Kaiming Li

Review of methods for functional brain connectivity detection using fMRI.

Since the mid of 1990s, functional connectivity study using fMRI (fcMRI) has drawn increasing attention of neuroscientists and computer scientists, since it opens a new window to explore functional network of human brain with relatively high resolution. A variety of methods for fcMRI study have been proposed. This paper intends to provide a technical review on computational methodologies developed for fcMRI analysis. From our perspective, these computational methods are classified into two general categories: model-driven methods and data-driven methods. Data-driven methods are a large family, and thus are further sub-classified into decomposition-based methods and clustering analysis methods. For each type of methods, principles, main contributors, and their advantages and drawbacks are discussed. Finally, potential applications of fcMRI are overviewed.

DICCCOL: Dense Individualized and Common Connectivity-Based Cortical Landmarks

Is there a common structural and functional cortical architecture that can be quantitatively encoded and precisely reproduced across individuals and populations? This question is still largely unanswered due to the vast complexity, variability, and nonlinearity of the cerebral cortex. Here, we hypothesize that the common cortical architecture can be effectively represented by group-wise consistent structural fiber connections and take a novel data-driven approach to explore the cortical architecture. We report a dense and consistent map of 358 cortical landmarks, named Dense Individualized and Common Connectivity-based Cortical Landmarks (DICCCOLs). Each DICCCOL is defined by group-wise consistent white-matter fiber connection patterns derived from diffusion tensor imaging (DTI) data. Our results have shown that these 358 landmarks are remarkably reproducible over more than one hundred human brains and possess accurate intrinsically established structural and functional cross-subject correspondences validated by large-scale functional magnetic resonance imaging data. In particular, these 358 cortical landmarks can be accurately and efficiently predicted in a new single brain with DTI data. Thus, this set of 358 DICCCOL landmarks comprehensively encodes the common structural and functional cortical architectures, providing opportunities for many applications in brain science including mapping human brain connectomes, as demonstrated in this work.

Complex span tasks and hippocampal recruitment during working memory

The working memory (WM) system is vital to performing everyday functions that require attentive, non-automatic processing of information. However, its interaction with long term memory (LTM) is highly debated. Here, we used fMRI to examine whether a popular complex WM span task, thought to force the displacement of to-be-remembered items in the focus of attention to LTM, recruited medial temporal regions typically associated with LTM functioning to a greater extent and in a different manner than traditional neuroimaging WM tasks during WM encoding and maintenance. fMRI scans were acquired while participants performed the operation span (OSPAN) task and an arithmetic task. Results indicated that performance of both tasks resulted in significant activation in regions typically associated with WM function. More importantly, significant bilateral activation was observed in the hippocampus, suggesting it is recruited during WM encoding and maintenance. Right posterior hippocampus activation was greater during OSPAN than arithmetic. Persitimulus graphs indicate a possible specialization of function for bilateral posterior hippocampus and greater involvement of the left for WM performance. Recall time-course activity within this region hints at LTM involvement during complex span.

Axonal Fiber Terminations Concentrate on Gyri

Convoluted cortical folding and neuronal wiring are 2 prominent attributes of the mammalian brain. However, the macroscale intrinsic relationship between these 2 general cross-species attributes, as well as the underlying principles that sculpt the architecture of the cerebral cortex, remains unclear. Here, we show that the axonal fibers connected to gyri are significantly denser than those connected to sulci. In human, chimpanzee, and macaque brains, a dominant fraction of axonal fibers were found to be connected to the gyri. This finding has been replicated in a range of mammalian brains via diffusion tensor imaging and high-angular resolution diffusion imaging. These results may have shed some lights on fundamental mechanisms for development and organization of the cerebral cortex, suggesting that axonal pushing is a mechanism of cortical folding.

Individualized ROI Optimization via Maximization of Group-wise Consistency of Structural and Functional Profiles

Studying connectivities among functional brain regions and the functional dynamics on brain networks has drawn increasing interest. A fundamental issue that affects functional connectivity and dynamics studies is how to determine the best possible functional brain regions or ROIs (regions of interest) for a group of individuals, since the connectivity measurements are heavily dependent on ROI locations. Essentially, identification of accurate, reliable and consistent corresponding ROIs is challenging due to the unclear boundaries between brain regions, variability across individuals, and nonlinearity of the ROIs. In response to these challenges, this paper presents a novel methodology to computationally optimize ROIs locations derived from task-based fMRI data for individuals so that the optimized ROIs are more consistent, reproducible and predictable across brains. Our computational strategy is to formulate the individual ROI location optimization as a group variance minimization problem, in which group-wise consistencies in functional/structural connectivity patterns and anatomic profiles are defined as optimization constraints. Our experimental results from multimodal fMRI and DTI data show that the optimized ROIs have significantly improved consistency in structural and functional profiles across individuals. These improved functional ROIs with better consistency could contribute to further study of functional interaction and dynamics in the human brain.

Gyral folding pattern analysis via surface profiling.

Folding is an essential shape characteristic of the human cerebral cortex. Descriptors of cortical folding patterns have been studied for decades. However, many previous studies are either based on local shape descriptors such as curvature, or based on global descriptors such as gyrification index or spherical wavelets. This paper proposes a gyrus-scale folding pattern analysis technique via cortical surface profiling. Firstly, we sample the cortical surface into 2D profiles and model them using a power function. This step provides both the flexibility of representing arbitrary shape by profiling and the compactness of representing shape by parametric modeling. Secondly, based on the estimated model parameters, we extract affine-invariant features on the cortical surface, and apply the affinity propagation clustering algorithm to parcellate the cortex into cortical regions with strict hierarchy and smooth transitions among them. Finally, a second-round surface profiling is performed on the parcellated cortical surface, and the number of hinges is detected to describe the gyral folding pattern. We have applied the surface profiling method to two normal brain datasets and a schizophrenia patient dataset. The experimental results demonstrate that the proposed method can accurately classify human gyri into 2-hinge, 3-hinge and 4-hinge patterns. The distribution of these folding patterns on brain lobes and the relationship between fiber density and gyral folding patterns are further investigated. Results from the schizophrenia dataset are consistent with commonly found abnormality in former studies by others, which demonstrates the potential clinical applications of the proposed technique.

