Joint independent component analysis for hypothesizing spatiotemporal relationships between longitudinal gray and white matter changes in preclinical Alzheimer's disease

Characterizing relationships between gray matter (GM) and white matter (WM) in early Alzheimer's disease (AD) would improve understanding of how and when AD impacts the brain. However, modeling these relationships across brain regions and longitudinally remains a challenge. Thus, we propose extending joint independent component analysis (jICA) into spatiotemporal modeling of regional cortical thickness and WM bundle volumes leveraging multimodal MRI. We jointly characterize these GM and WM features in a normal aging (n=316) and an age- and sex-matched preclinical AD cohort (n=81) at each of two imaging sessions spaced three years apart, training on the normal aging population in cross-validation and interrogating the preclinical AD cohort. We find this joint model identifies reproducible, longitudinal changes in GM and WM between the two imaging sessions and that these changes are associated with preclinical AD and are plausible considering the literature. We compare this joint model to two focused models: (1) GM features at the first session and WM at the second and (2) vice versa. The joint model identifies components that correlate poorly with those from the focused models, suggesting the different models resolve different patterns. We find the strength of association with preclinical AD is improved in the GM to WM model, which supports the hypothesis that medial temporal and frontal thinning precedes volume loss in the uncinate fasciculus and inferior anterior-posterior association fibers. These results suggest that jICA effectively generates spatiotemporal hypotheses about GM and WM in preclinical AD, especially when specific intermodality relationships are considered a priori.

Joint analysis of structural connectivity and cortical surface features: correlates with mild traumatic brain injury

Mild traumatic brain injury (mTBI) is a complex syndrome that affects up to 600 per 100,000 individuals, with a particular concentration among military personnel. About half of all mTBI patients experience a diverse array of chronic symptoms which persist long after the acute injury. Hence, there is an urgent need for better understanding of the white matter and gray matter pathologies associated with mTBI to map which specific brain systems are impacted and identify courses of intervention. Previous works have linked mTBI to disruptions in white matter pathways and cortical surface abnormalities. Herein, we examine these hypothesized links in an exploratory study of joint structural connectivity and cortical surface changes associated with mTBI and its chronic symptoms. Briefly, we consider a cohort of 12 mTBI and 26 control subjects. A set of 588 cortical surface metrics and 4,753 structural connectivity metrics were extracted from cortical surface regions and diffusion weighted magnetic resonance imaging in each subject. Principal component analysis (PCA) was used to reduce the dimensionality of each metric set. We then applied independent component analysis (ICA) both to each PCA space individually and together in a joint ICA approach. We identified a stable independent component across the connectivity-only and joint ICAs which presented significant group differences in subject loadings (p<0.05, corrected). Additionally, we found that two mTBI symptoms, slowed thinking and forgetfulness, were significantly correlated (p<0.05, corrected) with mTBI subject loadings in a surface-only ICA. These surface-only loadings captured an increase in bilateral cortical thickness.

Joint cortical surface and structural connectivity analysis of Alzheimer's Disease

Prior neuroimaging studies have demonstrated isolated structural and connectivity changes in the brain due to Alzheimer's Disease (AD). However, how these changes relate to each other is not well understood. We present a preliminary study to begin to fill this gap by leveraging joint independent component analysis (jICA). We explore how jICA performs in an analysis of T1 and diffusion weighted MRI by characterizing the joint changes of complex cortical surface and structural connectivity metrics in AD in subjects from the Baltimore Longitudinal Study of Aging. We calculate 588 region-based cortical metrics and 4,753 fractional anisotropy-based connectivity metrics and project them into a low-dimensional manifold with principal component analysis. We perform jICA on the manifold and subsequently backproject the independent components to the original data space. We demonstrate component stability with 3-fold cross validation and find differential component loadings between 776 cognitively unimpaired control subjects and 23 with AD that generalizes across folds. In addition, we perform the same analysis on the surface and connectivity metrics separately and find that the joint approach identifies both novel and similar components to the separate approaches. To illustrate the joint approach's primary utility, we provide an example hypothesis for how surface and connectivity components may vary together with AD. These preliminary results suggest jointly varying independent cortical surface and structural connectivity components can be consistently extracted from MRI data and provide a data-driven way for generating novel hypotheses about AD that may not be captured by separate analyses.

