Are you thinking what I'm thinking? Synchronization of resting fMRI time-series across subjects.

We describe BrainSync, an orthogonal transform that allows direct comparison of resting fMRI (rfMRI) time-series across subjects. For this purpose, we exploit the geometry of the rfMRI signal space to propose a novel orthogonal transformation that synchronizes rfMRI time-series across sessions and subjects. When synchronized, rfMRI signals become approximately equal at homologous locations across subjects. The method is based on the observation that rfMRI data exhibit similar connectivity patterns across subjects, as reflected in the pairwise correlations between different brain regions. We show that if the data for two subjects have similar correlation patterns then their time courses can be approximately synchronized by an orthogonal transformation. This transform is unique, invertible, efficient to compute, and preserves the connectivity structure of the original data for all subjects. Analogously to image registration, where we spatially align structural brain images, this temporal synchronization of brain signals across a population, or within-subject across sessions, facilitates cross-sectional and longitudinal studies of rfMRI data. The utility of the BrainSync transform is illustrated through demonstrative simulations and applications including quantification of rfMRI variability across subjects and sessions, cortical functional parcellation across a population, timing recovery in task fMRI data, comparison of task and resting state data, and an application to complex naturalistic stimuli for annotation prediction.

A hybrid high-resolution anatomical MRI atlas with sub-parcellation of cortical gyri using resting fMRI.

We present a new high-quality, single-subject atlas with sub-millimeter voxel resolution, high SNR, and excellent gray-white tissue contrast to resolve fine anatomical details. The atlas is labeled into two parcellation schemes: 1) the anatomical BCI-DNI atlas, which is manually labeled based on known morphological and anatomical features, and 2) the hybrid USCBrain atlas, which incorporates functional information to guide the sub-parcellation of cerebral cortex. In both cases, we provide consistent volumetric and cortical surface-based parcellation and labeling. The intended use of the atlas is as a reference template for structural coregistration and labeling of individual brains. A single-subject T1-weighted image was acquired five times at a resolution of 0.547 mm × 0.547 mm × 0.800 mm and averaged. Images were processed by an expert neuroanatomist using semi-automated methods in BrainSuite to extract the brain, classify tissue-types, and render anatomical surfaces. Sixty-six cortical and 29 noncortical regions were manually labeled to generate the BCI-DNI atlas. The cortical regions were further sub-parcellated into 130 cortical regions based on multi-subject connectivity analysis using resting fMRI (rfMRI) data from the Human Connectome Project (HCP) database to produce the USCBrain atlas. In addition, we provide a delineation between sulcal valleys and gyral crowns, which offer an additional set of 26 sulcal subregions per hemisphere. Lastly, a probabilistic map is provided to give users a quantitative measure of reliability for each gyral subdivision. Utility of the atlas was assessed by computing Adjusted Rand Indices (ARIs) between individual sub-parcellations obtained through structural-only coregistration to the USCBrain atlas and sub-parcellations obtained directly from each subject's resting fMRI data. Both atlas parcellations can be used with the BrainSuite, FreeSurfer, and FSL software packages.

[Comparison of endmember extraction at spectral unmixing for biological fluorescence imaging].

We applied two classical algorithms in hyperspectral imaging to extract endmember for biological fluorescence imaging. A combined algorithm was found to initialize the PPI with decreasing the number of multi-spectral pixels, with subsequent N-FINDR refinement, which could make a better result.

Loneliness and meaning in life are reflected in the intrinsic network architecture of the brain.

Social relationships imbue life with meaning, whereas loneliness diminishes one's sense of meaning in life. Yet the extent of interdependence between these psychological constructs remains poorly understood. We took a multivariate network approach to examine resting-state fMRI functional connectivity's association with loneliness and meaning in a large cohort of adults (N = 942). Loneliness and meaning in life were negatively correlated with one another. In their relationship with individually parcelled whole-brain measures of functional connectivity, a significant and reliable pattern was observed. Greater loneliness was associated with dense, and less modular, connections between default, frontoparietal, attention and perceptual networks. A greater sense of life meaning was associated with increased, and more modular, connectivity between default and limbic networks. Low loneliness was associated with more modular brain connectivity, and lower life meaning was associated with higher between-network connectivity. These findings advance our understanding of loneliness and life meaning as distinct, yet interdependent, features of sociality. The results highlight a potential role of the default network as a central hub, providing a putative neural mechanism for shifting between feelings of isolation and purpose.

rfDemons: Resting fMRI-based Cortical Surface Registration using the BrainSync Transform.

Cross subject functional studies of cerebral cortex require cortical registration that aligns functional brain regions. While cortical folding patterns are approximate indicators of the underlying cytoarchitecture, coregistration based on these features alone does not accurately align functional regions in cerebral cortex. This paper presents a method for cortical surface registration (rfDemons) based on resting fMRI (rfMRI) data that uses curvature-based anatomical registration as an initialization. In contrast to existing techniques that use connectivity-based features derived from rfMRI, the proposed method uses 'synchronized' resting rfMRI time series directly. The synchronization of rfMRI data is performed using the BrainSync transform which applies an orthogonal transform to the rfMRI time series to temporally align them across subjects. The rfDemons method was applied to rfMRI from the Human Connectome Project and evaluated using task fMRI data to explore the impact of cortical registration performed using resting fMRI data on functional alignment of the cerebral cortex.

BrainSync: An Orthogonal Transformation for Synchronization of fMRI Data Across Subjects.

We describe a method that allows direct comparison of resting fMRI (rfMRI) time series across subjects. For this purpose, we exploit the geometry of the rfMRI signal space to conjecture the existence of an orthogonal transformation that synchronizes fMRI time series across sessions and subjects. The method is based on the observation that rfMRI data exhibit similar connectivity patterns across subjects, as reflected in the pairwise correlations between different brain regions. The orthogonal transformation that performs the synchronization is unique, invertible, efficient to compute, and preserves the connectivity structure of the original data for all subjects. Similarly to image registration, where we spatially align the anatomical brain images, this synchronization of brain signals across a population or within subject across sessions facilitates longitudinal and cross-sectional studies of rfMRI data. The utility of this transformation is illustrated through applications to quantification of fMRI variability across subjects and sessions, joint cortical clustering of a population and comparison of task-related and resting fMRI.

Temporal Non-Local Means Filtering Reveals Real-Time Whole-Brain Cortical Interactions in Resting fMRI.

Intensity variations over time in resting BOLD fMRI exhibit spatial correlation patterns consistent with a set of large scale cortical networks. However, visualizations of this data on the brain surface, even after extensive preprocessing, are dominated by local intensity fluctuations that obscure larger scale behavior. Our novel adaptation of non-local means (NLM) filtering, which we refer to as temporal NLM or tNLM, reduces these local fluctuations without the spatial blurring that occurs when using standard linear filtering methods. We show examples of tNLM filtering that allow direct visualization of spatio-temporal behavior on the cortical surface. These results reveal patterns of activity consistent with known networks as well as more complex dynamic changes within and between these networks. This ability to directly visualize brain activity may facilitate new insights into spontaneous brain dynamics. Further, temporal NLM can also be used as a preprocessor for resting fMRI for exploration of dynamic brain networks. We demonstrate its utility through application to graph-based functional cortical parcellation. Simulations with known ground truth functional regions demonstrate that tNLM filtering prior to parcellation avoids the formation of false parcels that can arise when using linear filtering. Application to resting fMRI data from the Human Connectome Project shows significant improvement, in comparison to linear filtering, in quantitative agreement with functional regions identified independently using task-based experiments as well as in test-retest reliability.