Domain specific cues improve robustness of deep learning based segmentation of ct volumes

Machine Learning has considerably improved medical image analysis in the past years. Although data-driven approaches are intrinsically adaptive and thus, generic, they often do not perform the same way on data from different imaging modalities. In particular Computed tomography (CT) data poses many challenges to medical image segmentation based on convolutional neural networks (CNNs), mostly due to the broad dynamic range of intensities and the varying number of recorded slices of CT volumes. In this paper, we address these issues with a framework that combines domain-specific data preprocessing and augmentation with state-of-the-art CNN architectures. The focus is not limited to optimise the score, but also to stabilise the prediction performance since this is a mandatory requirement for use in automated and semi-automated workflows in the clinical environment. The framework is validated with an architecture comparison to show CNN architecture-independent effects of our framework functionality. We compare a modified U-Net and a modified Mixed-Scale Dense Network (MS-D Net) to compare dilated convolutions for parallel multi-scale processing to the U-Net approach based on traditional scaling operations. Finally, we propose an ensemble model combining the strengths of different individual methods. The framework performs well on a range of tasks such as liver and kidney segmentation, without significant differences in prediction performance on strongly differing volume sizes and varying slice thickness. Thus our framework is an essential step towards performing robust segmentation of unknown real-world samples

Cortical thickness and resting-state cardiac function across the lifespan: a cross-sectional pooled mega analysis

Understanding the association between autonomic nervous system [ANS] function and brain morphology across the lifespan provides important insights into neurovisceral mechanisms underlying health and disease. Resting state ANS activity, indexed by measures of heart rate [HR] and its variability [HRV] has been associated with brain morphology, particularly cortical thickness [CT]. While findings have been mixed regarding the anatomical distribution and direction of the associations, these inconsistencies may be due to sex and age differences in HR/HRV and CT. Previous studies have been limited by small sample sizes, which impede the assessment of sex differences and aging effects on the association between ANS function and CT. To overcome these limitations, 20 groups worldwide contributed data collected under similar protocols of CT assessment and HR/HRV recording to be pooled in a mega-analysis (N = 1,218 (50.5% female), mean age 36.7 years (range: 12-87)). Findings suggest a decline in HRV as well as CT with increasing age. CT, particularly in the orbitofrontal cortex, explained additional variance in HRV, beyond the effects of aging. This pattern of results may suggest that the decline in HRV with increasing age is related to a decline in orbitofrontal CT. These effects were independent of sex and specific to HRV; with no significant association between CT and HR. Greater CT across the adult lifespan may be vital for the maintenance of healthy cardiac regulation via the ANS – or greater cardiac vagal activity as indirectly reflected in HRV may slow brain atrophy. Findings reveal an important association between cortical thickness and cardiac parasympathetic activity with implications for healthy aging and longevity that should be studied further in longitudinal research

Comparative analysis of machine learning algorithms for multi-syndrome classification of neurodegenerative syndromes

Importance: The entry of artificial intelligence into medicine is pending. Several methods have been used for the predictions of structured neuroimaging data, yet nobody compared them in this context. Objective: Multi-class prediction is key for building computational aid systems for differential diagnosis. We compared support vector machine, random forest, gradient boosting, and deep feed-forward neural networks for the classification of different neurodegenerative syndromes based on structural magnetic resonance imaging. Design, setting, and participants: Atlas-based volumetry was performed on multi-centric T1-weighted MRI data from 940 subjects, i.e., 124 healthy controls and 816 patients with ten different neurodegenerative diseases, leading to a multi-diagnostic multi-class classification task with eleven different classes. Interventions: N.A. Main outcomes and measures: Cohen’s kappa, accuracy, and F1-score to assess model performance. Results: Overall, the neural network produced both the best performance measures and the most robust results. The smaller classes however were better classified by either the ensemble learning methods or the support vector machine, while performance measures for small classes were comparatively low, as expected. Diseases with regionally specific and pronounced atrophy patterns were generally better classified than diseases with widespread and rather weak atrophy. Conclusions and relevance: Our study furthermore underlines the necessity of larger data sets but also calls for a careful consideration of different machine learning methods that can handle the type of data and the classification task best

A functional connectome phenotyping dataset including cognitive state and personality measures

International audienceThe dataset enables exploration of higher-order cognitive faculties, self-generated mental experience, and personality features in relation to the intrinsic functional architecture of the brain. We provide multimodal magnetic resonance imaging (MRI) data and a broad set of state and trait phenotypic assessments: mindwandering, personality traits, and cognitive abilities. Specifically, 194 healthy participants (between 20 and 75 years of age) filled out 31 questionnaires, performed 7 tasks, and reported 4 probes of in-scanner mindwandering. The scanning session included four 15.5-min resting-state functional MRI runs using a multiband EPI sequence and a hig h-resolution structural scan using a 3D MP2RAGE sequence. This dataset constitutes one part of the MPI-Leipzig Mind-Brain-Body database

Behavioral data for "A functional connectome phenotyping dataset including cognitive state and personality measures"

This dataset enables exploration of higher-order cognitive faculties, self-generated mental experience, and personality features in relation to the intrinsic functional architecture of the brain. 194 healthy participants (between 20 and 75 years of age) filled out 31 questionnaires, performed 7 tasks, and reported 4 probes of in-scanner mind-wandering. This dataset constitutes one part of the Leipzig Study for Mind-Body-Emotion Interactions database, and contains the behavioral measures for download

