The code will be made available in this repository by October 8, 2023.
Free-breathing myocardial T1 mapping with Physically-Constrained Motion Correction
If you use PCMC-T1 in your research, please cite the paper as follows:
E. Hanania, I. Volovik, L. Barkat, I. Cohen, and M. Freiman, PCMC-T1: Free-Breathing Myocardial T1 Mapping with
Physically Constrained Motion Correction, Proc. 26th International Conference on Medical Image Computing and
Computer Assisted Intervention, MICCAI 2023, Vancouver, Canada, Oct. 8-12, 2023.
To use this project, follow these steps:
- Clone the Repository:
git clone https://github.com/eyalhana/PCMC-T1.git
- Install Dependecies
pip install -r requirements.txt
We utilized a publicly available myocardial T1 mapping dataset. To use this dataset, please download it in '.mat' format:
Use wget
(Linux/macOS) or curl
(Windows/Linux/macOS) to download the file:
- On Linux/macOS, use
wget
:wget -O data/T1Dataset210.mat [https://dataverse.harvard.edu/api/access/datafile/43188520](https://dataverse.harvard.edu/file.xhtml?persistentId=doi:10.7910/DVN/DHEUAV/H5WVDS)
- On Windows/Linux/macOS, use
curl
:curl -o data/T1Dataset210.mat [https://dataverse.harvard.edu/api/access/datafile/43188520](https://dataverse.harvard.edu/file.xhtml?persistentId=doi:10.7910/DVN/DHEUAV/H5WVDS)
To train using the MICCAI 2023 configuration (physically-constrained motion correction):
python /scripts/training.py --config /configs/miccai.yaml --fold 1
To train using the ISMRM 2023 configuration (group-wise mutual-information based motion correction):
python /scripts/training.py --config /configs/ismrm.yaml --fold 1
You can customize hyperparameters and file paths in the configuration files.
If you intend to train your own model using custom datasets or data formats, you'll likely need to customize the data-loading code in the following project files:
src/generators.py
src/data_preprocessing.py
config_loader.py
We used the
python /scripts/evaluation.py --config configs/miccai.yaml --model models/model_name.pt
For any code-related problems or questions please open an issue.
For other inquiries, please contact us via email at eyalhan at campus.technion.ac.il
.