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1.  Resting-state fMRI as a biomarker for Alzheimer's disease? 
Previous work indicates that resting-state functional magnetic resonance imaging (fMRI) is sensitive to functional brain changes related to Alzheimer's disease (AD) pathology across the clinical spectrum. Cross-sectional studies have found functional connectivity differences in the brain's default mode network in aging, mild cognitive impairment, and AD. In addition, two recent longitudinal studies have shown that functional connectivity changes track AD progression. This earlier work suggests that resting-state fMRI may be a promising biomarker for AD. However, some key issues still need to be addressed before resting-state fMRI can be successfully applied clinically. In a previous issue of Alzheimer's Research & Therapy, Vemuri and colleagues discuss the use of resting-state fMRI in the study of AD. In this commentary, I will highlight and expand upon some of their main conclusions.
doi:10.1186/alzrt106
PMCID: PMC3334541  PMID: 22423634
2.  Stability of Whole Brain and Regional Network Topology within and between Resting and Cognitive States 
PLoS ONE  2013;8(8):e70275.
Background
Graph-theory based analyses of resting state functional Magnetic Resonance Imaging (fMRI) data have been used to map the network organization of the brain. While numerous analyses of resting state brain organization exist, many questions remain unexplored. The present study examines the stability of findings based on this approach over repeated resting state and working memory state sessions within the same individuals. This allows assessment of stability of network topology within the same state for both rest and working memory, and between rest and working memory as well.
Methodology/Principal Findings
fMRI scans were performed on five participants while at rest and while performing the 2-back working memory task five times each, with task state alternating while they were in the scanner. Voxel-based whole brain network analyses were performed on the resulting data along with analyses of functional connectivity in regions associated with resting state and working memory. Network topology was fairly stable across repeated sessions of the same task, but varied significantly between rest and working memory. In the whole brain analysis, local efficiency, Eloc, differed significantly between rest and working memory. Analyses of network statistics for the precuneus and dorsolateral prefrontal cortex revealed significant differences in degree as a function of task state for both regions and in local efficiency for the precuneus. Conversely, no significant differences were observed across repeated sessions of the same state.
Conclusions/Significance
These findings suggest that network topology is fairly stable within individuals across time for the same state, but also fluid between states. Whole brain voxel-based network analyses may prove to be a valuable tool for exploring how functional connectivity changes in response to task demands.
doi:10.1371/journal.pone.0070275
PMCID: PMC3734135  PMID: 23940554
3.  Clinical Applications of Resting State Functional Connectivity 
During resting conditions the brain remains functionally and metabolically active. One manifestation of this activity that has become an important research tool is spontaneous fluctuations in the blood oxygen level-dependent (BOLD) signal of functional magnetic resonance imaging (fMRI). The identification of correlation patterns in these spontaneous fluctuations has been termed resting state functional connectivity (fcMRI) and has the potential to greatly increase the translation of fMRI into clinical care. In this article we review the advantages of the resting state signal for clinical applications including detailed discussion of signal to noise considerations. We include guidelines for performing resting state research on clinical populations, outline the different areas for clinical application, and identify important barriers to be addressed to facilitate the translation of resting state fcMRI into the clinical realm.
doi:10.3389/fnsys.2010.00019
PMCID: PMC2893721  PMID: 20592951
fMRI; fcMRI; neurological disease; psychiatric disease; brain; spontaneous activity; intrinsic activity
4.  The Influence of the Amplitude of Low-Frequency Fluctuations on Resting-State Functional Connectivity 
Studies of brain functional connectivity have provided a better understanding of organization and integration of large-scale brain networks. Functional connectivity using resting-state functional magnetic resonance imaging (fMRI) is typically based upon the correlations of the low-frequency fluctuation of fMRI signals. Reproducible spatial maps in the brain have also been observed using the amplitude of low-frequency fluctuations (ALFF) in resting-state. However, little is known about the influence of the ALFF on the functional connectivity measures. In the present study, we analyzed resting-state fMRI data on 79 healthy old individuals. Spatial independent component analysis and regions of interest (ROIs) based connectivity analysis were performed to obtain measures of functional connectivity. ALFF maps were also calculated. First, voxel-matched inter-subject correlations were computed between back-reconstructed IC and ALFF maps. For all the resting-state networks, there was a consistent correlation between ALFF variability and network strengths (within regions that had high IC strengths). Next, inter-subject variance of correlations across 160 functionally defined ROIs were correlated with the corresponding ALFF variance. The connectivity of several ROIs to other regions were more likely to correlate with its own regional ALFF. These regions were mainly located in the anterior cingulate cortex, medial prefrontal cortex, precuneus, insula, basal ganglia, and thalamus. These associations may suggest a functional significance of functional connectivity modulations. Alternatively, the fluctuation amplitudes may arise from physiological noises, and therefore, need to be controlled when studying resting-state functional connectivity.
doi:10.3389/fnhum.2013.00118
PMCID: PMC3613753  PMID: 23565090
ALFF; basal ganglia; brain network; default mode network; independent component analysis; insula; thalamus
5.  Modulation of Temporally Coherent Brain Networks Estimated Using ICA at Rest and During Cognitive Tasks 
Human brain mapping  2008;29(7):828-838.
