Development of a new MRI image reconstruction by the fusion of compressed sensing and deep learning

• Project/Area Number: 18K19917
• Research Category: Grant-in-Aid for Challenging Research (Exploratory)
• Allocation Type: Multi-year Fund
• Review Section: Medium-sized Section 90:Biomedical engineering and related fields
• Research Institution: Kyoto University
• Principal Investigator: Fujimoto Koji 京都大学, 医学研究科, 特定准教授 (10580110)
• Project Period (FY): 2018-06-29 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000); Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2019: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2018: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
• Keywords: 圧縮センシング / 深層学習 / compressed sensing / deep learning / MRI

Outline of Final Research Achievements

By using a measured data from radial scan MRI, simulated data with varying degree of time delay in the acquisition was generated. A correction method for this delay was reported at the international conference （international society for magnetic resonance in medicine, ISMRM 2020, abstract number #0657). For the deep learning network, a network consists of VGG19 and the following upsampling layers (Conv2DTranspose, Dropout, concatenate,　BatchNormalization, Activation) was constructed and trained with 5000 knee MRI images, with a successful image recovery.

Academic Significance and Societal Importance of the Research Achievements

画像再構成に深層学習の手法を融合させることができれば、画像再構成に要する時間の飛躍的な短縮がはかれ、臨床応用を加速する大きなポイントになりうる。深層学習を用いたMRI画像再構成研究はまだ萌芽期であり、ネットワークの構成、学習方法の最適化、画質評価の手法など今後も検討が必要である。画質劣化を伴わずにMRIの高速撮像が可能となれば、高齢者や小児など、臨床において長時間のMRI撮像が負担となる患者にとって、大きなメリットとなりうる。

