Healthy kidney segmentation in the dce-mr images using a convolutional neural network and temporal signal characteristics

Quantification of renal perfusion based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) requires determination of signal intensity time courses in the region of renal parenchyma. Thus, selection of voxels representing the kidney must be accomplished with special care and constitutes one of the major technical limitations which hampers wider usage of this technique as a standard clinical routine. Manual segmentation of renal compartments—even if performed by experts—is a common source of decreased repeatability and reproducibility. In this paper, we present a processing framework for the automatic kidney segmentation in DCE-MR images. The framework consists of two stages. Firstly, kidney masks are generated using a convolutional neural network. Then, mask voxels are classified to one of three regions—cortex, medulla, and pelvis–based on DCE-MRI signal intensity time courses. The proposed approach was evaluated on a cohort of 10 healthy volunteers who underwent the DCE-MRI examination. MRI scanning was repeated on two time events within a 10-day interval. For semantic segmentation task we employed a classic U-Net architecture, whereas experiments on voxel classification were performed using three alternative algorithms—support vector machines, logistic regression and extreme gradient boosting trees, among which SVM produced the most accurate results. Both segmentation and classification steps were accomplished by a series of models, each trained separately for a given subject using the data from other participants only. The mean achieved accuracy of the whole kidney segmentation was 94% in terms of IoU coefficient. Cortex, medulla and pelvis were segmented with IoU ranging from 90 to 93% depending on the tissue and body side. The results were also validated by comparing image-derived perfusion parameters with ground truth measurements of glomerular filtration rate (GFR). The repeatability of GFR calculation, as assessed by the coefficient of variation was determined at the level of 14.5 and 17.5% for the left and right kidney, respectively and it improved relative to manual segmentation. Reproduciblity, in turn, was evaluated by measuring agreement between image-derived and iohexol-based GFR values. The estimated absolute mean differences were equal to 9.4 and 12.9 mL/min/1.73 m2 for scanning sessions 1 and 2 and the proposed automated segmentation method. The result for session 2 was comparable with manual segmentation, whereas for session 1 reproducibility in the automatic pipeline was weaker.publishedVersio

Movement correction by object recognition-based anatomical tracking in functional magnetic resonance urography (fMRU): Proof of principle

Breathing motion is a challenge to analysis of imaging time series in many settings, especially in thorax and abdomen. We investigated in a software phantom as proof of principle, whether object recognition based tracking is capable of intensity-time-curve analysis. Images-time-series (no respiratory gating) of 100 kidneys were artificially generated (Matlab, TheMathworks, Natick, NA, USA). Respiratory movement was implemented by a sinusoidal coordinate shift with an amplitude of 3 cm and frequency of about 6 min-1. Renal intensity changes after contrast application were modeled using gamma functions for three anatomical compartments: cortex, pyramids and renal pelvis. Movement correction was carried out for half of the study population. Intensity-time-curves were extracted using automatically placed regions of interest relative to central coordinates of the kidney on the first image. Intensity changes over time extracted from the ROIs were subtracted from known intensity changes of the software model. Differences were assessed using Wilcox-Signed-Rank test for 50 kidneys with and 50 without movement correction. We used Bonferroni method to correct for multiple testing. Mean sum of differences between predicted and observed intensities across all kidneys and compartments was 0,072 with and 7,3 without movement correction. Significant difference between observation and model was not seen in any compartments of the tracking group (mean z-score: -0.8), whereas there was in 66 compartments in the non-tracking group (mean z-score: -3.2), signifying good agreement between theoretical model and observed intensity changes with object recognition-based tracking, and suboptimal agreement in the non-tracking-group due to movement artifacts. We conclude that object-recognition based anatomical tracking is feasible in fMRU as an alternative or addition to respiration gating. This may allow a higher temporal resolution of these studies in the future

Investigation of Neonatal Pulmonary Structure and Function via Proton and Hyperpolarized Gas Magnetic Resonance Imaging

