This repository hosts implementations of several projects I’ve contributed to, along with helpful preprocessing and post-processing utilities for medical image analysis. It also provides wrappers for selected external packages to enable seamless integration into TransMorph-like registration workflows.
Documentation is available at: https://junyuchen.me/MIR
Prerequisite: Install a CUDA-enabled PyTorch build before installing MIR.
git clone https://github.com/junyuchen245/MIR.git
cd MIR
python3.8 -m pip install -U pip
python3.8 -m pip install -e .
You can quickly benchmark several models on the IXI dataset using the scripts in tutorials/IXI_benchmarking. See the README there for dataset download and run commands.
Canonical workflow: run IXI_benchmarking.ipynb in that directory. The notebook handles dataset/checkpoint download, evaluates
TransMorph, TransMorphTVF, VFA, VFA-SPR, SITReg, SITReg-SPR, and ConvexAdam-MIND, and writes per-model CSV metrics to results/.
- deedsBCV integration is Linux-only. Windows users can still use MIR, but deedsBCV functionality is unavailable.
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Pretraining Deformable Image Registration Networks with Random Images
Chen, Junyu, et al. MIDL Short Papers, 2025.
[Paper] | [Repo] -
Correlation Ratio for Unsupervised Learning of Multi-modal Deformable Registration
Chen, Xiaojian, et al. SPIE Medical Imaging: Image Processing, 2025.
[Paper] | [Repo] -
Unsupervised Learning of Spatially Varying Regularization for Diffeomorphic Image Registration
Chen, Junyu, et al. Medical Image Analysis, 2025.
[Paper] | [Repo] -
Vector Field Attention for Deformable Image Registration
Liu, Yihao, et al. Journal of Medical Imaging, 2024.
[Paper] | [Repo] -
Unsupervised Learning of Multi-modal Affine Registration for PET/CT
Chen, Junyu, et al. IEEE NSS/MIC/RTSD, 2024.
[Paper] | [Repo] -
On Finite Difference Jacobian Computation in Deformable Image Registration
Liu, Yihao, et al. International Journal of Computer Vision, 2024.
[Paper] | [Repo] -
Deformable Cross-Attention Transformer for Medical Image Registration
Chen, Junyu, et al. MLMI Workshop, MICCAI 2023.
[Paper] | [Repo] -
Unsupervised Learning of Diffeomorphic Image Registration via TransMorph
Chen, Junyu, et al. WBIR, 2022. [Paper] | [Repo] -
TransMorph: Transformer for Unsupervised Medical Image Registration
Chen, Junyu, et al. Medical Image Analysis, 2022.
[Paper] | [Repo]
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Intensity Normalization Toolkit
Reinhold, Jacob C., et al. SPIE MI, 2019.
[Paper] | [Repo] -
ConvexAdam: Dual-Optimization-Based 3D Registration
Siebert, Hanna, et al. IEEE TMI, 2024.
[Paper] | [Repo] -
MultiMorph: On-demand Atlas Construction
Abulnaga, S. Mazdak, et al. CVPR, 2025.
[Paper] | [Repo] -
SITReg: Multi-resolution architecture for symmetric, inverse consistent, and topology preserving image registration.
Honkamaa, Joel, and Pekka Marttinen. MELBA, 2024.
[Paper] | [Repo] -
deedsBCV [Repo]
