Open-Source Skull Reconstruction with MONAI

We present a deep learning-based approach for skull reconstruction for MONAI, which has been pre-trained on the MUG500+ skull dataset. The implementation follows the MONAI contribution guidelines, hence, it can be easily tried out and used, and extended by MONAI users. The primary goal of this paper lies in the investigation of open-sourcing codes and pre-trained deep learning models under the MONAI framework. Nowadays, open-sourcing software, especially (pre-trained) deep learning models, has become increasingly important. Over the years, medical image analysis experienced a tremendous transformation. Over a decade ago, algorithms had to be implemented and optimized with low-level programming languages, like C or C++, to run in a reasonable time on a desktop PC, which was not as powerful as today's computers. Nowadays, users have high-level scripting languages like Python, and frameworks like PyTorch and TensorFlow, along with a sea of public code repositories at hand. As a result, implementations that had thousands of lines of C or C++ code in the past, can now be scripted with a few lines and in addition executed in a fraction of the time. To put this even on a higher level, the Medical Open Network for Artificial Intelligence (MONAI) framework tailors medical imaging research to an even more convenient process, which can boost and push the whole field. The MONAI framework is a freely available, community-supported, open-source and PyTorch-based framework, that also enables to provide research contributions with pre-trained models to others. Codes and pre-trained weights for skull reconstruction are publicly available at: https://github.com/Project-MONAI/research-contributions/tree/master/SkullRec

'A net for everyone': fully personalized and unsupervised neural networks trained with longitudinal data from a single patient

With the rise in importance of personalized medicine, we trained personalized neural networks to detect tumor progression in longitudinal datasets. The model was evaluated on two datasets with a total of 64 scans from 32 patients diagnosed with glioblastoma multiforme (GBM). Contrast-enhanced T1w sequences of brain magnetic resonance imaging (MRI) images were used in this study. For each patient, we trained their own neural network using just two images from different timepoints. Our approach uses a Wasserstein-GAN (generative adversarial network), an unsupervised network architecture, to map the differences between the two images. Using this map, the change in tumor volume can be evaluated. Due to the combination of data augmentation and the network architecture, co-registration of the two images is not needed. Furthermore, we do not rely on any additional training data, (manual) annotations or pre-training neural networks. The model received an AUC-score of 0.87 for tumor change. We also introduced a modified RANO criteria, for which an accuracy of 66% can be achieved. We show that using data from just one patient can be used to train deep neural networks to monitor tumor change.

Training β-VAE by Aggregating a Learned Gaussian Posterior with a Decoupled Decoder

The reconstruction loss and the Kullback-Leibler divergence (KLD) loss in a variational autoencoder (VAE) often play antagonistic roles, and tuning the weight of the KLD loss in $\beta$-VAE to achieve a balance between the two losses is a tricky and dataset-specific task. As a result, current practices in VAE training often result in a trade-off between the reconstruction fidelity and the continuity$/$disentanglement of the latent space, if the weight $\beta$ is not carefully tuned. In this paper, we present intuitions and a careful analysis of the antagonistic mechanism of the two losses, and propose, based on the insights, a simple yet effective two-stage method for training a VAE. Specifically, the method aggregates a learned Gaussian posterior $z \sim q_{\theta} (z|x)$ with a decoder decoupled from the KLD loss, which is trained to learn a new conditional distribution $p_{\phi} (x|z)$ of the input data $x$. Experimentally, we show that the aggregated VAE maximally satisfies the Gaussian assumption about the latent space, while still achieves a reconstruction error comparable to when the latent space is only loosely regularized by $\mathcal{N}(\mathbf{0},I)$. The proposed approach does not require hyperparameter (i.e., the KLD weight $\beta$) tuning given a specific dataset as required in common VAE training practices. We evaluate the method using a medical dataset intended for 3D skull reconstruction and shape completion, and the results indicate promising generative capabilities of the VAE trained using the proposed method. Besides, through guided manipulation of the latent variables, we establish a connection between existing autoencoder (AE)-based approaches and generative approaches, such as VAE, for the shape completion problem. Codes and pre-trained weights are available at https://github.com/Jianningli/skullVAE