Brain regions which exhibit temporally coherent fluctuations, have been increasingly studied using functional magnetic resonance imaging (fMRI). Such networks are often identified in the context of an fMRI scan collected during rest (and thus are called “resting state networks”); however, they are also present during (and modulated by) the performance of a cognitive task. In this article, we will refer to such networks as temporally coherent networks (TCNs). Although there is still some debate over the physiological source of these fluctuations, TCNs are being studied in a variety of ways. Recent studies have examined ways TCNs can be used to identify patterns associated with various brain disorders (e.g. schizophrenia, autism or Alzheimer’s disease). Independent component analysis (ICA) is one method being used to identify TCNs. ICA is a data driven approach which is especially useful for decomposing activation during complex cognitive tasks where multiple operations occur simultaneously. In this article we review recent TCN studies with emphasis on those that use ICA. We also present new results showing that TCNs are robust, and can be consistently identified at rest and during performance of a cognitive task in healthy individuals and in patients with schizophrenia. In addition, multiple TCNs show temporal and spatial modulation during the cognitive task versus rest. In summary, TCNs show considerable promise as potential imaging biological markers of brain diseases, though each network needs to be studied in more detail.
doi:10.1002/hbm.20581
PMCID: PMC2649823  PMID: 18438867
fMRI; auditory oddball; independent component analysis; P3; schizophrenia
6.  Understanding the Pathophysiology of Alzheimer's Disease and Mild Cognitive Impairment: A Mini Review on fMRI and ERP Studies 
The prevalence of Alzheimer's disease (AD) is predicted to increase rapidly in the coming decade, highlighting the importance of early detection and intervention in patients with AD and mild cognitive impairment (MCI). Recently, remarkable advances have been made in the application of neuroimaging techniques in investigations of AD and MCI. Among the various neuroimaging techniques, functional magnetic resonance imaging (fMRI) has many potential advantages, noninvasively detecting alterations in brain function that may be present very early in the course of AD and MCI. In this paper, we first review task-related and resting-state fMRI studies on AD and MCI. We then present our recent fMRI studies with additional event-related potential (ERP) experiments during a motion perception task in MCI. Our results indicate that fMRI, especially when combined with ERP recording, can be useful for detecting spatiotemporal functional changes in AD and MCI patients.
doi:10.1155/2012/719056
PMCID: PMC3135099  PMID: 21773027
7.  Large-Scale Spontaneous Fluctuations and Correlations in Brain Electrical Activity Observed with Magnetoencephalography 
NeuroImage  2010;51(1):102-111.
Knowledge about the intrinsic functional architecture of the human brain has been greatly expanded by the extensive use of resting-state functional magnetic resonance imaging (fMRI). However, the neurophysiological correlates and origins of spontaneous fMRI signal changes remain poorly understood. In the present study, we characterized the power modulations of spontaneous magnetoencephalography (MEG) rhythms recorded from human subjects during wakeful rest (with eyes open and eyes closed) and light sleep. Through spectral, correlation and coherence analyses, we found that resting-state MEG rhythms demonstrated ultraslow (<0.1 Hz) spontaneous power modulations that synchronized over a large spatial distance, especially between bilaterally homologous regions in opposite hemispheres. These observations are in line with the known spatio-temporal properties of spontaneous fMRI signals, and further suggest that the coherent power modulation of spontaneous rhythmic activity reflects the electrophysiological signature of the large-scale functional networks previously observed with fMRI in the resting brain.
doi:10.1016/j.neuroimage.2010.01.092
PMCID: PMC2847019  PMID: 20123024
Functional Connectivity; Resting State; Magnetoencephalography; Band-limited Power; Correlation; Coherence
8.  The Resting Brain: Unconstrained yet Reliable 
Cerebral Cortex (New York, NY)  2009;19(10):2209-2229.
