Nothing Special   »   [go: up one dir, main page]

skip to main content
research-article

A multi-scale large kernel attention with U-Net for medical image registration

Published: 23 October 2024 Publication History

Abstract

Deformable image registration minimizes the discrepancy between moving and fixed images by establishing linear and nonlinear spatial correspondences. It plays a crucial role in surgical navigation, image fusion and disease analysis. Its challenge lies in the large number of deformed parameters and the uncertainty of acquisition conditions. Benefiting from the powerful ability to capture hierarchical features and spatial relationships of convolutional neural networks, the medical image registration task has made great progress. Nowadays, the long-range relationship modeling and adaptive selection of self-attention show great potential and have also attracted much attention from researchers. Inspired by this, we propose a new method called Multi-scale Large Kernel Attention UNet (MLKA-Net), which combines a large kernel convolution with the attention mechanism using a multi-scale strategy, and uses a correction module to fine-tune the deformation field to achieve high-accuracy registration. Specifically, we first propose a multi-scale large kernel attention mechanism (MLKA), which generates attention maps by aggregating information from convolution kernels at different scales to improve local feature modeling capabilities of attention. Furthermore, we employ large kernel dilation convolution in proposed attention to construct sufficiently long-range relationships, while keeping lower number of parameters. Finally, to further improve local accuracy of the registration, we design an additional correction module and unsupervised framework to fine-tune the deformation field to solve the issue of original information loss in multilayer networks. Our method is compared qualitatively and quantitatively with 24 representative and advanced methods on the 3 public available 3D datasets from IXI database, LPBA40 dataset and OASIS database, respectively. The experiments demonstrate the excellent performance of the proposed method.

