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Automatic Artifact Detection Algorithm in Fetal MRI

Adam Lim, Justin Lo, Matthias W. Wagner, Birgit Ertl-Wagner, Dafna Sussman
2022 Frontiers in Artificial Intelligence  
Fetal MR imaging is subject to artifacts including motion, chemical shift, and radiofrequency artifacts. Currently, such artifacts are detected by the MRI operator, a process which is subjective, time consuming, and prone to errors. We propose a novel algorithm, RISE-Net, that can consistently, automatically, and objectively detect artifacts in 3D fetal MRI. It makes use of a CNN ensemble approach where the first CNN aims to identify and classify any artifacts in the image, and the second CNN
more » ... es regression to determine the severity of the detected artifacts. The main mechanism in RISE-Net is the stacked Residual, Inception, Squeeze and Excitation (RISE) blocks. This classification network achieved an accuracy of 90.34% and a F1 score of 90.39% and outperformed other state-of-the-art architectures, such as VGG-16, Inception, ResNet-50, ReNet-Inception, SE-ResNet, and SE-Inception. The severity regression network had an MSE of 0.083 across all classes. The presented algorithm facilitates rapid and accurate fetal MRI quality assurance that can be implemented into clinical use.
doi:10.3389/frai.2022.861791 pmid:35783351 pmcid:PMC9244144 fatcat:y5ywqqhxaraitgiblt2qvmayf4

Open-radiomics: A Research Protocol to Make Radiomics-based Machine Learning Pipelines Reproducible [article]

Ernest Namdar, Matthias W. Wagner, Birgit B. Ertl-Wagner, Farzad Khalvati
2022 arXiv   pre-print
The application of artificial intelligence (AI) techniques to medical imaging data has yielded promising results. As an important branch of AI pipelines in medical imaging, radiomics faces two major challenges namely reproducibility and accessibility. In this work, we introduce open-radiomics, a set of radiomics datasets, and a comprehensive radiomics pipeline that investigates the effects of radiomics feature extraction settings such as binWidth and image normalization on the reproducibility
more » ... the radiomics results performance. To make radiomics research more accessible and reproducible, we provide guidelines for building machine learning (ML) models on radiomics data, introduce Open-radiomics, an evolving collection of open-source radiomics datasets, and publish baseline models for the datasets.
arXiv:2207.14776v1 fatcat:n4ake6vx4rf3nmlndah7syovgy

Bayesian Pharmacokinetic Modeling of Dynamic Contrast-Enhanced Magnetic Resonance Imaging: Validation and Application [article]

Andreas Mittermeier, Birgit Ertl-Wagner, Jens Ricke, Olaf Dietrich, Michael Ingrisch
2019 arXiv   pre-print
Tracer-kinetic analysis of dynamic contrast-enhanced magnetic resonance imaging data is commonly performed with the well-known Tofts model and nonlinear least squares (NLLS) regression. This approach yields point estimates of model parameters, uncertainty of these estimates can be assessed e.g. by an additional bootstrapping analysis. Here, we present a Bayesian probabilistic modeling approach for tracer-kinetic analysis with a Tofts model, which yields posterior probability distributions of
more » ... fusion parameters and therefore promises a robust and information-enriched alternative based on a framework of probability distributions. In this manuscript, we use the Quantitative Imaging Biomarkers Alliance (QIBA) Tofts phantom to evaluate the Bayesian Tofts Model (BTM) against a bootstrapped NLLS approach. Furthermore, we demonstrate how Bayesian posterior probability distributions can be employed to assess treatment response in a breast cancer DCE-MRI dataset using Cohen's d. Accuracy and precision of the BTM posterior distributions were validated and found to be in good agreement with the NLLS approaches, and assessment of therapy response with respect to uncertainty in parameter estimates was found to be excellent. In conclusion, the Bayesian modeling approach provides an elegant means to determine uncertainty via posterior distributions within a single step and provides honest information about changes in parameter estimates.
arXiv:1904.01832v1 fatcat:ncccjmw37jbqhmevoq3fid2cvi

Volumetric Analysis of Hearing-Related Structures of Brain in Children with GJB2-Related Congenital Deafness

