CLAIRE: References

Go back to README.md.

If you plan on using CLAIRE in your research please cite the following two manuscripts:

• A. Mang, A. Gholami, C. Davatzikos & G. Biros. CLAIRE: A distributed-memory solver for constrained large deformation diffeomorphic image registration. SIAM Journal on Scientific Computing 41(5):C548–C584, 2019 [arxiv, sisc].
• M. Brunn, N. Himthani, G. Biros, M. Mehl & A. Mang. CLAIRE: Constrained Large Deformation Diffeomorphic Image Registration on Parallel Computing Architectures. Journal of Open Source Software, 6(61), 3038, 2021. [joss]

A BibTeX entry for LaTeX users are

@article{Mang:2019a,
author = "A. Mang and A. Gholami and C. Davatzikos and G. Biros",
title = "{CLAIRE}: A distributed-memory solver for constrained large deformation diffeomorphic image registration",
journal = "SIAM Journal on Scientific Computing",
volume = "41",
number = "5",
pages = "C548--C584",
year = "2019"}

@article{Brunn:2021a,
author = "M. Brunn and N. Himthani and G. Biros and M. Mehl and A. Mang",
title = "{CLAIRE}: Constrained large deformation diffeomorphic image registration on parallel computing architectures",
journal = "Journal of Open Source Software",
volume = "6",
number = "61",
pages = "3038",
year = "2021"}

If you want to refer to particular implementation or development aspects consider citing one of the works below.

Parallel CPU Implementation

• A. Mang, A. Gholami, C. Davatzikos & G. Biros. CLAIRE: A distributed-memory solver for constrained large deformation diffeomorphic image registration. SIAM Journal on Scientific Computing 41(5):C548–C584, 2019 [arxiv, sisc].
• A. Mang, A. Gholami & G. Biros. Distributed-memory large-deformation diffeomorphic 3D image registration. Proc ACM/IEEE Conference on SuperComputing, #72, 2016 [arxiv, ieee].

Parallel GPU Implementation

• M. Brunn, N. Himthani, G. Biros, M. Mehl & A. Mang. Multi-node multi-GPU diffeomorphic image registration for large-scale imaging problems. Proc ACM/IEEE Conference on Supercomputing 2020. [arxiv, ieee].
• M. Brunn, N. Himthani, G. Biros, M. Mehl & A. Mang. Fast GPU 3D diffeomorphic image registration. Journal of Parallel and Distributed Computing, 149:149-162, 2021 [arxiv, jpdc].

Algorithmic Developments

• A. Mang & G. Biros. An inexact Newton-Krylov algorithm for constrained diffeomorphic image registration. SIAM Journal on Imaging Sciences, 8(2):1030–1069, 2015. [arxiv, siims].
• A. Mang & G. Biros. Constrained H1 regularization schemes for diffeomorphic image registration. SIAM Journal on Imaging Sciences, 9(3):1154–1194, 2016 [arxiv, siims].
• A. Mang & G. Biros. A semi-Lagrangian two-level preconditioned Newton-Krylov solver for constrained diffeomorphic image registration. SIAM Journal on Scientific Computing, 39(6):B1064–B1101, 2017. [arxiv, sisc].
• M. Brunn, N. Himthani, G. Biros, M. Mehl & A. Mang. CLAIRE: Constrained Large Deformation Diffeomorphic Image Registration on Parallel Computing Architectures. Journal of Open Source Software, 6(61), 3038, 2021. [joss]