Research Products

• [Int'l Joint Research] ニューヨーク大学(米国)
• [Int'l Joint Research] New York University(米国)
• [Int'l Joint Research] New York University(米国)
• [Journal Article] Evaluation of image quality of pituitary dynamic contrast‐enhanced MRI using time‐resolved angiography with interleaved stochastic trajectories (TWIST) and iterative reconstruction TWIST (IT‐TWIST) (2020)
  • Author(s): Yokota Y, Fushimi Y, Okada T, Fujimoto K, Oshima S, Nakajima S, Fujii T, Tanji M, Inagaki N, Miyamoto S, Togashi K
  • Journal Title: Journal of Magnetic Resonance Imaging Volume: 51 Issue: 5 Pages: 1497-1506
  • DOI: 10.1002/jmri.26962
  • NAID: 120006840153
  • Peer Reviewed
• [Journal Article] Automatic segmentation of the uterus on MRI using a convolutional neural network (2019)
  • Author(s): Kurata Yasuhisa、Nishio Mizuho、Kido Aki、Fujimoto Koji、Yakami Masahiro、Isoda Hiroyoshi、Togashi Kaori
  • Journal Title: Computers in Biology and Medicine Volume: 114 Pages: 103438-103438
  • DOI: 10.1016/j.compbiomed.2019.103438
  • Peer Reviewed
• [Journal Article] Quantitative and Qualitative Evaluation of Convolutional Neural Networks with a Deeper U-Net for Sparse-View Computed Tomography Reconstruction (2019)
  • Author(s): Nakai Hirotsugu、Nishio Mizuho、Yamashita Rikiya、Ono Ayako、Nakao Kyoko Kameyama、Fujimoto Koji、Togashi Kaori
  • Journal Title: Academic Radiology Volume: 27 Issue: 4 Pages: 563-574
  • DOI: 10.1016/j.acra.2019.05.016
  • Peer Reviewed
• [Journal Article] Frequency and risk factors of thoracic metastases and optimisation of the use of cross-sectional chest imaging in follow-up patients with cervical cancer (2019)
  • Author(s): Nakao KK, Kido A, Imai T, Abiko K, Fujimoto K, Horie A, Minamiguchi S, Tanaka S, Mandai M, Togashi K
  • Journal Title: Clinical Radiology Volume: 74 Pages: 16-23
  • DOI: 10.1016/j.mri.2018.05.007
  • Peer Reviewed
• [Journal Article] Clinical Application of MR Imaging with Compressed Sensing in Neuroradiology (2018)
  • Author(s): 伏見育崇，藤 本 晃 司，岡 田 知 久，山 本 憲，富樫かおり
  • Journal Title: Japanese Journal of Magnetic Resonance in Medicine Volume: 38 Issue: 3 Pages: 87-92
  • DOI: 10.2463/jjmrm.2018-1656
  • NAID: 130007495571
  • ISSN: 0914-9457, 2434-0499
  • Year and Date: 2018-08-15
  • Peer Reviewed / Open Access
• [Journal Article] 3Dグラディエント撮像の技術と今後の展望 (2018)
  • Author(s): 藤本晃司
  • Journal Title: インナービジョン Volume: 33 Pages: 11-13
• [Journal Article] Complementary regional heterogeneity information from COPD patients obtained using oxygen-enhanced MRI and chest CT (2018)
  • Author(s): Fuseya Y, Muro S, Sato S, Tanabe N, Sato A, Tanimura K, Hasegawa K, Uemasu K, Kubo T, Kido A, Fujimoto K, Fushimi Y, Kusahara H, Sakashita N, Ohno Y, Togashi K, Mishima M, Hirai T.
  • Journal Title: PLoS One Volume: 30 Issue: 8 Pages: e0203273-e0203273
  • DOI: 10.1371/journal.pone.0203273
  • NAID: 120006817600
  • Peer Reviewed / Open Access
• [Journal Article] Automatic inference model construction for computer-aided diagnosis of lung nodule: Explanation adequacy, inference accuracy, and experts' knowledge. (2018)
  • Author(s): Kawagishi M, Kubo T, Sakamoto R, Yakami M, Fujimoto K, Aoyama G, Emoto Y, Sekiguchi H, Sakai K, Iizuka Y, Nishio M, Yamamoto H, Togashi K.
  • Journal Title: PLoS One Volume: 16 Issue: 11 Pages: e0207661-e0207661
  • DOI: 10.1371/journal.pone.0207661
  • NAID: 120006539611
  • Peer Reviewed / Open Access
• [Journal Article] Does the Diffusion Tensor Model Predict the Neurite Distribution of Cerebral Cortical Gray Matter? ? Cortical DTI-NODDI (2018)
  • Author(s): Hikaru Fukutomi, Matthew F. Glasser, Katsutoshi Murata, Thai Akasaka, Koji Fujimoto, Takayuki Yamamoto, Joonas A. Autio, Tomohisa Okada, Kaori Togashi, Hui Zhang, David C. Van Essen, Takuya Hayashi
  • Journal Title: biorxiv Volume: -
  • DOI: 10.1101/441659
  • Open Access / Int'l Joint Research
• [Presentation] A simple method to estimate gradient delay for MRF (2020)
  • Author(s): Koji Fiujimoto, Martijn A. Cloos, Tomohisa Okada
  • Organizer: ISMRM 2020 Annual Meeting
  • Int'l Joint Research
• [Presentation] 制約付きアンサンブル学習を用いた事後平均解の近似によるMR画像再構成 (2019)
  • Author(s): 久保田 菜々子, 原田 賢, 藤本 晃司, 岡田 知久, 井上 真郷
  • Organizer: 第３８回日本医用画像工学会大会
• [Presentation] Advantages and pitfalls in the imaging with human 7T MRI scanner (2019)