Matthias W. Wagner, Sharon L. Cushing, Makabongwe Tshuma, Karen A. Gordon, Birgit B. Ertl-Wagner, Logi Vidarsson
2022 Children  
Children with non-syndromic hereditary sensorineural hearing loss (SNHL) provide an opportunity to explore the impact of hearing on brain development. Objective: This study investigates volumetric differences of key hearing-related structures in children with gap junction protein beta 2 GJB2-related SNHL compared to controls. Materials and methods: Ninety-four children with SNHL (n = 15) or normal hearing (n = 79) were studied using automated volumetric segmentation. Heschl's gyrus (HG),
more » ... r HG (aHG), planum temporale (PT), medial geniculate nucleus (MGN), and nucleus accumbens (NA) were analyzed relative to total brain volume (TBV) at two different age groups: (1) 7–12 months and (2) 13 months–18 years. Two-sided t-tests were used to evaluate differences between groups. Differences were considered significant if p < 0.007. Results: Significantly smaller aHG-to-TBV ratios were found in 13-month-to-18-year-old patients (p < 0.0055). HG-, PT-, MGN-, and NA-to-TBV ratios were smaller in the same age group, without reaching a significant level. Conversely, HG- and NA-to-TBV were larger in the younger age group. No significant differences were found between the groups for age and TBV. Conclusions: In this exploratory volumetric analysis of key hearing-related structures, we observed age-related changes in volume in children with GJB2-related SNHL.
doi:10.3390/children9060800 pmid:35740737 pmcid:PMC9222099 fatcat:ihdznwnxm5bzjg4qvdlofxqr4i

Multiple Sclerosis

Nora N. Sommer, Tobias Saam, Eva Coppenrath, Hendrik Kooijman, Tania Kümpfel, Maximilian Patzig, Sebastian E. Beyer, Wieland H. Sommer, Maximilian F. Reiser, Birgit Ertl-Wagner, Karla M. Treitl
2018 Investigative Radiology  
Objectives: The aim of this study was to assess the diagnostic accuracy of a modified high-resolution whole-brain three-dimensional T1-weighted blackblood sequence (T1-weighted modified volumetric isotropic turbo spin echo acquisition [T1-mVISTA]) in comparison to a standard three-dimensional T1-weighted magnetization-prepared rapid gradient echo (MP-RAGE) sequence for detection of contrast-enhancing cerebral lesions in patients with relapsingremitting multiple sclerosis (MS). Materials and
more » ... ods: After institutional review board approval and informed consent, 22 patients (8 men; aged 31.0 ± 9.2 years) with relapsing-remitting MS were included in this monocentric prospective cohort study. Contrast-enhanced T1-mVISTA and MP-RAGE, both with 0.8 mm 3 resolution, were performed in all patients. In a substudy of 12 patients, T1-mVISTA was compared with a T1-mVISTAwith 1.0 mm 3 resolution (T1-mVISTA_1.0). Reference lesions were defined by an experienced neuroradiologist using all available sequences and served as the criterion standard. T1-mVISTA, T1-mVISTA_1.0, and MP-RAGE sequences were read in random order 4 weeks apart. Image quality, visual contrast enhancement, contrast-to-noise-ratio (CNR), diagnostic confidence, and lesion size were assessed and compared by Wilcoxon and Mann-Whitney U tests. Results: Eleven of 22 patients displayed contrast-enhancing lesions. Visual contrast enhancement, CNR, and diagnostic confidence of contrast-enhancing MS lesions were significantly increased in T1-mVISTA compared with MP-RAGE (P < 0.001). Significantly more contrast-enhancing lesions were detected with T1-mVISTA than with MP-RAGE (71 vs 39, respectively; P < 0.001). With MP-RAGE, 25.6% of lesions were missed in the initial reading, whereas only 4.2% of lesions were missed with T1-mVISTA. Increase of the voxel volume from 0.8 mm to 1.0 mm isotropic in T1-mVISTA_1.0 did not affect the detectability of lesions, whereas scan time was decreased from 4:43 to 1:55 minutes. Conclusions: Three-dimensional T1-mVISTA improves the detection rates of contrast-enhancing cerebral MS lesions compared with conventional 3D MP-RAGE sequences by increasing CNR of lesions and might, therefore, be useful in patient management.
doi:10.1097/rli.0000000000000410 pmid:28858894 fatcat:dtvorwzdpvd2pe4djm6iilayyu

Cross Attention Squeeze Excitation Network (CASE-Net) for Whole Body Fetal MRI Segmentation