References

[1]
Avants BB, Epstein CL, Grossman M, and Gee JC Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain Med Image Anal 2008 12 1 26-41
[2]
Faisal Beg Mirza, Miller Michael I, Alain Trouvé, and Laurent Younes Computing large deformation metric mappings via geodesic flows of diffeomorphisms Int J Comp Vision 2005 61 139-157
[3]
Heinrich Mattias P, Oskar Maier, and Heinz Handels Multi-modal multi-atlas segmentation using discrete optimisation and self-similarities VISCERAL Challenge@ISBI. 2015 1390 27
[4]
Marc Modat, Ridgway Gerard R, Taylor Zeike A, Manja Lehmann, Josephine Barnes, Hawkes David J, Fox Nick C, and Sébastien Ourselin Fast free-form deformation using graphics processing units Comp Method Programs Biomedicine 2010 98 3 278-284
[5]
Balakrishnan Guha, Zhao Amy, Sabuncu Mert R, Guttag John, and Dalca Adrian V Voxelmorph: A learning framework for deformable medical image registration IEEE Trans Med Imaging 2019 38 8 1788-1800
[6]
Chen Junyu, Frey Eric C, He Yufan, Segars William P, Li Ye, and Yong Du Transmorph: Transformer for unsupervised medical image registration Med Image Anal 2022 82
[7]
Xi Jia, Joseph Bartlett, Zhang Tianyang Lu, Wenqi Qiu Zhaowen, and Jinming Duan Lian Chunfeng, Cao Xiaohuan, Rekik Islem, Xuanang Xu, and Cui Zhiming U-net vs transformer: Is u-net outdated in medical image registration? Machine Learning Medical Imaging 2022 Cham. Springer Nature Switzerland 151-160
[8]
Kim B, Kim DH, Park SH, Kim J, Lee JG, and Ye JC CycleMorph: cycle consistent unsupervised deformable image registration Med Image Anal 2021 71
[9]
Shi Jiacheng, He Yuting, Kong Youyong, Coatrieux Jean-Louis, Shu Huazhong, Yang Guanyu, Li Shuo (2022) Xmorpher: Full transformer for deformable medical image registration via cross attention. In Linwei Wang, Qi Dou, P. Thomas Fletcher, Stefanie Speidel, and Shuo Li, (eds.), Medical Image Computing and Computer Assisted Intervention – MICCAI 2022, 217–226, Cham. Springer Nature Switzerland
[10]
Hessam Sokooti, De Vos Bob, Floris Berendsen, Lelieveldt Boudewijn PF, Ivana Išgum, and Marius Staring Nonrigid image registration using multi-scale 3d convolutional neural networks 2017 Cham Springer
[11]
Yutong Xie, Jianpeng Zhang, Chunhua Shen, and Yong Xia de Bruijne Marleen, Cattin Philippe C, Cotin Stéphane, Padoy Nicolas, Speidel Stefanie, Zheng Yefeng, and Essert Caroline Cotr: Efficiently bridging cnn and transformer for 3d medical image segmentation Medical Image Computing and Computer Assisted Intervention - MICCAI 2021 2021 Cham. Springer International Publishing 171-180
[12]
Yang Xiao, Kwitt Roland, Styner Martin, and Niethammer Marc Quicksilver: Fast predictive image registration – a deep learning approach Neuroimage 2017 158 378-396
[13]
Jaderberg Max, Simonyan Karen, Zisserman Andrew, Kavukcuoglu Koray (2015) Spatial transformer networks. In Proceedings of the 28th International Conference on Neural Information Processing Systems - Volume 2, NIPS’15, page 2017–2025, Cambridge, MA, USA. MIT Press
[14]
Olaf Ronneberger, Philipp Fischer, and Thomas Brox Navab Nassir, Hornegger Joachim, Wells William M, and Frangi Alejandro F U-net: Convolutional networks for biomedical image segmentation Medical Image Computing and Computer-Assisted Intervention - MICCAI 2015 2015 Cham. Springer International Publishing 234-241
[15]
Dosovitskiy Alexey, Beyer Lucas, Kolesnikov Alexander, Weissenborn Dirk, Zhai Xiaohua, Unterthiner Thomas, Dehghani Mostafa, Minderer Matthias, Heigold Georg, Gelly Sylvain, Uszkoreit Jakob, Houlsby Neil (2021) An image is worth 16x16 words: Transformers for image recognition at scale
[16]
Yungeng Zhang, Yuru Pei, and Hongbin Zha de Bruijne Marleen, Cattin Philippe C, Cotin Stéphane, Padoy Nicolas, Speidel Stefanie, Zheng Yefeng, and Essert Caroline Learning dual transformer network for diffeomorphic registration Medical Image Computing and Computer Assisted Intervention - MICCAI 2021–24th International Conference, Strasbourg, France, September 27 - October 1, 2021, Proceedings, Part IV 2021 Springer 129-138
[17]
Chen Xuxin, Wang Ximin, Zhang Ke, Fung Kar-Ming, Thai Theresa C, Moore Kathleen, Mannel Robert S, Liu Hong, Zheng Bin, and Qiu Yuchen Recent advances and clinical applications of deep learning in medical image analysis Med Image Anal 2022 79
[18]
He Kelei, Gan Chen, Li Zhuoyuan, Rekik Islem, Yin Zihao, Ji Wen, Gao Yang, Wang Qian, Zhang Junfeng, and Shen Dinggang Transformers in medical image analysis Intell Medicine 2023 3 1 59-78
[19]
