Brain segmentation in patients with perinatal arterial ischemic stroke.

BACKGROUND: Perinatal arterial ischemic stroke (PAIS) is associated with adverse neurological outcomes. Quantification of ischemic lesions and consequent brain development in newborn infants relies on labor-intensive manual assessment of brain tissues and ischemic lesions. Hence, we propose an automatic method utilizing convolutional neural networks (CNNs) to segment brain tissues and ischemic lesions in MRI scans of infants suffering from PAIS. MATERIALS AND METHODS: This single-center retrospective study included 115 patients with PAIS that underwent MRI after the stroke onset (baseline) and after three months (follow-up). Nine baseline and 12 follow-up MRI scans were manually annotated to provide reference segmentations (white matter, gray matter, basal ganglia and thalami, brainstem, ventricles, extra-ventricular cerebrospinal fluid, and cerebellum, and additionally on the baseline scans the ischemic lesions). Two CNNs were trained to perform automatic segmentation on the baseline and follow-up MRIs, respectively. Automatic segmentations were quantitatively evaluated using the Dice coefficient (DC) and the mean surface distance (MSD). Volumetric agreement between segmentations that were manually and automatically obtained was computed. Moreover, the scan quality and automatic segmentations were qualitatively evaluated in a larger set of MRIs without manual annotation by two experts. In addition, the scan quality was qualitatively evaluated in these scans to establish its impact on the automatic segmentation performance. RESULTS: Automatic brain tissue segmentation led to a DC and MSD between 0.78-0.92 and 0.18-1.08 mm for baseline, and between 0.88-0.95 and 0.10-0.58 mm for follow-up scans, respectively. For the ischemic lesions at baseline the DC and MSD were between 0.72-0.86 and 1.23-2.18 mm, respectively. Volumetric measurements indicated limited oversegmentation of the extra-ventricular cerebrospinal fluid in both the follow-up and baseline scans, oversegmentation of the ischemic lesions in the left hemisphere, and undersegmentation of the ischemic lesions in the right hemisphere. In scans without imaging artifacts, brain tissue segmentation was graded as excellent in more than 85% and 91% of cases, respectively for the baseline and follow-up scans. For the ischemic lesions at baseline, this was in 61% of cases. CONCLUSIONS: Automatic segmentation of brain tissue and ischemic lesions in MRI scans of patients with PAIS is feasible. The method may allow evaluation of the brain development and efficacy of treatment in large datasets.

Deep-Learning-Based Thrombus Localization and Segmentation in Patients with Posterior Circulation Stroke.

Thrombus volume in posterior circulation stroke (PCS) has been associated with outcome, through recanalization. Manual thrombus segmentation is impractical for large scale analysis of image characteristics. Hence, in this study we develop the first automatic method for thrombus localization and segmentation on CT in patients with PCS. In this multi-center retrospective study, 187 patients with PCS from the MR CLEAN Registry were included. We developed a convolutional neural network (CNN) that segments thrombi and restricts the volume-of-interest (VOI) to the brainstem (Polar-UNet). Furthermore, we reduced false positive localization by removing small-volume objects, referred to as volume-based removal (VBR). Polar-UNet is benchmarked against a CNN that does not restrict the VOI (BL-UNet). Performance metrics included the intra-class correlation coefficient (ICC) between automated and manually segmented thrombus volumes, the thrombus localization precision and recall, and the Dice coefficient. The majority of the thrombi were localized. Without VBR, Polar-UNet achieved a thrombus localization recall of 0.82, versus 0.78 achieved by BL-UNet. This high recall was accompanied by a low precision of 0.14 and 0.09. VBR improved precision to 0.65 and 0.56 for Polar-UNet and BL-UNet, respectively, with a small reduction in recall to 0.75 and 0.69. The Dice coefficient achieved by Polar-UNet was 0.44, versus 0.38 achieved by BL-UNet with VBR. Both methods achieved ICCs of 0.41 (95% CI: 0.27-0.54). Restricting the VOI to the brainstem improved the thrombus localization precision, recall, and segmentation overlap compared to the benchmark. VBR improved thrombus localization precision but lowered recall.

Domain- and task-specific transfer learning for medical segmentation tasks.

BACKGROUND AND OBJECTIVES: Transfer learning is a valuable approach to perform medical image segmentation in settings with limited cases available for training convolutional neural networks (CNN). Both the source task and the source domain influence transfer learning performance on a given target medical image segmentation task. This study aims to assess transfer learning-based medical segmentation task performance for various source task and domain combinations. METHODS: CNNs were pre-trained on classification, segmentation, and self-supervised tasks on two domains: natural images and T1 brain MRI. Next, these CNNs were fine-tuned on three target T1 brain MRI segmentation tasks: stroke lesion, MS lesions, and brain anatomy segmentation. In all experiments, the CNN architecture and transfer learning strategy were the same. The segmentation accuracy on all target tasks was evaluated using the mIOU or Dice coefficients. The detection accuracy was evaluated for the stroke and MS lesion target tasks only. RESULTS: CNNs pre-trained on a segmentation task on the same domain as the target tasks resulted in higher or similar segmentation accuracy compared to other source task and domain combinations. Pre-training a CNN on ImageNet resulted in a comparable, but not consistently higher lesion detection rate, despite the amount of training data used being 10 times larger. CONCLUSIONS: This study suggests that optimal transfer learning for medical segmentation is achieved with a similar task and domain for pre-training. As a result, CNNs can be effectively pre-trained on smaller datasets by selecting a source domain and task similar to the target domain and task.

Automated Final Lesion Segmentation in Posterior Circulation Acute Ischemic Stroke Using Deep Learning.

Final lesion volume (FLV) is a surrogate outcome measure in anterior circulation stroke (ACS). In posterior circulation stroke (PCS), this relation is plausibly understudied due to a lack of methods that automatically quantify FLV. The applicability of deep learning approaches to PCS is limited due to its lower incidence compared to ACS. We evaluated strategies to develop a convolutional neural network (CNN) for PCS lesion segmentation by using image data from both ACS and PCS patients. We included follow-up non-contrast computed tomography scans of 1018 patients with ACS and 107 patients with PCS. To assess whether an ACS lesion segmentation generalizes to PCS, a CNN was trained on ACS data (ACS-CNN). Second, to evaluate the performance of only including PCS patients, a CNN was trained on PCS data. Third, to evaluate the performance when combining the datasets, a CNN was trained on both datasets. Finally, to evaluate the performance of transfer learning, the ACS-CNN was fine-tuned using PCS patients. The transfer learning strategy outperformed the other strategies in volume agreement with an intra-class correlation of 0.88 (95% CI: 0.83-0.92) vs. 0.55 to 0.83 and a lesion detection rate of 87% vs. 41-77 for the other strategies. Hence, transfer learning improved the FLV quantification and detection rate of PCS lesions compared to the other strategies.