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MRI brain tumor medical images analysis using deep learning techniques: a systematic review

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Abstract

The substantial progress of medical imaging technology in the last decade makes it challenging for medical experts and radiologists to analyze and classify. Medical images contain massive information that can be used for diagnosis, surgical planning, training, and research. There is, therefore, a need for a technique that can automatically analyze and classify the images based on their respective contents. Deep Learning (DL) techniques have been recently used for medical image analysis, and this paper focuses on DL in the context of analyzing Magnetic Resonance Imaging (MRI) brain medical images. A comprehensive overview of the state-of-the-art processing of brain medical images using deep neural networks is detailed here. The scope of this research paper is restricted to three digital databases: (1) the Science Direct database, (2) the IEEEXplore Library of Engineering and Technology Technical Literature, and (3) Scopus database. 427 publications were evaluated and discussed in this research paper.

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References

  1. Muller H, M. Deserno T. Content-Based Medical Image Retrieval Henning. Biomedical Image Processing (Biological and Medical Physics, Biomedical Engineering). 2011;55–76. https://doi.org/10.1007/978-3-642-15816-2.

  2. Chen S, Ding C, Liu M. Dual-force convolutional neural networks for accurate brain tumor segmentation. Pattern Recogn. 2019;88:90–100. https://doi.org/10.1016/j.patcog.2018.11.009.

    Article  Google Scholar 

  3. Wachinger C, Reuter M, Klein T. DeepNAT: Deep convolutional neural network for segmenting neuroanatomy. NeuroImage. 2018;170:434–45. https://doi.org/10.1016/j.neuroimage.2017.02.035.

    Article  Google Scholar 

  4. Johnson DR, Guerin JB, Giannini C, Morris JM, Eckel LJ, Kaufmann TJ. 2016 updates to the WHO brain tumor classification system: What the radiologist needs to know. Radiographics. 2017;37(7):2164–80. https://doi.org/10.1148/rg.2017170037.

    Article  Google Scholar 

  5. DeAngelis. BRAIN TUMORS. 2001;344(2): 114–123.

  6. Saman S, Jamjala Narayanan S. Survey on brain tumor segmentation and feature extraction of MR images. International Journal of Multimedia Information Retrieval. 2019;8(2):79–99. https://doi.org/10.1007/s13735-018-0162-2.

    Article  Google Scholar 

  7. Brunese L, Mercaldo F, Reginelli A, Santone A. An ensemble learning approach for brain cancer detection exploiting radiomic features. Comput Methods Programs Biomed. 2020;185:105134. https://doi.org/10.1016/j.cmpb.2019.105134.

    Article  Google Scholar 

  8. Aiello M, Cavaliere C, D’Albore A, Salvatore M. The Challenges of Diagnostic Imaging in the Era of Big Data. Journal of Clinical Medicine. 2019;8(3):316. https://doi.org/10.3390/jcm8030316.

    Article  Google Scholar 

  9. Işın A, Direkoğlu C, Şah M. Review of MRI-based Brain Tumor Image Segmentation Using Deep Learning Methods. Procedia Computer Science. 2016;102:317–24. https://doi.org/10.1016/j.procs.2016.

    Article  Google Scholar 

  10. Kong Y, Gao J, Xu Y, Pan Y, Wang J, Liu J. Classification of autism spectrum disorder by combining brain connectivity and deep neural network classifier. Neurocomputing. 2019;324:63–8. https://doi.org/10.1016/j.neucom.2018.04.080.

    Article  Google Scholar 

  11. Menze B, Jakab A, Bauer S, Kalpathy-cramer J, Farahani K, Kirby J, Leemput K Van. Benchmark ( BRATS ) To cite this version : HAL Id : hal-00935640 The Multimodal Brain Tumor Image Segmentation Benchmark ( BRATS ). 2014.

  12. Havaei M, Davy A, Warde-farley D, Biard A, Courville A, Bengio Y, Larochelle H. Brain tumor segmentation with Deep Neural Networks. Med Image Anal. 2017;35:18–31. https://doi.org/10.1016/j.media.2016.05.004.

    Article  Google Scholar 

  13. Mallick PK, Ryu SH, Satapathy SK, Mishra S, Nguyen NG, Tiwari P. Brain MRI ImageClassification for Cancer Detection using Deep Wavelet Autoencoder based Deep Neural Network. IEEE Access, PP(c). 2019;1–1. https://doi.org/10.1109/access.2019.2902252.

  14. Mittal M, Goyal LM, Kaur S, Kaur I, Verma A, Jude Hemanth D. Deep learning based enhanced tumor segmentation approach for MR brain images. Applied Soft Computing Journal. 2019;78:346–54. https://doi.org/10.1016/j.asoc.2019.02.036.

    Article  Google Scholar 

  15. Talo M, Baloglu UB, Yıldırım Ö, Rajendra Acharya U. Application of deep transfer learning for automated brain abnormality classification using MR images. Cognitive Systems Research. 2019;54:176–88. https://doi.org/10.1016/j.cogsys.2018.12.007.

