A Tool for Interactive Data Visualization: Application to Over 10,000 Brain Imaging and Phantom MRI Data Sets.

In this paper we propose a web-based approach for quick visualization of big data from brain magnetic resonance imaging (MRI) scans using a combination of an automated image capture and processing system, nonlinear embedding, and interactive data visualization tools. We draw upon thousands of MRI scans captured via the COllaborative Imaging and Neuroinformatics Suite (COINS). We then interface the output of several analysis pipelines based on structural and functional data to a t-distributed stochastic neighbor embedding (t-SNE) algorithm which reduces the number of dimensions for each scan in the input data set to two dimensions while preserving the local structure of data sets. Finally, we interactively display the output of this approach via a web-page, based on data driven documents (D3) JavaScript library. Two distinct approaches were used to visualize the data. In the first approach, we computed multiple quality control (QC) values from pre-processed data, which were used as inputs to the t-SNE algorithm. This approach helps in assessing the quality of each data set relative to others. In the second case, computed variables of interest (e.g., brain volume or voxel values from segmented gray matter images) were used as inputs to the t-SNE algorithm. This approach helps in identifying interesting patterns in the data sets. We demonstrate these approaches using multiple examples from over 10,000 data sets including (1) quality control measures calculated from phantom data over time, (2) quality control data from human functional MRI data across various studies, scanners, sites, (3) volumetric and density measures from human structural MRI data across various studies, scanners and sites. Results from (1) and (2) show the potential of our approach to combine t-SNE data reduction with interactive color coding of variables of interest to quickly identify visually unique clusters of data (i.e., data sets with poor QC, clustering of data by site) quickly. Results from (3) demonstrate interesting patterns of gray matter and volume, and evaluate how they map onto variables including scanners, age, and gender. In sum, the proposed approach allows researchers to rapidly identify and extract meaningful information from big data sets. Such tools are becoming increasingly important as datasets grow larger.

Application of ICA to realistically simulated (1)H-MRS data.

INTRODUCTION: (1)H-MRS signals from brain tissues capture information on in vivo brain metabolism and neuronal biomarkers. This study aims to advance the use of independent component analysis (ICA) for spectroscopy data by objectively comparing the performance of ICA and LCModel in analyzing realistic data that mimics many of the known properties of in vivo data. METHODS: This work identifies key features of in vivo (1)H-MRS signals and presents methods to simulate realistic data, using a basis set of 12 metabolites typically found in the human brain. The realistic simulations provide a much needed ground truth to evaluate performances of various MRS analysis methods. ICA is applied to collectively analyze multiple realistic spectra and independent components identified with our generative model to obtain ICA estimates. These same data are also analyzed using LCModel and the comparisons between the ground-truth and the analysis estimates are presented. The study also investigates the potential impact of modeling inaccuracies by incorporating two sets of model resonances in simulations. RESULTS: The simulated fid signals incorporating line broadening, noise, and residual water signal closely resemble the in vivo signals. Simulation analyses show that the resolution performances of both LCModel and ICA are not consistent across metabolites and that while ICA resolution can be improved for certain resonances, ICA is as effective as, or better than, LCModel in resolving most model resonances. CONCLUSION: The results show that ICA can be an effective tool in comparing multiple spectra and complements existing approaches for providing quantified estimates.

Group independent component analysis of MR spectra.

This study investigates the potential of independent component analysis (ICA) to provide a data-driven approach for group level analysis of magnetic resonance (MR) spectra. ICA collectively analyzes data to identify maximally independent components, each of which captures covarying resonances, including those from different metabolic sources. A comparative evaluation of the ICA approach with the more established LCModel method in analyzing two different noise-free, artifact-free, simulated data sets of known compositions is presented. The results from such ideal simulations demonstrate the ability of data-driven ICA to decompose data and accurately extract components resembling modeled basis spectra from both data sets, whereas the LCModel results suffer when the underlying model deviates from assumptions, thus highlighting the sensitivity of model-based approaches to modeling inaccuracies. Analyses with simulated data show that independent component weights are good estimates of concentrations, even of metabolites with low intensity singlet peaks, such as scyllo-inositol. ICA is also applied to single voxel spectra from 193 subjects, without correcting for baseline variations, line-width broadening or noise. The results provide evidence that, despite the presence of confounding artifacts, ICA can be used to analyze in vivo spectra and extract resonances of interest. ICA is a promising technique for decomposing MR spectral data into components resembling metabolite resonances, and therefore has the potential to provide a data-driven alternative to the use of metabolite concentrations derived from curve-fitting individual spectra in making group comparisons.