Recent years have witnessed an upsurge in the usage of resting-state functional magnetic resonance imaging (fMRI) to examine functional connectivity (fcMRI), both in normal and pathological populations. Despite this increasing popularity, concerns about the psychologically unconstrained nature of the “resting-state” remain. Across studies, the patterns of functional connectivity detected are remarkably consistent. However, the test–retest reliability for measures of resting state fcMRI measures has not been determined. Here, we quantify the test–retest reliability, using resting scans from 26 participants at 3 different time points. Specifically, we assessed intersession (>5 months apart), intrasession (<1 h apart), and multiscan (across all 3 scans) reliability and consistency for both region-of-interest and voxel-wise analyses. For both approaches, we observed modest to high reliability across connections, dependent upon 3 predictive factors: 1) correlation significance (significantly nonzero > nonsignificant), 2) correlation valence (positive > negative), and 3) network membership (default mode > task positive network). Short- and long-term measures of the consistency of global connectivity patterns were highly robust. Finally, hierarchical clustering solutions were highly reproducible, both across participants and sessions. Our findings provide a solid foundation for continued examination of resting state fcMRI in typical and atypical populations.
doi:10.1093/cercor/bhn256
PMCID: PMC3896030  PMID: 19221144
fMRI; intraclass correlations; reliability; resting-state functional connectivity; test–retest
9.  Functional Magnetic Resonance Imaging in Narcolepsy and the Kleine–Levin Syndrome 
This work aims at reviewing the present state of the art when it comes to understanding the pathophysiology of narcolepsy and the Kleine–Levin syndrome (KLS) from a neuroimaging point of view. This work also aims at discussing future perspectives of functional neuroimaging in these sleep disorders. We focus on functional magnetic resonance imaging (fMRI), which is a technique for in vivo measurements of brain activation in neuronal circuitries under healthy and pathological conditions. fMRI has significantly increased the knowledge on the affected neuronal circuitries in narcolepsy and the Kleine–Levin syndrome. It has been shown that narcolepsy is accompanied with disturbances of the emotional and the closely related reward systems. In the Kleine Levin syndrome, fMRI has identified hyperactivation of the thalamus as a potential biomarker that could be used in the diagnostic procedure. The fMRI findings in both narcolepsy and the Kleine–Levin syndrome are in line with previous structural and functional imaging studies. We conclude that fMRI in combination with multi-modal imaging can reveal important details about the pathophysiology in narcolepsy and the Kleine–Levin syndrome. In the future, fMRI possibly gives opportunities for diagnostic support and prediction of treatment response in individual patients.
doi:10.3389/fneur.2014.00105
PMCID: PMC4069720
functional magnetic resonance imaging; narcolepsy; hypersomnia; Kleine–Levin syndrome; sleep; ascending arousal system; hypothalamus; thalamus
10.  Association of the interleukin 1 beta gene and brain spontaneous activity in amnestic mild cognitive impairment 
Purpose
The inflammatory response has been associated with the pathogenesis of Alzheimer’s disease (AD). The purpose of this study is to determine whether the rs1143627 polymorphism of the interleukin-1 beta (IL-1β) gene moderates functional magnetic resonance imaging (fMRI)-measured brain regional activity in amnestic mild cognitive impairment (aMCI).
Methods
Eighty older participants (47 with aMCI and 33 healthy controls) were recruited for this study. All of the participants were genotyped for variant rs1143627 in the IL1B gene and were scanned using resting-state fMRI. Brain activity was assessed by amplitude of low-frequency fluctuation (ALFF).
Results
aMCI patients had abnormal ALFF in many brain regions, including decreases in the inferior frontal gyrus, the superior temporal lobe and the middle temporal lobe, and increases in the occipital cortex (calcarine), parietal cortex (Pcu) and cerebellar cortex. The regions associated with an interaction of group X genotypes of rs1143627 C/T were the parietal cortex (left Pcu), frontal cortex (left superior, middle, and medial gyrus, right anterior cingulum), occipital cortex (left middle lobe, left cuneus) and the bilateral posterior lobes of the cerebellum. Regarding the behavioral significance, there were significant correlations between ALFF in different regions of the brain and with the cognitive scores of each genotype group.
