Effects of different smoothing on global and regional resting functional connectivity

Progressive alterations of resting-state hypothalamic dysconnectivity in schizophrenia

BACKGROUND

The hypothalamus may be involved in the pathogenesis of schizophrenia. Investigating hypothalamus dysfunction in schizophrenia and probing how it is related to symptoms and responds to antipsychotic medication is crucial for understanding the potential mechanism of hypothalamus dysfunction under the long-term illness.

METHODS

We recruited 216 patients with schizophrenia, including 140 antipsychotic-naïve first-episode patients (FES, including 44 patients with 1-year follow-up data), 76 chronically treated schizophrenia (CTS), and 210 healthy controls (HC). Hypothalamic seed-based functional connectivity (FC) was calculated and compared among the FES, CTS, and HC groups using analysis of covariance. Exploratory analysis was conducted between the FES patients at baseline and after 1-year follow-up. Significantly altered hypothalamic FCs were then related to clinical symptomology, while age- and illness-related regression analyses were also conducted and compared between diagnostic groups.

RESULTS

The FES patients showed decreased hypothalamic FCs with the midbrain and right thalamus, whereas the CTS patients showed more severe decreased hypothalamic FCs with the midbrain, right thalamus, left putamen, right caudate, and bilateral anterior cingulate cortex compared to HCs. These abnormalities were not correlated to the symptomology or illness duration, or not reversed by the antipsychotic treatment. Age-related hypothalamic FC decrease was also identified in the abovementioned regions, and a faster age-related decline of the hypothalamic FC was observed with the left putamen and bilateral anterior cingulate cortex.

CONCLUSION

Age-related hypothalamic FC decrease extends the functional alterations that characterize the neurodegenerative nature of schizophrenia. Future studies are required to further probe the hormonal or endocrinal underpinnings of such alterations and trace the precise progressive trajectories.

The multiverse of data preprocessing and analysis in graph-based fMRI: A systematic literature review of analytical choices fed into a decision support tool for informed analysis

The large number of different analytical choices used by researchers is partly responsible for the challenge of replication in neuroimaging studies. For an exhaustive robustness analysis, knowledge of the full space of analytical options is essential. We conducted a systematic literature review to identify the analytical decisions in functional neuroimaging data preprocessing and analysis in the emerging field of cognitive network neuroscience. We found 61 different steps, with 17 of them having debatable parameter choices. Scrubbing, global signal regression, and spatial smoothing are among the controversial steps. There is no standardized order in which different steps are applied, and the parameter settings within several steps vary widely across studies. By aggregating the pipelines across studies, we propose three taxonomic levels to categorize analytical choices: 1) inclusion or exclusion of specific steps, 2) parameter tuning within steps, and 3) distinct sequencing of steps. We have developed a decision support application with high educational value called METEOR to facilitate access to the data in order to design well-informed robustness (multiverse) analysis.

Amygdala functional connectivity in borderline personality disorder

Borderline personality disorder (BPD) is characterised by structural and functional brain alterations. Yet, there is little data on functional connectivity (FC) across different levels of brain networks and parameters. In this study, we applied a multi-level approach to analyse abnormal functional connectivity. We analysed resting-state functional magnetic resonance imaging (fMRI) data sets of 69 subjects: 17 female BPD patients and 51 age-matched psychiatrically healthy female controls. fMRI was analysed using CONN toolbox including: a) seed-based FC analysis of amygdala connectivity, b) independent component analysis (ICA) based network analysis of intra- and inter-network FC of selected resting-state networks (DMN, SN, FPN), as well as c) graph-theory based measures of network-level characteristics. We show group-level seed FC differences with higher amygdala to contralateral (superior) occipital cortex connectivity in BPD, which correlated with schema-therapy derived measures of symptoms/traits across the entire cohort. While there was no significant group effect on DMN, SN, or FPN intra-network or inter-network FC, we show a significant group difference for local efficiency and cluster coefficient for a DMN-linked cerebellum cluster. Our findings demonstrate BPD-linked changes in FC across multiple levels of observation, which supports a multi-level analysis for future studies to consider different aspects of functional connectome alterations.

A Comprehensive and Broad Approach to Resting-State Functional Connectivity in Adult Patients with Mild Traumatic Brain Injury

BACKGROUND AND PURPOSE

Several recent works using resting-state fMRI suggest possible alterations of resting-state functional connectivity after mild traumatic brain injury. However, the literature is plagued by various analysis approaches and small study cohorts, resulting in an inconsistent array of reported findings. In this study, we aimed to investigate differences in whole-brain resting-state functional connectivity between adult patients with mild traumatic brain injury within 1 month of injury and healthy control subjects using several comprehensive resting-state functional connectivity measurement methods and analyses.

