Sabine Heiland

Hao Li, Jianan Liu, Marianne Schell et al.

Shortening acquisition time and reducing motion artifacts are the most critical challenges in magnetic resonance imaging (MRI). Deep learning-based image restoration has emerged as a promising solution capable of generating high-resolution and motion-artifact-free MRI images from low-resolution images acquired with shortened acquisition times or from motion-artifact-corrupted images. To facilitate clinical integration, a time- and GPU-efficient network with reliable accuracy is essential. In this study, we adopted a unified 2D deep learning framework for pseudo-3D MRI image super-resolution reconstruction (SRR) and motion artifact reduction (MAR). The optimal down-sampling factors to optimize the acquisition time in SRR were identified. Training for MAR was performed using publicly available in vivo data, employing a novel standardized method to induce motion artifacts of varying severity in a controlled way. The accuracy of the network was evaluated through a pixel-wise uncertainty map, and performance was benchmarked against state-of-the-art methods. The results demonstrated that the down-sampling factor of 1x1x2 for x2 acceleration and 2x2x2 for x4 acceleration was optimal. For SRR, the proposed TS-RCAN outperformed the 3D networks of mDCSRN and ReCNN, with an improvement of more than 0.01 in SSIM and 1.5 dB in PSNR while reducing GPU load by up to and inference time by up to 90%. For MAR, TS-RCAN exceeded UNet's performance by up to 0.014 in SSIM and 1.48 dB in PSNR. Additionally, TS-RCAN provided uncertainty information, which can be used to estimate the quality of the reconstructed images. TS-RCAN has potential use for SRR and MAR in the clinical setting.

Jens Petersen, Fabian Isensee, Gregor Köhler et al.

The ability to estimate how a tumor might evolve in the future could have tremendous clinical benefits, from improved treatment decisions to better dose distribution in radiation therapy. Recent work has approached the glioma growth modeling problem via deep learning and variational inference, thus learning growth dynamics entirely from a real patient data distribution. So far, this approach was constrained to predefined image acquisition intervals and sequences of fixed length, which limits its applicability in more realistic scenarios. We overcome these limitations by extending Neural Processes, a class of conditional generative models for stochastic time series, with a hierarchical multi-scale representation encoding including a spatio-temporal attention mechanism. The result is a learned growth model that can be conditioned on an arbitrary number of observations, and that can produce a distribution of temporally consistent growth trajectories on a continuous time axis. On a dataset of 379 patients, the approach successfully captures both global and finer-grained variations in the images, exhibiting superior performance compared to other learned growth models.

Jens Petersen, Paul F. Jäger, Fabian Isensee et al.

Existing approaches to modeling the dynamics of brain tumor growth, specifically glioma, employ biologically inspired models of cell diffusion, using image data to estimate the associated parameters. In this work, we propose an alternative approach based on recent advances in probabilistic segmentation and representation learning that implicitly learns growth dynamics directly from data without an underlying explicit model. We present evidence that our approach is able to learn a distribution of plausible future tumor appearances conditioned on past observations of the same tumor.

Fabian Isensee, Marianne Schell, Irada Tursunova et al.

Brain extraction is a critical preprocessing step in the analysis of MRI neuroimaging studies and influences the accuracy of downstream analyses. The majority of brain extraction algorithms are, however, optimized for processing healthy brains and thus frequently fail in the presence of pathologically altered brain or when applied to heterogeneous MRI datasets. Here we introduce a new, rigorously validated algorithm (termed HD-BET) relying on artificial neural networks that aims to overcome these limitations. We demonstrate that HD-BET outperforms six popular, publicly available brain extraction algorithms in several large-scale neuroimaging datasets, including one from a prospective multicentric trial in neuro-oncology, yielding state-of-the-art performance with median improvements of +1.16 to +2.11 points for the DICE coefficient and -0.66 to -2.51 mm for the Hausdorff distance. Importantly, the HD-BET algorithm shows robust performance in the presence of pathology or treatment-induced tissue alterations, is applicable to a broad range of MRI sequence types and is not influenced by variations in MRI hardware and acquisition parameters encountered in both research and clinical practice. For broader accessibility our HD-BET prediction algorithm is made freely available (http://www.neuroAI-HD.org) and may become an essential component for robust, automated, high-throughput processing of MRI neuroimaging data.