ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

Metrics reloaded: Pitfalls and recommendations for image analysis validation

The field of automatic biomedical image analysis crucially depends on robust and meaningful performance metrics for algorithm validation. Current metric usage, however, is often ill-informed and does not reflect the underlying domain interest. Here, we present a comprehensive framework that guides researchers towards choosing performance metrics in a problem-aware manner. Specifically, we focus on biomedical image analysis problems that can be interpreted as a classification task at image, object or pixel level. The framework first compiles domain interest-, target structure-, data set- and algorithm output-related properties of a given problem into a problem fingerprint, while also mapping it to the appropriate problem category, namely image-level classification, semantic segmentation, instance segmentation, or object detection. It then guides users through the process of selecting and applying a set of appropriate validation metrics while making them aware of potential pitfalls related to individual choices. In this paper, we describe the current status of the Metrics Reloaded recommendation framework, with the goal of obtaining constructive feedback from the image analysis community. The current version has been developed within an international consortium of more than 60 image analysis experts and will be made openly available as a user-friendly toolkit after community-driven optimization.

Federated Learning Enables Big Data for Rare Cancer Boundary Detection

Although machine learning (ML) has shown promise in numerous domains, there are concerns about generalizability to out-of-sample data. This is currently addressed by centrally sharing ample, and importantly diverse, data from multiple sites. However, such centralization is challenging to scale (or even not feasible) due to various limitations. Federated ML (FL) provides an alternative to train accurate and generalizable ML models, by only sharing numerical model updates. Here we present findings from the largest FL study to-date, involving data from 71 healthcare institutions across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, utilizing the largest dataset of such patients ever used in the literature (25,256 MRI scans from 6,314 patients). We demonstrate a 33% improvement over a publicly trained model to delineate the surgically targetable tumor, and 23% improvement over the tumor's entire extent. We anticipate our study to: 1) enable more studies in healthcare informed by large and diverse data, ensuring meaningful results for rare diseases and underrepresented populations, 2) facilitate further quantitative analyses for glioblastoma via performance optimization of our consensus model for eventual public release, and 3) demonstrate the effectiveness of FL at such scale and task complexity as a paradigm shift for multi-site collaborations, alleviating the need for data sharing.

Deep Learning-based Type Identification of Volumetric MRI Sequences

The analysis of Magnetic Resonance Imaging (MRI) sequences enables clinical professionals to monitor the progression of a brain tumor. As the interest for automatizing brain volume MRI analysis increases, it becomes convenient to have each sequence well identified. However, the unstandardized naming of MRI sequences makes their identification difficult for automated systems, as well as makes it difficult for researches to generate or use datasets for machine learning research. In the face of that, we propose a system for identifying types of brain MRI sequences based on deep learning. By training a Convolutional Neural Network (CNN) based on 18-layer ResNet architecture, our system can classify a volumetric brain MRI as a FLAIR, T1, T1c or T2 sequence, or whether it does not belong to any of these classes. The network was evaluated on publicly available datasets comprising both, pre-processed (BraTS dataset) and non-pre-processed (TCGA-GBM dataset), image types with diverse acquisition protocols, requiring only a few slices of the volume for training. Our system can classify among sequence types with an accuracy of 96.81%.

Common Limitations of Image Processing Metrics: A Picture Story

While the importance of automatic image analysis is increasing at an enormous pace, recent meta-research revealed major flaws with respect to algorithm validation. Specifically, performance metrics are key for objective, transparent and comparative performance assessment, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. A common mission of several international initiatives is therefore to provide researchers with guidelines and tools to choose the performance metrics in a problem-aware manner. This dynamically updated document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts.

Combining unsupervised and supervised learning for predicting the final stroke lesion

Predicting the final ischaemic stroke lesion provides crucial information regarding the volume of salvageable hypoperfused tissue, which helps physicians in the difficult decision-making process of treatment planning and intervention. Treatment selection is influenced by clinical diagnosis, which requires delineating the stroke lesion, as well as characterising cerebral blood flow dynamics using neuroimaging acquisitions. Nonetheless, predicting the final stroke lesion is an intricate task, due to the variability in lesion size, shape, location and the underlying cerebral haemodynamic processes that occur after the ischaemic stroke takes place. Moreover, since elapsed time between stroke and treatment is related to the loss of brain tissue, assessing and predicting the final stroke lesion needs to be performed in a short period of time, which makes the task even more complex. Therefore, there is a need for automatic methods that predict the final stroke lesion and support physicians in the treatment decision process. We propose a fully automatic deep learning method based on unsupervised and supervised learning to predict the final stroke lesion after 90 days. Our aim is to predict the final stroke lesion location and extent, taking into account the underlying cerebral blood flow dynamics that can influence the prediction. To achieve this, we propose a two-branch Restricted Boltzmann Machine, which provides specialized data-driven features from different sets of standard parametric Magnetic Resonance Imaging maps. These data-driven feature maps are then combined with the parametric Magnetic Resonance Imaging maps, and fed to a Convolutional and Recurrent Neural Network architecture. We evaluated our proposal on the publicly available ISLES 2017 testing dataset, reaching a Dice score of 0.38, Hausdorff Distance of 29.21 mm, and Average Symmetric Surface Distance of 5.52 mm.