Neurometabolite concentration and clinical features of chronic alcohol use: a proton magnetic resonance spectroscopy study.

Chronic, heavy alcohol consumption may affect the concentration of neurometabolites assessed with proton magnetic resonance spectroscopy ((1)H-MRS). We investigated the largest sample reported to date (N=213) with the primary goal of determining how specific clinical features impact neurometabolite concentrations in an anterior cingulate gray matter voxel. This community-dwelling sample included both treatment-seeking and non-treatment-seeking individuals. A healthy control group (N=66) was matched for age and education. In multivariate analyses predicting neurometabolite concentrations, the heavy drinking group had greater concentrations overall. An age by group interaction was noted, as group difference across neurometabolites increased with age. More years drinking, but not more drinks per drinking day (DPDD), predicted greater concentrations of choline-containing compounds (Cho), creatine-phosphocreatine (Cre), glutamate-glutamine (Glx), and N-acetyl-aspartate (NAA). The effects of other clinical variables (depression, cigarette smoking, marijuana use) were negligible. After controlling for DPDD and years drinking, treatment-seeking status had no impact on neurometabolites. In the very oldest portion of the sample (mean age=50), however, a negative relationship was seen between NAA and years drinking. These results suggest that the nature of neurometabolite abnormalities in chronic heavy drinkers may vary as a function of duration of abuse.

Rare copy number deletions predict individual variation in human brain metabolite concentrations in individuals with alcohol use disorders.

BACKGROUND: Although variations in neurometabolite concentrations occur in diverse neuropsychiatric and neurodegenerative disorders, little is known about the nature of underlying genetic influences. The current study investigated the importance of a specific type of genetic mutation, copy number variation (CNV), for neurometabolite concentrations in a bilateral anterior cingulate voxel. METHODS: These neurometabolic signals were quantified using proton magnetic resonance spectroscopy ((1)H-MRS): N-acetylaspartate (NAA), creatine-phosphocreatine (Cre), glutamate/glutamine (Glx), myoinositol (mI), and phosphorylcholine-glycerol phosphorylcholine (Cho). Genetic data were collected using the Illumina 1MDuoBeadChip Array from a sample adults with alcohol use disorders (n = 146). RESULTS: The number of base pairs lost through rare copy number deletions (occurring in less than 5% of our sample) predicted lower NAA, Cre, mI, and Glx. More total rare deletions also predicted lower NAA, Cre, and Glx. Principal components analyses of the five neurometabolites identified two correlated components, the first comprised of NAA, Glx, and Cre, and the second comprised of Cho, mI, and to a lesser extent, Cre. The number and length of rare deletions were correlated with the first component, capturing approximately 10% of phenotypic variance, but not the second component. CONCLUSIONS: These results suggest that mutation load affects neurometabolite concentrations, potentially increasing risk for neuropsychiatric disorders. The greater effect of CVNs on NAA, Glx, and Cre may reflect a greater sensitivity to the effects of mutations (i.e., reduced canalization) for neurometabolites related to metabolic activity and cellular energetics, due to extensive recent selection pressure on these phenotypes in the human lineage.

Perturbation of the glutamate-glutamine system in alcohol dependence and remission.

