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基于支撑先验与深度图像先验的无预训练磁共振图像重建方法

赵地 赵莉芝 甘永进 覃斌毅

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基于支撑先验与深度图像先验的无预训练磁共振图像重建方法

赵地, 赵莉芝, 甘永进, 覃斌毅

Undersampled magnetic resonance image reconstruction based on support prior and deep image prior without pre-training

Zhao Di, Zhao Li-Zhi, Gan Yong-Jin, Qin Bin-Yi
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  • 基于深度学习的磁共振成像(magnetic resonance imaging, MRI)方法需要大规模、高质量的病患数据样本集进行预训练. 然而, 由于病患隐私及设备等因素限制, 获取大规模、高质量的磁共振数据集在实际临床应用中面临挑战. 本文提出一种新的基于深度学习的欠采样磁共振图像重建方法, 该方法无需预训练、不依赖训练数据集, 而是充分利用待重建的目标MR图像的结构先验和支撑先验, 并将其引入深度图像先验(deep image prior, DIP)框架, 从而削减对训练数据集的依赖, 提升学习效率. 基于参考图像与目标图像的相似性, 采用高分辨率参考图像作为深度网络输入, 将结构先验信息引入网络; 将参考图像在小波域中幅值大的系数索引集作为目标图像的已知支撑集, 构造正则化约束项, 将网络训练转化为网络参数的最优化求解过程. 实验结果表明, 本文方法可由欠采样k空间数据重建得到更精确的磁共振图像, 且在保留组织特征、细节纹理方面具有明显优势.
    Magnetic resonance imaging (MRI) method based on deep learning needs large-quantity and high-quality patient-based datasets for pre-training. However, this is a challenge to the clinical applications because it is difficult to obtain a sufficient quantity of patient-based MR datasets due to the limitation of equipment and patient privacy concerns. In this paper, we propose a novel undersampled MRI reconstruction method based on deep learning. This method does not require any pre-training procedures and does not depend on training datasets. The proposed method is inspired by the traditional deep image prior (DIP) framework, and integrates the structure prior and support prior of the target MR image to improve the efficiency of learning. Based on the similarity between the reference image and the target image, the high-resolution reference image obtained in advance is used as the network input, thereby incorporating the structural prior information into network. By taking the coefficient index set of the reference image with large amplitude in the wavelet domain as the known support of the target image, the regularization constraint term is constructed, and the network training is transformed into the optimization process of network parameters. Experimental results show that the proposed method can obtain more accurate reconstructions from undersampled k-space data, and has obvious advantages in preserving tissue features and detailed texture.
      通信作者: 赵莉芝, lizhi3285@126.com
    • 基金项目: 国家自然科学基金(批准号: 62041111, 61701554)、广西自然科学基金(批准号: 2021GXNSFBA220056, 2019GXNSFBA245076)和玉林师范学院科研基金 (批准号: G2019ZK03)资助的课题
      Corresponding author: Zhao Li-Zhi, lizhi3285@126.com
    • Funds: Project supported by the National Natural Science Foundation of China (Grant Nos. 62041111, 61701554), the Natural Science Foundation of Guangxi, China (Grant Nos. 2021GXNSFBA220056, 2019GXNSFBA245076), and the Research Funds of Yulin Normal University, China (Grant No. G2019ZK03)
    [1]

    Davenport M A, Duarte M F, Eldar Y C, et al. 2012 Compressed Sensing: Theory and Applications (Cambridge: Cambridge University Press) pp1–64

    [2]

    Lustig M, Donoho D L, Pauly J M 2007 Magn. Reson. Med. 58 1182Google Scholar

    [3]

    Qu X B, Guo D, Ning B D, Hou Y K, et al. 2012 Magn. Reson. Imaging 30 964Google Scholar

    [4]

    Liu J B, Wang S S, Peng X, Liang D 2015 Comput. Math. Methods Med. 2015 1

    [5]

    Zhan Z F, Cai J F, Guo D, Liu Y S, Chen Z, Qu X B 2016 IEEE Trans. Biomed. Eng. 63 1850Google Scholar

    [6]

    Liu Q G, Wang S S, Ying L, Peng X, et al. 2013 IEEE Trans. Image Process. 22 4652Google Scholar

    [7]

