TotalSegmentator: robust segmentation of 104 anatomical structures in CT images

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.Comment: Accepted at Radiology: Artificial Intelligenc

Liver Segmentation and its Application to Hepatic Interventions

The thesis addresses the development of an intuitive and accurate liver segmentation approach, its integration into software prototypes for the planning of liver interventions, and research on liver regeneration. The developed liver segmentation approach is based on a combination of the live wire paradigm and shape-based interpolation. Extended with two correction modes and integrated into a user-friendly workflow, the method has been applied to more than 5000 data sets. The combination of the liver segmentation with image analysis of hepatic vessels and tumors allows for the computation of anatomical and functional remnant liver volumes. In several projects with clinical partners world-wide, the benefit of the computer-assisted planning was shown. New insights about the postoperative liver function and regeneration could be gained, and most recent investigations into the analysis of MRI data provide the option to further improve hepatic intervention planning

Splenic nerve bundle stimulation in acute and chronic inflammation

Splenic neurovascular bundle stimulation holds potential to treat acute and chronic inflammatory conditions. In the first part of the thesis, the available literature on the interactions between the immune system and nervous system in the intestine is summarized. Then, it is shown that a specialized T-cell, that can produce the neurotransmitter acetylcholine, resides in the gut an plays a dual role in the development of experimental colitis in mice. Furthermore, electrical splenic neurovascular bundle stimulation ameliorated the outcomes of colitis in mice and reversed transcriptomic changes in the gut that were induced by colitis. The second part of the thesis focused on the translation of splenic neurovascular bundle stimulation to the human situation. It is shown that there are significant changes between murine and human innervation of the spleen. Using computed tomography (CT) images the course and the characteristics of the splenic artery were described. These data were used to develop a cuff electrode that could be used for electrical stimulation of the splenic neurovascular bundle in humans. Finally, it was demonstrated that splenic neurovascular bundle stimulation in humans was safe and feasible in a pilot study with patients that underwent esophagectomy

IMPROVING DAILY CLINICAL PRACTICE WITH ABDOMINAL PATIENT SPECIFIC 3D MODELS

This thesis proposes methods and procedures to proficiently introduce patient 3D models in the daily clinical practice for diagnosis and treatment of abdominal diseases. The objective of the work consists in providing and visualizing quantitative geometrical and topological information on the anatomy of interest, and to develop systems that allow to improve radiology and surgery. The 3D visualization drastically simplifies the interpretation process of medical images and provides benefits both in diagnosing and in surgical planning phases. Further advantages can be introduced registering virtual pre-operative information (3D models) with real intra-operative information (patient and surgical instruments). The surgeon can use mixed-reality systems that allow him/her to see covered structures before reaching them, surgical navigators for see the scene (anatomy and instruments) from different point of view and smart mechatronics devices, which, knowing the anatomy, assist him/her in an active way. All these aspects are useful in terms of safety, efficiency and financial resources for the physicians, for the patient and for the sanitary system too. The entire process, from volumetric radiological images acquisition up to the use of 3D anatomical models inside the surgical room, has been studied and specific applications have been developed. A segmentation procedure has been designed taking into account acquisition protocols commonly used in radiological departments, and a software tool, that allows to obtain efficient 3D models, have been implemented and tested. The alignment problem has been investigated examining the various sources of errors during the image acquisition, in the radiological department, and during to the execution of the intervention. A rigid body registration procedure compatible with the surgical environment has been defined and implemented. The procedure has been integrated in a surgical navigation system and is useful as starting initial registration for more accurate alignment methods based on deformable approaches. Monoscopic and stereoscopic 3D localization machine vision routines, using the laparoscopic and/or generic cameras images, have been implemented to obtain intra-operative information that can be used to model abdominal deformations. Further, the use of this information for fusion and registration purposes allows to enhance the potentialities of computer assisted surgery. In particular a precise alignment between virtual and real anatomies for mixed-reality purposes, and the development of tracker-free navigation systems, has been obtained elaborating video images and providing an analytical adaptation of the virtual camera to the real camera. Clinical tests, demonstrating the usability of the proposed solutions, are reported. Test results and appreciation of radiologists and surgeons, to the proposed prototypes, encourage their integration in the daily clinical practice and future developments

Case series of breast fillers and how things may go wrong: radiology point of view

INTRODUCTION: Breast augmentation is a procedure opted by women to overcome sagging breast due to breastfeeding or aging as well as small breast size. Recent years have shown the emergence of a variety of injectable materials on market as breast fillers. These injectable breast fillers have swiftly gained popularity among women, considering the minimal invasiveness of the procedure, nullifying the need for terrifying surgery. Little do they know that the procedure may pose detrimental complications, while visualization of breast parenchyma infiltrated by these fillers is also deemed substandard; posing diagnostic challenges. We present a case series of three patients with prior history of hyaluronic acid and collagen breast injections. REPORT: The first patient is a 37-year-old lady who presented to casualty with worsening shortness of breath, non-productive cough, central chest pain; associated with fever and chills for 2-weeks duration. The second patient is a 34-year-old lady who complained of cough, fever and haemoptysis; associated with shortness of breath for 1-week duration. CT in these cases revealed non thrombotic wedge-shaped peripheral air-space densities. The third patient is a 37‐year‐old female with right breast pain, swelling and redness for 2- weeks duration. Previous collagen breast injection performed 1 year ago had impeded sonographic visualization of the breast parenchyma. MRI breasts showed multiple non- enhancing round and oval shaped lesions exhibiting fat intensity. CONCLUSION: Radiologists should be familiar with the potential risks and hazards as well as limitations of imaging posed by breast fillers such that MRI is required as problem-solving tool

Characterization of alar ligament on 3.0T MRI: a cross-sectional study in IIUM Medical Centre, Kuantan

INTRODUCTION: The main purpose of the study is to compare the normal anatomy of alar ligament on MRI between male and female. The specific objectives are to assess the prevalence of alar ligament visualized on MRI, to describe its characteristics in term of its course, shape and signal homogeneity and to find differences in alar ligament signal intensity between male and female. This study also aims to determine the association between the heights of respondents with alar ligament signal intensity and dimensions. MATERIALS & METHODS: 50 healthy volunteers were studied on 3.0T MR scanner Siemens Magnetom Spectra using 2-mm proton density, T2 and fat-suppression sequences. Alar ligament is depicted in 3 planes and the visualization and variability of the ligament courses, shapes and signal intensity characteristics were determined. The alar ligament dimensions were also measured. RESULTS: Alar ligament was best depicted in coronal plane, followed by sagittal and axial planes. The orientations were laterally ascending in most of the subjects (60%), predominantly oval in shaped (54%) and 67% showed inhomogenous signal. No significant difference of alar ligament signal intensity between male and female respondents. No significant association was found between the heights of the respondents with alar ligament signal intensity and dimensions. CONCLUSION: Employing a 3.0T MR scanner, the alar ligament is best portrayed on coronal plane, followed by sagittal and axial planes. However, tremendous variability of alar ligament as depicted in our data shows that caution needs to be exercised when evaluating alar ligament, especially during circumstances of injury