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

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

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Automated detection of left ventricle in arterial input function images for inline perfusion mapping using deep learning: A study of 15,000 patients

Purpose: Quantification of myocardial perfusion has the potential to improve the detection of regional and global flow reduction. Significant effort has been made to automate the workflow, where one essential step is the arterial input function (AIF) extraction. Failure to accurately identify the left ventricle (LV) prevents AIF estimation required for quantification, therefore high detection accuracy is required. This study presents a robust LV detection method using the convolutional neural network (CNN). Methods: CNN models were trained by assembling 25,027 scans (N = 12,984 patients) from three hospitals, seven scanners. Performance was evaluated using a hold‐out test set of 5721 scans (N = 2805 patients). Model inputs were a time series of AIF images (2D+T). Two variations were investigated: (1) two classes (2CS) for background and foreground (LV mask), and (2) three classes (3CS) for background, LV, and RV. The final model was deployed on MRI scanners using the Gadgetron reconstruction software framework. Results: Model loading on the MRI scanner took ~340 ms and applying the model took ~180 ms. The 3CS model successfully detected the LV in 99.98% of all test cases (1 failure out of 5721). The mean Dice ratio for 3CS was 0.87 ± 0.08 with 92.0% of all cases having Dice >0.75. The 2CS model gave a lower Dice ratio of 0.82 ± 0.22 (P .2) comparing automatically extracted AIF signals with signals from manually drawn contours. Conclusions: A CNN‐based solution to detect the LV blood pool from the arterial input function image series was developed, validated, and deployed. A high LV detection accuracy of 99.98% was achieved

Automated Inline Analysis of Myocardial Perfusion MRI with Deep Learning

Recent development of quantitative myocardial blood flow (MBF) mapping allows direct evaluation of absolute myocardial perfusion, by computing pixel-wise flow maps. Clinical studies suggest quantitative evaluation would be more desirable for objectivity and efficiency. Objective assessment can be further facilitated by segmenting the myocardium and automatically generating reports following the AHA model. This will free user interaction for analysis and lead to a 'one-click' solution to improve workflow. This paper proposes a deep neural network based computational workflow for inline myocardial perfusion analysis. Adenosine stress and rest perfusion scans were acquired from three hospitals. Training set included N=1,825 perfusion series from 1,034 patients. Independent test set included 200 scans from 105 patients. Data were consecutively acquired at each site. A convolution neural net (CNN) model was trained to provide segmentation for LV cavity, myocardium and right ventricular by processing incoming 2D+T perfusion Gd series. Model outputs were compared to manual ground-truth for accuracy of segmentation and flow measures derived on global and per-sector basis. The trained models were integrated onto MR scanners for effective inference. Segmentation accuracy and myocardial flow measures were compared between CNN models and manual ground-truth. The mean Dice ratio of CNN derived myocardium was 0.93 +/- 0.04. Both global flow and per-sector values showed no significant difference, compared to manual results. The AHA 16 segment model was automatically generated and reported on the MR scanner. As a result, the fully automated analysis of perfusion flow mapping was achieved. This solution was integrated on the MR scanner, enabling 'one-click' analysis and reporting of myocardial blood flow.Comment: This work has been submitted to Radiology: Artificial Intelligence for possible publicatio

Simple Methods for Scanner Drift Normalization Validated for Automatic Segmentation of Knee Magnetic Resonance Imaging:with data from the Osteoarthritis Initiative

Scanner drift is a well-known magnetic resonance imaging (MRI) artifact characterized by gradual signal degradation and scan intensity changes over time. In addition, hardware and software updates may imply abrupt changes in signal. The combined effects are particularly challenging for automatic image analysis methods used in longitudinal studies. The implication is increased measurement variation and a risk of bias in the estimations (e.g. in the volume change for a structure). We proposed two quite different approaches for scanner drift normalization and demonstrated the performance for segmentation of knee MRI using the fully automatic KneeIQ framework. The validation included a total of 1975 scans from both high-field and low-field MRI. The results demonstrated that the pre-processing method denoted Atlas Affine Normalization significantly removed scanner drift effects and ensured that the cartilage volume change quantifications became consistent with manual expert scores

An Automatic Technique for MRI Based Murine Abdominal Fat Measurement

Because of the well-known relationship between obesity and high incidence of diseases, fat related research using mice models is being widely investigated in preclinical experiments. In the present study, we developed a technique to automatically measure mice abdominal adipose volume and determine the depot locations using Magnetic Resonance Imaging (MRI). Our technique includes an innovative method to detect fat tissues from MR images which not only utilizes the T1 weighted intensity information, but also takes advantage of the transverse relaxation time(T2) calculated from the multiple echo data. The technique contains both a fat optimized MRI imaging acquisition protocol that works well at 7T and a newly designed post processing methodology that can automatically accomplish the fat extraction and depot recognition without user intervention in the segmentation procedure. The post processing methodology has been integrated into easy-to-use software that we have made available via free download. The method was validated by comparing automated results with two independent manual analyses in 26 mice exhibiting different fat ratios from the obesity research project. The comparison confirms a close agreement between the results in total adipose tissue size and voxel-by-voxel overlaps