BOLD Noise Assumptions in fMRI

This paper discusses the assumption of Gaussian noise in the blood-oxygenation-dependent (BOLD) contrast for functional MRI (fMRI). In principle, magnitudes in MRI images follow a Rice distribution. We start by reviewing differences between Rician and Gaussian noise. An analytic expression is derived for the null (resting-state) distribution of the difference between two Rician distributed images. This distribution is shown to be symmetric, and an exact expression for its standard deviation is derived. This distribution can be well approximated by a Gaussian, with very high precision for high SNR, and high precision for lower SNR. Tests on simulated and real MR images show that subtracting the time-series mean in fMRI yields asymmetrically distributed temporal noise. Subtracting a resting-state time series from the first results in symmetric and nearly Gaussian noise. This has important consequences for fMRI analyses using standard statistical tests

Interactive Segmentation and Visualization of DTI Data Using a Hierarchical Watershed Representation

Magnetic resonance diffusion tensor imaging (DTI) measures diffusion of water molecules and is used to characterize orientation of white matter fibers and connectivity of neurological structures. Segmentation and visualization of DT images is challenging, because of low data quality and complexity of anatomical structures. In this paper, we propose an interactive segmentation approach, based on a hierarchical representation of the input DT image through a tree structure. The tree is obtained by successively merging watershed regions, based on the morphological waterfall approach, hence the name watershed tree. Region merging is done according to a combined similarity and homogeneity criterion. We introduce filters that work on the proposed tree representation, and that enable region-based attribute filtering of DTI data. Linked views between the visualizations of the simplified DT image and the tree enable a user to visually explore both data and tree at interactive rates. The coupling of filtering, semiautomatic segmentation by labeling nodes in the tree, and various interaction mechanisms support the segmentation task. Our method is robust against noise, which we demonstrate on synthetic and real DTI data

Distinguishing Patients With a Coordination Disorder From Healthy Controls Using Local Features of Movement Trajectories During the Finger-to-Nose Test

Assessment of coordination disorders is valuable for monitoring progression of patients, distinguishing healthy and pathological conditions, and ultimately aiding in clinical decision making, thereby offering the possibility to improve medical care or rehabilitation. A common method to assess movement disorders is by using clinical rating scales. However, rating scales depend on the evaluation and interpretation of an observer, implying that subjective phenotypic assignment precedes the application of the scales. Objective and more accurate methods are under continuous development but gold standards are still scarce. Here, we show how a method we previously developed, originally aimed at assessing dynamic balance by a probabilistic generalized linear model, can be used to assess a broader range of functional movements. In this paper, the method is applied to distinguish patients with coordination disorders from healthy controls. We focused on movements recorded during the finger-to-nose task (FNT), which is commonly used to assess coordination disorders. We also compared clinical FNT scores and model scores. Our method achieved 84% classification accuracy in distinguishing patients and healthy participants, using only two features. Future work could entail testing the reliability of the method by using additional features and other clinical tests such as finger chasing, quiet standing, and/or usage of tracking devices such as depth cameras or force plates

Efficient Computation of Greyscale Path Openings

Path openings are morphological operators that are used to preserve long, thin, and curved structures in images. They have the ability to adapt to local image structures,which allows them to detect lines that are not perfectly straight. They are applicable in extracting cracks, roads, and similar structures. Although path openings are very efficient to implement for binary images, the greyscale case is more problematic. This study provides an analysis of the main existing greyscale algorithm, and shows that although its time complexity can be quadratic in the number of pixels, this is optimal in terms of the output (if the full opening transform is created). Also, it is shown that under many circumstances the worst-case running time is much less than quadratic. Finally, a new algorithm is provided,which has the same time complexity, but is simpler, faster in practice and more amenable to parallelizatio

Improving Utility of GPU in Accelerating Industrial Applications with User-centred Automatic Code Translation

SMEs (Small and medium-sized enterprises), particularly those whose business is focused on developing innovative produces, are limited by a major bottleneck on the speed of computation in many applications. The recent developments in GPUs have been the marked increase in their versatility in many computational areas. But due to the lack of specialist GPU (Graphics processing units) programming skills, the explosion of GPU power has not been fully utilized in general SME applications by inexperienced users. Also, existing automatic CPU-to-GPU code translators are mainly designed for research purposes with poor user interface design and hard-to-use. Little attentions have been paid to the applicability, usability and learnability of these tools for normal users. In this paper, we present an online automated CPU-to-GPU source translation system, (GPSME) for inexperienced users to utilize GPU capability in accelerating general SME applications. This system designs and implements a directive programming model with new kernel generation scheme and memory management hierarchy to optimize its performance. A web-service based interface is designed for inexperienced users to easily and flexibly invoke the automatic resource translator. Our experiments with non-expert GPU users in 4 SMEs reflect that GPSME system can efficiently accelerate real-world applications with at least 4x and have a better applicability, usability and learnability than existing automatic CPU-to-GPU source translators

