Application of deep learning for automatic segmentation of brain tumors on magnetic resonance imaging: a heuristic approach in the clinical scenario

Antonio Di Ieva*, Carlo Russo, Sidong Liu, Anne Jian, Michael Y. Bai, Yi Qian, John S. Magnussen

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


Purpose: Accurate brain tumor segmentation on magnetic resonance imaging (MRI) has wide-ranging applications such as radiosurgery planning. Advances in artificial intelligence, especially deep learning (DL), allow development of automatic segmentation that overcome the labor-intensive and operator-dependent manual segmentation. We aimed to evaluate the accuracy of the top-performing DL model from the 2018 Brain Tumor Segmentation (BraTS) challenge, the impact of missing MRI sequences, and whether a model trained on gliomas can accurately segment other brain tumor types. Methods: We trained the model using Medical Decathlon dataset, applied it to the BraTS 2019 glioma dataset, and developed additional models using individual and multimodal MRI sequences. The Dice score was calculated to assess the model’s accuracy compared to ground truth labels by neuroradiologists on BraTS dataset. The model was then applied to a local dataset of 105 brain tumors, performance of which was qualitatively evaluated. Results: The DL model using pre- and post-gadolinium contrast T1 and T2 FLAIR sequences performed best, with a Dice score 0.878 for whole tumor, 0.732 tumor core, and 0.699 active tumor. Lack of T1 or T2 sequences did not significantly degrade performance, but FLAIR and T1C were important contributors. All segmentations performed by the model in the local dataset, including non-glioma cases, were considered accurate by a pool of specialists. Conclusion: The DL model could use available MRI sequences to optimize glioma segmentation and adopt transfer learning to segment non-glioma tumors, thereby serving as a useful tool to improve treatment planning and personalized surveillance of patients.

Original languageEnglish
Pages (from-to)1253-1262
Number of pages10
Issue number8
Early online date26 Jan 2021
Publication statusPublished - Aug 2021


  • Artificial intelligence
  • Brain tumor
  • Convolutional neural network
  • Deep learning
  • Segmentation


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