direct-e2e-ads-recon-reg

DIRECT — Adaptive Sampling, Reconstruction & Registration

Pretrained models that jointly learn adaptive (k)-space sampling, reconstruction, and motion registration for dynamic MRI.

• Paper: arXiv:2411.18249
• Companion (sampling + recon only, MIDL 2026): PMLR · Hub NKI-AI/direct-e2e-ads-recon
• Framework: DIRECT

Dataset

Models

Each experiment is a .yaml + .pt pair:

Full training configs: projects/e2e_ads_recon_reg.

Training protocol

Same data domain as the companion E2E-ADS-Recon models: CMRxRecon cine with mixed discrete accelerations (typically (R \in {4.0327, 6, 8.2}), or init variants) and ACS center_fractions of matching length (usually 0.04).

Released inference YAMLs pin one active (R) / ACS (default val-4x). Other rates are commented under masking — uncomment to switch (same {name}.pt).

Install DIRECT

git clone https://github.com/NKI-AI/direct.git
cd direct
conda create --name direct python=3.12
conda activate direct
pip install meson-python meson ninja
pip install --no-build-isolation -e ".[dev]"

Usage

hf download NKI-AI/direct-e2e-ads-recon-reg --local-dir ./e2e_ads_recon_reg

direct predict ./predictions \
  --cfg ./e2e_ads_recon_reg/vsharp_ads_1d_phase_reg.yaml \
  --checkpoint ./e2e_ads_recon_reg/vsharp_ads_1d_phase_reg.pt \
  --data-root /path/to/cmrxrecon \
  --num-gpus 1

The first argument is the prediction output directory.

These models include a registration_model, so inference YAMLs enable registration transforms that build a reference_image (default: drop frame index 6 via FROM_KEY). Volumes must have enough temporal frames for that index. To use a different reference frame, edit:

transforms:
  registration:
    registration: true
    registration_simulate_reference: FROM_KEY
    registration_simulate_reference_from_key_index: 6
    registration_estimate_displacement: false

Citation

If you use these models or DIRECT, please cite the DIRECT toolkit and the method paper(s) below.

DIRECT

@article{DIRECTTOOLKIT,
  title={DIRECT: Deep Image REConstruction Toolkit},
  author={Yiasemis, George and Moriakov, Nikita and Karkalousos, Dimitrios and Caan, Matthan and Teuwen, Jonas},
  journal={Journal of Open Source Software},
  volume={7},
  number={73},
  pages={4278},
  year={2022},
  doi={10.21105/joss.04278},
  url={https://doi.org/10.21105/joss.04278}
}

Method

@article{yiasemis2024e2eadsreg,
  title={Deep End-to-End Adaptive k-Space Sampling, Reconstruction, and Registration for Dynamic {MRI}},
  author={Yiasemis, George and Moriakov, Nikita and Sonke, Jan-Jakob and Teuwen, Jonas},
  journal={arXiv preprint arXiv:2411.18249},
  year={2024}
}