    Article  Google Scholar 

  16. Menze BH, Jakab A, Bauer S, Kalpathy-Cramer J, Farahani K, Kirby J, Van Leemput K. The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS). IEEE Trans Med Imaging. 2015;34(10):1993–2024. https://doi.org/10.1109/TMI.2014.2377694.

    Article  Google Scholar 

  17. Zhang J, Xie Y, Wu Q, Xia Y. Medical image classification using synergic deep learning. Med Image Anal. 2019;54:10–9. https://doi.org/10.1016/j.media.2019.02.010.

    Article  Google Scholar 

  18. Litjens G, Kooi T, Bejnordi BE, Setio AAA, Ciompi F, Ghafoorian M, Sánchez CI. A survey on deep learning in medical image analysis. Med Image Anal. 2017;42:60–88. https://doi.org/10.1016/j.media.2017.07.005.

    Article  Google Scholar 

  19. Zhang L, Ji Q. A Bayesian Network Model for Automatic and Interactive Image Segmentation. IEEE Trans Image Process. 2011;20(9):2582–93. https://doi.org/10.1109/tip.2011.2121080.

    Article  MathSciNet  MATH  Google Scholar 

  20. Anwar SM, Majid M, Qayyum A, Awais M, Alnowami M, Khan MK. Medical Image Analysis using Convolutional Neural Networks: A Review. J Med Syst. 2018;42(11):1–13. https://doi.org/10.1007/s10916-018-1088-1.

    Article  Google Scholar 

  21. Ayachi R, Ben Amor N. Brain tumor segmentation using support vector machines. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5590 LNAI. 2009;736–747. https://doi.org/10.1007/978-3-642-02906-6_63.

  22. Liaw A, Wiener M. Classification and Regression by randomForest. R News. 2002;2(3):18–22.

    Google Scholar 

  23. Saba T, Mohamed AS, El-Affendi M, Amin J, Sharif M. Brain tumor detection using fusion of hand crafted and deep learning features. Cognitive Systems Research. 2020;59:221–30. https://doi.org/10.1016/j.cogsys.2019.09.007.

    Article  Google Scholar 

  24. Pereira S, Meier R, McKinley R, Wiest R, Alves V, Silva CA, Reyes M. Enhancing interpretability of automatically extracted machine learning features: application to a RBM-Random Forest system on brain lesion segmentation. Medical Image Analysis. 2018;44:228–44. https://doi.org/10.1016/j.media.2017.12.009.

    Article  Google Scholar 

  25. Thaha MM, Kumar KPM, Murugan BS, Dhanasekeran S, Vijayakarthick P, Selvi AS. Brain Tumor Segmentation Using Convolutional Neural Networks in MRI Images 2. J Med Syst. 2019;43(9):1240–51. https://doi.org/10.1007/s10916-019-1416-0.

    Article  Google Scholar 

  26. Maier A, Syben C, Lasser T, Riess C. A gentle introduction to deep learning in medical image processing. Z Med Phys. 2019;29(2):86–101. https://doi.org/10.1016/j.zemedi.2018.12.003.

    Article  Google Scholar 

  27. Ronneberger O, Fischer P, Brox T. U-net: Convolutional networks for biomedical image segmentation. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2015;9351:234–41. https://doi.org/10.1007/978-3-319-24574-4_28.

    Article  Google Scholar 

  28. Nema S, Dudhane A, Murala S, Naidu S. RescueNet: An unpaired GAN for brain tumor segmentation. Biomedical Signal Processing and Control. 2020;55. https://doi.org/10.1016/j.bspc.2019.101641.

  29. Li H, Li A, Wang M. A novel end-to-end brain tumor segmentation method using improved fully convolutional networks. Comput Biol Med. 2019;108:150–60. https://doi.org/10.1016/j.compbiomed.2019.03.014.

    Article  Google Scholar 

  30. Gonella G, Binaghi E, Nocera P, Mordacchini C. Investigating the behaviour of machine learning techniques to segment brain metastases in radiation therapy planning. Applied Sciences (Switzerland). 2019;9(16). https://doi.org/10.3390/app9163335.

  31. Pereira S, Pinto A, Alves V, Silva CA. Brain Tumor Segmentation Using Convolutional Neural Networks in MRI Images. 2016;35(5):1240–51.

    Google Scholar 

  32. Kamnitsas K, Ledig C, Newcombe VFJJ, Simpson JP, Kane AD, Menon DK, Glocker B. Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation. Med Image Anal. 2017;36:61–78. https://doi.org/10.1016/j.media.2016.10.004.

    Article  Google Scholar 

  33. Sharif MI, Li JP, Khan MA, Saleem MA. Active Deep neural Network Features Selection for Segmentation and Recognition of Brain Tumors using MRI Images. Pattern Recogn Lett. 2019. https://doi.org/10.1016/j.patrec.2019.11.019.

    Article  Google Scholar 

  34. Deng W, Shi Q, Luo K, Yang Y, Ning N. Brain Tumor Segmentation Based on Improved Convolutional Neural Network in Combination with Non-quantifiable Local Texture Feature. Journal of Medical Systems. 2019;43(6). https://doi.org/10.1007/s10916-019-1289-2.

