Automatic segmentation of adipose tissue from thigh magnetic resonance images

Automatic segmentation of adipose tissue in thigh magnetic resonance imaging (MRI) scans is challenging and rarely reported in the literature. To address this problem, we propose a fully automated unsupervised segmentation method involving the use of spatial intensity constraints to guide the segmentation process. The novelty of this method lies in two aspects: firstly, an adaptive distance classifier, incorporating intra-slice spatial continuity, is used for robust region growing and segmentation estimation; secondly, polynomial based intensity inhomogeneity maps are generated to model inter- and intra-slice intensity variation of each pixel class and thus refine the initial classification. Our experimental results have demonstrated the effectiveness of imposing 3D intensity constraints to successfully classify the adipose tissue from muscles in the presence of image noise and considerable amounts of non-uniform MRI intensity. © 2013 Springer-Verlag

Feasibility of MR-Based Body Composition Analysis in Large Scale Population Studies

Introduction Quantitative and accurate measurements of fat and muscle in the body are important for prevention and diagnosis of diseases related to obesity and muscle degeneration. Manually segmenting muscle and fat compartments in MR body-images is laborious and time-consuming, hindering implementation in large cohorts. In the present study, the feasibility and success-rate of a Dixon-based MR scan followed by an intensity-normalised, non-rigid, multi-atlas based segmentation was investigated in a cohort of 3,000 subjects. Materials and Methods 3,000 participants in the in-depth phenotyping arm of the UK Biobank imaging study underwent a comprehensive MR examination. All subjects were scanned using a 1.5 T MR-scanner with the dual-echo Dixon Vibe protocol, covering neck to knees. Subjects were scanned with six slabs in supine position, without localizer. Automated body composition analysis was performed using the AMRA Profiler™ system, to segment and quantify visceral adipose tissue (VAT), abdominal subcutaneous adipose tissue (ASAT) and thigh muscles. Technical quality assurance was performed and a standard set of acceptance/rejection criteria was established. Descriptive statistics were calculated for all volume measurements and quality assurance metrics. Results Of the 3,000 subjects, 2,995 (99.83%) were analysable for body fat, 2,828 (94.27%) were analysable when body fat and one thigh was included, and 2,775 (92.50%) were fully analysable for body fat and both thigh muscles. Reasons for not being able to analyse datasets were mainly due to missing slabs in the acquisition, or patient positioned so that large parts of the volume was outside of the field-of-view. Discussion and Conclusions In conclusion, this study showed that the rapid UK Biobank MR-protocol was well tolerated by most subjects and sufficiently robust to achieve very high success-rate for body composition analysis. This research has been conducted using the UK Biobank Resource

Automatic Segmentation of Muscle Tissue and Inter-muscular Fat in Thigh and Calf MRI Images

Magnetic resonance imaging (MRI) of thigh and calf muscles is one of the most effective techniques for estimating fat infiltration into muscular dystrophies. The infiltration of adipose tissue into the diseased muscle region varies in its severity across, and within, patients. In order to efficiently quantify the infiltration of fat, accurate segmentation of muscle and fat is needed. An estimation of the amount of infiltrated fat is typically done visually by experts. Several algorithmic solutions have been proposed for automatic segmentation. While these methods may work well in mild cases, they struggle in moderate and severe cases due to the high variability in the intensity of infiltration, and the tissue's heterogeneous nature. To address these challenges, we propose a deep-learning approach, producing robust results with high Dice Similarity Coefficient (DSC) of 0.964, 0.917 and 0.933 for muscle-region, healthy muscle and inter-muscular adipose tissue (IMAT) segmentation, respectively.Comment: 9 pages, 4 figures, 2 tables, MICCAI 2019, the 22nd International Conference on Medical Image Computing and Computer Assisted Interventio

Advanced body composition assessment: from body mass index to body composition profiling