    Du H Q, Lam F 2012 Magn. Reson. Imaging 30 954Google Scholar

    [8]

    Peng X, Du H Q, Lam F, Babacan D, Liang Z P 2011 In: Proceedings of IEEE International Symposium on Biomedical Imaging Chicago, USA, March 30, 2011 p89

    [9]

    Manduca A, Trzasko J D, Li Z B. 2010 In: Proceedings of SPIE, The International Society for Optical Engineering (California-2010.2.13) p762223

    [10]

    Han Y, Du H Q, Gao X Z, Mei W B 2017 IET Image Proc. 11 155Google Scholar

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    Stojnic M, Parvaresh F, Hassibi B 2009 IEEE Trans. Signal Process. 57 3075Google Scholar

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    Usman M, Prieto C, Schaeffter T, et al. 2011 Magn. Reson. Med. 66 1163Google Scholar

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    Blumensath T 2011 IEEE Trans. Inf. Theory 57 4660Google Scholar

    [14]

    Litjens G, Kooi T, Bejnordi B E, Setio A A A, Ciompi F, Ghafoorian M, van der Laak J A W M, van Ginneken B, Sánchez C I 2017 Med. Image Anal. 42 60Google Scholar

    [15]

    Wang S S, Xiao T H, Liu Q G, Zheng H R 2021 Biomed. Signal Process. Control 68 102579Google Scholar

    [16]

    Liang D, Cheng J, Ke Z W, Ying L 2020 IEEE Signal Processing Mag. 37 141Google Scholar

    [17]

    Schlemper J, Caballero J, Hajnal J V, Price A N, Rueckert D 2018 IEEE Trans. Med. Imaging 37 491Google Scholar

    [18]

    Yang G, Yu S, Dong H, Slabaugh G, Dragotti P L, Ye X J, Liu F D, Arridge S, Keegan J, Guo Y K, Firmin D 2018 IEEE Trans. Med. Imaging 37 1310Google Scholar

    [19]

    Wang S S, Su Z H, Ying L, Peng X, Zhu S, Liang F, Feng D G, Liang D 2016 In: IEEE 13th International Symposium on Biomedical Imaging Prague, Czech Republic, April 01, 2016 p514

    [20]

    Akcakaya M, Moeller S, Weingartner S, Ugurbil K 2019 Magn. Reson. Med. 81 439Google Scholar

    [21]

    Aggarwal H K, Mani M P, Jacob M 2019 IEEE Trans. Med. Imaging 38 394Google Scholar

    [22]

    Yang Y, Sun J, Li H B, Xu Z B 2016 In: Advances in Neural Information Processing Systems Barcelona, Spain, December 05, 2016 p10

    [23]

    Qin C, Schlemper J, Caballero J, Price A N, Hajnal J V, Rueckert D 2019 IEEE Trans. Med. Imaging 38 280Google Scholar

    [24]

    Ulyanov D, Vedaldi A, Lempitsky V 2018 In: IEEE/CVF Conference on Computer Vision and Pattern Recognition Salt Lake City, USA, June 18, 2018 p9446

    [25]

    Gong K, Catana C, Qi J Y, Li Q Z 2019 IEEE Trans. Med. Imaging 38 1655Google Scholar

    [26]

    Gary M, Michael E, Peyman M 2019 arXiv: 1903.10176

    [27]

    Sagel A, Roumy A, Guillemot C 2020 In: IEEE International Conference on Acoustics, Speech and Signal Processing Barcelona, Spain, May 04, 2020 p2513

    [28]

    Liu J M, Sun Y, Xu X J, Kamilov U S 2019 In: IEEE International Conference on Acoustics, Speech and Signal Processing Brighton, Britain, May 12, 2019 p7715

    [29]

    Hashimoto F, Ohba H, Ote K, Teramoto A, Sukada H 2019 IEEE Access 7 96594Google Scholar

    [30]

    Dave van Veen, Ajil J, Mahdi S, Eric P, Sriram V, Alexandros G D 2018 arXiv: 1806.06438

    [31]

    Daniel O B, Johannes L, Maximilian S 2020 Inverse Problems 36 094004Google Scholar

    [32]

    Yoo J, Jin K H, Gupta H, Yerly J, Stuber M, Unser M 2021 IEEE Trans. Med. Imaging (Early Access)

    [33]

    Vaswani N, Lu W 2010 IEEE Trans. Signal Process. 58 4595Google Scholar

    [34]

    Wang Z, Bovik A C, Sheikh H R, Simoncelli E P 2004 IEEE Trans. Image Process. 13 600Google Scholar

  • 图 1  方法总览图 (a)本文重建方法总体步骤; (b)本文重建方法采用的网络架构[24]

    Fig. 1.  Overview of the proposed method: (a) Overall process for the proposed reconstruction method; (b) network architecture[24] used in the proposed method.