The HoloLens in Medicine: A systematic Review and Taxonomy

The HoloLens (Microsoft Corp., Redmond, WA), a head-worn, optically see-through augmented reality display, is the main player in the recent boost in medical augmented reality research. In medical settings, the HoloLens enables the physician to obtain immediate insight into patient information, directly overlaid with their view of the clinical scenario, the medical student to gain a better understanding of complex anatomies or procedures, and even the patient to execute therapeutic tasks with improved, immersive guidance. In this systematic review, we provide a comprehensive overview of the usage of the first-generation HoloLens within the medical domain, from its release in March 2016, until the year of 2021, were attention is shifting towards it's successor, the HoloLens 2. We identified 171 relevant publications through a systematic search of the PubMed and Scopus databases. We analyze these publications in regard to their intended use case, technical methodology for registration and tracking, data sources, visualization as well as validation and evaluation. We find that, although the feasibility of using the HoloLens in various medical scenarios has been shown, increased efforts in the areas of precision, reliability, usability, workflow and perception are necessary to establish AR in clinical practice.

GAN-based generation of realistic 3D data: A systematic review and taxonomy

Data has become the most valuable resource in today's world. With the massive proliferation of data-driven algorithms, such as deep learning-based approaches, the availability of data is of great interest. In this context, high-quality training, validation and testing datasets are particularly needed. Volumetric data is a very important resource in medicine, as it ranges from disease diagnoses to therapy monitoring. When the dataset is sufficient, models can be trained to help doctors with these tasks. Unfortunately, there are scenarios and applications where large amounts of data is unavailable. For example, in the medical field, rare diseases and privacy issues can lead to restricted data availability. In non-medical fields, the high cost of obtaining a sufficient amount of high-quality data can also be a concern. A solution to these problems can be the generation of synthetic data to perform data augmentation in combination with other more traditional methods of data augmentation. Therefore, most of the publications on 3D Generative Adversarial Networks (GANs) are within the medical domain. The existence of mechanisms to generate realistic synthetic data is a good asset to overcome this challenge, especially in healthcare, as the data must be of good quality and close to reality, i.e. realistic, and without privacy issues. In this review, we provide a summary of works that generate realistic 3D synthetic data using GANs. We therefore outline GAN-based methods in these areas with common architectures, advantages and disadvantages. We present a novel taxonomy, evaluations, challenges and research opportunities to provide a holistic overview of the current state of GANs in medicine and other fields.

k-strip: A novel segmentation algorithm in k-space for the application of skull stripping

Objectives: Present a novel deep learning-based skull stripping algorithm for magnetic resonance imaging (MRI) that works directly in the information rich k-space. Materials and Methods: Using two datasets from different institutions with a total of 36,900 MRI slices, we trained a deep learning-based model to work directly with the complex raw k-space data. Skull stripping performed by HD-BET (Brain Extraction Tool) in the image domain were used as the ground truth. Results: Both datasets were very similar to the ground truth (DICE scores of 92\%-98\% and Hausdorff distances of under 5.5 mm). Results on slices above the eye-region reach DICE scores of up to 99\%, while the accuracy drops in regions around the eyes and below, with partially blurred output. The output of k-strip often smoothed edges at the demarcation to the skull. Binary masks are created with an appropriate threshold. Conclusion: With this proof-of-concept study, we were able to show the feasibility of working in the k-space frequency domain, preserving phase information, with consistent results. Future research should be dedicated to discovering additional ways the k-space can be used for innovative image analysis and further workflows.

Back to the Roots: Reconstructing Large and Complex Cranial Defects using an Image-based Statistical Shape Model

Designing implants for large and complex cranial defects is a challenging task, even for professional designers. Current efforts on automating the design process focused mainly on convolutional neural networks (CNN), which have produced state-of-the-art results on reconstructing synthetic defects. However, existing CNN-based methods have been difficult to translate to clinical practice in cranioplasty, as their performance on complex and irregular cranial defects remains unsatisfactory. In this paper, a statistical shape model (SSM) built directly on the segmentation masks of the skulls is presented. We evaluate the SSM on several cranial implant design tasks, and the results show that, while the SSM performs suboptimally on synthetic defects compared to CNN-based approaches, it is capable of reconstructing large and complex defects with only minor manual corrections. The quality of the resulting implants is examined and assured by experienced neurosurgeons. In contrast, CNN-based approaches, even with massive data augmentation, fail or produce less-than-satisfactory implants for these cases. Codes are publicly available at https://github.com/Jianningli/ssm