Shen Dinggang, Davatzikos C (2001) Hammer: hierarchical attribute matching mechanism for elastic registration. In Proceedings IEEE Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA 2001), 29–36
[20]
Xavier Pennec, Pascal Cachier, and Nicholas Ayache Taylor Chris and Colchester Alain Understanding the “demon’s algorithm”: 3d non-rigid registration by gradient descent Medical Image Computing and Computer-Assisted Intervention - MICCAI’99, 597–605, Berlin, Heidelberg 1999 Berlin Heidelberg Springer
[21]
Rueckert D, Sonoda LI, Hayes C, Hill DLG, Leach MO, and Hawkes DJ Nonrigid registration using free-form deformations: application to breast mr images IEEE Trans Med Imaging 1999 18 8 712-721
[22]
Ashburner John A fast diffeomorphic image registration algorithm Neuroimage 2007 38 1 95-113
[23]
Vercauteren Tom, Pennec Xavier, Perchant Aymeric, and Ayache Nicholas Diffeomorphic demons: Efficient non-parametric image registration Neuroimage 2009 45 S61-S72
[24]
Shun Miao, Jane Wang Z, and Rui Liao A cnn regression approach for real-time 2d/3d registration IEEE Transa Medical Imaging 2016 35 5 1352-1363
[25]
de Vos Bob D, Berendsen Floris F, Viergever Max A, Staring Marius, Išgum Ivana (2017) End-to-end unsupervised deformable image registration with a convolutional neural network. volume 10553 LNCS of Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 204–212. Springer Verlag
[26]
Dongyang Kuang and Tanya Schmah Suk Heung-Il, Liu Mingxia, Yan Pingkun, and Lian Chunfeng Faim - a convnet method for unsupervised 3d medical image registration Machine Learning in Medical Imaging 2019 Cham. Springer International Publishing 646-654
[27]
Zhao Shengyu, et al., (2019) Recursive cascaded networks for unsupervised medical image registration. 2019 IEEE/CVF International Conference on Computer Vision (ICCV), pages 10599–10609
[28]
Boah Kim, Hwan Kim Dong, Ho Park Seong, Jieun Kim, June-Goo Lee, and Chul Ye Jong Cyclemorph: Cycle consistent unsupervised deformable image registration Med Image Anal 2021 71
[29]
Xiaojun Hu, Miao Kang, Weilin Huang, Scott Matthew R, Roland Wiest, and Mauricio Reyes Shen Dinggang, Liu Tianming, Peters Terry M, Staib Lawrence H, Essert Caroline, Zhou Sean, Yap Pew-Thian, and Khan Ali Dual-stream pyramid registration network Medical Image Computing and Computer Assisted Intervention - MICCAI 2019 2019 Cham. Springer International Publishing 382-390
[30]
Qian Lijun, Zhou Qing, Cao Xiaohuan, Shen Wenjun, Suo Shiteng, Ma Shanshan, Guoxiang Qu, Gong Xuhua, Yan Yunqi, Jianrong Xu, and Jiang Luan A cascade-network framework for integrated registration of liver dce-mr images Comput Med Imaging Graph 2021 89
[31]
Zhao Yao et al. A transformer-based hierarchical registration framework for multimodality deformable image registration Computerized Medical Imaging Graphics 2023 108
[32]
Chen Junyu, He Yufan, Frey Eric C., Li Ye, Du Yong (2021) Vit-v-net: Vision transformer for unsupervised volumetric medical image registration. arXiv preprint http://arxiv.org/abs/2104.06468arXiv:2104.06468
[33]
Ze Liu, Yutong Lin, Cao Yue Hu, Han Wei Yixuan, Zheng Zhang, Stephen Lin, and Baining Guo Swin transformer: Hierarchical vision transformer using shifted windows IEEE/CVF Int Conf Computer Vision (ICCV) 2021 2021 9992-10002
[34]
Fan Jingfan, Cao Xiaohuan, Wang Qian, Yap Pew-Thian, and Shen Dinggang Adversarial learning for mono- or multi-modal registration Med Image Anal 2019 58
[35]
Chitchaya Suwanraksa, Jidapa Bridhikitti, Thiansin Liamsuwan, and Sitthichok Chaichulee Cbct-to-ct translation using registration-based generative adversarial networks in patients with head and neck cancer Cancers. 2023 15 7 2017
[36]
Kim Boah, Han Inhwa, Ye Jong Chul (2022) Diffusemorph: Unsupervised deformable image registration using diffusion model. In Shai Avidan, Gabriel Brostow, Moustapha Cissé, Giovanni Maria Farinella, and Tal Hassner, (eds.), 347–364, Cham. Springer Nature Switzerland
[37]
Cai Linqin, Fang Haodu, and Li Zhiqing Pre-trained multilevel fuse network based on vision-conditioned reasoning and bilinear attentions for medical image visual question answering J Supercomput 2023 79 12 13696-13723
[38]
La Salvia Marco, Torti Emanuele, Marenzi Elisa, Danese Giovanni, and Leporati Francesco Edge and cloud computing approaches in the early diagnosis of skin cancer with attention-based vision transformer through hyperspectral imaging J Supercomput 2024 80 11 16368-16392
[39]
Liu Yu, Ao Yongcai (August 2024) Deformable attention mechanism-based YOLOv7 structure for lung nodule detection. The Journal of Supercomputing. 1-20
