Kathinka D. Kurz

Luca Tomasetti, Mahdieh Khanmohammadi, Kjersti Engan et al.

Time is a fundamental factor during stroke treatments. A fast, automatic approach that segments the ischemic regions helps treatment decisions. In clinical use today, a set of color-coded parametric maps generated from computed tomography perfusion (CTP) images are investigated manually to decide a treatment plan. We propose an automatic method based on a neural network using a set of parametric maps to segment the two ischemic regions (core and penumbra) in patients affected by acute ischemic stroke. Our model is based on a convolution-deconvolution bottleneck structure with multi-input and slow fusion. A loss function based on the focal Tversky index addresses the data imbalance issue. The proposed architecture demonstrates effective performance and results comparable to the ground truth annotated by neuroradiologists. A Dice coefficient of 0.81 for penumbra and 0.52 for core over the large vessel occlusion test set is achieved. The full implementation is available at: https://git.io/JtFGb.

Luca Tomasetti, Kjersti Engan, Liv Jorunn Høllesli et al.

Precise and fast prediction methods for ischemic areas comprised of dead tissue, core, and salvageable tissue, penumbra, in acute ischemic stroke (AIS) patients are of significant clinical interest. They play an essential role in improving diagnosis and treatment planning. Computed Tomography (CT) scan is one of the primary modalities for early assessment in patients with suspected AIS. CT Perfusion (CTP) is often used as a primary assessment to determine stroke location, severity, and volume of ischemic lesions. Current automatic segmentation methods for CTP mostly use already processed 3D parametric maps conventionally used for clinical interpretation by radiologists as input. Alternatively, the raw CTP data is used on a slice-by-slice basis as 2D+time input, where the spatial information over the volume is ignored. In addition, these methods are only interested in segmenting core regions, while predicting penumbra can be essential for treatment planning. This paper investigates different methods to utilize the entire 4D CTP as input to fully exploit the spatio-temporal information, leading us to propose a novel 4D convolution layer. Our comprehensive experiments on a local dataset of 152 patients divided into three groups show that our proposed models generate more precise results than other methods explored. Adopting the proposed 4D mJ-Net, a Dice Coefficient of 0.53 and 0.23 is achieved for segmenting penumbra and core areas, respectively. The code is available on https://github.com/Biomedical-Data-Analysis-Laboratory/4D-mJ-Net.git.

Luca Tomasetti, Stine Hansen, Mahdieh Khanmohammadi et al.

Precise ischemic lesion segmentation plays an essential role in improving diagnosis and treatment planning for ischemic stroke, one of the prevalent diseases with the highest mortality rate. While numerous deep neural network approaches have recently been proposed to tackle this problem, these methods require large amounts of annotated regions during training, which can be impractical in the medical domain where annotated data is scarce. As a remedy, we present a prototypical few-shot segmentation approach for ischemic lesion segmentation using only one annotated sample during training. The proposed approach leverages a novel self-supervised training mechanism that is tailored to the task of ischemic stroke lesion segmentation by exploiting color-coded parametric maps generated from Computed Tomography Perfusion scans. We illustrate the benefits of our proposed training mechanism, leading to considerable improvements in performance in the few-shot setting. Given a single annotated patient, an average Dice score of 0.58 is achieved for the segmentation of ischemic lesions.

Sam Narimani, Solveig Roth Hoff, Kathinka Dæhli Kurz et al.

Purpose: Annotation of medical breast images is an essential step toward better diagnostic but a time consuming task. This research aims to focus on different selecting sample strategies within deep active learning on Breast Region Segmentation (BRS) to lessen computational cost of training and effective use of resources. Methods: The Stavanger breast MRI dataset containing 59 patients was used in this study, with FCN-ResNet50 adopted as a sustainable deep learning (DL) model. A novel sample selection approach based on Breast Anatomy Geometry (BAG) analysis was introduced to group data with similar informative features for DL. Patient positioning and Breast Size were considered the key selection criteria in this process. Four selection strategies including Random Selection, Nearest Point, Breast Size, and a hybrid of all three strategies were evaluated using an active learning framework. Four training data proportions of 10%, 20%, 30%, and 40% were used for model training, with the remaining data reserved for testing. Model performance was assessed using Dice score, Intersection over Union, precision, and recall, along with 5-fold cross-validation to enhance generalizability. Results: Increasing the training data proportion from 10% to 40% improved segmentation performance for nearly all strategies, except for Random Selection. The Nearest Point strategy consistently achieved the lowest carbon footprint at 30% and 40% data proportions. Overall, combining the Nearest Point strategy with 30% of the training data provided the best balance between segmentation performance, efficiency, and environmental sustainability. Keywords: Deep Active Learning, Breast Region Segmentation, Human-center analysis

Sam Narimani, Solveig Roth Hoff, Kathinka Dahli Kurz et al.

Purpose: Segmentation of the breast lesion in dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is an essential step to accurately diagnose and plan treatment and monitor progress. This study aims to highlight the impact of breast region segmentation (BRS) on deep learning-based breast lesion segmentation (BLS) in breast DCE-MRI. Methods Using the Stavanger Dataset containing primarily 59 DCE-MRI scans and UNet++ as deep learning models, four different process were conducted to compare effect of BRS on BLS. These four approaches included the whole volume without BRS and with BRS, BRS with the selected lesion slices and lastly optimal volume with BRS. Preprocessing methods like augmentation and oversampling were used to enhance the small dataset, data shape uniformity and improve model performance. Optimal volume size were investigated by a precise process to ensure that all lesions existed in slices. To evaluate the model, a hybrid loss function including dice, focal and cross entropy along with 5-fold cross validation method were used and lastly a test dataset which was randomly split used to evaluate the model performance on unseen data for each of four mentioned approaches. Results Results demonstrate that using BRS considerably improved model performance and validation. Significant improvement in last approach -- optimal volume with BRS -- compared to the approach without BRS counting around 50 percent demonstrating how effective BRS has been in BLS. Moreover, huge improvement in energy consumption, decreasing up to 450 percent, introduces a green solution toward a more environmentally sustainable approach for future work on large dataset.