README.md

February 24, 2026 · View on GitHub

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Overview

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

Installation

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 .

Quick start: IXI benchmarking

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/.

Platform notes

  • deedsBCV integration is Linux-only. Windows users can still use MIR, but deedsBCV functionality is unavailable.

📄 Included Projects

  1. Pretraining Deformable Image Registration Networks with Random Images
    Chen, Junyu, et al. MIDL Short Papers, 2025.
    [Paper] | [Repo]

  2. Correlation Ratio for Unsupervised Learning of Multi-modal Deformable Registration
    Chen, Xiaojian, et al. SPIE Medical Imaging: Image Processing, 2025.
    [Paper] | [Repo]

  3. Unsupervised Learning of Spatially Varying Regularization for Diffeomorphic Image Registration
    Chen, Junyu, et al. Medical Image Analysis, 2025.
    [Paper] | [Repo]

  4. Vector Field Attention for Deformable Image Registration
    Liu, Yihao, et al. Journal of Medical Imaging, 2024.
    [Paper] | [Repo]

  5. Unsupervised Learning of Multi-modal Affine Registration for PET/CT
    Chen, Junyu, et al. IEEE NSS/MIC/RTSD, 2024.
    [Paper] | [Repo]

  6. On Finite Difference Jacobian Computation in Deformable Image Registration
    Liu, Yihao, et al. International Journal of Computer Vision, 2024.
    [Paper] | [Repo]

  7. Deformable Cross-Attention Transformer for Medical Image Registration
    Chen, Junyu, et al. MLMI Workshop, MICCAI 2023.
    [Paper] | [Repo]

  8. Unsupervised Learning of Diffeomorphic Image Registration via TransMorph
    Chen, Junyu, et al. WBIR, 2022. [Paper] | [Repo]

  9. TransMorph: Transformer for Unsupervised Medical Image Registration
    Chen, Junyu, et al. Medical Image Analysis, 2022.
    [Paper] | [Repo]

🔌 External Wrappers Included

  1. Intensity Normalization Toolkit
    Reinhold, Jacob C., et al. SPIE MI, 2019.
    [Paper] | [Repo]

  2. ConvexAdam: Dual-Optimization-Based 3D Registration
    Siebert, Hanna, et al. IEEE TMI, 2024.
    [Paper] | [Repo]

  3. MultiMorph: On-demand Atlas Construction
    Abulnaga, S. Mazdak, et al. CVPR, 2025.
    [Paper] | [Repo]

  4. SITReg: Multi-resolution architecture for symmetric, inverse consistent, and topology preserving image registration.
    Honkamaa, Joel, and Pekka Marttinen. MELBA, 2024.
    [Paper] | [Repo]

  5. deedsBCV [Repo]

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