Justin Lo, Saiee Nithiyanantham, Jillian Cardinell, Dylan Young, Sherwin Cho, Abirami Kirubarajan, Matthias W. Wagner, Roxana Azma, Steven Miller, Mike Seed, Birgit Ertl-Wagner, Dafna Sussman
2021 Sensors  
Segmentation of the fetus from 2-dimensional (2D) magnetic resonance imaging (MRI) can aid radiologists with clinical decision making for disease diagnosis. Machine learning can facilitate this process of automatic segmentation, making diagnosis more accurate and user independent. We propose a deep learning (DL) framework for 2D fetal MRI segmentation using a Cross Attention Squeeze Excitation Network (CASE-Net) for research and clinical applications. CASE-Net is an end-to-end segmentation
more » ... tecture with relevant modules that are evidence based. The goal of CASE-Net is to emphasize localization of contextual information that is relevant in biomedical segmentation, by combining attention mechanisms with squeeze-and-excitation (SE) blocks. This is a retrospective study with 34 patients. Our experiments have shown that our proposed CASE-Net achieved the highest segmentation Dice score of 87.36%, outperforming other competitive segmentation architectures.
doi:10.3390/s21134490 pmid:34209154 fatcat:fydedwhrz5drhcum3vvmrtexmu

Gas exchange mechanisms in preterm infants on HFOV – a computational approach

Christian J. Roth, Kai M. Förster, Anne Hilgendorff, Birgit Ertl-Wagner, Wolfgang A. Wall, Andreas W. Flemmer
2018 Scientific Reports  
High-frequency oscillatory ventilation (HFOV) is a commonly used therapy applied to neonates requiring ventilatory support during their first weeks of life. Despite its wide application, the underlying gas exchange mechanisms promoting the success of HVOF in neonatal care are not fully understood until today. In this work, a highly resolved computational lung model, derived from Magnetic Resonance Imaging (MRI) and Infant Lung Function Testing (ILFT), is used to reveal the reason for highly
more » ... cient gas exchange during HFOV, in the preterm infant. In total we detected six mechanisms that facilitate gas exchange during HFOV: (i) turbulent vortices in large airways; (ii) asymmetric in-and expiratory flow profiles; (iii) radial mixing in main bronchi; (iv) laminar flow in higher generations of the respiratory tract; (v) pendelluft; (vi) direct ventilation of central alveoli. The illustration of six specific gas transport phenomena during HFOV in preterm infants advances general knowledge on protective ventilation in neonatal care and can support decisions on various modes of ventilatory therapy at high frequencies. patient, which governs the passive behaviour of the lung especially during expiration. This novel computational lung model can be subjected to representative conditions of HFOV and is perfectly suited to reconfirm the previously hypothesised gas transport mechanisms in HFOV 6 .
doi:10.1038/s41598-018-30830-x pmid:30158557 fatcat:nqlqjl7v35eo3lynqjmojs65eu

The effect of radio-adaptive doses on HT29 and GM637 cells

Silke B Schwarz, Pamela M Schaffer, Ulrike Kulka, Birgit Ertl-Wagner, Roswitha Hell, Moshe Schaffer
2008 Radiation Oncology  
The shape of the dose-response curve at low doses differs from the linear quadratic model. The effect of a radio-adaptive response is the centre of many studies and well known inspite that the clinical applications are still rarely considered. Methods: We studied the effect of a low-dose pre-irradiation (0.03 Gy -0.1 Gy) alone or followed by a 2.0 Gy challenging dose 4 h later on the survival of the HT29 cell line (human colorectal cancer cells) and on the GM637 cell line (human fibroblasts).
doi:10.1186/1748-717x-3-12 pmid:18433479 pmcid:PMC2387149 fatcat:sve3wneedrbvjbww2k5yg2iiqy

Primary versus Secondary Headache in Children: A Frequent Diagnostic Challenge in Clinical Routine

Michaela Bonfert, Friedrich Ebinger, Markus Blankenburg, Birgit Ertl-Wagner, Florian Heinen, Timo Roser
2013 Neuropediatrics  
doi:10.1055/s-0032-1332743 pmid:23303551 fatcat:r5zze34inva7ho7qcvicc4bpty

Fetal magnetic resonance imaging: indications, technique, anatomical considerations and a review of fetal abnormalities