Fairy Tales versus Facts: Genre Matters to the Developing Brain

Neurobiological studies of discourse comprehension have almost exclusively focused on narrative comprehension. However, successful engagement in modern society, particularly in educational settings, also requires comprehension with an aim to learn new information (i.e., "expository comprehension"). Despite its prevalence, no studies to date have neurobiologically characterized expository comprehension as compared with narrative. In the current study, we used functional magnetic resonance imaging in typically developing children to test whether different genres require specialized brain networks. In addition to expected activations in language and comprehension areas in the default mode network (DMN), expository comprehension required significantly greater activation in the frontoparietal control network (FPN) than narrative comprehension, and relied significantly less on posterior regions in the DMN. Functional connectivity analysis revealed that, compared with narrative, the FPN robustly correlated with the DMN, and this inter-network communication was higher with increased reading expertise. These findings suggest that, relative to narrative comprehension, expository comprehension shows (1) a unique configuration of the DMN, potentially to support non-social comprehension processes, and (2) increased utilization of top-down regions to help support goal-directed comprehension processes in the DMN. More generally, our findings reveal that different types of discourse-level comprehension place diverse neural demands on the developing brain.

Anatomical context improves deep learning on the brain age estimation task

Deep learning has shown remarkable improvements in the analysis of medical images without the need for engineered features. In this work, we hypothesize that deep learning is complementary to traditional feature estimation. We propose a network design to include traditional structural imaging features alongside deep convolutional ones and illustrate this approach on the task of imaging-based age prediction in two separate contexts: T1-weighted brain magnetic resonance imaging (MRI) (N = 5121, ages 4-96, healthy controls) and computed tomography (CT) of the head (N = 1313, ages 1-97, healthy controls). In brain MRI, we can predict age with a mean absolute error of 4.08 years by combining raw images along with engineered structural features, compared to 5.00 years using image-derived features alone and 8.23 years using structural features alone. In head CT, we can predict age with a median absolute error of 9.99 years combining features, compared to 11.02 years with image-derived features alone and 13.28 years with structural features alone. These results show that we can complement traditional feature estimation using deep learning to improve prediction tasks. As the field of medical image processing continues to integrate deep learning, it will be important to use the new techniques to complement traditional imaging features instead of fully displacing them.

Applying a network framework to the neurobiology of reading and dyslexia

Background

There is a substantial literature on the neurobiology of reading and dyslexia. Differences are often described in terms of individual regions or individual cognitive processes. However, there is a growing appreciation that the brain areas subserving reading are nested within larger functional systems, and new network analysis methods may provide greater insight into how reading difficulty arises. Yet, relatively few studies have adopted a principled network-based approach (e.g., connectomics) to studying reading. In this study, we combine data from previous reading literature, connectomics studies, and original data to investigate the relationship between network architecture and reading.

Methods

First, we detailed the distribution of reading-related areas across many resting-state networks using meta-analytic data from NeuroSynth. Then, we tested whether individual differences in modularity, the brain’s tendency to segregate into resting-state networks, are related to reading skill. Finally, we determined whether brain areas that function atypically in dyslexia, as identified by previous meta-analyses, tend to be concentrated in hub regions.

Results

We found that most resting-state networks contributed to the reading network, including those subserving domain-general cognitive skills such as attention and executive function. There was also a positive relationship between the global modularity of an individual’s brain network and reading skill, with the visual, default mode and cingulo-opercular networks showing the highest correlations. Brain areas implicated in dyslexia were also significantly more likely to have a higher participation coefficient (connect to multiple resting-state networks) than other areas.

