Abstract
It is still hard to deal with artifacts in magnetic resonance images (MRIs), particularly when the latter are to be segmented. This paper introduces a novel deep-based scheme for tumor segmentation in brain MRIs. According to the proposed scheme, a large set of partial sub-images are paved form sliced from an MRI volume then inputted to an ensemble of convolutional neural networks (CNNs) in order to label the voxels in the centers of the sub-images, according to the classes to which they should belong. Partial sub-images, that capture local patterns around central voxels, have allowed to speed-up both the training and the prediction steps, allowing efficient use of such a scheme for real MRI-based tumor diagnosis. Experiments were performed using the BraTS (brain tumor segmentation) database, where the obtained results show that the proposed scheme allows both fast and accurate brain tumor detection and segmentation in pathological MRIs.
Similar content being viewed by others
References
Amin J, Sharif M, Yasmin M, Fernandes SL (2018) Big data analysis for brain tumor detection: deep convolutional neural networks. Fut Gener Comput Syst 87:290–297. https://doi.org/10.1016/j.future.2018.04.065
Bennai MT, Guessoum Z, Mazouzi S, Cormier S, Mezghiche M (2020) A stochastic multi-agent approach for medical-image segmentation: application to tumor segmentation in brain MR images. Artif Intell Med 110:101980. https://doi.org/10.1016/j.artmed.2020.101980
Bezdek J, Ehrlich R, Full WE (1984) FCM: the fuzzy C-means clustering algorithm. Comput Geosci 10:191–203
Bringmann B, Nijssen S, Zimmermann A (2010) From local patterns to classification models. In: Dzeroski S, Goethals B, Panov P (eds) Inductive databases and constraint-based data mining. Springer, pp. 127–154. https://doi.org/10.1007/978-1-4419-7738-0_6
Chen G, Li Q, Shi F, Rekik I, Pan Z (2020) RFDCR: automated brain lesion segmentation using cascaded random forests with dense conditional random fields. NeuroImage 211:116620. https://doi.org/10.1016/j.neuroimage.2020.116620
Choudhury CL, Mahanty C, Kumar R, Mishra BK (2020) Brain tumor detection and classification using convolutional neural network and deep neural network. In: 2020 international conference on computer science, engineering and applications (ICCSEA), pp 1–4. https://doi.org/10.1109/ICCSEA49143.2020.9132874
Coupé P, Mansencal B, Clément M, Giraud R, de Senneville BD, Ta VT, Lepetit V, Manjon JV (2020) AssemblyNet: a large ensemble of CNNs for 3D whole brain MRI segmentation. NeuroImage 219:117026. https://doi.org/10.1016/j.neuroimage.2020.117026
de Brébisson A, Montana G (2015) Deep neural networks for anatomical brain segmentation. In: Proceedings of the IEEE conference on computer vision and pattern recognition workshops, pp 20–28
Freund Y, Schapire R (1999) A short introduction to boosting. J Jpn Soc Artif Intell 14(771–780):1612
Fülöp T, Győrfi Á, Surányi B, Kovács L, Szilágyi L (2020) Brain tumor segmentation from MRI data using ensemble learning and multi-atlas. In: 2020 IEEE 18th world symposium on applied machine intelligence and informatics (SAMI), pp 111–116. https://doi.org/10.1109/SAMI48414.2020.9108752
Gordillo N, Montseny E, Sobrevilla P (2013) State of the art survey on MRI brain tumor segmentation. Magn Resonance Imaging 31(8):1426–1438. https://doi.org/10.1016/j.mri.2013.05.002
Hornik K (1991) Approximation capabilities of multilayer feedforward networks. Neural Netw 4(2):251–257. https://doi.org/10.1016/0893-6080(91)90009-T
Hu K, Gan Q, Zhang Y, Deng S, Xiao F, Huang W, Cao C, Gao X (2019) Brain tumor segmentation using multi-cascaded convolutional neural networks and conditional random field. IEEE Access 7:92615–92629. https://doi.org/10.1109/ACCESS.2019.2927433
Kaleem M, Sanaullah M, Hussain MA, Jaffar MA, Choi TS (2012) Segmentation of brain tumor tissue using marker controlled watershed transform method. In: Chowdhry BS, Shaikh FK, Hussain DMA, Uqaili MA (eds) Emerging trends and applications in information communication technologies. Springer, Berlin, pp 222–227
Knerr S, Personnaz L, Dreyfus G (1990) Single-layer learning revisited: a stepwise procedure for building and training a neural network. In: Fogelman Soulié F, Hérault J (eds) Neurocomputing: algorithms, architectures and applications, NATO ASI Series, vol F68. Springer, Berlin, pp 41–50
Kumar N, Kaur N, Gupta D (2020) Major convolutional neural networks in image classification: a survey. In: Dutta M, Krishna CR, Kumar R, Kalra M (eds) Proceedings of international conference on iot inclusive life (ICIIL 2019), NITTTR Chandigarh, India. Springer Singapore, Singapore, pp 243–258
Kwon D, Shinohara RT, Akbari H, Davatzikos C (2014) Combining generative models for multifocal glioma segmentation and registration. In: Golland P, Hata N, Barillot C, Hornegger J, Howe R (eds) Medical image computing and computer-assisted intervention—MICCAI 2014. Springer, Cham, pp 763–770
Li SZ (2009) Markov random field modeling in image analysis. Springer, Berlin