    图 2  参考图像和目标图像的结构相似性及小波域支撑分布 (a), (b)同一病人的脑部扫描MR图像; (c), (d)对应的小波系数分布(Haar小波, 9层小波分解)

    Fig. 2.  Structural similarity between the reference and target images and support distributions in the wavelet domain: (a), (b) Brain MR images from the same patient; (c), (d) corresponding wavelet coefficient distributions (Using Haar wavelet at level 9).

    图 3  实验数据. 第一组 (a)参考图像; (b)待重建的目标图像1. 第二组 (c)参考图像; (d)待重建的目标图像2; (e)待重建的目标图像3

    Fig. 3.  MR images used in the experiments. Group one: (a) Reference image; (b) target image 1. Group two: (c) Reference image; (d) target image 2; (e) target image 3.

    图 4  降采样模板 (a)笛卡尔采样模板; (b)径向采样模板; (c)变密度采样模板

    Fig. 4.  Undersampling masks used in the experiments: (a) Cartesian mask; (b) radial mask; (c) variable density mask.

    图 5  笛卡尔采样模板40%采样率下目标图像1的重建结果对比. 第一行为目标图像1与各方法重建结果, 第二行为对应的误差图像, 第三行为对应的局部放大图

    Fig. 5.  Comparison of reconstructions of target image 1 using Cartesian undersampled mask with 40% sampling rate: Target image 1 and reconstruction results (1st row), the corresponding error images (2nd row), and the corresponding zoom-in images (3rd row)

    图 6  笛卡尔采样模板20%采样率下目标图像2的重建结果对比. 第一行为目标图像2与各方法重建结果, 第二行为对应的误差图像, 第三行为对应的局部放大图

    Fig. 6.  Comparison of reconstructions of target image 2 using Cartesian undersampled mask with 20% sampling rate: Target image 2 and reconstruction results (1st row), the corresponding error images (2nd row), and the corresponding zoom-in images (3rd row)

    图 7  笛卡尔采样模板30%采样率下目标图像3的重建结果对比. 第一行为目标图像3与各方法重建结果, 第二行为对应的误差图像, 第三行为对应的局部放大图

    Fig. 7.  Comparison of reconstructions of target image 3 using Cartesian undersampled mask with 30% sampling rate: Target image 3 and reconstruction results (1st row), the corresponding error images (2nd row), and the corresponding zoom-in images (3rd row)

    图 8  变密度采样模板30%采样率下目标图像1的重建结果对比. 第一行为目标图像1与各方法重建结果, 第二行为对应的误差图像, 第三行为对应的局部放大图

    Fig. 8.  Comparison of reconstructions of target image 1 using variable density undersampled mask with 30% sampling rate: Target image 1 and reconstruction results (1st row), the corresponding error images (2nd row), and the corresponding zoom-in images (3rd row).

    图 9  径向采样模板10%采样率下目标图像3的重建结果对比. 第一行为目标图像3与各方法重建结果, 第二行为对应的误差图像, 第三行为对应的局部放大图

    Fig. 9.  Comparison of reconstructions of target image 3 using radial undersampled mask with 10% sampling rate: Target image 3 and reconstruction results (1st row), the corresponding error images (2nd row), and the corresponding zoom-in images (3rd row).

