Deep learning for segmentation of brain tumors: Impact of cross-institutional training and testing Academic Article uri icon

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  • Background and purpose

    Convolutional neural networks (CNNs) are commonly used for segmentation of brain tumors. In this work, we assess the effect of cross-institutional training on the performance of CNNs.


    We selected 44 glioblastoma (GBM) patients from two institutions in The Cancer Imaging Archive dataset. The images were manually annotated by outlining each tumor component to form ground truth. To automatically segment the tumors in each patient, we trained three CNNs: (a) one using data for patients from the same institution as the test data, (b) one using data for the patients from the other institution and (c) one using data for the patients from both of the institutions. The performance of the trained models was evaluated using Dice similarity coefficients as well as Average Hausdorff Distance between the ground truth and automatic segmentations. The 10-fold cross-validation scheme was used to compare the performance of different approaches.


    Performance of the model significantly decreased (P < 0.0001) when it was trained on data from a different institution (dice coefficients: 0.68 ± 0.19 and 0.59 ± 0.19) as compared to training with data from the same institution (dice coefficients: 0.72 ± 0.17 and 0.76 ± 0.12). This trend persisted for segmentation of the entire tumor as well as its individual components.


    There is a very strong effect of selecting data for training on performance of CNNs in a multi-institutional setting. Determination of the reasons behind this effect requires additional comprehensive investigation.

publication date

  • 2018