Menze B, Jakab A, Bauer S, Kalpathy-Cramer J, Farahani K, Kirby J, Burren Y, Porz N, Slotboom J, Wiest R, Lanczi L, Gerstner E, Weber MA, Arbel T, Avants B, Ayache N, Buendia P, Collins L, Cordier N, Corso J, Criminisi A, Das T, Delingette H, Demiralp C, Durst C, Dojat M, Doyle S, Festa J, Forbes F, Geremia E, Glocker B, Golland P, Guo X, Hamamci A, Iftekharuddin K, Jena R, John N, Konukoglu E, Lashkari D, Antonio Mariz J, Meier R, Pereira S, Precup D, Price SJ, Riklin-Raviv T, Reza S, Ryan M, Schwartz L, Shin HC, Shotton J, Silva C, Sousa N, Subbanna N, Szekely G, Taylor T, Thomas O, Tustison N, Unal G, Vasseur F, Wintermark M, Hye Ye D, Zhao L, Zhao B, Zikic D, Prastawa M, Reyes M, Van Leemput K (2014) The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans Med Imag. https://doi.org/10.1109/TMI.2014.2377694
Oliveira GC, Varoto R, Cliquet Jr A (2018) Brain tumor segmentation in magnetic resonance images using genetic algorithm clustering and AdaBoost classifier. In: Proceedings of the 11th international joint conference on biomedical engineering systems and technologies—BioImaging, vol 2. INSTICC, SciTePress, pp 77–82. https://doi.org/10.5220/0006534900770082
Pan Y, Huang W, Lin Z, Zhu W, Zhou J, Wong J, Ding Z (2015) Brain tumor grading based on neural networks and convolutional neural networks. In: 2015 37th annual international conference of the IEEE engineering in medicine and biology society (EMBC), pp 699–702. https://doi.org/10.1109/EMBC.2015.7318458
Park J, Sandberg IW (1993) Approximation and radial-basis-function networks. Neural Comput 5(2):305–316. https://doi.org/10.1162/neco.1993.5.2.305
Pereia S, Pinto A, Alves V, Silva CA (2016) Brain tumor segmentation using convolutional neural networks in MRI images. IEEE Trans Med Imaging 35(5):1240–1251. https://doi.org/10.1109/TMI.2016.2538465
Rabeh AB, Benzarti F, Amiri H (2017) Segmentation of brain MRI using active contour model. Int J Imaging Syst Technol 27(1):3–11. https://doi.org/10.1002/IMA.22205
Rajasree R, Columbus CC (2015) Brain tumour image segmentation and classification system based on the modified AdaBoost classifier. Int J Appl Eng Res 10(14):11911–11916
Roma AA, Diaz De Vivar A, Park KJ, Alvarado-Cabrero I, Rasty G, Chanona-Vilchis JG, Mikami Y, Hong SR, Teramoto N, Ali-Fehmi R, Rutgers JKL, Barbuto D, Silva EG (2015) Invasive endocervical adenocarcinoma: a new pattern-based classification system with important clinical significance. Am J Surg Pathol 39(5):667–672. https://doi.org/10.1097/pas.0000000000000402
Schölkopf B, Burges C, Vapnik V (1995) Extracting support data for a given task. In: Proceedings of the 1st international conference on knowledge discovery & data mining, pp 252–257
Subbanna NK, Precup D, Collins DL, Arbel T (2013) Hierarchical probabilistic gabor and MRF segmentation of brain tumours in MRI volumes. In: Mori K, Sakuma I, Sato Y, Barillot C, Navab N (eds) Medical image computing and computer-assisted intervention—MICCAI 2013. Springer, Berlin, pp 751–758
Yamanakkanavar N, Choi JY, Lee B (2020) MRI segmentation and classification of human brain using deep learning for diagnosis of alzheimer’s disease: a survey. Sensors 20(11):3243. https://doi.org/10.3390/s20113243
Yousaf S, RaviPrakash H, Anwar SM, Sohail N, Bagci U (2020) State-of-the-art in brain tumor segmentation and current challenges. In: Kia SM, Mohy-ud-Din H, Abdulkadir A, Bass C, Habes M, Rondina JM, Tax CMW, Wang H, Wolfers T, Rathore S, Ingalhalikar M (eds) Machine learning in clinical neuroimaging and radiogenomics in neuro-oncology—third international workshop, MLCN 2020, and second international workshop, RNO-AI 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 4-8, 2020, Proceedings, Lecture notes in computer science, vol 12449. Springer, Berlin, pp 189–198. https://doi.org/10.1007/978-3-030-66843-3_19
Zhang D, Huang G, Zhang Q, Han J, Han J, Wang Y, Yu Y (2020) Exploring task structure for brain tumor segmentation from multi-modality MR images. IEEE Trans Image Process 29:9032–9043. https://doi.org/10.1109/TIP.2020.3023609
Zhang D, Huang G, Zhang Q, Han J, Han J, Yu Y (2021) Cross-modality deep feature learning for brain tumor segmentation. Pattern Recognit 110:107562. https://doi.org/10.1016/j.patcog.2020.107562
Zhang W, Li R, Deng H, Wang L, Lin W, Ji S, Shen D (2015) Deep convolutional neural networks for multi-modality isointense infant brain image segmentation. Neuroimage 108:214–224
Zhou C, Cule B, Goethals B (2016) Pattern based sequence classification. IEEE Trans Knowl Data Eng 28:1285–1298
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors have no conflicts of interest to declare that are relevant to the content of this article.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Bouchaour, N., Mazouzi, S. Deep pattern-based tumor segmentation in brain MRIs. Neural Comput & Applic 34, 14317–14326 (2022). https://doi.org/10.1007/s00521-022-07422-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00521-022-07422-y