DCP: A pipeline toolbox for diffusion connectome.

The brain structural network derived from diffusion magnetic resonance imaging (dMRI) reflects the white matter connections between brain regions, which can quantitatively describe the anatomical connection pattern of the entire brain. The development of structural brain connectome leads to the emergence of a large number of dMRI processing packages and network analysis toolboxes. However, the fully automated network analysis based on dMRI data remains challenging. In this study, we developed a cross-platform MATLAB toolbox named "Diffusion Connectome Pipeline" (DCP) for automatically constructing brain structural networks and calculating topological attributes of the networks. The toolbox integrates a few developed packages, including FSL, Diffusion Toolkit, SPM, Camino, MRtrix3, and MRIcron. It can process raw dMRI data collected from any number of participants, and it is also compatible with preprocessed files from public datasets such as HCP and UK Biobank. Moreover, a friendly graphical user interface allows users to configure their processing pipeline without any programming. To prove the capacity and validity of the DCP, two tests were conducted with using DCP. The results showed that DCP can reproduce the findings in our previous studies. However, there are some limitations of DCP, such as relying on MATLAB and being unable to fixel-based metrics weighted network. Despite these limitations, overall, the DCP software provides a standardized, fully automated computational workflow for white matter network construction and analysis, which is beneficial for advancing future human brain connectomics application research.

A systematic literature review of fMRI and EEG resting-state functional connectivity in Dementia with Lewy Bodies: Underlying mechanisms, clinical manifestation, and methodological considerations.

Previous studies suggest that there may be important links between functional connectivity, disease mechanisms underpinning the Dementia with Lewy Body (DLB) and the key clinical symptoms, but the exact relationship remains unclear. We performed a systematic literature review to address this gap by summarising the research findings while critically considering the impact of methodological differences on findings. The main methodological choices of fMRI articles included data-driven, seed-based or regions of interest approaches, or their combinations. Most studies focused on examining large-scale resting-state networks, which revealed a consistent decrease in connectivity and some associations with non-cognitive symptoms. Although the inter-network connectivity showed mixed results, the main finding is consistent with theories positing disconnection between visual and attentional areas of the brain implicated in the aetiology of psychotic symptoms in the DLB. The primary methodological choice of EEG studies was implementing the phase lag index and using graph theory. The EEG studies revealed a consistent decrease in connectivity on alpha and beta frequency bands. While the overall trend of findings showed decreased connectivity, more subtle changes in the directionality of connectivity were observed when using a hypothesis-driven approach. Problems with cognition were also linked with greater functional connectivity disturbances. In summary, connectivity measures can capture brain disturbances in the DLB and remain crucial in uncovering the causal relationship between the networks' disorganisation and underlying mechanisms resulting in psychotic, motor, and cognitive symptoms of the DLB.

Differences in Grey Matter Concentrations and Functional Connectivity between Young Carriers and Non-Carriers of the APOE ε4 Genotype.

Background: The pathophysiology of Alzheimer's disease (AD) may begin developing years or even decades prior to the manifestation of its first symptoms. The APOE ε4 genotype is a prominent genetic risk for AD that has been found to be associated with brain changes across the lifespan since early adulthood. Thus, studying brain changes that may occur in young adults with an APOE ε4 status is highly relevant. Objective: Examine potential differences in grey matter (GM) and functional connectivity (FC) in brains of cognitively healthy young APOE ε4 carriers and non-carriers, denoted here as ε4(+) and ε4(-), respectively. Methods: Three Tesla magnetic resonance imaging (MRI) brain scans were acquired from cognitively healthy young participants aged approximately 20 years (n = 151). Voxel-based morphometry (VBM) analysis was employed to identify potential structural differences in GM between ε4(+) and ε4(-). In a subsequent seed-based connectivity (SBC) analysis, brain regions that structurally differed in the VBM analysis were considered as seeds and correlated with all the remaining voxels across the brains to then measure the differences in FC between groups. Results: The VBM analysis suggested that ε4(+) (n = 28) had greater GM densities relative to ε4(-) (n = 123) in the left hippocampus and the left posterior insula (puncorr < 0.001). However, the effect did not survive the correction for multiple comparisons, suggesting minimal structural differences in this age range. In contrast, the SBC analysis indicated that ε4(+) exhibited significantly decreased FC between the left hippocampus and areas of the left middle temporal gyrus (n = 27) compared to ε4(-) (n = 102). These results remained significant after multiple comparisons (pFDR < 0.05). Lastly, no statistically significant differences in FC between groups were observed for the left insular seed (pFDR > 0.05). Discussion: These results suggest early structural and functional brain changes associated with the APOE ε4 genotype on young adults. Yet, they must be cautiously interpreted and contrasted with both older adults with genetic risk for AD and patients diagnosed with AD.

