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We report a fully differential study of ionization of the Ne L-shell by Compton scattering of 20 keV photons. We find two physical mechanisms which modify the Compton-electron emission. Firstly, we observe scattering of the Compton electrons at their parent nucleus. Secondly, we find a distinct maximum in the electron momentum distribution close-to-zero momentum which we attribute to a focusing of the electrons by the Coulomb potential., Comment: 5 pages, 4 figures

The hypothalamus plays a crucial role in the regulation of a broad range of physiological, behavioural, and cognitive functions. However, despite its importance, only a few small-scale neuroimaging studies have investigated its substructures, likely due to the lack of fully automated segmentation tools to address scalability and reproducibility issues of manual segmentation. While the only previous attempt to automatically sub-segment the hypothalamus with a neural network showed promise for 1.0 mm isotropic T1-weighted (T1w) MRI, there is a need for an automated tool to sub-segment also high-resolutional (HiRes) MR scans, as they are becoming widely available, and include structural detail also from multi-modal MRI. We, therefore, introduce a novel, fast, and fully automated deep learning method named HypVINN for sub-segmentation of the hypothalamus and adjacent structures on 0.8 mm isotropic T1w and T2w brain MR images that is robust to missing modalities. We extensively validate our model with respect to segmentation accuracy, generalizability, in-session test-retest reliability, and sensitivity to replicate hypothalamic volume effects (e.g. sex-differences). The proposed method exhibits high segmentation performance both for standalone T1w images as well as for T1w/T2w image pairs. Even with the additional capability to accept flexible inputs, our model matches or exceeds the performance of state-of-the-art methods with fixed inputs. We, further, demonstrate the generalizability of our method in experiments with 1.0 mm MR scans from both the Rhineland Study and the UK Biobank. Finally, HypVINN can perform the segmentation in less than a minute (GPU) and will be available in the open source FastSurfer neuroimaging software suite, offering a validated, efficient, and scalable solution for evaluating imaging-derived phenotypes of the hypothalamus., Comment: Accepted in Imaging Neuroscience

Head motion is an omnipresent confounder of magnetic resonance image (MRI) analyses as it systematically affects morphometric measurements, even when visual quality control is performed. In order to estimate subtle head motion, that remains undetected by experts, we introduce a deep learning method to predict in-scanner head motion directly from T1-weighted (T1w), T2-weighted (T2w) and fluid-attenuated inversion recovery (FLAIR) images using motion estimates from an in-scanner depth camera as ground truth. Since we work with data from compliant healthy participants of the Rhineland Study, head motion and resulting imaging artifacts are less prevalent than in most clinical cohorts and more difficult to detect. Our method demonstrates improved performance compared to state-of-the-art motion estimation methods and can quantify drift and respiration movement independently. Finally, on unseen data, our predictions preserve the known, significant correlation with age.

Exploration of bias has significant impact on the transparency and applicability of deep learning pipelines in medical settings, yet is so far woefully understudied. In this paper, we consider two separate groups for which training data is only available at differing image resolutions. For group H, available images and labels are at the preferred high resolution while for group L only deprecated lower resolution data exist. We analyse how this resolution-bias in the data distribution propagates to systematically biased predictions for group L at higher resolutions. Our results demonstrate that single-resolution training settings result in significant loss of volumetric group differences that translate to erroneous segmentations as measured by DSC and subsequent classification failures on the low resolution group. We further explore how training data across resolutions can be used to combat this systematic bias. Specifically, we investigate the effect of image resampling, scale augmentation and resolution independence and demonstrate that biases can effectively be reduced with multi-resolution approaches.

Leading neuroimaging studies have pushed 3T MRI acquisition resolutions below 1.0 mm for improved structure definition and morphometry. Yet, only few, time-intensive automated image analysis pipelines have been validated for high-resolution (HiRes) settings. Efficient deep learning approaches, on the other hand, rarely support more than one fixed resolution (usually 1.0 mm). Furthermore, the lack of a standard submillimeter resolution as well as limited availability of diverse HiRes data with sufficient coverage of scanner, age, diseases, or genetic variance poses additional, unsolved challenges for training HiRes networks. Incorporating resolution-independence into deep learning-based segmentation, i.e., the ability to segment images at their native resolution across a range of different voxel sizes, promises to overcome these challenges, yet no such approach currently exists. We now fill this gap by introducing a Voxelsize Independent Neural Network (VINN) for resolution-independent segmentation tasks and present FastSurferVINN, which (i) establishes and implements resolution-independence for deep learning as the first method simultaneously supporting 0.7-1.0 mm whole brain segmentation, (ii) significantly outperforms state-of-the-art methods across resolutions, and (iii) mitigates the data imbalance problem present in HiRes datasets. Overall, internal resolution-independence mutually benefits both HiRes and 1.0 mm MRI segmentation. With our rigorously validated FastSurferVINN we distribute a rapid tool for morphometric neuroimage analysis. The VINN architecture, furthermore, represents an efficient resolution-independent segmentation method for wider application, Comment: accepted at NeuroImage

