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Item type:Publication, Access status: with files , Guided reconstruction with conditioned diffusion models for unsupervised anomaly detection in brain MRIs(2025-01-22); ; ; ; The application of supervised models to clinical screening tasks is challenging due to the need for annotated data for each considered pathology. Unsupervised Anomaly Detection (UAD) is an alternative approach that aims to identify any anomaly as an outlier from a healthy training distribution. A prevalent strategy for UAD in brain MRI involves using generative models to learn the reconstruction of healthy brain anatomy for a given input image. As these models should fail to reconstruct unhealthy structures, the reconstruction errors indicate anomalies. However, a significant challenge is to balance the accurate reconstruction of healthy anatomy and the undesired replication of abnormal structures. While diffusion models have shown promising results with detailed and accurate reconstructions, they face challenges in preserving intensity characteristics, resulting in false positives. We propose conditioning the denoising process of diffusion models with additional information derived from a latent representation of the input image. We demonstrate that this conditioning allows for accurate and local adaptation to the general input intensity distribution while avoiding the replication of unhealthy structures. We compare the novel approach to different state-of-the-art methods and for different data sets. Our results show substantial improvements in the segmentation performance, with the Dice score improved by 11.9%, 20.0%, and 44.6%, for the BraTS, ATLAS and MSLUB data sets, respectively, while maintaining competitive performance on the WMH data set. Furthermore, our results indicate effective domain adaptation across different MRI acquisitions and simulated contrasts, an important attribute for general anomaly detection methods. The code for our work is available at https://github.com/FinnBehrendt/Conditioned-Diffusion-Models-UAD.Publicationtype: Journal Article39 40 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Three-dimensional deep learning with spatial erasing for unsupervised anomaly segmentation in brain MRI(Springer, 2021-07-12); ; ; ; Purpose: Brain Magnetic Resonance Images (MRIs) are essential for the diagnosis of neurological diseases. Recently, deep learning methods for unsupervised anomaly detection (UAD) have been proposed for the analysis of brain MRI. These methods rely on healthy brain MRIs and eliminate the requirement of pixel-wise annotated data compared to supervised deep learning. While a wide range of methods for UAD have been proposed, these methods are mostly 2D and only learn from MRI slices, disregarding that brain lesions are inherently 3D and the spatial context of MRI volumes remains unexploited. Methods: We investigate whether using increased spatial context by using MRI volumes combined with spatial erasing leads to improved unsupervised anomaly segmentation performance compared to learning from slices. We evaluate and compare 2D variational autoencoder (VAE) to their 3D counterpart, propose 3D input erasing, and systemically study the impact of the data set size on the performance. Results: Using two publicly available segmentation data sets for evaluation, 3D VAEs outperform their 2D counterpart, highlighting the advantage of volumetric context. Also, our 3D erasing methods allow for further performance improvements. Our best performing 3D VAE with input erasing leads to an average DICE score of 31.40% compared to 25.76% for the 2D VAE. Conclusions: We propose 3D deep learning methods for UAD in brain MRI combined with 3D erasing and demonstrate that 3D methods clearly outperform their 2D counterpart for anomaly segmentation. Also, our spatial erasing method allows for further performance improvements and reduces the requirement for large data sets.Publicationtype: Journal ArticleScopus© Citations 19 133 215 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Multiple sclerosis lesion activity segmentation with attention-guided two-path CNNsMultiple sclerosis is an inflammatory autoimmune demyelinating disease that is characterized by lesions in the central nervous system. Typically, magnetic resonance imaging (MRI) is used for tracking disease progression. Automatic image processing methods can be used to segment lesions and derive quantitative lesion parameters. So far, methods have focused on lesion segmentation for individual MRI scans. However, for monitoring disease progression, lesion activity in terms of new and enlarging lesions between two time points is a crucial biomarker. For this problem, several classic methods have been proposed, e.g., using difference volumes. Despite their success for single-volume lesion segmentation, deep learning approaches are still rare for lesion activity segmentation. In this work, convolutional neural networks (CNNs) are studied for lesion activity segmentation from two time points. For this task, CNNs are designed and evaluated that combine the information from two points in different ways. In particular, two-path architectures with attention-guided interactions are proposed that enable effective information exchange between the two time point's processing paths. It is demonstrated that deep learning-based methods outperform classic approaches and it is shown that attention-guided interactions significantly improve performance. Furthermore, the attention modules produce plausible attention maps that have a masking effect that suppresses old, irrelevant lesions. A lesion-wise false positive rate of 26.4% is achieved at a true positive rate of 74.2%, which is not significantly different from the interrater performance.Publicationtype: Journal Article183