Magnetic resonance imaging (MRI) is a modality that utilizes the phenomenon of nuclear magnetic resonance (NMR) to yield tomographic images of the body. Proton (1H) MRI has historically been successful in soft tissues but has suffered in the lung due to a variety of technical challenges, such as the low proton-density, rapid T2* relaxation time of the lung parenchymal tissue, and inherent physiological motion in the chest. Recent developments in radial ultrashort echo time (UTE) MRI have in part overcome these issues. In addition, there has been much progress in techniques for hyperpolarization of noble gases (3He and 129Xe) out of thermal equilibrium via spin exchange optical pumping, which can greatly enhance the gas NMR signal such that it is detectable within the airspaces of the lung on MRI. The lung is a unique organ due to its complex structural and functional dynamics, and its early development through the neonatal (newborn) period is not yet well understood in normal or abnormal conditions. Pulmonary morbidities are relatively common in infants and are present in a majority of patients admitted to the neonatal intensive care unit, often stemming from preterm birth and/or congenital defects. Current clinical lung imaging in these patients is typically limited to chest x-ray radiography, which does not provide tomographic information and so has lowered sensitivity. More rarely, x-ray computed tomography (CT) is used but exposes infants to ionizing radiation and typically requires sedation, both of which pose increased risks to pediatric patients. Thus the opportunity is ripe for application of novel pulmonary MRI techniques to the infant population. However, MR imaging of very small pulmonary structure and microstructure requires fundamental changes in the imaging theory of both 1H UTE MRI and hyperpolarized gas diffusion MRI. Furthermore, such young patients are often non-compliant, yielding a need for new and innovative techniques for monitoring respiratory and bulk motion. This dissertation describes methodology development and provides experimental results in both 1H UTE MRI and hyperpolarized 3He and 129Xe gas diffusion MRI, with investigation into the structure and function of infant lungs at both the macrostructural and microstructural level. In particular, anisotropically restricted gas diffusion within infant alveolar microstructure is investigated as a measurement of airspace size and geometry. Additionally, the phenomenon of respiratory and bulk motion-tracking via modulation of the k-space center\u27s magnitude and phase is explored and applied via UTE MRI in various neonatal pulmonary conditions to extract imaging-based metrics of diagnostic value. Further, the proton-density regime of pulmonary UTE MRI is validated in translational applications. These techniques are applied in infants with various pulmonary conditions, including patients diagnosed with bronchopulmonary dysplasia, congenital diaphragmatic hernia, esophageal atresia/tracheoesophageal fistula, tracheomalacia, and no suspected lung disease. In addition, explanted lung specimens from both infants with and without lung disease are examined. Development and implementation of these techniques involves a strong understanding of the physics-based theory of NMR, hyperpolarization, and MR imaging, in addition to foundations in hardware, software, and image analysis techniques. This thesis first outlines the theory and background of NMR, MRI, and pulmonary physiology and development (Part I), then proceeds into the theory, equipment, and imaging experiments for hyperpolarized gas diffusion MRI in infant lung airspaces (Part II), and finally details the theory, data processing methods, and applications of pulmonary UTE MRI in infant patients (Part III). The potential for clinical translation of the neonatal pulmonary MRI methods presented in this dissertation is very high, with the foundations of these techniques firmly rooted in the laws of physics

Assessment of morphological and functional properties of the genitourinary system using high resolution MRI