pymia: A Python package for data handling and evaluation in deep learning-based medical image analysis

Background and Objective: Deep learning enables tremendous progress in medical image analysis. One driving force of this progress are open-source frameworks like TensorFlow and PyTorch. However, these frameworks rarely address issues specific to the domain of medical image analysis, such as 3-D data handling and distance metrics for evaluation. pymia, an open-source Python package, tries to address these issues by providing flexible data handling and evaluation independent of the deep learning framework. Methods: The pymia package provides data handling and evaluation functionalities. The data handling allows flexible medical image handling in every commonly used format (e.g., 2-D, 2.5-D, and 3-D; full- or patch-wise). Even data beyond images like demographics or clinical reports can easily be integrated into deep learning pipelines. The evaluation allows stand-alone result calculation and reporting, as well as performance monitoring during training using a vast amount of domain-specific metrics for segmentation, reconstruction, and regression. Results: The pymia package is highly flexible, allows for fast prototyping, and reduces the burden of implementing data handling routines and evaluation methods. While data handling and evaluation are independent of the deep learning framework used, they can easily be integrated into TensorFlow and PyTorch pipelines. The developed package was successfully used in a variety of research projects for segmentation, reconstruction, and regression. Conclusions: The pymia package fills the gap of current deep learning frameworks regarding data handling and evaluation in medical image analysis. It is available at https://github.com/rundherum/pymia and can directly be installed from the Python Package Index using pip install pymia.

Learning Bloch Simulations for MR Fingerprinting by Invertible Neural Networks

Magnetic resonance fingerprinting (MRF) enables fast and multiparametric MR imaging. Despite fast acquisition, the state-of-the-art reconstruction of MRF based on dictionary matching is slow and lacks scalability. To overcome these limitations, neural network (NN) approaches estimating MR parameters from fingerprints have been proposed recently. Here, we revisit NN-based MRF reconstruction to jointly learn the forward process from MR parameters to fingerprints and the backward process from fingerprints to MR parameters by leveraging invertible neural networks (INNs). As a proof-of-concept, we perform various experiments showing the benefit of learning the forward process, i.e., the Bloch simulations, for improved MR parameter estimation. The benefit especially accentuates when MR parameter estimation is difficult due to MR physical restrictions. Therefore, INNs might be a feasible alternative to the current solely backward-based NNs for MRF reconstruction.

Spatially Regularized Parametric Map Reconstruction for Fast Magnetic Resonance Fingerprinting

Magnetic resonance fingerprinting (MRF) provides a unique concept for simultaneous and fast acquisition of multiple quantitative MR parameters. Despite acquisition efficiency, adoption of MRF into the clinics is hindered by its dictionary-based reconstruction, which is computationally demanding and lacks scalability. Here, we propose a convolutional neural network-based reconstruction, which enables both accurate and fast reconstruction of parametric maps, and is adaptable based on the needs of spatial regularization and the capacity for the reconstruction. We evaluated the method using MRF T1-FF, an MRF sequence for T1 relaxation time of water and fat fraction mapping. We demonstrate the method's performance on a highly heterogeneous dataset consisting of 164 patients with various neuromuscular diseases imaged at thighs and legs. We empirically show the benefit of incorporating spatial regularization during the reconstruction and demonstrate that the method learns meaningful features from MR physics perspective. Further, we investigate the ability of the method to handle highly heterogeneous morphometric variations and its generalization to anatomical regions unseen during training. The obtained results outperform the state-of-the-art in deep learning-based MRF reconstruction. Coupled with fast MRF sequences, the proposed method has the potential of enabling multiparametric MR imaging in clinically feasible time.

Dual-Stream Pyramid Registration Network

We propose a Dual-Stream Pyramid Registration Network (referred as Dual-PRNet) for unsupervised 3D medical image registration. Unlike recent CNN-based registration approaches, such as VoxelMorph, which explores a single-stream encoder-decoder network to compute a registration fields from a pair of 3D volumes, we design a two-stream architecture able to compute multi-scale registration fields from convolutional feature pyramids. Our contributions are two-fold: (i) we design a two-stream 3D encoder-decoder network which computes two convolutional feature pyramids separately for a pair of input volumes, resulting in strong deep representations that are meaningful for deformation estimation; (ii) we propose a pyramid registration module able to predict multi-scale registration fields directly from the decoding feature pyramids. This allows it to refine the registration fields gradually in a coarse-to-fine manner via sequential warping, and enable the model with the capability for handling significant deformations between two volumes, such as large displacements in spatial domain or slice space. The proposed Dual-PRNet is evaluated on two standard benchmarks for brain MRI registration, where it outperforms the state-of-the-art approaches by a large margin, e.g., having improvements over recent VoxelMorph [2] with 0.683->0.778 on the LPBA40, and 0.511->0.631 on the Mindboggle101, in term of average Dice score.