Automatic Segmentation of Stroke Lesions in Non-contrast Computed Tomography Datasets with Convolutional Neural Networks

Citation Author(s):
University of Calgary
University of Calgary
University of Calgary
University Medical Center Hamburg-Eppendorf
University Medical Center Hamburg-Eppendorf
University of Calgary
Submitted by:
Anup Tuladhar
Last updated:
Wed, 06/10/2020 - 20:23
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This dataset contains the trained model that accompanies the publication of the same name:

 Anup Tuladhar*, Serena Schimert*, Deepthi Rajashekar, Helge C. Kniep, Jens Fiehler, Nils D. Forkert, "Automatic Segmentation of Stroke Lesions in Non-Contrast Computed Tomography Datasets With Convolutional Neural Networks," in IEEE Access, vol. 8, pp. 94871-94879, 2020, doi:10.1109/ACCESS.2020.2995632. *: Co-first authors


Publication Abstract

Non-contrast computed tomography (NCCT) is commonly used for volumetric follow-up assessment of ischemic strokes. However, manual lesion segmentation is time-consuming and subject to high inter-observer variability. The aim of this study was to develop and establish a baseline convolutional neural network (CNN) model for automatic NCCT lesion segmentation. A total of 252 multi center clinical NCCT datasets, acquired from 22 centers, and corresponding manual segmentations were used to train  (204 datasets) and validate (48 datasets) a 3D multi scale CNN model for lesion segmentation. Post processing methods were implemented to improve the CNN-based lesion segmentations. The final CNN model and post processing method was evaluated using 39 out of distribution holdout test datasets, acquired at seven centers that did not contribute to the training or validation datasets. Each test image was segmented by two or three neuroradiologists. The Dice similarity coefficient (DSC) and predicted lesion volumes were used to evaluate the segmentations. The CNN model achieved a mean DSC score of 0.47 on the validation NCCT datasets. Post-processing significantly improved the DSC to 0.50 (P<0.01). On the holdout test set, the CNN model achieved a mean DSC score of 0.42, which was also significantly improved to 0.45 (P<0.05) by post processing. Importantly, the automatically segmented lesion volumes were not significantly different from the lesion volumes determined by the expert observers (P>0.05) and showed excellent agreement with manual lesion segmentation volumes (intraclass correlation coefficient, ICC = 0.88). The proposed CNN model can automatically and reliably segment ischemic stroke lesions in clinical NCCT datasets. Post processing techniques can further improve accuracy. As the model was trained and evaluated on datasets from multiple centers, it is broadly applicable and is publicly available.



The dataset contains 3 parts:

  • Pre-processing: Script to extract brain volume from surrounding skull in non-contrast computed tomography (NCCT) scans and instructions for further pre-processing.
  • Trained convolutional neural network (CNN) to perform automated segmentations
  • Post-processing script to improve CNN-based segmentations


Independent Instructions for each part are also contained within each folder.