Awesome
Slice-to-Volume Registration Transformer (SVoRT)
This repo is the official implementation of the paper 'SVoRT: Iterative Transformer for Slice-to-Volume Registration in Fetal Brain MRI'
Resources
Requirements
- python 3.9
- pytorch 1.10
- pyyaml
- scikit-image
- antpy
- scipy
- nibabel
Training from scratch
Generate training data
To generate training data, please download the CRL atlas and FeTA dataset v2.1, unzip them in dataset/
, and run preprocessing.py
. You may also add your own training data (see RegisteredDataset
in .src/data/dataset.py
).
Modify hyperparameters
The hyperparameters of data simulation and model are stored in ./src/config/
.
Run the training script
python train.py --config ./config/config_SVoRTv2.yaml \
--output ../results/SVoRTv2
Pretrained model
To use the pretrained model, please first download the pretrain weights.
Testing
python test.py --config ./config/config_SVoRTv2.yaml \
--output ../results/SVoRTv2/test_output \
--checkpoint ../results/SVoRTv2/checkpoint.pt
Citation
@inproceedings{xu2022svort,
title={SVoRT: Iterative Transformer for Slice-to-Volume Registration in Fetal Brain MRI},
author={Xu, Junshen and Moyer, Daniel and Grant, P Ellen and Golland, Polina and Iglesias, Juan Eugenio and Adalsteinsson, Elfar},
booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
pages={3--13},
year={2022},
organization={Springer}
}
Contact
For questions, please send an email to junshen@mit.edu