Cortical Thickness and Resting State Cardiac Function Across the Lifespan: A Cross-Sectional Pooled Mega Analysis

Understanding the association between autonomic nervous system [ANS] function and brain morphology across the lifespan provides important insights into neurovisceral mechanisms underlying health and disease. Resting state ANS activity, indexed by measures of heart rate [HR] and its variability [HRV] has been associated with brain morphology, particularly cortical thickness [CT]. While findings have been mixed regarding the anatomical distribution and direction of the associations, these inconsistencies may be due to sex and age differences in HR/HRV and CT. Previous studies have been limited by small sample sizes, which impede the assessment of sex differences and aging effects on the association between ANS function and CT. To overcome these limitations, 20 groups worldwide contributed data collected under similar protocols of CT assessment and HR/HRV recording to be pooled in a mega-analysis (N = 1,218 (50.5% female), mean age 36.7 years (range: 12-87)). Findings suggest that the decline in HRV with increasing age is related to a decline in prefrontal CT, particularly in the orbitofrontal cortex. These effects were independent of sex and specific to HRV; with no significant association between CT and HR. Greater CT across the adult lifespan may be vital for the maintenance of healthy cardiac regulation via the ANS. Nonetheless, in the absence of longitudinal data, alternative explanations need to be considered. Findings reveal an important association between cortical thickness and cardiac parasympathetic activity with implications for healthy aging and longevity

Cortical Thickness and Resting State Cardiac Function Across the Lifespan: A Cross-Sectional Pooled Mega Analysis

Resting state autonomic nervous system activity [ANS] indexed by measures of heart rate [HR] and its variability [HRV], is associated with brain morphology, in particular cortical thickness [CT]. However, findings have been mixed regarding the regions of interest [ROI] associated with HR/HRV and the direction of the association. Sex and age differences in HR/HRV and CT may explain some of the existing inconsistencies. Understanding the association between ANS function and brain morphology across aging, may provide important insights into neurovisceral mechanisms underlying health and disease. Previous studies have been limited by small sample sizes, prohibiting the assessment of sex differences, and effects of aging, in the association between ANS function and CT. In an effort to overcome these limitations, data from researchers worldwide, applying similar protocols in the assessment of CT and recording of HR/HRV, will be pooled for a mega-analysis. This preprint details the hypotheses, strategies for pooling of data and planned analyses of this project

A mind-brain-body dataset of MRI, EEG, cognition, emotion, and peripheral physiology in young and old adults

We present a publicly available dataset of 227 healthy participants comprising a young (N=153, 25.1±3.1 years, range 20-35 years, 45 female) and an elderly group (N=74, 67.6±4.7 years, range 59-77 years, 37 female) acquired cross-sectionally in Leipzig, Germany, between 2013 and 2015 to study mind-body-emotion interactions. During a two-day assessment, participants completed MRI at 3 Tesla (resting-state fMRI, quantitative T1 (MP2RAGE), T2-weighted, FLAIR, SWI/QSM, DWI) and a 62-channel EEG experiment at rest. During task-free resting-state fMRI, cardiovascular measures (blood pressure, heart rate, pulse, respiration) were continuously acquired. Anthropometrics, blood samples, and urine drug tests were obtained. Psychiatric symptoms were identified with Standardized Clinical Interview for DSM IV (SCID-I), Hamilton Depression Scale, and Borderline Symptoms List. Psychological assessment comprised 6 cognitive tests as well as 21 questionnaires related to emotional behavior, personality traits and tendencies, eating behavior, and addictive behavior. We provide information on study design, methods, and details of the data. This dataset is part of the larger MPI Leipzig Mind-Brain-Body database

Cortical thickness and resting-state cardiac function across the lifespan: A cross-sectional pooled mega-analysis

Understanding the association between autonomic nervous system [ANS] function and brain morphology across the lifespan provides important insights into neurovisceral mechanisms underlying health and disease. Resting-state ANS activity, indexed by measures of heart rate [HR] and its variability [HRV] has been associated with brain morphology, particularly cortical thickness [CT]. While findings have been mixed regarding the anatomical distribution and direction of the associations, these inconsistencies may be due to sex and age differences in HR/HRV and CT. Previous studies have been limited by small sample sizes, which impede the assessment of sex differences and aging effects on the association between ANS function and CT. To overcome these limitations, 20 groups worldwide contributed data collected under similar protocols of CT assessment and HR/HRV recording to be pooled in a mega-analysis (N = 1,218 (50.5% female), mean age 36.7 years (range: 12–87)). Findings suggest a decline in HRV as well as CT with increasing age. CT, particularly in the orbitofrontal cortex, explained additional variance in HRV, beyond the effects of aging. This pattern of results may suggest that the decline in HRV with increasing age is related to a decline in orbitofrontal CT. These effects were independent of sex and specific to HRV; with no significant association between CT and HR. Greater CT across the adult lifespan may be vital for the maintenance of healthy cardiac regulation via the ANS—or greater cardiac vagal activity as indirectly reflected in HRV may slow brain atrophy. Findings reveal an important association between CT and cardiac parasympathetic activity with implications for healthy aging and longevity that should be studied further in longitudinal research