venv/bin/activate
- Install requirements:
pip install -r requirements.txt
Use the "MultiTrain" scripts to launch the trainings, providing the neccesary parameters. Those in the COMET folder accepts a .ini configuration file (see COMET/train_config_files for example configurations).
For instance:
python TrainingScripts/Train_3d.py
Use Evaluate_network to test the trained models. On the Brain folder, use "Evaluate_network__test_fixed.py" instead.
For instance:
python EvaluationScripts/evaluation.py
Please, consider citing our paper, if you find the work useful:
@misc{perezdefrutos2022ddmr, title = {Train smarter, not harder: learning deep abdominal CT registration on scarce data}, author = {Pérez de Frutos, Javier and Pedersen, André and Pelanis, Egidijus and Bouget, David and Survarachakan, Shanmugapriya and Langø, Thomas and Elle, Ole-Jakob and Lindseth, Frank}, year = {2022}, doi = {10.48550/ARXIV.2211.15717}, publisher = {arXiv}, copyright = {Creative Commons Attribution 4.0 International}, note = {preprint on arXiv at https://arxiv.org/abs/2211.15717} }
This project is based on VoxelMorph library, and its related publication:
@article{VoxelMorph2019, title={VoxelMorph: A Learning Framework for Deformable Medical Image Registration}, author={Balakrishnan, Guha and Zhao, Amy and Sabuncu, Mert R. and Guttag, John and Dalca, Adrian V.}, journal={IEEE Transactions on Medical Imaging}, year={2019}, volume={38}, number={8}, pages={1788-1800}, doi={10.1109/TMI.2019.2897538} }