    图 10  笛卡尔采样模板下本文方法的相对误差曲线

    Fig. 10.  Relative errors curves of the proposed method under Cartesian undersampled mask

    图 11  参考图像与目标图像间存在对比度差异及运动偏移情况下本文方法的重建结果 (a)参考图像; (b)待重建目标图像; (c)本文方法对(b)的重建结果; (d)待重建目标图像(存在运动偏移); (e)本文方法对(d)的重建结果; (a)—(c) 相对误差为2.19%, PSNR = 40.8788 dB, SSIM = 0.9937; (d), (e) 相对误差为2.54%, PSNR = 39.0825 dB, SSIM = 0.9937

    Fig. 11.  Reconstructions of the proposed method when there is contrast difference and motion between the reference image and the target image: (a) Reference image; (b) target image to be reconstructed; (c) reconstruction of (b) by the proposed method; (d) target image to be reconstructed(with motion effects); (e) reconstruction of (d) by the proposed method; (a)—(c) the relative error is 2.19%, PSNR = 40.8788 dB, SSIM = 0.9937; (d), (e) relative error 2.54%, PSNR = 39.0825 dB, SSIM = 0.9937.

    表 1  实验参数设置

    Table 1.  Parameter setting for experiments

    参数图像
    目标图像1目标图像2目标图像3
    网络超参数学习率0.0050.0030.003
    L666
    $n_{\rm{d}}$[32, 64, 64, 64, 128, 128][16, 32, 64, 64, 128, 128][16, 32, 64, 64, 128, 128]
    $n_{\rm{u}}$[32, 64, 64, 64, 128, 128][16, 32, 64, 64, 128, 128][16, 32, 64, 64, 128, 128]
    $n_{\rm{s}}$[16, 16, 16, 16, 16, 16][16, 16, 16, 16, 16, 16][16, 16, 16, 16, 16, 16]
    $k_{\rm{d}}$[3, 3, 3, 3, 3, 3][3, 3, 3, 3, 3, 3][3, 3, 3, 3, 3, 3]
    $k_{\rm{u}}$[3, 3, 3, 3, 3, 3][3, 3, 3, 3, 3, 3][3, 3, 3, 3, 3, 3]
    $k_{\rm{s}}$[1, 1, 1, 1, 1, 1][1, 1, 1, 1, 1, 1][1, 1, 1, 1, 1, 1]
    迭代次数500030003000
    小波参数小波函数HaarHaarHaar
    分解层数788
    P135005500052000
    λ1 × 10–101 × 10–61 × 10–9
    下载: 导出CSV

    表 2  笛卡尔采样模板下不同重建方法的相对误差、PSNR及SSIM

    Table 2.  Relative errors, PSNR and SSIM values of reconstruction by different methods under Cartesian undersampled mask

    待重建MR图像重建方法10% 20%
    相对误差/%PSNR/dBSSIM相对误差/%PSNR/dBSSIM
    目标图像1零填充35.6418.73650.5543 16.1425.61850.7135
    CS-WS34.5319.01010.559013.7427.01390.7998
    DIP32.5119.53440.666612.4927.84400.8989
    本文方法19.8923.80040.81729.4330.28520.9793
    目标图像2零填充19.6622.56250.7550 13.3625.92040.8065
    CS-WS17.1423.75300.765410.3428.14260.8507
    DIP15.0924.90870.84735.4133.78140.9619
    本文方法7.5130.92880.94543.4837.59150.9788
    目标图像3零填充17.6423.57160.7857 12.7626.38070.8266
    CS-WS15.2424.83950.81399.8728.61440.8774
    DIP14.9025.06600.85855.4333.82640.9607
    本文方法7.3131.22280.94913.5337.54880.9806
    待重建MR图像重建方法30% 40%
    相对误差/%PSNR/dBSSIM相对误差/%PSNR/dBSSIM
    目标图像1零填充11.5328.53610.7657 7.7132.03370.8087
    CS-WS9.4030.31260.86896.6833.27360.9136
    DIP9.0530.63860.93426.9832.89330.9605
    本文方法7.0632.79700.95905.6434.73950.9728
    目标图像2零填充4.6135.16770.8677 3.4637.66300.8830
    CS-WS2.6140.08830.93771.9542.63380.9438
    DIP2.8039.49920.98582.3341.10080.9892
    本文方法2.0842.04690.99051.7343.64370.9931
    目标图像3零填充4.3135.81820.8813 3.2438.29610.8997
    CS-WS2.4540.71930.94441.8443.19580.9601
    DIP3.2238.56320.98242.5440.43240.9885
    本文方法2.0542.24840.99081.6444.20510.9939
    下载: 导出CSV

