BackgroundPrevious studies using hierarchical clustering approach to analyze resting-state fMRI data were limited to a few slices or regions-of-interest (ROIs) after substantial data reduction.PurposeTo develop a framework that can perform voxel-wise hierarchical clustering of whole-brain resting-state fMRI data from a group of subjects.Materials and MethodsResting-state fMRI measurements were conducted for 86 adult subjects using a single-shot echo-planar imaging (EPI) technique. After pre-processing and co-registration to a standard template, pair-wise cross-correlation coefficients (CC) were calculated for all voxels inside the brain and translated into absolute Pearson's distances after imposing a threshold CC≥0.3. The group averages of the Pearson's distances were then used to perform hierarchical clustering with the developed framework, which entails gray matter masking and an iterative scheme to analyze the dendrogram.ResultsWith the hierarchical clustering framework, we identified most of the functional connectivity networks reported previously in the literature, such as the motor, sensory, visual, memory, and the default-mode functional networks (DMN). Furthermore, the DMN and visual system were split into their corresponding hierarchical sub-networks.ConclusionIt is feasible to use the proposed hierarchical clustering scheme for voxel-wise analysis of whole-brain resting-state fMRI data. The hierarchical clustering result not only confirmed generally the finding in functional connectivity networks identified previously using other data processing techniques, such as ICA, but also revealed directly the hierarchical structure within the functional connectivity networks.

Different machine learning algorithms have recently been used for assisting automated classification of independent component analysis (ICA) results from resting-state fMRI data. The success of this approach relies on identification of artifact components and meaningful functional networks. A limiting factor of ICA is the uncertainty of the number of independent components (NIC). We aim to develop a framework based on support vector machines (SVM) and optimized feature-selection for automated classification of independent components (ICs) and use the framework to investigate the effects of input NIC on the ICA results. Seven different resting-state fMRI datasets were studied. 18 features were devised by mimicking the empirical criteria for manual evaluation. The five most significant (p < 0.01) features were identified by general linear modeling and used to generate a classification model for the framework. This feature-optimized classification of ICs with SVM (FOCIS) framework was used to classify both group and single subject ICA results. The classification results obtained using FOCIS and previously published FSL-FIX were compared against manually evaluated results. On average the false negative rate in identifying artifact contaminated ICs for FOCIS and FSL-FIX were 98.27 and 92.34%, respectively. The number of artifact and functional network components increased almost linearly with the input NIC. Through tracking, we demonstrate that incrementing NIC affects most ICs when NIC < 33, whereas only a few limited ICs are affected by direct splitting when NIC is incremented beyond NIC > 40. For a given IC, its changes with increasing NIC are individually specific irrespective whether the component is a potential resting-state functional network or an artifact component. Using FOCIS, we investigated experimentally the ICA dimensionality of resting-state fMRI datasets and found that the input NIC can critically affect the ICA results of resting-state fMRI data.

PurposeCharacterize the static and dynamic functional connectivity for subjects with juvenile myoclonic epilepsy (JME) using a quantitative data-driven analysis approach.MethodsWhole-brain resting-state functional MRI data were acquired on a 3 T whole-body clinical MRI scanner from 18 subjects clinically diagnosed with JME and 25 healthy control subjects. 2-min sliding-window approach was incorporated in the quantitative data-driven data analysis framework to assess both the dynamic and static functional connectivity in the resting brains. Two-sample t-tests were performed voxel-wise to detect the differences in functional connectivity metrics based on connectivity strength and density.ResultsThe static functional connectivity metrics based on quantitative data-driven analysis of the entire 10-min acquisition window of resting-state functional MRI data revealed significantly enhanced functional connectivity in JME patients in bilateral dorsolateral prefrontal cortex, dorsal striatum, precentral and middle temporal gyri. The dynamic functional connectivity metrics derived by incorporating a 2-min sliding window into quantitative data-driven analysis demonstrated significant hyper dynamic functional connectivity in the dorsolateral prefrontal cortex, middle temporal gyrus and dorsal striatum. Connectivity strength metrics (both static and dynamic) can detect more extensive functional connectivity abnormalities in the resting-state functional networks (RFNs) and depict also larger overlap between static and dynamic functional connectivity results.ConclusionIncorporating a 2-min sliding window into quantitative data-driven analysis of resting-state functional MRI data can reveal additional information on the temporally fluctuating RFNs of the human brain, which indicate that RFNs involving dorsolateral prefrontal cortex have temporal varying hyper dynamic characteristics in JME patients. Assessing dynamic along with static functional connectivity may provide further insights into the abnormal function connectivity underlying the pathological brain functioning in JME.