Birgit Ertl-Wagner, Andreas Lienemann, Alexander Strauss, Maximilian F. Reiser
2002 European Radiology  
Fetal MR imaging often poses a diagnostic challenge for the radiologist. Both fetal anatomy and pathology differ decidedly from pediatric and adult MR imaging. While ultrasound remains the method of choice for screening examinations of the fetus, MR imaging is playing an increasingly important role in the detection and classification of malformations not diagnosable by ultrasonography alone. Recently, advances in fast single-shot MR sequences have allowed high-resolution, highquality imaging of
more » ... the moving fetus. Preferable sequences to be applied are a true fast imaging steady precession (true-FISP) or a half-Fourier acquired single-shot turbo spin-echo (HASTE) sequence. Premedication is generally no longer required. In all fetal MR imaging, every aspect of fetal anatomy has to be scrutinized. Subsequently, any abnormalities need to be described and classified. A close collaboration with the referring obstetrician is of paramount importance.
doi:10.1007/s00330-002-1383-5 pmid:12136311 fatcat:p5ljy77zyvcphfyah4is75a3u4

Cost-Effectiveness of Endovascular Stroke Therapy

Wolfgang G. Kunz, M.G. Myriam Hunink, Wieland H. Sommer, Sebastian E. Beyer, Felix G. Meinel, Franziska Dorn, Stefan Wirth, Maximilian F. Reiser, Birgit Ertl-Wagner, Kolja M. Thierfelder
2016 Stroke  
doi:10.1161/strokeaha.116.014147 pmid:27758942 fatcat:gj2ajhzjtvdhjbt34hirttpxay

Expanding spectrum of neurologic manifestations in patients withNLRP3low-penetrance mutations

Elisabeth Schuh, Peter Lohse, Birgit Ertl-Wagner, Matthias Witt, Markus Krumbholz, Marion Frankenberger, Lisa-Ann Gerdes, Reinhard Hohlfeld, Tania Kümpfel
2015 Neurology: Neuroimmunology & Neuroinflammation  
Objective: To evaluate the frequency of the cryoporin/NLRP3 low-penetrance mutations V198M and Q703K in patients who reported at least 2 symptoms compatible with cryopyrin-associated periodic syndromes (CAPS) and to characterize the phenotype in mutation-positive patients. Methods: The frequency of the V198M and Q703K mutations was investigated in a selected cohort of 108 patients from our neuroimmunology department. We describe the clinical, neurologic, immunologic, and neuroradiologic features of the mutation carriers.
doi:10.1212/nxi.0000000000000109 pmid:26020059 pmcid:PMC4436598 fatcat:5acx6c7vjrdp7l33wtaphbzzuq

CT and MRI Findings in Cerebral Aspergilloma

Friederike Gärtner, Julia Forstenpointner, Birgit Ertl-Wagner, Babak Hooshmand, Christian Riedel, Olav Jansen
2017 RöFo. Fortschritte auf dem Gebiet der Röntgenstrahlen und der bildgebenden Verfahren (Print)  
Purpose Invasive aspergillosis usually affects immunocompromised patients. It carries a high risk of morbidity and mortality and usually has a nonspecific clinical presentation. Early diagnosis is essential in order to start effective treatment and improve clinical outcome. Materials and Methods In a retrospective search of the PACS databases from two medical centers, we identified 9 patients with histologically proven cerebral aspergilloma. We systematically analyzed CT and MRI imaging
more » ... to identify typical imaging appearances of cerebral aspergilloma. Results CT did not show a typical appearance of the aspergillomas. In 100 % (9/9) there was a rim-attenuated diffusion restriction on MRI imaging. Multiple hypointense layers in the aspergillus wall, especially on the internal side, were detected in 100 % on T2-weighted imaging (9/9). Aspergillomas were T1-hypointense in 66 % of cases (6/9) and partly T1-hyperintense in 33 % (3/9). In 78 % (7/9) of cases, a rim-attenuated diffusion restriction was detected after contrast agent application. Conclusion Nine cases were identified. Whereas CT features were less typical, we observed the following imaging features on MRI: A strong, rim-attenuated diffusion restriction (9/9); onion layer-like hypointense zones, in particular in the innermost part of the abscess wall on T2-weighted images (9/9). Enhancement of the lesion border was present in the majority of the cases (7/9). Key points Citation Format
doi:10.1055/s-0043-120766 pmid:29156474 fatcat:5xt42pj3ubeflgam5eo27mxdwu

