Andreas Husch

Mehri Baniasadi, Mikkel V. Petersen, Jorge Goncalves et al.

Segmenting deep brain structures from magnetic resonance images is important for patient diagnosis, surgical planning, and research. Most current state-of-the-art solutions follow a segmentation-by-registration approach, where subject MRIs are mapped to a template with well-defined segmentations. However, registration-based pipelines are time-consuming, thus, limiting their clinical use. This paper uses deep learning to provide a robust and efficient deep brain segmentation solution. The method consists of a pre-processing step to conform all MRI images to the same orientation, followed by a convolutional neural network using the nnU-Net framework. We use a total of 14 datasets from both research and clinical collections. Of these, seven were used for training and validation and seven were retained for independent testing. We trained the network to segment 30 deep brain structures, as well as a brain mask, using labels generated from a registration-based approach. We evaluated the generalizability of the network by performing a leave-one-dataset-out cross-validation, and extensive testing on external datasets. Furthermore, we assessed cross-domain transportability by evaluating the results separately on different domains. We achieved an average DSC of 0.89 $\pm$ 0.04 on the independent testing datasets when compared to the registration-based gold standard. On our test system, the computation time decreased from 42 minutes for a reference registration-based pipeline to 1 minute. Our proposed method is fast, robust, and generalizes with high reliability. It can be extended to the segmentation of other brain structures. The method is publicly available on GitHub, as well as a pip package for convenient usage.

Beatriz Garcia Santa Cruz, Jan Sölter, Matias Nicolas Bossa et al.

Machine learning based methods for diagnosis and progression prediction of COVID-19 from imaging data have gained significant attention in the last months, in particular by the use of deep learning models. In this context hundreds of models where proposed with the majority of them trained on public datasets. Data scarcity, mismatch between training and target population, group imbalance, and lack of documentation are important sources of bias, hindering the applicability of these models to real-world clinical practice. Considering that datasets are an essential part of model building and evaluation, a deeper understanding of the current landscape is needed. This paper presents an overview of the currently public available COVID-19 chest X-ray datasets. Each dataset is briefly described and potential strength, limitations and interactions between datasets are identified. In particular, some key properties of current datasets that could be potential sources of bias, impairing models trained on them are pointed out. These descriptions are useful for model building on those datasets, to choose the best dataset according the model goal, to take into account the specific limitations to avoid reporting overconfident benchmark results, and to discuss their impact on the generalisation capabilities in a specific clinical setting

Florian Bernard, Johan Thunberg, Peter Gemmar et al.

The alignment of a set of objects by means of transformations plays an important role in computer vision. Whilst the case for only two objects can be solved globally, when multiple objects are considered usually iterative methods are used. In practice the iterative methods perform well if the relative transformations between any pair of objects are free of noise. However, if only noisy relative transformations are available (e.g. due to missing data or wrong correspondences) the iterative methods may fail. Based on the observation that the underlying noise-free transformations can be retrieved from the null space of a matrix that can directly be obtained from pairwise alignments, this paper presents a novel method for the synchronisation of pairwise transformations such that they are transitively consistent. Simulations demonstrate that for noisy transformations, a large proportion of missing data and even for wrong correspondence assignments the method delivers encouraging results.