Conclusions

These results contribute to the growing literature on the relationship between reading and brain network architecture. They suggest that an efficient network organization, i.e., one in which brain areas form cohesive resting-state networks, is important for skilled reading, and that dyslexia can be characterized by abnormal functioning of hub regions that map information between multiple systems. Overall, use of a connectomics framework opens up new possibilities for investigating reading difficulty, especially its commonalities across other neurodevelopmental disorders.

Electronic supplementary material

The online version of this article (10.1186/s11689-018-9251-z) contains supplementary material, which is available to authorized users.

Structural covariance across the lifespan: Brain development and aging through the lens of inter-network relationships

Recent studies have revealed that brain development is marked by morphological synchronization across brain regions. Regions with shared growth trajectories form structural covariance networks (SCNs) that not only map onto functionally identified cognitive systems, but also correlate with a range of cognitive abilities across the lifespan. Despite advances in within-network covariance examinations, few studies have examined lifetime patterns of structural relationships across known SCNs. In the current study, we used a big-data framework and a novel application of covariate-adjusted restricted cubic spline regression to identify volumetric network trajectories and covariance patterns across 13 networks (n = 5,019, ages = 7-90). Our findings revealed that typical development and aging are marked by significant shifts in the degree that networks preferentially coordinate with one another (i.e., modularity). Specifically, childhood showed higher modularity of networks compared to adolescence, reflecting a shift over development from segregation to desegregation of inter-network relationships. The shift from young to middle adulthood was marked by a significant decrease in inter-network modularity and organization, which continued into older adulthood, potentially reflecting changes in brain organizational efficiency with age. This study is the first to characterize brain development and aging in terms of inter-network structural covariance across the lifespan.

Prefrontal mediation of the reading network predicts intervention response in dyslexia

A primary challenge facing the development of interventions for dyslexia is identifying effective predictors of intervention response. While behavioral literature has identified core cognitive characteristics of response, the distinction of reading versus executive cognitive contributions to response profiles remains unclear, due in part to the difficulty of segregating these constructs using behavioral outputs. In the current study we used functional neuroimaging to piece apart the mechanisms of how/whether executive and reading network relationships are predictive of intervention response. We found that readers who are responsive to intervention have more typical pre-intervention functional interactions between executive and reading systems compared to nonresponsive readers. These findings suggest that intervention response in dyslexia is influenced not only by domain-specific reading regions, but also by contributions from intervening domain-general networks. Our results make a significant gain in identifying predictive bio-markers of outcomes in dyslexia, and have important implications for the development of personalized clinical interventions.

Comprehending text versus reading words in young readers with varying reading ability: distinct patterns of functional connectivity from common processing hubs

Skilled reading depends on recognizing words efficiently in isolation (word-level processing; WL) and extracting meaning from text (discourse-level processing; DL); deficiencies in either result in poor reading. FMRI has revealed consistent overlapping networks in word and passage reading, as well as unique regions for DL processing; however, less is known about how WL and DL processes interact. Here we examined functional connectivity from seed regions derived from where BOLD signal overlapped during word and passage reading in 38 adolescents ranging in reading ability, hypothesizing that even though certain regions support word- and higher-level language, connectivity patterns from overlapping regions would be task modulated. Results indeed revealed that the left-lateralized semantic and working memory (WM) seed regions showed task-dependent functional connectivity patterns: during DL processes, semantic and WM nodes all correlated with the left angular gyrus, a region implicated in semantic memory/coherence building. In contrast, during WL, these nodes coordinated with a traditional WL area (left occipitotemporal region). In addition, these WL and DL findings were modulated by decoding and comprehension abilities, respectively, with poorer abilities correlating with decreased connectivity. Findings indicate that key regions may uniquely contribute to multiple levels of reading; we speculate that these connectivity patterns may be especially salient for reading outcomes and intervention response.