[40]
Rane Chinmay, Mehrotra Raj, Bhattacharyya Shubham, Sharma Mukta, and Bhattacharya Mahua A novel attention fusion network-based framework to ensemble the predictions of CNNs for lymph node metastasis detection J Supercomput 2021 77 4 4201-4220
[41]
Shuai L, Guo ZH, Zhang P, Wan J, Pu X, and Wang ZL Stretchable, self-healing, conductive hydrogel fibers for strain sensing and triboelectric energy-harvesting smart textiles Nano Energy 2020 78
[42]
Vaswani Ashish et al. Guyon I, Von Luxburg U, Bengio S, Wallach H, Fergus R, Vishwanathan S, Garnett R, et al. Attention is all you need Advances in Neural Information Processing Systems 2017 Curran Associates Inc
[43]
Dalca Adrian V, Balakrishnan Guha, Guttag John, and Sabuncu Mert R Unsupervised learning of probabilistic diffeomorphic registration for images and surfaces Med Image Anal 2019 57 226-236
[44]
Vincent Arsigny, Olivier Commowick, Xavier Pennec, and Nicholas Ayache A log-euclidean framework for statistics on diffeomorphisms. Medical image computing and computer-assisted intervention : MICCAI Int Conf Medical Image Comp Comp-Assist Interv 2006 1 924-31
[45]
Shattuck David W, Mirza Mubeena, Adisetiyo Vitria, Hojatkashani Cornelius, Salamon Georges, Narr Katherine L, Poldrack Russell A, Bilder Robert M, and Toga Arthur W Construction of a 3d probabilistic atlas of human cortical structures Neuroimage 2008 39 3 1064-1080
[46]
Marcus Daniel S, Wang Tracy H, Parker Jamie, Csernansky John G, Morris John C, and Buckner Randy L Open access series of imaging studies (oasis): Cross-sectional mri data in young, middle aged, nondemented, and demented older adults J Cogn Neurosci 2007 19 9 1498-1507
[47]
Alessa Hering, Lasse Hansen, Mok Tony CW, Chung Albert CS, Hanna Siebert, Stephanie Hager, Annkristin Lange, Sven Kuckertz, Stefan Heldmann, Wei Shao, Sulaiman Vesal, Mirabela Rusu, et al. Geoffrey Sonn. Learn2reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning IEEE Transa Medical Imaging 2023 3 697-712
[48]
Dalca Adrian V, Balakrishnan Guha, Guttag John, Sabuncu Mert R (2018) Unsupervised Learning for Fast Probabilistic Diffeomorphic Registration, 729–738. Springer International Publishing
[49]
Lee Raymond Dice Measures of the amount of ecologic association between species Ecology 1945 26 297-302
[50]
Qiu Huaqi, Qin Chen, Schuh Andreas, Hammernik Kerstin, Rueckert Daniel (2021) Learning diffeomorphic and modality-invariant registration using b-splines. In Medical Imaging with Deep Learning
[51]
Wang Wenhai, Xie Enze, Li Xiang, Fan Deng-Ping, Song Kaitao, Liang Ding, Tong Lu, Luo Ping, and Shao Ling Pvt v2: Improved baselines with pyramid vision transformer Computational Visual Media 2022 8 3 415-424
[52]
Zhou Hong-Yu, Guo Jiansen, Zhang Yinghao, Yu Lequan, Wang Liansheng, Yu Yizhou (2021) nnformer: Interleaved transformer for volumetric segmentation. CoRR, abs/2109.03201
[53]
Hanna Siebert, Lasse Hansen, and Heinrich Mattias P Aubreville Marc, Zimmerer David, and Heinrich Mattias Fast 3d registration with accurate optimisation and little learning for learn2reg 2021 Biomedical Image Registration, Domain Generalisation and Out-of-Distribution Analysis 2022 Cham. Springer International Publishing 174-179
[54]
Mok Tony CW, Chung Albert CS (2020) Large deformation diffeomorphic image registration with laplacian pyramid networks. In Anne L. Martel, Purang Abolmaesumi, Danail Stoyanov, Diana Mateus, Maria A. Zuluaga, S. Kevin Zhou, Daniel Racoceanu, and Leo Joskowicz (eds.), Medical Image Computing and Computer Assisted Intervention – MICCAI 2020, 211–221, Cham. Springer International Publishing

Recommendations

Comments

Please enable JavaScript to view thecomments powered by Disqus.

Information & Contributors

Information

Published In

cover image The Journal of Supercomputing
The Journal of Supercomputing  Volume 81, Issue 1
Jan 2025
4237 pages

Publisher

Kluwer Academic Publishers

United States

Publication History

Published: 23 October 2024
Accepted: 02 October 2024

Author Tags

  1. Medical image registration
  2. Attention
  3. U-Net

Qualifiers

  • Research-article

Funding Sources

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • 0
    Total Citations
  • 0
    Total Downloads
  • Downloads (Last 12 months)0
  • Downloads (Last 6 weeks)0
Reflects downloads up to 14 Dec 2024

Other Metrics

Citations

View Options

View options

Media

Figures

Other

Tables

Share

Share

Share this Publication link

Share on social media