  35. Kermi A, Mahmoudi I, Khadir MT. Deep convolutional neural networks using U-Net for automatic brain tumor segmentation in multimodal MRI volumes. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2019. https://doi.org/10.1007/978-3-030-11726-9_4.

    Article  Google Scholar 

  36. Benson E, Pound MP, French AP, Jackson AS, Pridmore TP. Deep hourglass for brain tumor segmentation. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2019. https://doi.org/10.1007/978-3-030-11726-9_37.

    Article  Google Scholar 

  37. Kuzina A, Egorov E, Burnaev E. Bayesian generative models for knowledge transfer in MRI semantic segmentation problems. Frontiers in Neuroscience. 2019;13(JUL). https://doi.org/10.3389/fnins.2019.00844.

  38. Mlynarski P, Delingette H, Criminisi A, Ayache N. 3D convolutional neural networks for tumor segmentation using long-range 2D context. Comput Med Imaging Graph. 2019;73:60–72. https://doi.org/10.1016/j.compmedimag.2019.02.001.

    Article  Google Scholar 

  39. Sun L, Zhang S, Chen H, Luo L. Brain tumor segmentation and survival prediction using multimodal MRI scans with deep learning. Frontiers in Neuroscience. 2019;13(JUL). https://doi.org/10.3389/fnins.2019.00810.

  40. Zhai J, Li H. An Improved Full Convolutional Network Combined with Conditional Random Fields for Brain MR Image Segmentation Algorithm and its 3D Visualization Analysis. Journal of Medical Systems. 2019;43(9). https://doi.org/10.1007/s10916-019-1424-0.

  41. Sun J, Chen W, Peng S, Liu B. DRRNet: Dense Residual Refine Networks for Automatic Brain Tumor Segmentation. Journal of Medical Systems. 2019;43(7). https://doi.org/10.1007/s10916-019-1358-6.

  42. Amin J, Sharif M, Yasmin M, Saba T, Anjum MA, Fernandes SL. A New Approach for Brain Tumor Segmentation and Classification Based on Score Level Fusion Using Transfer Learning. J Med Syst. 2019;43(11):326. https://doi.org/10.1007/s10916-019-1453-8.

    Article  Google Scholar 

  43. Kong X, Sun G, Wu Q, Liu J, Lin F. Hybrid pyramid u-net model for brain tumor segmentation. In IFIP Advances in Information and Communication Technology. 2018;(Vol. 538). https://doi.org/10.1007/978-3-030-00828-4_35.

  44. Hoseini F, Shahbahrami A, Bayat P. An Efficient Implementation of Deep Convolutional Neural Networks for MRI Segmentation. J Digit Imaging. 2018;31(5):738–47. https://doi.org/10.1007/s10278-018-0062-2.

    Article  Google Scholar 

  45. Hu Y, Xia Y. 3D deep neural network-based brain tumor segmentation using multimodality magnetic resonance sequences. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2018. https://doi.org/10.1007/978-3-319-75238-9_36.

    Article  Google Scholar 

  46. Zhao X, Wu Y, Song G, Li Z, Zhang Y, Fan Y. A deep learning model integrating FCNNs and CRFs for brain tumor segmentation. Med Image Anal. 2018;43:98–111. https://doi.org/10.1016/j.media.2017.10.002.

    Article  Google Scholar 

  47. Naceur MB, Saouli R, Akil M, Kachouri R. Fully Automatic Brain Tumor Segmentation using End-To-End Incremental Deep Neural Networks in MRI images. Comput Methods Programs Biomed. 2018;166:39–49. https://doi.org/10.1016/j.cmpb.2018.09.007.

    Article  Google Scholar 

  48. Ramírez I, Martín A, Schiavi E, Ramirez I, Martin A, Schiavi E. Optimization of a variational model using deep learning: An application to brain tumor segmentation. 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), 2018-April(Isbi). 2018;631–634. https://doi.org/10.1109/ISBI.2018.8363654.

  49. Charron O, Lallement A, Jarnet D, Noblet V, Clavier JB, Meyer P. Automatic detection and segmentation of brain metastases on multimodal MR images with a deep convolutional neural network. Comput Biol Med. 2018;95:43–54. https://doi.org/10.1016/j.compbiomed.2018.02.004.

    Article  Google Scholar 

  50. Liu D, Zhang H, Zhao M, Yu X, Yao S, Zhou W. Brain Tumor Segmention Based on Dilated Convolution Refine Networks. Proceedings - 2018 IEEE/ACIS 16th International Conference on Software Engineering Research, Management and Application, SERA 2018. 2018;113–120. https://doi.org/10.1109/SERA.2018.8477213.

  51. Iqbal S, Ghani MU, Saba T, Rehman A. Brain tumor segmentation in multi-spectral MRI using convolutional neural networks (CNN). Microsc Res Tech. 2018;81(4):419–27. https://doi.org/10.1002/jemt.22994.

    Article  Google Scholar 

  52. Baid U, Talbar S, Rane S, Gupta S, Thakur MH, Moiyadi A, Mahajan A. Deep learning radiomics algorithm for gliomas (DRAG) model: A novel approach using 3D UNET based deep convolutional neural network for predicting survival in gliomas. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2019. https://doi.org/10.1007/978-3-030-11726-9_33.