Ziel dieser Arbeit war die Untersuchung und Darstellbarkeit einzelner Kompartimente des Urogenitaltrakts mittels hochaufgelöster Magnetresonanztomografie (MRT). Im Kontext der Schließmuskelregeneration wurde mit Hilfe der MRT der urethrale Schließmuskel eines Tiermodells visualisiert, wodurch im zeitlichen Verlauf die Lokalisierung und Anpassungsfähigkeit des Muskelgewebes nach Injektion von markierten Stammzellen untersucht werden konnte. Hierfür wurde eine robuste, sensitive und nicht-invasive Methode angewendet, um ein essentielles Verständnis der biologischen Effekte im Sphinkter zu erhalten und somit neue zellbasierte Therapien zu entwickeln. Zur Untersuchung weiterer Kompartimente des Urogenitaltrakts wurden die renalen Strukturen Cortex, Medulla und Pelvis ohne die Verwendung von Kontrastmittel anhand hochauflösender MR-Methoden im Probanden evaluiert. Unter Zuhilfenahme optimierter MR-Sequenzen konnten die einzelnen Kompartimente klar strukturiert und durch einen selbstentwickelten automatischen Algorithmus segmentiert werden. Im Vergleich zur manuellen Segmentierung zeigten die berechneten Koeffizienten eine hohe Übereinstimmung zur automatischen Segmentierung der gesamten Nierenregion. Zusätzlich wurde durch den vorgestellten Algorithmus sowohl die Medulla als auch das Nierenbecken automatisch segmentiert. Bisher sind keine Ansätze aus der Literatur bekannt, die das Nierenbecken aus nativen MR-Bildern segmentierten und evaluierten. Die Kombination aus optimierten MR-Bildern, Bildregistrierung und automatischer Segmentierung liefert zuverlässige und wiederholbare Ergebnisse der Volumenbestimmung der gesamten Niere und der renalen Strukturen ohne Zuhilfenahme von Kontrastmittel. Bei einer möglichen Übertragung des entwickelten Algorithmus in die klinische Routine eröffnen sich neue nicht-invasive Möglichkeiten zur Bewertung und Überwachung morphologischer Veränderungen. Zur weiteren Anwendung wurden die segmentierten Areale auf entzerrungskorrigierte funktionelle Diffusionsdatensätze überlagert, um eine regionenbasierte Darstellung der fraktionellen Anisotropie (FA) und der mittleren Diffusivität (MD) zu erhalten. Die Durchführung der Verzerrungskorrektur wurde anhand der „reversed gradient“ Methode verwirklicht. Die erfolgreiche Verzerrungskorrektur konnte durch einen Vergleich der manuellen Segmentierung der MD Karten und den automatisch generierten Masken aus den Anatomiedatensätzen dargelegt werden. Die manuelle Segmentierung ist sehr zeitaufwändig und auf Grund der unscharfen Außenkontur der Niere in den MD Karten äußerst schwierig zu realisieren. Daher erbringt die Fusion von hochaufgelösten, anatomisch segmentierten Masken mit verzerrungskorrigierten funktionellen Daten Vorteile für eine zuverlässige Auswertung. Die berechneten funktionellen Werte zeigten eine gute Übereinstimmung mit Literaturwerten. Lediglich verringerte medullare FA-Werte sind auf die Tatsache zurückzuführen, dass die bisherigen Bewertungsmethoden nur Regionen aus den hellsten Bereichen der funktionellen Bilder mit einbezogen haben. Ein weiterer Vorteil des entwickelten Algorithmus ist somit eine schichtweise Quantifizierung der gesamten Nierenstrukturen, wobei lokale Nierenerkrankungen, wie Zysten oder eine partielle Nekrose, durch eine erweiterte Segmentierung mit in die Beurteilung einbezogen werden können. Die Verhältnisse der Volumina innerhalb der Niere, unter Berücksichtigung der Funktionalität der einzelnen Regionen, ermöglichen nun weitere Erkenntnisse in der Nierendiagnostik

Diseases of the Abdomen and Pelvis 2018-2021: Diagnostic Imaging - IDKD Book

Gastrointestinal disease; PET/CT; Radiology; X-ray; IDKD; Davo

In vivo methods and applications of xenon-129 magnetic resonance

Hyperpolarised gas lung MRI using xenon-129 can provide detailed 3D images of the ventilated lung airspaces, and can be applied to quantify lung microstructure and detailed aspects of lung function such as gas exchange. It is sensitive to functional and structural changes in early lung disease and can be used in longitudinal studies of disease progression and therapy response. The ability of 129Xe to dissolve into the blood stream and its chemical shift sensitivity to its local environment allow monitoring of gas exchange in the lungs, perfusion of the brain and kidneys, and blood oxygenation. This article reviews the methods and applications of in vivo 129Xe MR in humans, with a focus on the physics of polarisation by optical pumping, radiofrequency coil and pulse sequence design, and the in vivo applications of 129Xe MRI and MRS to examine lung ventilation, microstructure and gas exchange, blood oxygenation, and perfusion of the brain and kidneys