    表 3  径向采样模板及变密度采样模板下不同重建方法的相对误差、PSNR及SSIM

    Table 3.  Relative errors, PSNR and SSIM values of reconstruction by different methods under radial undersampled mask and variable density undersampled mask

    待重建MR图像采样模板(采样率)重建方法相对误差/%PSNR/dBSSIM
    目标图像1径向(20%)零填充14.3426.64260.7852
    CS-WS12.1128.11290.8519
    DIP10.9528.98450.9169
    本文方法7.9231.79600.9547
    变密度(30%)零填充15.0326.23730.7735
    CS-WS11.1528.82640.8662
    DIP9.2630.44410.9321
    本文方法6.4333.61990.9648
    目标图像2径向(10%)零填充8.0530.32020.7960
    CS-WS5.7333.28030.9010
    DIP4.4035.58140.9662
    本文方法3.5437.44340.9760
    变密度(20%)零填充6.4732.22130.8778
    CS-WS3.5637.41950.9625
    DIP3.1538.47640.9821
    本文方法2.5740.22430.9850
    目标图像3径向(10%)零填充7.0331.55760.8177
    CS-WS5.1834.21110.9158
    DIP4.7335.03030.9629
    本文方法3.5537.48520.9751
    变密度(20%)零填充5.8233.21060.8978
    CS-WS3.2738.21610.9675
    DIP3.0138.97860.9819
    本文方法2.5440.42290.9852
    下载: 导出CSV

    表 4  径向采样模板及变密度采样模板下不同重建方法的相对误差、PSNR及SSIM

    Table 4.  Relative errors, PSNR and SSIM values of reconstructions by different methods under radial undersampled mask and variable density undersampled mask

    采样模板(采样率)重建方法相对误差/%PSNR/dBSSIM
    径向 (20%)DIP + Ref8.8830.91800.9478
    DIP + Sup10.3529.47390.9264
    DIP + Ref + Sup8.2431.55300.9512
    DIP + Ref + Sup + Cor7.9231.79600.9547
    变密度 (30%)DIP + Ref7.3832.41160.9583
    DIP + Sup9.0830.61040.9583
    DIP + Ref + Sup6.7133.23600.9620
    DIP + Ref + Sup + Cor6.4333.61990.9648
    下载: 导出CSV

    表 5  笛卡尔采样下不同重建方法的计算时间

    Table 5.  Computational time for different reconstruction methods under the Cartesian mask

    待重建MR图像重建方法计算时间
    10%20%30%40%
    目标图像1CS-WS46 s46 s49 s46 s
    DIP2 min 53 s2 min 43 s2 min 47 s2 min 45 s
    本文方法3 min 55 s3 min 56 s3 min 54 s3 min 56 s
    图11(d)所示目标图像CS-WS42 s42 s45 s44 s
    DIP2 min 33 s2 min 35 s2 min 35 s2 min 34 s
    本文方法3 min 14 s3 min 15 s3 min 15 s3 min 13 s
    下载: 导出CSV
  • [1]

    Davenport M A, Duarte M F, Eldar Y C, et al. 2012 Compressed Sensing: Theory and Applications (Cambridge: Cambridge University Press) pp1–64

    [2]

    Lustig M, Donoho D L, Pauly J M 2007 Magn. Reson. Med. 58 1182Google Scholar

    [3]

    Qu X B, Guo D, Ning B D, Hou Y K, et al. 2012 Magn. Reson. Imaging 30 964Google Scholar

    [4]

    Liu J B, Wang S S, Peng X, Liang D 2015 Comput. Math. Methods Med. 2015 1

    [5]

    Zhan Z F, Cai J F, Guo D, Liu Y S, Chen Z, Qu X B 2016 IEEE Trans. Biomed. Eng. 63 1850Google Scholar

    [6]

    Liu Q G, Wang S S, Ying L, Peng X, et al. 2013 IEEE Trans. Image Process. 22 4652Google Scholar

    [7]

    Du H Q, Lam F 2012 Magn. Reson. Imaging 30 954Google Scholar

    [8]

    Peng X, Du H Q, Lam F, Babacan D, Liang Z P 2011 In: Proceedings of IEEE International Symposium on Biomedical Imaging Chicago, USA, March 30, 2011 p89

