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Constrained Probabilistic Mask Learning for Task-specific Undersampled MRI Reconstruction

Code for the paper Constrained Probabilistic Mask Learning for Task-specific Undersampled MRI Reconstruction @ WACV 2024.

Undersampling is a common method in Magnetic Resonance Imaging (MRI) to subsample the number of data points in k-space, reducing acquisition times at the cost of decreased image quality. A popular approach is to employ undersampling patterns following various strategies, e.g., variable density sampling or radial trajectories. In this work, we propose a method that directly learns the undersampling masks from data points, thereby also providing task- and domain-specific patterns. To solve the resulting discrete optimization problem, we propose a general optimization routine called ProM: A fully probabilistic, differentiable, versatile, and model-free framework for mask optimization that enforces acceleration factors through a convex constraint. Analyzing knee, brain, and cardiac MRI datasets with our method, we discover that different anatomic regions reveal distinct optimal undersampling masks, demonstrating the benefits of using custom masks, tailored for a downstream task. For example, ProM can create undersampling masks that maximize performance in downstream tasks like segmentation with networks trained on fully-sampled MRIs. Even with extreme acceleration factors, ProM yields reasonable performance while being more versatile than existing methods, paving the way for data-driven all-purpose mask generation.

Requirements:

Required packages are listed in the requirements.txt file, which can be install e.g. over pip:

pip install -r requirements.txt

We use Python 3.9.

Datasets

Our repository uses ACDC, BraTS and fastMRI Knee. Additionally, please download the knee annotations from fastMRI+ into the fastMRI Knee directory. Per default, the data is supposed to be located at data.

The pre-processing of the datasets will be triggered on the first call of the respective dataset objects: ACDCDataset, BrainDataset, KneeDataset in src/datasets.py.

Use Own Data

In general, a target dataset needs to fulfill the requirement of implementing a subclass of ProMDataset in src/datasets.py. This implies that the __get_item__ method should return a dictionary containing tensors of the image in image space, k-space and a segmentation. Hereby, the segmentation maybe an empty dummy if the segmentation downstream task is not applied. Also an image size should be supplied.

The run_dataset_optim, which kicks off the training procedure, allows passing a custom dataset directly like:

run_dataset_optim(cfg=cfg, ds=MyCustomDataset())

Train ProM

The subfolder scripts contains a few starter scripts on how to use apply ProM to a PyTorch dataset. The first script 01_run_prom_reconstruction.py shows how to configure and train ProM for a classic reconstruct task. 02_train_unet.py trains the U-nets used for the segmentation downstream tasks in our paper. These are also available in the models directory. Subsequently, 03_run_prom_segmentation.py applies the trained networks in the ProM procedure. Lastly, use 04_eval_mask.py to obtain metrics.

Citation

If you use our repository in your research, please cite our paper Constrained Probabilistic Mask Learning for Task-specific Undersampled MRI Reconstruction:

@inproceedings{weber2024constrained,
  title={Constrained Probabilistic Mask Learning for Task-specific Undersampled MRI Reconstruction},
  author={Weber, Tobias and Ingrisch, Michael and Bischl, Bernd and R{\"u}gamer, David},
    booktitle = {Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV)},
    year      = {2024},
}