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PET image denoising using unsupervised deep learning

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European Journal of Nuclear Medicine and Molecular Imaging Aims and scope Submit manuscript

Abstract

Purpose

Image quality of positron emission tomography (PET) is limited by various physical degradation factors. Our study aims to perform PET image denoising by utilizing prior information from the same patient. The proposed method is based on unsupervised deep learning, where no training pairs are needed.

Methods

In this method, the prior high-quality image from the patient was employed as the network input and the noisy PET image itself was treated as the training label. Constrained by the network structure and the prior image input, the network was trained to learn the intrinsic structure information from the noisy image and output a restored PET image. To validate the performance of the proposed method, a computer simulation study based on the BrainWeb phantom was first performed. A 68Ga-PRGD2 PET/CT dataset containing 10 patients and a 18F-FDG PET/MR dataset containing 30 patients were later on used for clinical data evaluation. The Gaussian, non-local mean (NLM) using CT/MR image as priors, BM4D, and Deep Decoder methods were included as reference methods. The contrast-to-noise ratio (CNR) improvements were used to rank different methods based on Wilcoxon signed-rank test.

Results

For the simulation study, contrast recovery coefficient (CRC) vs. standard deviation (STD) curves showed that the proposed method achieved the best performance regarding the bias-variance tradeoff. For the clinical PET/CT dataset, the proposed method achieved the highest CNR improvement ratio (53.35% ± 21.78%), compared with the Gaussian (12.64% ± 6.15%, P = 0.002), NLM guided by CT (24.35% ± 16.30%, P = 0.002), BM4D (38.31% ± 20.26%, P = 0.002), and Deep Decoder (41.67% ± 22.28%, P = 0.002) methods. For the clinical PET/MR dataset, the CNR improvement ratio of the proposed method achieved 46.80% ± 25.23%, higher than the Gaussian (18.16% ± 10.02%, P < 0.0001), NLM guided by MR (25.36% ± 19.48%, P < 0.0001), BM4D (37.02% ± 21.38%, P < 0.0001), and Deep Decoder (30.03% ± 20.64%, P < 0.0001) methods. Restored images for all the datasets demonstrate that the proposed method can effectively smooth out the noise while recovering image details.

Conclusion

The proposed unsupervised deep learning framework provides excellent image restoration effects, outperforming the Gaussian, NLM methods, BM4D, and Deep Decoder methods.

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Funding

This work was supported by the National Institutes of Health under grant 1RF1AG052653-01A1, 1P41EB022544-01A1, NIH C06 CA059267, by the National Natural Science Foundation of China (No: U1809204, 61525106, 61427807, 61701436), by the National Key Technology Research and Development Program of China (No: 2017YFE0104000, 2016YFC1300302), and by Shenzhen Innovation Funding (No: JCYJ20170818164343304, JCYJ20170816172431715). Jianan Cui is a PhD student in Zhejiang University and was supported by the China Scholarship Council for 2-year study at Massachusetts General Hospital.

Author information

Author notes

  1. Jianan Cui and Kuang Gong contributed equally to this work.

Authors and Affiliations

  1. Center for Advanced Medical Computing and Analysis, Massachusetts General Hospital, 55 Fruit St, White 427, Boston, MA, 02114, USA

    Jianan Cui, Kuang Gong, Ning Guo, Chenxi Wu, Xiaxia Meng, Kyungsang Kim & Quanzheng Li

  2. State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, 38 Zheda Road, No.3 Teaching Building, 405, Hangzhou, 310027, China

    Jianan Cui & Huafeng Liu

  3. Gordon Center for Medical Imaging, Massachusetts General Hospital/Harvard Medical School, 55 Fruit St, White 427, Boston, MA, 02114, USA

    Kuang Gong, Ning Guo, Kyungsang Kim & Quanzheng Li

  4. Department of Nuclear Medicine, First Hospital of Shanxi Medical University, Taiyuan, China

    Xiaxia Meng & Zhifang Wu

  5. Department of Nuclear Medicine, Peking Union Medical College Hospital, Beijing, China

    Kun Zheng & Zhaohui Zhu

  6. Department of Nuclear Medicine, The Chinese PLA General Hospital, Beijing, China

    Liping Fu, Baixuan Xu & Jiahe Tian

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  1. Jianan Cui
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Corresponding authors

Correspondence to Huafeng Liu or Quanzheng Li.

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Conflict of interest

Author Quanzheng Li has received research support from Siemens Medical Solutions. Other authors declare that they have no conflict of interest.

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

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Electronic supplementary material

Suppl. figure 1

Comparisons between using the noise image as input and using anatomical prior image as input (proposed) based on the simulated BrainWeb phantom. (PNG 64 kb)

High Resolution Image (TIFF 1566 kb)

Suppl. figure 2

Network structure of the modified 3D U-net employed in the proposed method. (PNG 4489 kb)

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Suppl. figure 3

Comparison of the normalized cost values for the Adam, Nesterov’s accelerated gradient (NAG) and L-BFGS algorithms based on one PET/CT dataset. The normalized cost value is defined as \( {L}_n=\left({\varnothing}_{Adam}^{ref}-{\varnothing}^n\right)/\left({\varnothing}_{Adam}^{ref}-{\varnothing}_{Adam}^1\right) \), where \( {\varnothing}_{Adam}^{ref} \) and \( {\varnothing}_{Adam}^1 \) are the cost value using the Adam algorithm running 700 epochs and 1 epoch, respectively. (PNG 23 kb)

High Resolution Image (TIFF 985 kb)

Suppl. figure 4

The lesion contrast .vs standard deviations in reference ROIs by varying FWHMs (gray) of the Gaussian filter, window sizes (blue) of the NLM method, noise standard deviation (light blue) of the BM4D, and training epochs of the Deep Decoder (green) and the proposed method (orange). Left plot is based on one patient scan from the PET/CT dataset. Right plot is based on one patient scan from the PET/MR dataset. (PNG 48 kb)

High Resolution Image (TIFF 56.3 kb)

Suppl. figure 5

Tumor size, SUVmax, SUVmean and TLG versus CNR improvement ratios. Left: PET/CT data set; Right: PET/MR data set. (PNG 6112 kb)

High Resolution Image (TIFF 36565 kb)

Suppl. figure 6

A mismatch example from PET/CT dataset. Zoomed regions shown on top row indicate the tumor structure mismatches between the CT prior and the noisy PET image. (PNG 97 kb)

High Resolution Image (TIFF 1845 kb)

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(DOCX 56.1 kb)

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Cui, J., Gong, K., Guo, N. et al. PET image denoising using unsupervised deep learning. Eur J Nucl Med Mol Imaging 46, 2780–2789 (2019). https://doi.org/10.1007/s00259-019-04468-4

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