MATERIALS AND METHODS

A total of 123 subjects (72 patients with mild traumatic brain injury and 51 healthy controls) were included. A standard fMRI preprocessing pipeline was used. ROI/seed-based analyses were conducted using 4 standard brain parcellation methods, and the independent component analysis method was applied to measure resting-state functional connectivity. The fractional amplitude of low-frequency fluctuations was also measured. Group comparisons were performed on all measurements with appropriate whole-brain multilevel statistical analysis and correction.

RESULTS

There were no significant differences in age, sex, education, and hand preference between groups as well as no significant correlation between all measurements and these potential confounders. We found that each resting-state functional connectivity measurement revealed various regions or connections that were different between groups. However, after we corrected for multiple comparisons, the results showed no statistically significant differences between groups in terms of resting-state functional connectivity across methods and analyses.

CONCLUSIONS

Although previous studies point to multiple regions and networks as possible mild traumatic brain injury biomarkers, this study shows that the effect of mild injury on brain resting-state functional connectivity has not survived after rigorous statistical correction. A further study using subject-level connectivity analyses may be necessary due to both subtle and variable effects of mild traumatic brain injury on brain functional connectivity across individuals.

Effective connectivity between deep brain stimulation targets in individuals with treatment-resistant depression

The therapeutic effect of deep brain stimulation on patients with treatment-resistant depression is strongly dependent on the connectivity of the stimulation region with other regions associated with depression. The aims of this study are to characterize the effective connectivity between the brain regions playing important roles in depression and further investigate the underlying pathophysiological mechanisms of treatment-resistant depression and the mechanisms involving deep brain stimulation. Thirty-three individuals with treatment-resistant depression and 29 healthy control subjects were examined. All subjects underwent resting-state functional MRI scanning. The coupling parameters reflecting the causal interactions among deep brain stimulation targets and medial prefrontal cortex were estimated using spectral dynamic causal modelling. Our results showed that compared to the healthy control subjects, in the left hemisphere of treatment-resistant depression patients, the nucleus accumbens was inhibited by the inferior thalamic peduncle and excited the ventral caudate and the subcallosal cingulate gyrus, which in turn excited the lateral habenula. In the right hemisphere, the lateral habenula inhibited the ventral caudate and the nucleus accumbens, both of which inhibited the inferior thalamic peduncle, which in turn inhibited the cingulate gyrus. The ventral caudate excited the lateral habenula and the cingulate gyrus, which excited the medial prefrontal cortex. Furthermore, these effective connectivity links varied between males and females, and the left and right hemispheres. Our findings suggest that intrinsic excitatory/inhibitory connections between deep brain stimulation targets are impaired in treatment-resistant depression patients, and that these connections are sex dependent and hemispherically lateralized. This knowledge can help to better understand the underlying mechanisms of treatment-resistant depression, and along with tractography, structural imaging, and other relevant clinical information, may assist to determine the appropriate region for deep brain stimulation therapy in each treatment-resistant depression patient.

The Cerebellum's Orchestra: Understanding the Functional Connectivity of Its Lobes and Deep Nuclei in Coordination and Integration of Brain Networks

The cerebellum, a crucial brain region, significantly contributes to various brain functions. Although it occupies a small portion of the brain, it houses nearly half of the neurons in the nervous system. Previously thought to be solely involved in motor activities, the cerebellum has since been found to play a role in cognitive, sensory, and associative functions. To further elucidate the intricate neurophysiological characteristics of the cerebellum, we investigated the functional connectivity of cerebellar lobules and deep nuclei with 8 major functional brain networks in 198 healthy subjects. Our findings revealed both similarities and differences in the functional connectivity of key cerebellar lobules and nuclei. Despite robust functional connectivity among these lobules, our results demonstrated that they exhibit heterogeneous functional integration with different functional networks. For instance, lobules 4, 5, 6, and 8 were linked to sensorimotor networks, while lobules 1, 2, and 7 were associated with higher-order, non-motor, and complex functional networks. Notably, our study uncovered a lack of functional connectivity in lobule 3, strong connections between lobules 4 and 5 with the default mode networks, and connections between lobules 6 and 8 with the salience, dorsal attention, and visual networks. Additionally, we found that cerebellar nuclei, particularly the dentate cerebellar nuclei, were connected to sensorimotor, salience, language, and default-mode networks. This study provides valuable insights into the diverse functional roles of the cerebellum in cognitive processing.

Resting-state functional connectivity correlates of antipsychotic treatment in unmedicated schizophrenia

BACKGROUND

Antipsychotics may modulate the resting state functional connectivity(rsFC) to improve clinical symptoms in schizophrenia(Sz). Existing literature has potential confounders like past medication effects and evaluating preselected regions/networks. We aimed to evaluate connectivity pattern changes with antipsychotics in unmedicated Sz using Multivariate pattern analysis(MVPA), a data-driven technique for whole-brain connectome analysis.