    Article  Google Scholar 

  53. Cui S, Mao L, Jiang J, Liu C, Xiong S. Automatic semantic segmentation of brain gliomas from MRI images using a deep cascaded neural network. Journal of Healthcare Engineering. 2018. https://doi.org/10.1155/2018/4940593.

  54. Islam M, Ren H. Multi-modal PixelNet for brain tumor segmentation. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2018. https://doi.org/10.1007/978-3-319-75238-9_26.

    Article  Google Scholar 

  55. Pinto A, Pereira S, Rasteiro D, Silva CA. Hierarchical brain tumour segmentation using extremely randomized trees. Pattern Recogn. 2018;82:105–17. https://doi.org/10.1016/j.patcog.2018.05.006.

    Article  Google Scholar 

  56. Qamar S, Jin H, Zheng R, Ahmad P. 3D Hyper-Dense Connected Convolutional Neural Network for Brain Tumor Segmentation. Proceedings - 2018 14th International Conference on Semantics, Knowledge and Grids, SKG 2018. 2018;123–130. https://doi.org/10.1109/SKG.2018.00024.

  57. Soltaninejad M, Yang G, Lambrou T, Allinson N, Jones TL, Barrick TR, Ye X. Supervised learning based multimodal MRI brain tumour segmentation using texture features from supervoxels. Comput Methods Programs Biomed. 2018;157:69–84. https://doi.org/10.1016/j.cmpb.2018.01.003.

    Article  Google Scholar 

  58. Soltaninejad M, Zhang L, Lambrou T, Yang G, Allinson N, Ye X. MRI brain tumor segmentation and patient survival prediction using random forests and fully convolutional networks. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2018. https://doi.org/10.1007/978-3-319-75238-9_18.

    Article  Google Scholar 

  59. Wang G, Li W, Zuluaga MA, Pratt R, Patel PA, Aertsen M, Vercauteren T. Interactive Medical Image Segmentation Using Deep Learning with Image-Specific Fine Tuning. IEEE Trans Med Imaging. 2018;37(7):1562–73. https://doi.org/10.1109/TMI.2018.2791721.

    Article  Google Scholar 

  60. Wang Y, Li C, Zhu T, Zhang J. Multimodal brain tumor image segmentation using WRN-PPNet. Comput Med Imaging Graph. 2019. https://doi.org/10.1016/j.compmedimag.2019.04.001.

    Article  Google Scholar 

  61. Zhang Z, Odaibo D, Skidmore FMM, Tanik MMM. A big data analytics approach in medical imaging segmentation using deep convolutional neural networks. Big Data and Visual Analytics. 2018. https://doi.org/10.1007/978-3-319-63917-8_10.

    Article  Google Scholar 

  62. Takacs P, Manno-Kovacs A. MRI brain tumor segmentation combining saliency and convolutional network features. Proceedings - International Workshop on Content-Based Multimedia Indexing, 2018-Septe. https://doi.org/10.1109/CBMI.2018.8516544.

  63. Thillaikkarasi R, Saravanan S. An Enhancement of Deep Learning Algorithm for Brain Tumor Segmentation Using Kernel Based CNN with M-SVM. Journal of Medical Systems. 2019;43(4). https://doi.org/10.1007/s10916-019-1223-7.

  64. Chen H, Dou Q, Yu L, Qin J, Heng P-A. VoxResNet: Deep voxelwise residual networks for brain segmentation from 3D MR images. NeuroImage. 2018;170:446–55. https://doi.org/10.1016/j.neuroimage.2017.04.041.

    Article  Google Scholar 

  65. Gottapu RD, Dagli CH. DenseNet for Anatomical Brain Segmentation. Procedia Computer Science. 2018;140:179–85. https://doi.org/10.1016/j.procs.2018.10.327.

    Article  Google Scholar 

  66. Li H, Jiang G, Zhang J, Wang R, Wang Z, Zheng W-S, Menze B. Fully convolutional network ensembles for white matter hyperintensities segmentation in MR images. NeuroImage. 2018;183:650–65. https://doi.org/10.1016/j.neuroimage.2018.07.005.

    Article  Google Scholar 

  67. Teoh EJ, Tan KC, Xiang C. Estimating the number of hidden neurons in a feedforward network using the singular value decomposition. IEEE Trans Neural Networks. 2006;17(6):1623–9. https://doi.org/10.1109/TNN.2006.880582.

    Article  Google Scholar 

  68. Wang G, Zuluaga MA, Li W, Pratt R, Patel PA, Aertsen M, Vercauteren T. DeepIGeoS: A Deep Interactive Geodesic Framework for Medical Image Segmentation. IEEE Trans Pattern Anal Mach Intell. 2019;41(7):1559–72. https://doi.org/10.1109/TPAMI.2018.2840695.

    Article  Google Scholar 

  69. Li J, Yu ZL, Gu Z, Liu H, Li Y. MMAN: Multi-modality aggregation network for brain segmentation from MR images. Neurocomputing. 2019;358:10–9. https://doi.org/10.1016/j.neucom.2019.05.025.