Predicting Functional Cortical ROIs via DTI-Derived Fiber Shape Models

Studying structural and functional connectivities of human cerebral cortex has drawn significant interest and effort recently. A fundamental and challenging problem arises when attempting to measure the structural and/or functional connectivities of specific cortical networks: how to identify and localize the best possible regions of interests (ROIs) on the cortex? In our view, the major challenges come from uncertainties in ROI boundary definition, the remarkable structural and functional variability across individuals and high nonlinearities within and around ROIs. In this paper, we present a novel ROI prediction framework that localizes ROIs in individual brains based on their learned fiber shape models from multimodal task-based functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) data. In the training stage, shape models of white matter fibers are learnt from those emanating from the functional ROIs, which are activated brain regions detected from task-based fMRI data. In the prediction stage, functional ROIs are predicted in individual brains based only on DTI data. Our experiment results show that the average ROI prediction error is around 3.94 mm, in comparison with benchmark data provided by working memory and visual task-based fMRI. Our work demonstrated that fiber bundle shape models derived from DTI data are good predictors of functional cortical ROIs.

Connectome-scale assessments of structural and functional connectivity in MCI

Mild cognitive impairment (MCI) has received increasing attention not only because of its potential as a precursor for Alzheimers disease but also as a predictor of conversion to other neurodegenerative diseases. Although MCI has been defined clinically, accurate and efficient diagnosis is still challenging. Although neuroimaging techniques hold promise, compared to commonly used biomarkers including amyloid plaques, tau protein levels and brain tissue atrophy, neuroimaging biomarkers are less well validated. In this article, we propose a connectomes‐scale assessment of structural and functional connectivity in MCI via two independent multimodal DTI/fMRI datasets. We first used DTI‐derived structural profiles to explore and tailor the most common and consistent landmarks, then applied them in a whole‐brain functional connectivity analysis. The next step fused the results from two independent datasets together and resulted in a set of functional connectomes with the most differentiation power, hence named as “connectome signatures.” Our results indicate that these “connectome signatures” have significantly high MCI‐vs‐controls classification accuracy, at more than 95%. Interestingly, through functional meta‐analysis, we found that the majority of “connectome signatures” are mainly derived from the interactions among different functional networks, for example, cognition–perception and cognition–action domains, rather than from within a single network. Our work provides support for using functional “connectome signatures” as neuroimaging biomarkers of MCI. Hum Brain Mapp 35:2911–2923, 2014.

Representing and Retrieving Video Shots in Human-Centric Brain Imaging Space

Meaningful representation and effective retrieval of video shots in a large-scale database has been a profound challenge for the image/video processing and computer vision communities. A great deal of effort has been devoted to the extraction of low-level visual features, such as color, shape, texture, and motion for characterizing and retrieving video shots. However, the accuracy of these feature descriptors is still far from satisfaction due to the well-known semantic gap. In order to alleviate the problem, this paper investigates a novel methodology of representing and retrieving video shots using human-centric high-level features derived in brain imaging space (BIS) where brain responses to natural stimulus of video watching can be explored and interpreted. At first, our recently developed dense individualized and common connectivity-based cortical landmarks (DICCCOL) system is employed to locate large-scale functional brain networks and their regions of interests (ROIs) that are involved in the comprehension of video stimulus. Then, functional connectivities between various functional ROI pairs are utilized as BIS features to characterize the brains comprehension of video semantics. Then an effective feature selection procedure is applied to learn the most relevant features while removing redundancy, which results in the formation of the final BIS features. Afterwards, a mapping from low-level visual features to high-level semantic features in the BIS is built via the Gaussian process regression (GPR) algorithm, and a manifold structure is then inferred, in which video key frames are represented by the mapped feature vectors in the BIS. Finally, the manifold-ranking algorithm concerning the relationship among all data is applied to measure the similarity between key frames of video shots. Experimental results on the TRECVID 2005 dataset demonstrate the superiority of the proposed work in comparison with traditional methods.

Bridging the Semantic Gap via Functional Brain Imaging

The multimedia content analysis community has made significant efforts to bridge the gaps between low-level features and high-level semantics perceived by humans. Recent advances in brain imaging and neuroscience in exploring the human brains responses during multimedia comprehension demonstrated the possibility of leveraging cognitive neuroscience knowledge to bridge the semantic gaps. This paper presents our initial effort in this direction by using functional magnetic resonance imaging (fMRI). Specifically, task-based fMRI (T-fMRI) was performed to accurately localize the brain regions involved in video comprehension. Then, natural stimulus fMRI (N-fMRI) data were acquired when subjects watched the multimedia clips selected from the TRECVID datasets. The responses in the localized brain regions were measured and used to extract high-level features as the representation of the brains comprehension of semantics in the videos. A novel computational framework was developed to learn the most relevant low-level feature sets that best correlate the fMRI-derived semantic features based on the training videos with fMRI scans, and then the learned model was applied to larger scale TRECVID video datasets without fMRI scans for category classification. Our experimental results demonstrate: 1) there are meaningful couplings between brains fMRI-derived responses and video stimuli, suggesting the validity of linking semantics and low-level features via fMRI and 2) the computationally learned low-level features can significantly (p <; 0.01) improve video classification in comparison with original low-level features and extracted low-level features resulted from well-known feature projection algorithms.