METHODS

Forty-seven unmedicated patients with Sz(DSM-IV-TR) underwent clinical evaluation and neuroimaging at baseline and after 3-months of antipsychotic treatment. Resting-state functional MRI was analysed using group-MVPA to derive 5-components. The brain region with significant connectivity pattern changes with antipsychotics was identified, and post-hoc seed-to-voxel analysis was performed to identify connectivity changes and their association with symptom changes.

RESULTS

Connectome-MVPA analysis revealed the connectivity pattern of a cluster localised to left anterior cingulate and paracingulate gyri (ACC/PCG) (peak coordinates:x = -04,y = +30,z = +26;k = 12;cluster-p_FWE=0.002) to differ significantly after antipsychotics. Specifically, its connections with clusters of precuneus/posterior cingulate cortex(PCC) and left inferior temporal gyrus(ITG) correlated with improvement in positive and negative symptoms scores, respectively.

CONCLUSION

ACC/PCG, a hub of the default mode network, seems to mediate the antipsychotic effects in unmedicated Sz. Evaluating causality models with data from randomised controlled design using the MVPA approach would further enhance our understanding of therapeutic connectomics in Sz.

Functional connectivity of sub-cortical brain regions: disparities and similarities

Sub-cortical grey matter structures, such as the putamen, pallidum, caudate, thalamus, amygdala and hippocampus, play substantial roles in both simple and complex brain functions, including regulation of pleasure and emotions; control of movements; learning; decision-making; language development; and sensory, cognitive, social and other higher-order functions. Most of these regions act as information hubs for the nervous system, relaying and controlling the flow of information to various portions of the brain. To further understand the complex neurophysiological characteristics of sub-cortical areas, the aim of this study was to investigate the functional integrations of six sub-cortical areas to different major functional brain networks. One hundred ninety-eight healthy individuals were examined using resting-state functional MRI. The seeds identified in this study were six sub-cortical deep grey matter regions, namely putamen, pallidum, caudate, thalamus, amygdala and hippocampus. The analysis indicated that the link between the sub-cortical regions and some functional brain networks was similar in some aspects, but there were disparities in the mechanism underlying such a link and in the existence of functional connections between these regions and networks. Despite the substantial functional connectivity linkages between the sub-cortical regions, discrepancies were still noted. On the basis of the connections to the majority of the major brain networks, this study demonstrated the essential functional roles and involvements of the sub-cortical regions. This finding is consistent with an earlier report that revealed a substantial role of the sub-cortical regions in several brain functions.

Empirical evaluation of human fetal fMRI preprocessing steps

Increased study and methodological innovation have led to growth in the field of fetal brain fMRI. An important gap yet to be addressed is optimization of fetal fMRI preprocessing. Rapid developmental changes, imaged within the maternal compartment using an abdominal coil, introduce novel constraints that challenge established methods used in adult fMRI. This study evaluates the impact of (1) normalization to a group mean-age template versus normalization to an age-matched template; (2) independent components analysis (ICA) denoising at two criterion thresholds; and (3) smoothing using three kernel sizes. Data were collected from 121 fetuses (25-39 weeks, 43.8% female). Results indicate that the mean age template is superior in older fetuses, but less optimal in younger fetuses. ICA denoising at a more stringent threshold is superior to less stringent denoising. A larger smoothing kernel can enhance cross-hemisphere functional connectivity. Overall, this study provides improved understanding of the impact of specific steps on fetal image quality. Findings can be used to inform a common set of best practices for fetal fMRI preprocessing.

Lag-Optimized Blood Oxygenation Level Dependent Cerebrovascular Reactivity Estimates Derived From Breathing Task Data Have a Stronger Relationship With Baseline Cerebral Blood Flow

Cerebrovascular reactivity (CVR), an important indicator of cerebrovascular health, is commonly studied with the Blood Oxygenation Level Dependent functional MRI (BOLD-fMRI) response to a vasoactive stimulus. Theoretical and empirical evidence suggests that baseline cerebral blood flow (CBF) modulates BOLD signal amplitude and may influence BOLD-CVR estimates. We address how acquisition and modeling choices affect the relationship between baseline cerebral blood flow (bCBF) and BOLD-CVR: whether BOLD-CVR is modeled with the inclusion of a breathing task, and whether BOLD-CVR amplitudes are optimized for hemodynamic lag effects. We assessed between-subject correlations of average GM values and within-subject spatial correlations across cortical regions. Our results suggest that a breathing task addition to a resting-state acquisition, alongside lag-optimization within BOLD-CVR modeling, can improve BOLD-CVR correlations with bCBF, both between- and within-subjects, likely because these CVR estimates are more physiologically accurate. We report positive correlations between bCBF and BOLD-CVR, both between- and within-subjects. The physiological explanation of this positive correlation is unclear; research with larger samples and tightly controlled vasoactive stimuli is needed. Insights into what drives variability in BOLD-CVR measurements and related measurements of cerebrovascular function are particularly relevant when interpreting results in populations with altered vascular and/or metabolic baselines or impaired cerebrovascular reserve.