Review of Disentanglement Approaches for Medical Applications -- Towards Solving the Gordian Knot of Generative Models in Healthcare

Deep neural networks are commonly used for medical purposes such as image generation, segmentation, or classification. Besides this, they are often criticized as black boxes as their decision process is often not human interpretable. Encouraging the latent representation of a generative model to be disentangled offers new perspectives of control and interpretability. Understanding the data generation process could help to create artificial medical data sets without violating patient privacy, synthesizing different data modalities, or discovering data generating characteristics. These characteristics might unravel novel relationships that can be related to genetic traits or patient outcomes. In this paper, we give a comprehensive overview of popular generative models, like Generative Adversarial Networks (GANs), Variational Autoencoders (VAEs), and Flow-based Models. Furthermore, we summarize the different notions of disentanglement, review approaches to disentangle latent space representations and metrics to evaluate the degree of disentanglement. After introducing the theoretical frameworks, we give an overview of recent medical applications and discuss the impact and importance of disentanglement approaches for medical applications.

Stochastic Modeling of Inhomogeneities in the Aortic Wall and Uncertainty Quantification using a Bayesian Encoder-Decoder Surrogate

Inhomogeneities in the aortic wall can lead to localized stress accumulations, possibly initiating dissection. In many cases, a dissection results from pathological changes such as fragmentation or loss of elastic fibers. But it has been shown that even the healthy aortic wall has an inherent heterogeneous microstructure. Some parts of the aorta are particularly susceptible to the development of inhomogeneities due to pathological changes, however, the distribution in the aortic wall and the spatial extent, such as size, shape, and type, are difficult to predict. Motivated by this observation, we describe the heterogeneous distribution of elastic fiber degradation in the dissected aortic wall using a stochastic constitutive model. For this purpose, random field realizations, which model the stochastic distribution of degraded elastic fibers, are generated over a non-equidistant grid. The random field then serves as input for a uni-axial extension test of the pathological aortic wall, solved with the finite-element (FE) method. To include the microstructure of the dissected aortic wall, a constitutive model developed in a previous study is applied, which also includes an approach to model the degradation of inter-lamellar elastic fibers. Then to assess the uncertainty in the output stress distribution due to this stochastic constitutive model, a convolutional neural network, specifically a Bayesian encoder-decoder, was used as a surrogate model that maps the random input fields to the output stress distribution obtained from the FE analysis. The results show that the neural network is able to predict the stress distribution of the FE analysis while significantly reducing the computational time. In addition, it provides the probability for exceeding critical stresses within the aortic wall, which could allow for the prediction of delamination or fatal rupture.

MOMO -- Deep Learning-driven classification of external DICOM studies for PACS archivation

Patients regularly continue assessment or treatment in other facilities than they began them in, receiving their previous imaging studies as a CD-ROM and requiring clinical staff at the new hospital to import these studies into their local database. However, between different facilities, standards for nomenclature, contents, or even medical procedures may vary, often requiring human intervention to accurately classify the received studies in the context of the recipient hospital's standards. In this study, the authors present MOMO (MOdality Mapping and Orchestration), a deep learning-based approach to automate this mapping process utilizing metadata substring matching and a neural network ensemble, which is trained to recognize the 76 most common imaging studies across seven different modalities. A retrospective study is performed to measure the accuracy that this algorithm can provide. To this end, a set of 11,934 imaging series with existing labels was retrieved from the local hospital's PACS database to train the neural networks. A set of 843 completely anonymized external studies was hand-labeled to assess the performance of our algorithm. Additionally, an ablation study was performed to measure the performance impact of the network ensemble in the algorithm, and a comparative performance test with a commercial product was conducted. In comparison to a commercial product (96.20% predictive power, 82.86% accuracy, 1.36% minor errors), a neural network ensemble alone performs the classification task with less accuracy (99.05% predictive power, 72.69% accuracy, 10.3% minor errors). However, MOMO outperforms either by a large margin in accuracy and with increased predictive power (99.29% predictive power, 92.71% accuracy, 2.63% minor errors).