    Article  Google Scholar 

  70. Roy S, Maji P. An accurate and robust skull stripping method for 3-D magnetic resonance brain images. Magn Reson Imaging. 2018;54:46–57. https://doi.org/10.1016/j.mri.2018.07.014.

    Article  Google Scholar 

  71. Dolz J, Desrosiers C, Ben Ayed I. 3D fully convolutional networks for subcortical segmentation in MRI: A large-scale study. NeuroImage. 2018;170:456–70. https://doi.org/10.1016/j.neuroimage.2017.04.039.

    Article  Google Scholar 

  72. Lakshmi VK, Feroz CA, Merlin JAJ. Automated Detection and Segmentation of Brain Tumor Using Genetic Algorithm. International Conference on Smart Systems and Inventive Technology (ICSSIT). 2018;2018:583–9. https://doi.org/10.1109/ICSSIT.2018.8748487.

    Article  Google Scholar 

  73. Wang W, Liang D, Chen Q, Iwamoto Y, Han XH, Zhang Q, Chen YW. Medical Image Classification Using Deep Learning BT - Deep Learning in Healthcare: Paradigms and Applications (Y.-W. Chen & L. C. Jain, eds.). 2020. https://doi.org/10.1007/978-3-030-32606-7_3.

  74. Cheng J, Huang W, Cao S, Yang R, Yang W, Yun Z, Feng Q. Enhanced performance of brain tumor classification via tumor region augmentation and partition. PLoS ONE. 2015;10(10):1–13. https://doi.org/10.1371/journal.pone.0140381.

    Article  Google Scholar 

  75. Sheela CJJ, Suganthi G. Automatic Brain Tumor Segmentation from MRI using Greedy Snake Model and Fuzzy C-Means Optimization. Journal of King Saud University - Computer and Information Sciences. 2019. https://doi.org/10.1016/j.jksuci.2019.04.006.

    Article  Google Scholar 

  76. Deepak S, Ameer PM. Brain tumor classification using deep CNN features via transfer learning. Comput Biol Med. 2019;111(March):103345. https://doi.org/10.1016/j.compbiomed.2019.103345.

    Article  Google Scholar 

  77. Zyad MA, Gouskir M, Bouikhalene B. Classification of brain tumor from magnetic resonance imaging using convolutional neural networks. International Journal of Advanced Science and Technology. 2019;126:31–8. https://doi.org/10.33832/ijast.2019.126.04.

    Article  Google Scholar 

  78. Ghassemi N, Shoeibi A, Rouhani M. Deep neural network with generative adversarial networks pre-training for brain tumor classification based on MR images. Biomed Signal Process Control. 2020;57:101678. https://doi.org/10.1016/j.bspc.2019.101678.

    Article  Google Scholar 

  79. Sajjad M, Khan S, Muhammad K, Wu W, Ullah A, Baik SW. Multi-grade brain tumor classification using deep CNN with extensive data augmentation. Journal of Computational Science. 2019;30:174–82. https://doi.org/10.1016/j.jocs.2018.12.003.

    Article  Google Scholar 

  80. Swati ZNK, Zhao Q, Kabir M, Ali F, Ali Z, Ahmed S, Lu J. Brain tumor classification for MR images using transfer learning and fine-tuning. Comput Med Imaging Graph. 2019;75:34–46. https://doi.org/10.1016/j.compmedimag.2019.05.001.

    Article  Google Scholar 

  81. Pashaei A, Sajedi H, Jazayeri N. Brain tumor classification via convolutional neural network and extreme learning machines. 2018 8th International Conference on Computer and Knowledge Engineering, ICCKE 2018. 2018;314–319. https://doi.org/10.1109/ICCKE.2018.8566571.

  82. Afshar P, Mohammadi A, Plataniotis KN. Brain Tumor Type Classification via Capsule Networks. Proceedings - International Conference on Image Processing, ICIP. 2018;3129–3133. https://doi.org/10.1109/ICIP.2018.8451379.

  83. Lu S, Lu Z, Zhang Y-D. Pathological brain detection based on AlexNet and transfer learning. Journal of Computational Science. 2019;30:41–7. https://doi.org/10.1016/j.jocs.2018.11.008.

    Article  Google Scholar 

  84. Saxena N, Sharma R, Joshi K, Rana HS. Identification of glioma from MR images using convolutional neural network. In Advances in Intelligent Systems and Computing. 2019;(Vol. 880). https://doi.org/10.1007/978-3-030-02686-8_44.

  85. Özyurt F, Sert E, Avcı D. An expert system for brain tumor detection: Fuzzy C-means with super resolution and convolutional neural network with extreme learning machine. Medical Hypotheses. 2020;134. https://doi.org/10.1016/j.mehy.2019.109433.

  86. Isselmou AEK, Xu G, Zhang S, Saminu S, Javaid I. Deep learning algorithm for brain tumor detection and analysis using MR brain images. ACM International Conference Proceeding Series. 2019;28–32. https://doi.org/10.1145/3348416.3348421.