This paper gives a brief overview of common non-invasive techniques for body composition analysis and a more in-depth review of a body composition assessment method based on fatreferenced quantitative MRI. Earlier published studies of this method are summarized, and a previously unpublished validation study, based on 4753 subjects from the UK Biobank imaging cohort, comparing the quantitative MRI method with dualenergy X-ray absorptiometry (DXA) is presented. For whole-body measurements of adipose tissue (AT) or fat and lean tissue (LT), DXA and quantitative MRIs show excellent agreement with linear correlation of 0.99 and 0.97, and coefficient of variation (CV) of 4.5 and 4.6 per cent for fat (computed from AT) and LT, respectively, but the agreement was found significantly lower for visceral adipose tissue, with a CV of >20 per cent. The additional ability of MRI to also measure muscle volumes, muscle AT infiltration and ectopic fat, in combination with rapid scanning protocols and efficient image analysis tools, makes quantitative MRI a powerful tool for advanced body composition assessment

Semi-Supervised Deep Learning for Multi-Tissue Segmentation from Multi-Contrast MRI

Segmentation of thigh tissues (muscle, fat, inter-muscular adipose tissue (IMAT), bone, and bone marrow) from magnetic resonance imaging (MRI) scans is useful for clinical and research investigations in various conditions such as aging, diabetes mellitus, obesity, metabolic syndrome, and their associated comorbidities. Towards a fully automated, robust, and precise quantification of thigh tissues, herein we designed a novel semi-supervised segmentation algorithm based on deep network architectures. Built upon Tiramisu segmentation engine, our proposed deep networks use variational and specially designed targeted dropouts for faster and robust convergence, and utilize multi-contrast MRI scans as input data. In our experiments, we have used 150 scans from 50 distinct subjects from the Baltimore Longitudinal Study of Aging (BLSA). The proposed system made use of both labeled and unlabeled data with high efficacy for training, and outperformed the current state-of-the-art methods with dice scores of 97.52%, 94.61%, 80.14%, 95.93%, and 96.83% for muscle, fat, IMAT, bone, and bone marrow tissues, respectively. Our results indicate that the proposed system can be useful for clinical research studies where volumetric and distributional tissue quantification is pivotal and labeling is a significant issue. To the best of our knowledge, the proposed system is the first attempt at multi-tissue segmentation using a single end-to-end semi-supervised deep learning framework for multi-contrast thigh MRI scans.Comment: 20 pages, 9 figures, Journal of Signal Processing System

Quantitative body shape analysis for obesity evaluation

Obesity is a public health concern as it is associated with a number of diseases, such as diabetes mellitus type 2, cardiovascular disease, some forms of renal failure and certain types of cancers. Growing evidence suggests that it is not only the amount of fat, but also its distribution in the body that is important to predict metabolic risk factors and adverse changes in organs. In this respect, it is necessary to develop convenient and inexpensive measures to characterize human body fat distribution and to investigate the unknown linkage between intrinsic adiposity and external body shape. This dissertation research aims to improve the obesity assessment by developing new quantitative measurements that comprehensively characterize body shape, and are highly relevant to intrinsic abdominal adiposity conditions. The proposed body shape descriptors were defined based on three-dimensional body images reconstructed from a custom-made stereovision body imaging system, which is particularly suitable for clinical use as an obesity monitoring equipment for its high portability and affordability. In this study, we developed a fully-automated algorithm to process T1-weighted magnetic resonance imaging (MRI) slices for abdominal adiposity measurements. This algorithm dramatically reduces the processing time and workload compared with traditional manual or semi-automatic methods for MRI processing, and greatly improves the repeatability and objectivity of fat assessments. A new obesity categorization method was then defined based on MRI adiposity data to depict characteristics of abdominal fat distribution, and the associations between the body shape descriptors and the MRI abdominal adiposity were explored. It was shown that the proposed body shape descriptors are able to capture the body shape differences between the subjects with dissimilar internal fat distribution (i.e., different categories), and to provide excellent prediction for the category of fat distribution through an optimized support-vector-machine classifier. The predictive models established in this dissertation demonstrate that the novel body shape descriptors were also effective for prediction of the volumes of abdominal visceral fat and subcutaneous fat accumulated in male and female adults. This dissertation introduces an innovative approach to assess obesity and fat distribution based on newly defined shape descriptors, and provides new findings that reveal the associations of intrinsic fat distribution with external body shapes, which enable both qualitative and quantitative assessment of obesity from body shape measurements.Biomedical Engineerin