Effect of smoking status on neuronal responses to graphic cigarette warning labels

Tobias Rüther, Yannick Schultz, Christina Wirth, Agnieszka Chrobok, Andrea Rabenstein, Daniel Keeser, Birgit Ertl-Wagner, Oliver Pogarell, Susanne Karch
2018 PLoS ONE  
Smoking is responsible for a large proportion of cancer, respiratory and cardiovascular deaths. Nevertheless the health risks of smoking are still underestimated in many smokers. The present study aimed to examine neurobiological responses to graphical warnings on cigarette packings in non-smokers and patients with tobacco dependence. Twenty non-smokers and twenty-four patients with tobacco dependence participated in a functional MRI study during that pictures of different categories were
more » ... ted ((a) EU-warning pictures, (b) text-only warnings, (c) neutral pictures with short information). Patients contributed twice in the experiment (after 10 hours nicotine withdrawal / about 5 minutes after nicotine consumption). Smokers during withdrawal demonstrated increased neuronal responses predominantly in subcortical, temporal and frontal brain regions that are associated with emotional and cognitive processes during the presentation of graphical warnings compared to neutral pictures. In smokers after smoking and non-smokers, the differences between graphical warnings and neutral pictures were increased compared to smokers during withdrawal. The comparison of the graphical warnings with text-only labels demonstrated the importance of affective brain regions especially in smokers after smoking and in non-smokers. During withdrawal, the neural responses associated with graphical warnings and text-only labels differed only marginally. The results suggest that emotional and cognitive reactions to graphical warnings are predominantly seen in smokers after smoking and in non-smokers. The impact of these pictures during withdrawal seems to be less pronounced; in this case, more unspecific processes seem to be important, including the projection of sensory signals to the cerebral cortex.
doi:10.1371/journal.pone.0201360 pmid:30235214 pmcid:PMC6147412 fatcat:pqkd2ni76vgd3pyhthnwndb4ja

Imaging-Based Features of Headaches in Chiari Malformation Type I

Noam Alperin, James R. Loftus, Carlos J. Oliu, Ahmet M. Bagci, Sang H. Lee, Birgit Ertl-Wagner, Raymond Sekula, Terry Lichtor, Barth A. Green
2015 Neurosurgery  
Background-Sub-occipital cough-induced headaches are considered a hallmark symptom of Chiari Malformation Type I (CMI). However, non-Valsalva-related suboccipital headaches and headaches in other locations are also common in CMI. The diagnostic significance and the underlying factors associated with these different headaches types are not well understood. Objective-This imaging-based study compares cranial morphology and hydrodynamics in three types of headaches in CMI to better understand the
more » ... athophysiological basis for the different headache characteristics. Methods-Twenty-two cranial physiologic and morphologic measures were obtained using specialized MRI scans from 63 symptomatic pretreated CMI patients, 40 with suboccipitalheadaches induced by Valsalva maneuvers (34F, 36±10years), 15 with non-Valsalva related suboccipital-headaches (10F, 33±9years), 8 with non-suboccipital non-Valsalva induced headaches (8F, 39±13years), and 37 control subjects (24F, age 36±12years). Group differences were identified using two-tailed Student's t-test. Results-Posterior cranial fossa markers of CMI were similar among the three headache subtypes. However, the Valsalva-related suboccipital-headaches cohort demonstrated significantly lower intracranial compliance index than the non-Valsalva-related suboccipital-headaches cohort (7.5±3.4 vs. 10.9±4.9), lower intracranial volume change during the cardiac cycle (0.48±0.19 vs. 0.61±0.16mL), and higher MRICP (11.1±4.3 vs. 7.7±2.8mmHg, p=0.02). The Valsalva-related suboccipital-headaches cohort had smaller intracranial and lateral ventricles volumes compared to the healthy cohort. The non-Valsalva-related suboccipital-headaches cohort had reduced venous drainage through the jugular veins. Conclusion-Valsalva-induced worsening of occipital-headaches appears related to a small intracranial volume rather than the smaller posterior cranial fossa. This explains the reduced intracranial compliance and corresponding higher pressure measured in CMI patients with headaches affected by Valsalva maneuvers.
doi:10.1227/neu.0000000000000740 pmid:25812067 pmcid:PMC4854289 fatcat:bfkueixfdbdblnt6hcbujyif7u
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