  87. Sengupta A, Agarwal S, Gupta PK, Ahlawat S, Patir R, Gupta RK, Singh A. On differentiation between vasogenic edema and non-enhancing tumor in high-grade glioma patients using a support vector machine classifier based upon pre and post-surgery MRI images. Eur J Radiol. 2018;106:199–208. https://doi.org/10.1016/j.ejrad.2018.07.018.

    Article  Google Scholar 

  88. Ge C, Gu IY-H, Jakola AS, Yang J. Deep Learning and Multi-Sensor Fusion for Glioma Classification Using Multistream 2D Convolutional Networks. Conference Proceedings : … Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference. 2018;2018:5894–7. https://doi.org/10.1109/EMBC.2018.8513556.

    Article  Google Scholar 

  89. Bakas S, Reyes M, Jakab A, Bauer S, Rempfler M, Crimi A, Menze B. Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge. 2018;(November). Retrieved from http://arxiv.org/abs/1811.02629.

  90. Schmainda KM, Prah MA, Rand SD, Liu Y, Logan B, Muzi M, Quarles CC. Multisite concordance of DSC-MRI analysis for brain tumors: Results of a National Cancer Institute Quantitative Imaging Network Collaborative Project. American Journal of Neuroradiology. 2018;39(6):1008–16. https://doi.org/10.3174/ajnr.A5675.

    Article  Google Scholar 

  91. ParthaSarathi M, Ansari MA. Multimodal Retrieval Framework for Brain Volumes in 3D MR Volumes. Journal of Medical and Biological Engineering. 2018;38(2):261–72. https://doi.org/10.1007/s40846-017-0287-4.

    Article  Google Scholar 

  92. Lee JK, Wang J, Sa JK, Ladewig E, Lee HO, Lee IH, Nam DH. Spatiotemporal genomic architecture informs precision oncology in glioblastoma. Nat Genet. 2017;49(4):594–9. https://doi.org/10.1038/ng.3806.

    Article  Google Scholar 

  93. Beig N, Patel J, Prasanna P, Partovi S, Varadan V, Madabhushi A, Tiwari P. Radiogenomic analysis of hypoxia pathway reveals computerized MRI descriptors predictive of overall survival in glioblastoma. 2017;10134:101341U. https://doi.org/10.1117/12.2255694.

    Article  Google Scholar 

  94. Czarnek N, Clark K, Peters KB, Mazurowski MA. Algorithmic three-dimensional analysis of tumor shape in MRI improves prognosis of survival in glioblastoma: a multi-institutional study. J Neurooncol. 2017;132(1):55–62. https://doi.org/10.1007/s11060-016-2359-7.

    Article  Google Scholar 

  95. Tian Q, Wang L, Liu Y, Li B, Liang Z, Gao P, Liu Y. Relationship between Glioblastoma Heterogeneity and Survival Time: An MR Imaging Texture Analysis. J Magn Reson Imaging. 2017;38(9):1695–701. https://doi.org/10.1002/jmri.2596010.3174/ajnr.A5279.

    Article  Google Scholar 

  96. Kanas VG, Zacharaki EI, Thomas GA, Zinn PO, Megalooikonomou V, Colen RR. Learning MRI-based classification models for MGMT methylation status prediction in glioblastoma. Comput Methods Programs Biomed. 2017;140:249–57. https://doi.org/10.1016/j.cmpb.2016.12.018.

    Article  Google Scholar 

  97. Dunn Jr WD, Hwang SN, Cooper LA, Aerts HJWL, Holder CA. Assessing the Effects of Software Platforms on Volumetric Segmentation of Glioblastoma. Journal of Neuroimaging in Psychiatry and Neurology. 2016;64–72. https://doi.org/10.17756/jnpn.2016-008.

  98. Chaddad A, Desrosiers C, Toews M. Radiomic analysis of multi-contrast brain MRI for the prediction of survival in patients with glioblastoma multiforme. Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, 2016-Octob. 2016;4035–4038. https://doi.org/10.1109/EMBC.2016.7591612.

  99. Le Reste P-J, Stindel E, Morvan Y, Upadhaya T, Hatt M. Prognosis classification in glioblastoma multiforme using multimodal MRI derived heterogeneity textural features: impact of pre-processing choices. Medical Imaging 2016: Computer-Aided Diagnosis. 2016;9785, 97850W. https://doi.org/10.1117/12.2217151.

  100. Wiest R, Aerts HJWL, Rios Velazquez E, Meier R, Reyes M, Alexander B, Bauer S. Fully automatic GBM segmentation in the TCGA-GBM dataset: Prognosis and correlation with VASARI features. Scientific Reports. 2015;5(1):1–10. https://doi.org/10.1038/srep16822.

    Article  Google Scholar 

  101. Nabizadeh N, Kubat M. Brain tumors detection and segmentation in MR images: Gabor wavelet vs. statistical features. Comput Electr Eng. 2015;45:286–301. https://doi.org/10.1016/j.compeleceng.2015.02.007.

    Article  Google Scholar 

  102. Jothi NVSN, J. A. A. . Automatic Classification of Brain MRI Images Using SVM and Neural Network Classifiers. Advances in Intelligent Systems and Computing. 2015;320:621–31. https://doi.org/10.1007/978-3-319-11218-3.