As acute ethanol exposure inhibits N-methyl-D-aspartate glutamate (Glu) receptors, sudden withdrawal from chronic alcohol use may lead to an increased activation of these receptors with excitotoxic effects. In the longer term, brain levels of Glu and its metabolites, such as glutamine (Gln), are likely to be chronically altered by alcohol, possibly providing a measure of overall abnormal Glu-Gln cycling. However, few studies have assessed concentrations of these metabolites in clinical populations of individuals with alcohol use disorders. Glu and Gln levels were compared in groups of 17 healthy controls and in 13 participants with alcohol dependence. Within the alcohol-dependent group, seven participants had current alcohol use disorder (AUD), and six had AUD in remission for at least 1 year (AUD-R). Neurometabolite concentrations were measured with proton magnetic resonance spectroscopy ((1)H-MRS) in a predominantly gray matter voxel that included the bilateral anterior cingulate gyri. Tissue segmentation provided an assessment of the proportion of gray matter in the (1)H-MRS voxel. The Drinker Inventory of Consequences (DrInC) and Form-90 were administered to all participants to quantify alcohol consequences and use. Glu level was lower and Gln level was higher in the AUD and AUD-R groups relative to the control group; creatine, choline, myo-inositol, and total N-acetyl groups, primarily N-acetylaspartate did not differ across groups. These results were not confounded by age, sex, or proportion of gray matter in the (1)H-MRS voxel. Neurometabolite concentrations did not differ between AUD and AUD-R groups. Subsequent regressions in the combined clinical group, treating voxel gray matter proportion as a covariate, revealed that total score on the DrInC was positively correlated with Gln but negatively correlated with both Glu and gray matter proportion. Regression analyses, including DrInC scores and smoking variables, identified a marginal independent effect of smoking on Gln. The current findings of higher Gln and lower Glu in the combined AUD and AUD-R groups might indicate a perturbation of the Glu-Gln cycle in alcohol use disorders. The absence of differences in mean Glu and Gln between the AUD and AUD-R groups suggests that altered Glu-Gln metabolism may either predate the onset of abuse or persist during prolonged abstinence.

A baseline for the multivariate comparison of resting-state networks.

As the size of functional and structural MRI datasets expands, it becomes increasingly important to establish a baseline from which diagnostic relevance may be determined, a processing strategy that efficiently prepares data for analysis, and a statistical approach that identifies important effects in a manner that is both robust and reproducible. In this paper, we introduce a multivariate analytic approach that optimizes sensitivity and reduces unnecessary testing. We demonstrate the utility of this mega-analytic approach by identifying the effects of age and gender on the resting-state networks (RSNs) of 603 healthy adolescents and adults (mean age: 23.4 years, range: 12-71 years). Data were collected on the same scanner, preprocessed using an automated analysis pipeline based in SPM, and studied using group independent component analysis. RSNs were identified and evaluated in terms of three primary outcome measures: time course spectral power, spatial map intensity, and functional network connectivity. Results revealed robust effects of age on all three outcome measures, largely indicating decreases in network coherence and connectivity with increasing age. Gender effects were of smaller magnitude but suggested stronger intra-network connectivity in females and more inter-network connectivity in males, particularly with regard to sensorimotor networks. These findings, along with the analysis approach and statistical framework described here, provide a useful baseline for future investigations of brain networks in health and disease.

Mining the mind research network: a novel framework for exploring large scale, heterogeneous translational neuroscience research data sources.

A neuroinformatics (NI) system is critical to brain imaging research in order to shorten the time between study conception and results. Such a NI system is required to scale well when large numbers of subjects are studied. Further, when multiple sites participate in research projects organizational issues become increasingly difficult. Optimized NI applications mitigate these problems. Additionally, NI software enables coordination across multiple studies, leveraging advantages potentially leading to exponential research discoveries. The web-based, Mind Research Network (MRN), database system has been designed and improved through our experience with 200 research studies and 250 researchers from seven different institutions. The MRN tools permit the collection, management, reporting and efficient use of large scale, heterogeneous data sources, e.g., multiple institutions, multiple principal investigators, multiple research programs and studies, and multimodal acquisitions. We have collected and analyzed data sets on thousands of research participants and have set up a framework to automatically analyze the data, thereby making efficient, practical data mining of this vast resource possible. This paper presents a comprehensive framework for capturing and analyzing heterogeneous neuroscience research data sources that has been fully optimized for end-users to perform novel data mining.