The effects of APOEe4 allele on cerebral structure, function, and related interactions with cognition in young adults.

In the last decade, extensive research has emerged into understanding the impact of risk factors for Alzheimer's Disease (AD) on brain in pre-symptomatic stages. We investigated the neuroimaging correlates of the APOEe4 genetic risk factor for AD in young adulthood, its relationship with cognition, and potential effects of other variables on the findings. While conventional volumetric analyses revealed no consistent differences, more sophisticated analyses identified subtle structural differences between APOEe4 carriers and non-carriers. Findings from diffusion studies were limited, but functional studies demonstrated consistent alterations in connectivity and activity. The complex relationship between APOE genotype, neuroimaging variables, and cognition revealed no consensus on the directionality of findings. Methodological choices, including analytical approaches, sample size, and the influence of other genes, gender, and ethnicity, varied across studies, impacting comparability and generalizability. Recommendations for future research include multimodal and longitudinal imaging, standardisation of pipelines, advanced analytical techniques, and collaborative data pooling.

Genetic risk factors of Alzheimer's Disease disrupt resting-state functional connectivity in cognitively intact young individuals.

BACKGROUND: Past evidence shows that changes in functional brain connectivity in multiple resting-state networks occur in cognitively healthy individuals who have non-modifiable risk factors for Alzheimer's Disease. Here, we aimed to investigate how those changes differ in early adulthood and how they might relate to cognition. METHODS: We investigated the effects of genetic risk factors of AD, namely APOEe4 and MAPTA alleles, on resting-state functional connectivity in a cohort of 129 cognitively intact young adults (aged 17-22 years). We used Independent Component Analysis to identify networks of interest, and Gaussian Random Field Theory to compare connectivity between groups. Seed-based analysis was used to quantify inter-regional connectivity strength from the clusters that exhibited significant between-group differences. To investigate the relationship with cognition, we correlated the connectivity and the performance on the Stroop task. RESULTS: The analysis revealed a decrease in functional connectivity in the Default Mode Network (DMN) in both APOEe4 carriers and MAPTA carriers in comparison with non-carriers. APOEe4 carriers showed decreased connectivity in the right angular gyrus (size = 246, p-FDR = 0.0079), which was correlated with poorer performance on the Stroop task. MAPTA carriers showed decreased connectivity in the left middle temporal gyrus (size = 546, p-FDR = 0.0001). In addition, we found that only MAPTA carriers had a decreased connectivity between the DMN and multiple other brain regions. CONCLUSIONS: Our findings indicate that APOEe4 and MAPTA alleles modulate brain functional connectivity in the brain regions within the DMN in cognitively intact young adults. APOEe4 carriers also showed a link between connectivity and cognition.

Resting-state brain connectivity in healthy young and middle-aged adults at risk of progressive Alzheimer's disease.

Functional brain connectivity of the resting-state networks has gained recent attention as a possible biomarker of Alzheimer's Disease (AD). In this paper, we review the literature of functional connectivity differences in young adults and middle-aged cognitively intact individuals with non-modifiable risk factors of AD (n = 17). We focus on three main intrinsic resting-state networks: The Default Mode network, Executive network, and the Salience network. Overall, the evidence from the literature indicated early vulnerability of functional connectivity across different at-risk groups, particularly in the Default Mode Network. While there was little consensus on the interpretation on directionality, the topography of the findings showed frequent overlap across studies, especially in regions that are characteristic of AD (i.e., precuneus, posterior cingulate cortex, and medial prefrontal cortex areas). We conclude that while resting-state functional connectivity markers have great potential to identify at-risk individuals, implementing more data-driven approaches, further longitudinal and cross-validation studies, and the analysis of greater sample sizes are likely to be necessary to fully establish the effectivity and utility of resting-state network-based analyses.