    Article  Google Scholar 

  103. Reza SMS, Mays R, Iftekharuddin KM. Multi-fractal detrended texture feature for brain tumor classification. Medical Imaging 2015: Computer-Aided Diagnosis. 2015;9414, 941410. https://doi.org/10.1117/12.2083596.

  104. Rubin DL, Westbroek EM, Gevaert O, Achrol AS, Rodriguez S, Loya JJ, Feroze AH. Magnetic resonance image features identify glioblastoma phenotypic subtypes with distinct molecular pathway activities. Science Translational Medicine. 2015;7(303):303ra138. https://doi.org/10.1126/scitranslmed.aaa7582.

    Article  Google Scholar 

  105. Han L, Kamdar MR. MRI to MGMT: predicting methylation status in glioblastoma patients using convolutional recurrent neural networks. Anal Chem. 2015;25(4):368–79. https://doi.org/10.1142/9789813235533_0031.

    Article  Google Scholar 

  106. Kirby J, Colen R, Rubin DL, Hu Y, Buetow K, Mikkelsen T, Meerzaman D. Addition of MR imaging features and genetic biomarkers strengthens glioblastoma survival prediction in TCGA patients. Journal of Neuroradiology. 2014;42(4):212–21. https://doi.org/10.1016/j.neurad.2014.02.006.

    Article  Google Scholar 

  107. Huang E, Gutman DA, Jilwan-Nicolas M, Hwang SN, Jain R, Rubin D, Wintermark M. Imaging genomic mapping of an invasive MRI phenotype predicts patient outcome and metabolic dysfunction: a TCGA glioma phenotype research group project. BMC Med Genomics. 2014;7(1):1–9. https://doi.org/10.1186/1755-8794-7-30.

    Article  Google Scholar 

  108. Kwon D, Shinohara RT, Akbari H, Davatzikos C. Combining generative models for multifocal glioma segmentation and registration. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8673 LNCS(PART 1), 2014;763–770. https://doi.org/10.1007/978-3-319-10404-1_95.

  109. Kirby J, Jaffe CC, Poisson LM, Mikkelsen T, Flanders A, Rao A, Freymann J. Outcome Prediction in Patients with Glioblastoma by Using Imaging, Clinical, and Genomic Biomarkers: Focus on the Nonenhancing Component of the Tumor. Radiology. 2014;272(2):484–93. https://doi.org/10.1148/radiol.14131691.

    Article  Google Scholar 

  110. Mazurowski MA, Zhang J, Peters KB, Hobbs H. Computer-extracted MR imaging features are associated with survival in glioblastoma patients. J Neurooncol. 2014;120(3):483–8. https://doi.org/10.1007/s11060-014-1580-5.

    Article  Google Scholar 

  111. Ge C, Gu IY, Jakola AS, Yang J. Cross-Modality Augmentation of Brain Mr Images Using a Novel Pairwise Generative Adversarial Network for Enhanced Glioma Classification. IEEE International Conference on Image Processing (ICIP). 2019;2019:559–63. https://doi.org/10.1109/ICIP.2019.8803808.

    Article  Google Scholar 

  112. Frid-Adar M, Klang E, Amitai M, Goldberger J, Greenspan H. Synthetic data augmentation using GAN for improved liver lesion classification. Proceedings - International Symposium on Biomedical Imaging, 2018-April;289–293. https://doi.org/10.1109/ISBI.2018.8363576.

  113. Shin H-C, Tenenholtz NA, Rogers JK, Schwarz CG, Senjem ML, Gunter JL, Michalski M. Medical image synthesis for data augmentation and anonymization using generative adversarial networks. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2018. https://doi.org/10.1007/978-3-030-00536-8_1.

    Article  Google Scholar 

  114. Krizhevsky A, Sutskever I, Hinton GE. ImageNet classification with deep convolutional neural networks. Adv Neural Inf Process Syst. 2012;2:1097–105.

    Google Scholar 

  115. Géron A. Hands-On Machine Learning with Scikit-Learn, Keras, and TensorFlow: Concepts, Tools, and Techniques to Build Intelligent Systems. O'Reilly Media. (2019).

  116. He K. PReLu5. 2014;1026–1034. https://doi.org/10.1109/ICCV.2015.123.

  117. Lundervold AS, Lundervold A. An overview of deep learning in medical imaging focusing on MRI. Zeitschrift Für Medizinische Physik. 2019;29(2):102–27. https://doi.org/10.1016/j.zemedi.2018.11.002.

    Article  Google Scholar 

  118. Trakoolwilaiwan T, Behboodi B, Lee J, Kim K, Choi J-W. Convolutional neural network for high-accuracy functional near- infrared spectroscopy in a brain– computer interface. Neurophoton. 2017;5(1). https://doi.org/10.1117/1.NPh.5.1.

  119. Wang SH, Phillips P, Sui Y, Liu B, Yang M, Cheng H. Classification of Alzheimer’s Disease Based on Eight-Layer Convolutional Neural Network with Leaky Rectified Linear Unit and Max Pooling. J Med Syst. 2018;42(5):85. https://doi.org/10.1007/s10916-018-0932-7.