Conclusions
The present study provided evidence that aMCI patients had abnormal ALFF in many brain regions. Specifically, the rs1143627 C/T polymorphism of the IL1B gene may modulate regional spontaneous brain activity in aMCI patients.
doi:10.1186/1742-2094-9-263
PMCID: PMC3541073  PMID: 23199001
Amnestic mild cognitive impairment; Functional magnetic resonance imaging; Amplitude of low-frequency fluctuation; Interleukin-1 beta; Cognition
11.  Prediction of Task-Related BOLD fMRI with Amplitude Signatures of Resting-State fMRI 
Blood oxygen contrast-functional magnetic resonance imaging (fMRI) signals are a convolution of neural and vascular components. Several studies indicate that task-related (T-fMRI) or resting-state (R-fMRI) responses linearly relate to hypercapnic task responses. Based on the linearity of R-fMRI and T-fMRI with hypercapnia demonstrated by different groups using different study designs, we hypothesized that R-fMRI and T-fMRI signals are governed by a common physiological mechanism and that resting-state fluctuation of amplitude (RSFA) should be linearly related to T-fMRI responses. We tested this prediction in a group of healthy younger humans where R-fMRI, T-fMRI, and hypercapnic (breath hold, BH) task measures were obtained form the same scan session during resting state and during performance of motor and BH tasks. Within individual subjects, significant linear correlations were observed between motor and BH task responses across voxels. When averaged over the whole brain, the subject-wise correlation between the motor and BH tasks showed a similar linear relationship within the group. Likewise, a significant linear correlation was observed between motor-task activity and RSFA across voxels and subjects. The linear rest–task (R–T) relationship between motor activity and RSFA suggested that R-fMRI and T-fMRI responses are governed by similar physiological mechanisms. A practical use of the R–T relationship is its potential to estimate T-fMRI responses in special populations unable to perform tasks during fMRI scanning. Using the R–T relationship determined from the first group of 12 healthy subjects, we predicted the T-fMRI responses in a second group of 7 healthy subjects. RSFA in both the lower and higher frequency ranges robustly predicted the magnitude of T-fMRI responses at the subject and voxel levels. We propose that T-fMRI responses are reliably predictable to the voxel level in situations where only R-fMRI measures are possible, and may be useful for assessing neural activity in task non-compliant clinical populations.
doi:10.3389/fnsys.2012.00007
PMCID: PMC3294272  PMID: 22408609
breath hold; resting-state fluctuations; BOLD; fMRI; hypercapnia; motor cortex; prediction; vascular
12.  Acupuncture Modulates Resting State Hippocampal Functional Connectivity in Alzheimer Disease 
PLoS ONE  2014;9(3):e91160.
Our objective is to clarify the effects of acupuncture on hippocampal connectivity in patients with Alzheimer disease (AD) using functional magnetic resonance imaging (fMRI). Twenty-eight right-handed subjects (14 AD patients and 14 healthy elders) participated in this study. Clinical and neuropsychological examinations were performed on all subjects. MRI was performed using a SIEMENS verio 3-Tesla scanner. The fMRI study used a single block experimental design. We first acquired baseline resting state data during the initial 3 minutes and then performed acupuncture stimulation on the Tai chong and He gu acupoints for 3 minutes. Last, we acquired fMRI data for another 10 minutes after the needle was withdrawn. The preprocessing and data analysis were performed using statistical parametric mapping (SPM5) software. Two-sample t-tests were performed using data from the two groups in different states. We found that during the resting state, several frontal and temporal regions showed decreased hippocampal connectivity in AD patients relative to control subjects. During the resting state following acupuncture, AD patients showed increased connectivity in most of these hippocampus related regions compared to the first resting state. In conclusion, we investigated the effect of acupuncture on AD patients by combing fMRI and traditional acupuncture. Our fMRI study confirmed that acupuncture at Tai chong and He gu can enhance the hippocampal connectivity in AD patients.
doi:10.1371/journal.pone.0091160
PMCID: PMC3946345  PMID: 24603951
13.  Functional Connectivity Variations in Mild Cognitive Impairment: Associations with Cognitive Function 
Participants with mild cognitive impairment (MCI) have a higher likelihood of developing Alzheimer's disease (AD) compared to those without MCI, and functional magnetic resonance neuroimaging (fMRI) used with MCI participants may prove to be an important tool in identifying early biomarkers for AD. We tested the hypothesis that functional connectivity differences exist between older adults with and without MCI using resting-state fMRI. Data were collected on over 200 participants of the Rush Memory and Aging Project, a community-based, clinical-pathological cohort study of aging. From the cohort, 40 participants were identified as having MCI, and were compared to 40 demographically matched participants without cognitive impairment. MCI participants showed lesser functional connectivity between the posterior cingulate cortex and right and left orbital frontal, right middle frontal, left putamen, right caudate, left superior temporal, and right posterior cingulate regions; and greater connectivity with right inferior frontal, left fusiform, left rectal, and left precentral regions. Furthermore, in an alternate sample of 113, connectivity values in regions of difference correlated with episodic memory and processing speed. Results suggest functional connectivity values in regions of difference are associated with cognitive function and may reflect the presence of AD pathology and increased risk of developing clinical AD.
doi:10.1017/S1355617711001299
PMCID: PMC3368801  PMID: 22005016
Mild cognitive impairment (MCI); Resting-state fMRI; Functional connectivity; Posterior cingulate cortex; Memory; Basal ganglia; Striatum
14.  Low Frequency Fluctuations Reveal Integrated and Segregated Processing among the Cerebral Hemispheres 
NeuroImage  2010;54(1):517-527.
