Deep Dive into MRI: Exploring Deep Learning Applications in 0.55T and 7T MRI

The development of magnetic resonance imaging (MRI) for medical imaging has provided a leap forward in diagnosis, providing a safe, non-invasive alternative to techniques involving ionising radiation exposure for diagnostic purposes. It was described by Block and Purcel in 1946, and it was not until 1980 that the first clinical application of MRI became available. Since that time the MRI has gone through many advances and has altered the way diagnosing procedures are performed. Due to its ability to improve constantly, MRI has become a commonly used practice among several specialisations in medicine. Particularly starting 0.55T and 7T MRI technologies have pointed out enhanced preservation of image detail and advanced tissue characterisation. This review examines the integration of deep learning (DL) techniques into these MRI modalities, disseminating and exploring the study applications. It highlights how DL contributes to 0.55T and 7T MRI data, showcasing the potential of DL in improving and refining these technologies. The review ends with a brief overview of how MRI technology will evolve in the coming years.

How we won BraTS 2023 Adult Glioma challenge? Just faking it! Enhanced Synthetic Data Augmentation and Model Ensemble for brain tumour segmentation

Deep Learning is the state-of-the-art technology for segmenting brain tumours. However, this requires a lot of high-quality data, which is difficult to obtain, especially in the medical field. Therefore, our solutions address this problem by using unconventional mechanisms for data augmentation. Generative adversarial networks and registration are used to massively increase the amount of available samples for training three different deep learning models for brain tumour segmentation, the first task of the BraTS2023 challenge. The first model is the standard nnU-Net, the second is the Swin UNETR and the third is the winning solution of the BraTS 2021 Challenge. The entire pipeline is built on the nnU-Net implementation, except for the generation of the synthetic data. The use of convolutional algorithms and transformers is able to fill each other's knowledge gaps. Using the new metric, our best solution achieves the dice results 0.9005, 0.8673, 0.8509 and HD95 14.940, 14.467, 17.699 (whole tumour, tumour core and enhancing tumour) in the validation set.

Deep PCCT: Photon Counting Computed Tomography Deep Learning Applications Review

Medical imaging faces challenges such as limited spatial resolution, interference from electronic noise and poor contrast-to-noise ratios. Photon Counting Computed Tomography (PCCT) has emerged as a solution, addressing these issues with its innovative technology. This review delves into the recent developments and applications of PCCT in pre-clinical research, emphasizing its potential to overcome traditional imaging limitations. For example PCCT has demonstrated remarkable efficacy in improving the detection of subtle abnormalities in breast, providing a level of detail previously unattainable. Examining the current literature on PCCT, it presents a comprehensive analysis of the technology, highlighting the main features of scanners and their varied applications. In addition, it explores the integration of deep learning into PCCT, along with the study of radiomic features, presenting successful applications in data processing. While acknowledging these advances, it also discusses the existing challenges in this field, paving the way for future research and improvements in medical imaging technologies. Despite the limited number of articles on this subject, due to the recent integration of PCCT at a clinical level, its potential benefits extend to various diagnostic applications.

Multilingual Natural Language Processing Model for Radiology Reports -- The Summary is all you need!

The impression section of a radiology report summarizes important radiology findings and plays a critical role in communicating these findings to physicians. However, the preparation of these summaries is time-consuming and error-prone for radiologists. Recently, numerous models for radiology report summarization have been developed. Nevertheless, there is currently no model that can summarize these reports in multiple languages. Such a model could greatly improve future research and the development of Deep Learning models that incorporate data from patients with different ethnic backgrounds. In this study, the generation of radiology impressions in different languages was automated by fine-tuning a model, publicly available, based on a multilingual text-to-text Transformer to summarize findings available in English, Portuguese, and German radiology reports. In a blind test, two board-certified radiologists indicated that for at least 70% of the system-generated summaries, the quality matched or exceeded the corresponding human-written summaries, suggesting substantial clinical reliability. Furthermore, this study showed that the multilingual model outperformed other models that specialized in summarizing radiology reports in only one language, as well as models that were not specifically designed for summarizing radiology reports, such as ChatGPT.

MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision

We present MedShapeNet, a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D surgical instrument models. Prior to the deep learning era, the broad application of statistical shape models (SSMs) in medical image analysis is evidence that shapes have been commonly used to describe medical data. Nowadays, however, state-of-the-art (SOTA) deep learning algorithms in medical imaging are predominantly voxel-based. In computer vision, on the contrary, shapes (including, voxel occupancy grids, meshes, point clouds and implicit surface models) are preferred data representations in 3D, as seen from the numerous shape-related publications in premier vision conferences, such as the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), as well as the increasing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models) in computer vision research. MedShapeNet is created as an alternative to these commonly used shape benchmarks to facilitate the translation of data-driven vision algorithms to medical applications, and it extends the opportunities to adapt SOTA vision algorithms to solve critical medical problems. Besides, the majority of the medical shapes in MedShapeNet are modeled directly on the imaging data of real patients, and therefore it complements well existing shape benchmarks comprising of computer-aided design (CAD) models. MedShapeNet currently includes more than 100,000 medical shapes, and provides annotations in the form of paired data. It is therefore also a freely available repository of 3D models for extended reality (virtual reality - VR, augmented reality - AR, mixed reality - MR) and medical 3D printing. This white paper describes in detail the motivations behind MedShapeNet, the shape acquisition procedures, the use cases, as well as the usage of the online shape search portal: https://medshapenet.ikim.nrw/

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

AutoPET Challenge: Combining nn-Unet with Swin UNETR Augmented by Maximum Intensity Projection Classifier

Tumor volume and changes in tumor characteristics over time are important biomarkers for cancer therapy. In this context, FDG-PET/CT scans are routinely used for staging and re-staging of cancer, as the radiolabeled fluorodeoxyglucose is taken up in regions of high metabolism. Unfortunately, these regions with high metabolism are not specific to tumors and can also represent physiological uptake by normal functioning organs, inflammation, or infection, making detailed and reliable tumor segmentation in these scans a demanding task. This gap in research is addressed by the AutoPET challenge, which provides a public data set with FDG-PET/CT scans from 900 patients to encourage further improvement in this field. Our contribution to this challenge is an ensemble of two state-of-the-art segmentation models, the nn-Unet and the Swin UNETR, augmented by a maximum intensity projection classifier that acts like a gating mechanism. If it predicts the existence of lesions, both segmentations are combined by a late fusion approach. Our solution achieves a Dice score of 72.12\% on patients diagnosed with lung cancer, melanoma, and lymphoma in our cross-validation. Code: https://github.com/heiligerl/autopet_submission

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.

Generation of Synthetic Rat Brain MRI scans with a 3D Enhanced Alpha-GAN

Translational brain research using Magnetic Resonance Imaging (MRI) is becoming increasingly popular as animal models are an essential part of scientific studies and more ultra-high-field scanners are becoming available. Some disadvantages of MRI are the availability of MRI scanners and the time required for a full scanning session (it usually takes over 30 minutes). Privacy laws and the 3Rs ethics rule also make it difficult to create large datasets for training deep learning models. Generative Adversarial Networks (GANs) can perform data augmentation with higher quality than other techniques. In this work, the alpha-GAN architecture is used to test its ability to produce realistic 3D MRI scans of the rat brain. As far as the authors are aware, this is the first time that a GAN-based approach has been used for data augmentation in preclinical data. The generated scans are evaluated using various qualitative and quantitative metrics. A Turing test conducted by 4 experts has shown that the generated scans can trick almost any expert. The generated scans were also used to evaluate their impact on the performance of an existing deep learning model developed for segmenting the rat brain into white matter, grey matter and cerebrospinal fluid. The models were compared using the Dice score. The best results for whole brain and white matter segmentation were obtained when 174 real scans and 348 synthetic scans were used, with improvements of 0.0172 and 0.0129, respectively. Using 174 real scans and 87 synthetic scans resulted in improvements of 0.0038 and 0.0764 for grey matter and CSF segmentation, respectively. Thus, by using the proposed new normalisation layer and loss functions, it was possible to improve the realism of the generated rat MRI scans and it was shown that using the generated data improved the segmentation model more than using the conventional data augmentation.