    Article  Google Scholar 

  120. Zhang YD, Hou XX, Chen Y, Chen H, Yang M, Yang J, Wang SH. Voxelwise detection of cerebral microbleed in CADASIL patients by leaky rectified linear unit and early stopping. Multimedia Tools and Applications. 2018;77(17):21825–45. https://doi.org/10.1007/s11042-017-4383-9.

    Article  Google Scholar 

  121. Wang S, Jiang Y, Hou X, Cheng H, Du S. Cerebral Micro-Bleed Detection Based on the Convolution Neural Network with Rank Based Average Pooling. IEEE Access. 2017;5:16576–83. https://doi.org/10.1109/ACCESS.2017.2736558.

    Article  Google Scholar 

  122. Hang ST, Aono M. Bi-linearly weighted fractional max pooling: An extension to conventional max pooling for deep convolutional neural network. Multimedia Tools and Applications. 2017;76(21):22095–117. https://doi.org/10.1007/s11042-017-4840-5.

    Article  Google Scholar 

  123. Simonyan K, Zisserman A. Very deep convolutional networks for large-scale image recognition. 3rd International Conference on Learning Representations, ICLR 2015 - Conference Track Proceedings, 2015;1–14.

  124. Lin M, Chen Q, Yan S. Network in network. 2nd International Conference on Learning Representations, ICLR 2014 - Conference Track Proceedings, 2014;1–10.

  125. Szegedy C, Liu W, Jia Y, Sermanet P, Reed S, Anguelov D, Rabinovich A. Going deeper with convolutions. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 07–12-June, 2015;1–9. https://doi.org/10.1109/CVPR.2015.7298594.

  126. He K, Zhang X, Ren S, Sun J. Deep residual learning for image recognition. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. 2016-Decem;770–778. https://doi.org/10.1109/CVPR.2016.90.

  127. Abdelaziz Ismael SA, Mohammed A, Hefny H. An enhanced deep learning approach for brain cancer MRI images classification using residual networks. Artificial Intelligence in Medicine. 2020;102(December). https://doi.org/10.1016/j.artmed.2019.101779.

  128. Xie S, Girshick R, Dollár P, Tu Z, He K. Aggregated residual transformations for deep neural networks. Proceedings - 30th IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2017, 2017-Janua. 2017;5987–5995. https://doi.org/10.1109/CVPR.2017.634.

  129. Hara K, Kataoka H, Satoh Y. Can Spatiotemporal 3D CNNs Retrace the History of 2D CNNs and ImageNet? Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2018;6546–6555. https://doi.org/10.1109/CVPR.2018.00685.

  130. Milletari F, Navab N, Ahmadi SA. V-Net: Fully convolutional neural networks for volumetric medical image segmentation. Proceedings - 2016 4th International Conference on 3D Vision, 3DV 2016. 2016;565–571. https://doi.org/10.1109/3DV.2016.79.

  131. Hu J, Shen L, Sun G. Squeeze-and-Excitation Networks. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. 2018;7132–7141. https://doi.org/10.1109/CVPR.2018.00745.

  132. Pan SJ, Yang Q. A Survey on Transfer Learning. IEEE Trans Knowl Data Eng. 2010;22(10):1345–59. https://doi.org/10.1109/TKDE.2009.191.

    Article  Google Scholar 

  133. Abd-Ellah MK, Awad AI, Khalaf AAM, Hamed HFA. Two-phase multi-model automatic brain tumour diagnosis system from magnetic resonance images using convolutional neural networks. Eurasip Journal on Image and Video Processing. 2018;1. https://doi.org/10.1186/s13640-018-0332-4.

  134. Ahammed Muneer KV, Rajendran VR, Paul Joseph K. Glioma Tumor Grade Identification Using Artificial Intelligent Techniques. Journal of Medical Systems. 2019;43(5). https://doi.org/10.1007/s10916-019-1228-2.

  135. Banerjee I, Crawley A, Bhethanabotla M, Daldrup-Link HE, Rubin DL. Transfer learning on fused multiparametric MR images for classifying histopathological subtypes of rhabdomyosarcoma. Comput Med Imaging Graph. 2018;65:167–75. https://doi.org/10.1016/j.compmedimag.2017.05.002.

    Article  Google Scholar 

  136. Banzato T, Bernardini M, Cherubini GB, Zotti A. A methodological approach for deep learning to distinguish between meningiomas and gliomas on canine MR-images. BMC Veterinary Research. 2018;14(1). https://doi.org/10.1186/s12917-018-1638-2.

  137. Rehman A, Naz S, Razzak MI, Akram F, Imran M. A Deep Learning-Based Framework for Automatic Brain Tumors Classification Using Transfer Learning. Circuits, Systems, and Signal Processing. 2019. https://doi.org/10.1007/s00034-019-01246-3.

    Article  Google Scholar 

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Al-Galal, S.A.Y., Alshaikhli, I.F.T. & Abdulrazzaq, M. MRI brain tumor medical images analysis using deep learning techniques: a systematic review. Health Technol. 11, 267–282 (2021). https://doi.org/10.1007/s12553-020-00514-6

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