We present a keypoint-based foundation model for general purpose brain MRI registration, based on the recently-proposed KeyMorph framework. Our model, called BrainMorph, serves as a tool that supports multi-modal, pairwise, and scalable groupwise registration. BrainMorph is trained on a massive dataset of over 100,000 3D volumes, skull-stripped and non-skull-stripped, from nearly 16,000 unique healthy and diseased subjects. BrainMorph is robust to large misalignments, interpretable via interrogating automatically-extracted keypoints, and enables rapid and controllable generation of many plausible transformations with different alignment types and different degrees of nonlinearity at test-time. We demonstrate the superiority of BrainMorph in solving 3D rigid, affine, and nonlinear registration on a variety of multi-modal brain MRI scans of healthy and diseased subjects, in both the pairwise and groupwise setting. In particular, we show registration accuracy and speeds that surpass many classical and learning-based methods, especially in the context of large initial misalignments and large group settings. All code and models are available at https://github.com/alanqrwang/brainmorph
Image registration · Multi-modal · Keypoint detection · Foundation model · Brain MRI
@article{melba:2025:010:wang,
title = "BrainMorph: A Foundational Keypoint Model for Robust and Flexible Brain MRI Registration",
author = "Wang, Alan Q. and Saluja, Rachit and Kim, Heejong and He, Xinzi and Dalca, Adrian and Sabuncu, Mert R.",
journal = "Machine Learning for Biomedical Imaging",
volume = "3",
issue = "May 2025 issue",
year = "2025",
pages = "181--215",
issn = "2766-905X",
doi = "https://doi.org/10.59275/j.melba.2025-59g7",
url = "https://melba-journal.org/2025:010"
}
TY - JOUR
AU - Wang, Alan Q.
AU - Saluja, Rachit
AU - Kim, Heejong
AU - He, Xinzi
AU - Dalca, Adrian
AU - Sabuncu, Mert R.
PY - 2025
TI - BrainMorph: A Foundational Keypoint Model for Robust and Flexible Brain MRI Registration
T2 - Machine Learning for Biomedical Imaging
VL - 3
IS - May 2025 issue
SP - 181
EP - 215
SN - 2766-905X
DO - https://doi.org/10.59275/j.melba.2025-59g7
UR - https://melba-journal.org/2025:010
ER -