  • Author(s): Koji Fujimoto, Tomohisa Okada, Dinh Ha Duy Thuy, Toru Ishii, Martijn A. Cloos, Yuta Urushibata, Hideto Kuribayashi, Tobias Kober, Nouha Salibi, Ravi Seethamraju, John Grinstead, Tadashi Isa
  • Organizer: 2019 RSNA
  • Int'l Joint Research
• [Presentation] Compressed Sensing MR Angiography from Simulation Research to Clinical Practices (2019)
  • Author(s): Sayo Otani, Yasutaka Fushimi, Koji Fujimoto, Takayuki Yamamoto, Azusa Ota, Krishna W. Pandu, Sonoko Oshima, Yusuke Yokota, Satoshi Nakajima, Akihiko Sakata, Akira Yamamoto, Peter Speier, Christoph Forman, Michaela Schmidt, Tomohisa Okada, Kaori Togashi
  • Organizer: 2019 RSNA
  • Int'l Joint Research
• [Presentation] Age-related changes in tissue T1, T2 values of the human brain quantified by 2D PnP-MRF at 7T MRI (2019)
  • Author(s): Koji Fujimoto, Martijn A Cloos, Atsushi Shima, Dinh Ha Duy Thuy, Nobukatsu Sawamoto, Ryosuke Takahashi, Tadashi Isa, Tomohisa Okada
  • Organizer: ISMRM 2019 Annual Meeting
  • Int'l Joint Research
• [Presentation] Evaluation of image quality of pituitary dynamic contrast-enhanced MRI using TWIST and IT-TWIST (2019)
  • Author(s): Yusuke Yokota, Yasutaka Fushimi, Tomohisa Okada, Hikaru Fukutomi, Akira Yamamoto, Satoshi Nakajima, Gosuke Okubo, Sonoko Oshima, Koji Fujimoto, and Kaori Togashi
  • Organizer: ISMRM 2019 Annual Meeting
  • Int'l Joint Research
• [Presentation] Age-related changes in the brain tissue T1, T2 values quantified by 2D MRF in normal healthy volunteers measured at 7T MRI (2018)
  • Author(s): Koji Fujimoto1, Martijn A. Cloos2, Dinh Ha Duy Thuy1, Atsushi Shima3, Nobukatsu Sawamoto4, Ryosuke Takahashi3, Tadashi Isa1,5, Tomohisa Okada1
  • Organizer: 第46回日本磁気共鳴医学会大会
• [Presentation] In Vivo Evaluation of MR Fingerprinting at 7T (2018)
  • Author(s): Thai Akasaka1, Koji Fujimoto2, Martijn Cloos3, Tomohisa Okada2, Kaori Togashi2
  • Organizer: ISMRM 2018 Annual Meeting
  • Int'l Joint Research
• [Presentation] Test-retest reproducibility of quantitative proton MRS using short-TE STEAM and semi-LASER sequences in young adult volunteer brains at 7T (2018)
  • Author(s): Tomohisa Okada1, Hideto Kuribayashi2, Lana G Kaiser 2, Yuta Urushibata 2, Nouha Salibi3, Ravi Teja Seethamraju3, Sinyeob Ahn3, Tadashi Isa1, Koji Fujimoto 1
  • Organizer: ISMRM 2018 Annual Meeting
  • Int'l Joint Research
• [Presentation] Cortical T2* and QSM maps at 7T: test-retest reproducibility, similarity and differences (2018)
  • Author(s): Tomohisa Okada1, Yuta Urushibata2, Tobias Kober3,4,5, Benjamin Schmitt6, Koji Fujimoto1
  • Organizer: ISMRM 2018 Annual Meeting
  • Int'l Joint Research
• [Presentation] Cortical T1 mapping with 3D MR Fingerprinting at 7T using a single transmit channel (2018)
  • Author(s): Koji Fiujimoto1, Martijn A. Cloos2, Yuta Urushibata3, Tomohisa Okada1
  • Organizer: ISMRM 2018 Annual Meeting
  • Int'l Joint Research
• [Presentation] Age-related neurochemical changes in normal human brain: a proton MR spectroscopy study at 7T (2018)
  • Author(s): Toru Ishii, Koji Fujimoto, Hideto Kuribayashi, Yuta Urushibata, Nouha Salibi, Ravi Seethamraju, Ahn Sinyeob, Tadashi Isa, Tomohisa Okada
  • Organizer: ISMRM 2018 Annual Meeting
  • Int'l Joint Research
• [Presentation] Test-retest reproducibility of cortical thickness, B1+, and R1 in healthy young adults measured at 7T (2018)
  • Author(s): Koji Fujimoto1, Yuta Urushibata2, Hideto Kuribayashi2, Tobias Kober3,4,5, Tadashi Isa1, Tomohisa Okada1
  • Organizer: ISMRM 2018 Annual Meeting
  • Int'l Joint Research
• [Presentation] Age-related changes in cortical thickness and R1 values measured at 7T (2018)
  • Author(s): Koji Fujimoto1, Yuta Urushibata2, Hideto Kuribayashi2, Tobias Kober3,4,5, Tadashi Isa1, Tomohisa Okada1
  • Organizer: ISMRM 2018 Annual Meeting
  • Int'l Joint Research
• [Presentation] Automatic segmentation of uterus with malignant tumor on MRI using U-net (2018)
  • Author(s): Yasuhisa Kurata, Mizuho Nishio, Koji Fujimoto, Masahiro Yakami, Aki Kido, Hiroyoshi Isoda, Kaori Togashi
  • Organizer: CARS, 2018-Computer Assisted Radiology and Surgery Proceedings of the 32nd International Congress and Exhibition
  • Int'l Joint Research
• [Presentation] Age-related changes in thickness, R1 and R2* values of the cortex at 7T (2018)
  • Author(s): Tomohisa Okada1, Koji Fujimoto1, Yuta Urushibata2, Hideto Kuribayashi2, Tobias Kober3,4,5, Tadashi Isa1
  • Organizer: i2i workshop
  • Int'l Joint Research