    [9]

    Manduca A, Trzasko J D, Li Z B. 2010 In: Proceedings of SPIE, The International Society for Optical Engineering (California-2010.2.13) p762223

    [10]

    Han Y, Du H Q, Gao X Z, Mei W B 2017 IET Image Proc. 11 155Google Scholar

    [11]

    Stojnic M, Parvaresh F, Hassibi B 2009 IEEE Trans. Signal Process. 57 3075Google Scholar

    [12]

    Usman M, Prieto C, Schaeffter T, et al. 2011 Magn. Reson. Med. 66 1163Google Scholar

    [13]

    Blumensath T 2011 IEEE Trans. Inf. Theory 57 4660Google Scholar

    [14]

    Litjens G, Kooi T, Bejnordi B E, Setio A A A, Ciompi F, Ghafoorian M, van der Laak J A W M, van Ginneken B, Sánchez C I 2017 Med. Image Anal. 42 60Google Scholar

    [15]

    Wang S S, Xiao T H, Liu Q G, Zheng H R 2021 Biomed. Signal Process. Control 68 102579Google Scholar

    [16]

    Liang D, Cheng J, Ke Z W, Ying L 2020 IEEE Signal Processing Mag. 37 141Google Scholar

    [17]

    Schlemper J, Caballero J, Hajnal J V, Price A N, Rueckert D 2018 IEEE Trans. Med. Imaging 37 491Google Scholar

    [18]

    Yang G, Yu S, Dong H, Slabaugh G, Dragotti P L, Ye X J, Liu F D, Arridge S, Keegan J, Guo Y K, Firmin D 2018 IEEE Trans. Med. Imaging 37 1310Google Scholar

    [19]

    Wang S S, Su Z H, Ying L, Peng X, Zhu S, Liang F, Feng D G, Liang D 2016 In: IEEE 13th International Symposium on Biomedical Imaging Prague, Czech Republic, April 01, 2016 p514

    [20]

    Akcakaya M, Moeller S, Weingartner S, Ugurbil K 2019 Magn. Reson. Med. 81 439Google Scholar

    [21]

    Aggarwal H K, Mani M P, Jacob M 2019 IEEE Trans. Med. Imaging 38 394Google Scholar

    [22]

    Yang Y, Sun J, Li H B, Xu Z B 2016 In: Advances in Neural Information Processing Systems Barcelona, Spain, December 05, 2016 p10

    [23]

    Qin C, Schlemper J, Caballero J, Price A N, Hajnal J V, Rueckert D 2019 IEEE Trans. Med. Imaging 38 280Google Scholar

    [24]

    Ulyanov D, Vedaldi A, Lempitsky V 2018 In: IEEE/CVF Conference on Computer Vision and Pattern Recognition Salt Lake City, USA, June 18, 2018 p9446

    [25]

    Gong K, Catana C, Qi J Y, Li Q Z 2019 IEEE Trans. Med. Imaging 38 1655Google Scholar

    [26]

    Gary M, Michael E, Peyman M 2019 arXiv: 1903.10176

    [27]

    Sagel A, Roumy A, Guillemot C 2020 In: IEEE International Conference on Acoustics, Speech and Signal Processing Barcelona, Spain, May 04, 2020 p2513

    [28]

    Liu J M, Sun Y, Xu X J, Kamilov U S 2019 In: IEEE International Conference on Acoustics, Speech and Signal Processing Brighton, Britain, May 12, 2019 p7715

    [29]

    Hashimoto F, Ohba H, Ote K, Teramoto A, Sukada H 2019 IEEE Access 7 96594Google Scholar

    [30]

    Dave van Veen, Ajil J, Mahdi S, Eric P, Sriram V, Alexandros G D 2018 arXiv: 1806.06438

    [31]

    Daniel O B, Johannes L, Maximilian S 2020 Inverse Problems 36 094004Google Scholar

    [32]

    Yoo J, Jin K H, Gupta H, Yerly J, Stuber M, Unser M 2021 IEEE Trans. Med. Imaging (Early Access)

    [33]

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出版历程
  • 收稿日期:  2021-09-22
  • 修回日期:  2021-10-18
  • 上网日期:  2022-02-21
  • 刊出日期:  2022-03-05

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