We investigate the Cauchy problem for a class of nonlinear elliptic operators with $C^\infty$-coefficients at a regular set $\Omega \subset R^n$. The Cauchy data are given at a manifold $\Gamma \subset \partial\Omega$ and our goal is to reconstruct the trace of the $H^1(\Omega)$ solution of a nonlinear elliptic equation at $\partial \Omega / \Gamma$. We propose two iterative methods based on the segmenting Mann iteration applied to fixed point equations, which are closely related to the original problem. The first approach consists in obtaining a corresponding linear Cauchy problem and analyzing a linear fixed point equation; a convergence proof is given and convergence rates are obtained. On the second approach a nonlinear fixed point equation is considered and a fully nonlinear iterative method is investigated; some preliminary convergence results are proven and a numerical analysis is provided., Comment: 23 pages, 6 figures

Deep learning approaches for diffusion MRI have so far focused primarily on voxel-based segmentation of lesions or white-matter fiber tracts. A drawback of representing tracts as volumetric labels, rather than sets of streamlines, is that it precludes point-wise analyses of microstructural or geometric features along a tract. Traditional tractography pipelines, which do allow such analyses, can benefit from detailed whole-brain segmentations to guide tract reconstruction. Here, we introduce fast, deep learning-based segmentation of 170 anatomical regions directly on diffusion-weighted MR images, removing the dependency of conventional segmentation methods on T 1-weighted images and slow pre-processing pipelines. Working natively in diffusion space avoids non-linear distortions and registration errors across modalities, as well as interpolation artifacts. We demonstrate consistent segmentation results between 0 .70 and 0 .87 Dice depending on the tissue type. We investigate various combinations of diffusion-derived inputs and show generalization across different numbers of gradient directions. Finally, integrating our approach to provide anatomical priors for tractography pipelines, such as TRACULA, removes hours of pre-processing time and permits processing even in the absence of high-quality T 1-weighted scans, without degrading the quality of the resulting tract estimates., Comment: Christian Ewert and David K\"ugler contributed equally. Accepted at MICCAI 2020 International Workshop on Computational Diffusion MRI

Despite recent successes, the advances in Deep Learning have not yet been fully translated to Computer Assisted Intervention (CAI) problems such as pose estimation of surgical instruments. Currently, neural architectures for classification and segmentation tasks are adopted ignoring significant discrepancies between CAI and these tasks. We propose an automatic framework (AutoSNAP) for instrument pose estimation problems, which discovers and learns the architectures for neural networks. We introduce 1)~an efficient testing environment for pose estimation, 2)~a powerful architecture representation based on novel Symbolic Neural Architecture Patterns (SNAPs), and 3)~an optimization of the architecture using an efficient search scheme. Using AutoSNAP, we discover an improved architecture (SNAPNet) which outperforms both the hand-engineered i3PosNet and the state-of-the-art architecture search method DARTS., Comment: Accepted at MICCAI 2020 Preparing code for release at https://github.com/MECLabTUDA/AutoSNAP

Purpose: Electromagnetic Tracking (EMT) can potentially complement fluoroscopic navigation, reducing radiation exposure in a hybrid setting. Due to the susceptibility to external distortions, systematic error in EMT needs to be compensated algorithmically. Compensation algorithms for EMT in guidewire procedures are only practical in an online setting. Methods: We collect positional data and train a symmetric Artificial Neural Network (ANN) architecture for compensating navigation error. The results are evaluated in both online and offline scenarios and are compared to polynomial fits. We assess spatial uncertainty of the compensation proposed by the ANN. Simulations based on real data show how this uncertainty measure can be utilized to improve accuracy and limit radiation exposure in hybrid navigation. Results: ANNs compensate unseen distortions by more than 70%, outperforming polynomial regression. Working on known distortions, ANNs outperform polynomials as well. We empirically demonstrate a linear relationship between tracking accuracy and model uncertainty. The effectiveness of hybrid tracking is shown in a simulation experiment. Conclusion: ANNs are suitable for EMT error compensation and can generalize across unseen distortions. Model uncertainty needs to be assessed when spatial error compensation algorithms are developed, so that training data collection can be optimized. Finally, we find that error compensation in EMT reduces the need for x-ray images in hybrid navigation.

Failure cases of black-box deep learning, e.g. adversarial examples, might have severe consequences in healthcare. Yet such failures are mostly studied in the context of real-world images with calibrated attacks. To demystify the adversarial examples, rigorous studies need to be designed. Unfortunately, complexity of the medical images hinders such study design directly from the medical images. We hypothesize that adversarial examples might result from the incorrect mapping of image space to the low dimensional generation manifold by deep networks. To test the hypothesis, we simplify a complex medical problem namely pose estimation of surgical tools into its barest form. An analytical decision boundary and exhaustive search of the one-pixel attack across multiple image dimensions let us localize the regions of frequent successful one-pixel attacks at the image space., Comment: Figure 4 corrected from published Version to correct y-axis labels

Though analysis of Medical Images by Deep Learning achieves unprecedented results across various applications, the effect of \emph{noisy training annotations} is rarely studied in a systematic manner. In Medical Image Analysis, most reports addressing this question concentrate on studying segmentation performance of deep learning classifiers. The absence of continuous ground truth annotations in these studies limits the value of conclusions for applications, where regression is the primary method of choice. In the application of surgical instrument pose estimation, where precision has a direct clinical impact on patient outcome, studying the effect of \emph{noisy annotations} on deep learning pose estimation techniques is of supreme importance. Real x-ray images are inadequate for this evaluation due to the unavailability of ground truth annotations. We circumvent this problem by generating synthetic radiographs, where the ground truth pose is known and therefore the pose estimation error made by the medical-expert can be estimated from experiments. Furthermore, this study shows the property of deep neural networks to learn dominant signals from noisy annotations with sufficient data in a regression setting.