Topography of hippocampal connectivity with sensorimotor cortex revealed by optimizing smoothing kernel and voxel size

Studies of the hippocampus use smaller voxel sizes and smoothing kernels than cortical activation studies, typically using a multivoxel seed with specified radius for connectivity analysis. This study identified optimal processing parameters for evaluating hippocampal connectivity with sensorimotor cortex (SMC), comparing effectiveness by varying parameters during both activation and connectivity analysis. Using both 3mm and 4mm isovoxels, smoothing kernels of 0-10mm were evaluated on the amplitude and extent of motor activation and hippocampal connectivity with SMC. Psychophysiological interactions (PPI) identified hippocampal connectivity with SMC during volitional movements, and connectivity effects from multivoxel seeds were compared with alternate methods; a structural seed represented the mean connectivity map from all voxels within a region, whereas a functional seed represented the regional voxel with maximal SMC connectivity. With few exceptions, the same parameters were optimal for activation and connectivity. Larger isovoxels showed larger activation volumes in both SMC and the hippocampus; connectivity volumes from structural seeds were also larger, except from the posterior hippocampus. Regardless of voxel size, the 10mm smoothing kernel generated larger activation and connectivity volumes from structural seeds, as well as larger beta estimates at connectivity maxima; structural seeds also produced larger connectivity volumes than multivoxel seeds. Functional seeds showed lesser effects from voxel size and smoothing kernels. Optimal parameters revealed topography in structural seed connectivity along both the longitudinal axis and mediolateral axis of the hippocampus. These results indicate larger voxels and smoothing kernels can improve sensitivity for detecting both cortical activation and hippocampal connectivity.

The Influence of Spatial Smoothing Kernel Size on the Temporal Features of Intrinsic Connectivity Networks

Spatial smoothing is a common preprocessing step in the analysis of functional magnetic resonance imaging (fMRI) data. However, little is known about the effect of spatial smoothing kernel size on the temporal properties of functional brain networks. This study presents a pilot investigation on the influence of spatial smoothing using independent component analysis (ICA) as a data-driven technique to extract functional networks of brain in the form of intrinsic connectivity networks (ICNs). BOLD resting state fMRI data were collected from 22 healthy subjects on a 3.0 T MRI scanner. 3D spatial smoothing was applied using a Gaussian filter with full width at half maximum (FWHM) kernel sizes of 4 mm, 8 mm, and 12 mm in the preprocessing step. Group ICA with the Infomax algorithm was performed at 75-IC decomposition. Network temporal features including functional network connectivity (FNC) and BOLD power spectra were calculated and compared pairwise using a paired t-test with a false discovery rate (FDR) correction for multiple comparisons. Results revealed robust effects of smoothing kernel size on FNC measures of most ICNs, largely indicating a decrease in inter-network connectivity as the smoothing kernel size decreased. Power spectra analysis showed increased high-frequency power (0.15 - 0.25 Hz) but decreased low-frequency power (0.01 - 0.10 Hz) with a decrease in the smoothing kernel size (corrected p< 0.01). These findings provide a preliminary observation on the effect of spatial smoothing kernel size on the FNC and power spectra.

Investigating the sub-regions of the superior parietal cortex using functional magnetic resonance imaging connectivity

Objectives

Traditionally, the superior parietal lobule (SPL) is usually investigated as one region of interest, particularly in functional magnetic resonance imaging (fMRI) studies. However, cytoarchitectonic analysis has shown that the SPL has a complex, heterogeneous topology that comprises more than seven sub-regions. Since previous studies have shown how the SPL is significantly involved in different neurological functions—such as visuomotor, cognitive, sensory, higher order, working memory and attention—this study aims to investigate whether these cytoarchitecturally different sub-regions have different functional connectivity to different functional brain networks.

Methods

This study examined 198 healthy subjects using resting-state fMRI and investigated the functional connectivity of seven sub-regions of the SPL to eight regional functional networks.

Results

The findings showed that most of the seven sub-regions were functionally connected to these targeted networks and that there are differences between these sub-regions and their functional connectivity patterns. The most consistent functional connectivity was observed with the visual and attention networks. There were also clear functional differences between Brodmann area (BA) 5 and BA7. BA5, with its three sub-regions, had strong functional connectivity to both the sensorimotor and salience networks.

Conclusion

These findings have enhanced our understanding of the functional organisations of the complexity of the SPL and its varied topology and also provide clear evidence of the functional patterns and involvements of the SPL in major brain functions.