Parkinson's disease-related perfusion and glucose metabolic brain patterns identified with PCASL-MRI and FDG-PET imaging

AbstractIntroductionUnder normal conditions, the spatial distribution of resting cerebral blood flow and cerebral metabolic rate of glucose are closely related. A relatively new magnetic resonance (MR) technique, pseudo-continuous arterial spin labeling (PCASL), can be used to measure regional brain perfusion. We identified a Parkinson's disease (PD)-related perfusion and metabolic covariance pattern in the same patients using PCASL and FDG-PET imaging and assessed (dis)similarities in the disease-related pattern between perfusion and metabolism in PD patients.MethodsNineteen PD patients and seventeen healthy controls underwent [18F]-fluorodeoxyglucose positron emission tomography (FDG-PET) imaging. Of 14 PD patients and all healthy controls PCASL-MRI could be obtained. Data were analyzed using scaled subprofile model/principal component analysis (SSM/PCA).ResultsUnique Parkinson's disease-related perfusion and metabolic covariance patterns were identified using PCASL and FDG-PET in the same patients. The PD-related metabolic covariance brain pattern is in high accordance with previously reports. Also our disease-related perfusion pattern is comparable to the earlier described perfusion pattern. The most marked difference between our perfusion and metabolic patterns is the larger perfusion decrease in cortical regions including the insula.ConclusionWe identified PD-related perfusion and metabolic brain patterns using PCASL and FDG-PET in the same patients which were comparable with results of existing research. In this respect, PCASL appears to be a promising addition in the early diagnosis of individual parkinsonian patients

Assessing Dynamic Balance Performance during Exergaming based on Speed and Curvature of Body Movements

Improving balance performance among the elderly is of utmost importance because of the increasing number of injuries and fatalities caused by fall incidences. Digital games controlled by body movements (exergames) have been proposed as a way to improve balance among older people. However, the assessment of balance performance in real-time during exergaming remains a challenging task. This assessment could be used to provide instantaneous feedback and automatically adjust the exergame difficulty. Such features could potentially increase the motivation of the player, thus augmenting the effectiveness of exergames. As clear differences in balance performance have been identified between older and younger people, distinguishing between older and younger adults can help identifying measures of balance performance. We used generalized linear models to investigate whether the assessment of balance performance based on movement speed can be improved by incorporating curvature of the movement trajectory into the analysis. Indeed, our results indicated that curvature improves the performance of the models. Five-fold cross validation indicated that our method is promising for the assessment of balance performance in real-time by showing more than 90% classification accuracy. Finally, this method could be valuable not only for exergaming but also for real-time assessment of body movements in sports, rehabilitation and medicine

Visual Data Exploration for Balance Quantification in Real-Time During Exergaming

Unintentional injuries are among the ten leading causes of death in older adults; falls cause 60% of these deaths. Despite their effectiveness to improve balance and reduce the risk of falls, balance training programs have several drawbacks in practice, such as lack of engaging elements, boring exercises, and the effort and cost of travelling, ultimately resulting in low adherence. Exergames, that is, digital games controlled by body movements, have been proposed as an alternative to improve balance. One of the main challenges for exergames is to automatically quantify balance during game-play in order to adapt the game difficulty according to the skills of the player. Here we perform a multidimensional exploratory data analysis, using visualization techniques, to find useful measures for quantifying balance in real-time. First, we visualize exergaming data, derived from 400 force plate recordings of 40 participants from 20 to 79 years and 10 trials per participant, as heat maps and violin plots to get quick insight into the nature of the data. Second, we extract known and new features from the data, such as instantaneous speed, measures of dispersion, turbulence measures derived from speed, and curvature values. Finally, we analyze and visualize these features using several visualizations such as a heat map, overlapping violin plots, a parallel coordinate plot, a projection of the two first principal components, and a scatter plot matrix. Our visualizations and findings suggest that heat maps and violin plots can provide quick insight and directions for further data exploration. The most promising measures to quantify balance in real-time are speed, curvature and a turbulence measure, because these measures show age-related changes in balance performance. The next step is to apply the present techniques to data of whole body movements as recorded by devices such as Kinect