Long-term outcome after hypothermia-treated hypoxic-ischaemic encephalopathy

Hypoxic-ischaemic encephalopathy (HIE) is a major cause of acquired brain injury in newborn infants. It is a potentially life-threatening condition that leaves survivors at substantial risk of life-long debilitating sequelae including cerebral palsy, epilepsy, intellectual disability, sensory disruption, behavioural issues, executive difficulties and autism spectrum disorder. More subtle cognitive impairments are common among survivors free of major neuromotor disability. Therapeutic hypothermia (TH) reduces the risk of death and disability in nearterm/term new-born infants with moderate and severe HIE. Outcomes in adolescence and adulthood following HIE treated with TH are not yet known. The majority of infants with HIE also suffer multi-organ dysfunction resulting from the hypoxic-ischaemic insult. The kidneys are particularly sensitive to hypoxia-ischaemia, with up to 72% of asphyxiated infants suffering acute kidney injury (AKI) prior to the advent of TH. Evidence point to AKI being independently associated with increased neonatal morbidity and mortality. To date, very little is known about long-term renal consequences following neonatal AKI in asphyxiated infants treated with TH. The overall aim of this thesis was to contribute to the improved treatment and care of infants with HIE by means of increased knowledge about the predictive value of early aEEG, neonatal AKI, and long-term outcomes in the era of TH. In a small population-based cohort, the predictive value of early amplitude-integrated EEG (aEEG) was demonstrated to be altered in infants treated with TH due to HIE. Poor outcome at the age of 1 year was only seen among infants with a persisting abnormal aEEG background pattern at and beyond 24 hours of age. In a population-based, prospective, longitudinal study including all children treated with TH between 2007 and 2009 in Stockholm, Sweden, we assessed neuromotor, neurologic, cognitive and behavioural outcomes at 6-8 and 10-12 years of age. Seventeen per cent of survivors developed CP. Survivors free of major neuromotor impairment had cognitive abilities within normal range. Repeated assessment in early adolescence revealed new deficits in 26% of children with previously favourable outcome. The proportion of children with executive difficulties in this patient population appears to be higher than in the general population. Outcomes in children with a history of moderate HIE remain heterogenous also in the era of TH. In a population-based cohort of all children treated with TH between 2007 and 2009 in Stockholm, Sweden, 45% suffered neonatal AKI. Severe AKI necessitating kidney support therapy was rare. Among infants with AKI, 20% fulfilled only the urinary output criterion of the neonatal modified KDIGO (Kidney Disease Improving Global Outcomes) definition. Mortality was higher among infants with AKI. At 10-12 years of age, 21% of children had decreased glomerular filtration rate (GFR) estimated from creatinine with the Schwartz-Lyon equation. A more in-depth assessment of renal functions in the above-mentioned population-based cohort demonstrated that renal sequelae (defined as decreased GFR, albuminuria, hypertension or normal high blood pressure, reduced renal volume on magnetic resonance imaging, or elevated Fibroblast Growth Factor 23) were rare at 10-12 years of age following perinatal asphyxia and TH. The Schwarz-Lyon equation appears to underestimate GFR in this patient population

Diseases of the Chest, Breast, Heart and Vessels 2019-2022

This open access book focuses on diagnostic and interventional imaging of the chest, breast, heart, and vessels. It consists of a remarkable collection of contributions authored by internationally respected experts, featuring the most recent diagnostic developments and technological advances with a highly didactical approach. The chapters are disease-oriented and cover all the relevant imaging modalities, including standard radiography, CT, nuclear medicine with PET, ultrasound and magnetic resonance imaging, as well as imaging-guided interventions. As such, it presents a comprehensive review of current knowledge on imaging of the heart and chest, as well as thoracic interventions and a selection of "hot topics". The book is intended for radiologists, however, it is also of interest to clinicians in oncology, cardiology, and pulmonology