Automatic signal and image-based assessments of spinal cord injury and treatments.

Spinal cord injury (SCI) is one of the most common sources of motor disabilities in humans that often deeply impact the quality of life in individuals with severe and chronic SCI. In this dissertation, we have developed advanced engineering tools to address three distinct problems that researchers, clinicians and patients are facing in SCI research. Particularly, we have proposed a fully automated stochastic framework to quantify the effects of SCI on muscle size and adipose tissue distribution in skeletal muscles by volumetric segmentation of 3-D MRI scans in individuals with chronic SCI as well as non-disabled individuals. We also developed a novel framework for robust and automatic activation detection, feature extraction and visualization of the spinal cord epidural stimulation (scES) effects across a high number of scES parameters to build individualized-maps of muscle recruitment patterns of scES. Finally, in the last part of this dissertation, we introduced an EMG time-frequency analysis framework that implements EMG spectral analysis and machine learning tools to characterize EMG patterns resulting in independent or assisted standing enabled by scES, and identify the stimulation parameters that promote muscle activation patterns more effective for standing. The neurotechnological advancements proposed in this dissertation have greatly benefited SCI research by accelerating the efforts to quantify the effects of SCI on muscle size and functionality, expanding the knowledge regarding the neurophysiological mechanisms involved in re-enabling motor function with epidural stimulation and the selection of stimulation parameters and helping the patients with complete paralysis to achieve faster motor recovery

Automated measurement of fat infiltration in the hip abductors from Dixon magnetic resonance imaging

PURPOSE: Intramuscular fat infiltration is a dynamic process, in response to exercise and muscle health, which can be quantified by estimating fat fraction (FF) from Dixon MRI. Healthy hip abductor muscles are a good indicator of a healthy hip and an active lifestyle as they have a fundamental role in walking. The automated measurement of the abductors' FF requires the challenging task of segmenting them. We aimed to design, develop and evaluate a multi-atlas based method for automated measurement of fat fraction in the main hip abductor muscles: gluteus maximus (GMAX), gluteus medius (GMED), gluteus minimus (GMIN) and tensor fasciae latae (TFL). METHOD: We collected and manually segmented Dixon MR images of 10 healthy individuals and 7 patients who underwent MRI for hip problems. Twelve of them were selected to build an atlas library used to implement the automated multi-atlas segmentation method. We compared the FF in the hip abductor muscles for the automated and manual segmentations for both healthy and patients groups. Measures of average and spread were reported for FF for both methods. We used the root mean square error (RMSE) to quantify the method accuracy. A linear regression model was used to explain the relationship between FF for automated and manual segmentations. RESULTS: The automated median (IQR) FF was 20.0(16.0-26.4) %, 14.3(10.9-16.5) %, 15.5(13.9-18.6) % and 16.2(13.5-25.6) % for GMAX, GMED, GMIN and TFL respectively, with a FF RMSE of 1.6%, 0.8%, 2.1%, 2.7%. A strong linear correlation (R2 = 0.93, p < .001, m = 0.99) was found between the FF from automated and manual segmentations. The mean FF was higher in patients than in healthy subjects. CONCLUSION: The automated measurement of FF of hip abductor muscles from Dixon MRI had good agreement with FF measurements from manually segmented images. The method was accurate for both healthy and patients groups