Resting-state functional magnetic resonance imaging (fMRI) has provided a novel approach for examining interhemispheric interaction, demonstrating a high degree of functional connectivity between homotopic regions in opposite hemispheres. However, heterotopic resting state functional connectivity (RSFC) remains relatively uncharacterized. In the present study, we examine non-homotopic regions, characterizing heterotopic RSFC and comparing it to intrahemispheric RSFC, to examine the impact of hemispheric separation on the integration and segregation of processing in the brain. Resting-state fMRI scans were acquired from 59 healthy participants to examine interregional correlations in spontaneous low frequency fluctuations in BOLD signal. Using a probabilistic atlas, we correlated probability-weighted time series from 112 regions (56 per hemisphere) distributed throughout the entire cerebrum. We compared RSFC for pairings of non-homologous regions located in different hemispheres (heterotopic connectivity) to RSFC for the same pairings when located within hemisphere (intrahemispheric connectivity). For positive connections, connectivity strength was greater within each hemisphere, consistent with integrated intrahemispheric processing. However, for negative connections, RSFC strength was greater between the hemispheres, consistent with segregated interhemispheric processing. These patterns were particularly notable for connections involving frontal and heteromodal regions. The distribution of positive and negative connectivity was nearly identical within and between the hemispheres, though we demonstrated detailed regional variation in distribution. We discuss implications for leading models of interhemispheric interaction. The future application of our analyses may provide important insight into impaired interhemispheric processing in clinical and aging populations.
doi:10.1016/j.neuroimage.2010.05.073
PMCID: PMC3134281  PMID: 20570737
15.  Longitudinal Changes of Resting-State Functional Connectivity during Motor Recovery after Stroke 
Background and Purpose
Functional magnetic resonance imaging (fMRI) studies could provide crucial information on the neural mechanisms of motor recovery in stroke patients. Resting-state fMRI is applicable to stroke patients who are not capable of proper performance of the motor task. In this study, we explored neural correlates of motor recovery in stroke patients by investigating longitudinal changes in resting-state functional connectivity of the ipsilesional primary motor cortex (M1).
Methods
A longitudinal observational study using repeated fMRI experiments was conducted in 12 patients with stroke. Resting-state fMRI data were acquired four times over a period of 6 months. Patients participated in the first session of fMRI shortly after onset, and thereafter in subsequent sessions at 1, 3, and 6 months after onset. Resting-state functional connectivity of the ipsilesional M1 was assessed and compared with that of healthy subjects.
Results
Compared with healthy subjects, patients demonstrated higher functional connectivity with the ipsilesional frontal and parietal cortices, bilateral thalamus, and cerebellum. Instead, functional connectivity with the contralesional M1 and occipital cortex were decreased in stroke patients. Functional connectivity between the ipsilesional and contralesional M1 showed the most asymmetry at 1 month after onset to the ipsilesional side. Functional connectivity of the ipsilesional M1 with the contralesional thalamus, supplementary motor area, and middle frontal gyrus at onset was positively correlated with motor recovery at 6 months after stroke.
Conclusions
Resting-state fMRI elicited distinctive but comparable results with previous task-based fMRI, presenting complementary and practical values for use in the study of stroke patients.
doi:10.1161/STROKEAHA.110.596155
PMCID: PMC3589816  PMID: 21441147
Resting-state fMRI; Stroke; Motor recovery; Functional connectivity
16.  Resting-State Brain Activity in Adult Males Who Stutter 
PLoS ONE  2012;7(1):e30570.
Although developmental stuttering has been extensively studied with structural and task-based functional magnetic resonance imaging (fMRI), few studies have focused on resting-state brain activity in this disorder. We investigated resting-state brain activity of stuttering subjects by analyzing the amplitude of low-frequency fluctuation (ALFF), region of interest (ROI)-based functional connectivity (FC) and independent component analysis (ICA)-based FC. Forty-four adult males with developmental stuttering and 46 age-matched fluent male controls were scanned using resting-state fMRI. ALFF, ROI-based FCs and ICA-based FCs were compared between male stuttering subjects and fluent controls in a voxel-wise manner. Compared with fluent controls, stuttering subjects showed increased ALFF in left brain areas related to speech motor and auditory functions and bilateral prefrontal cortices related to cognitive control. However, stuttering subjects showed decreased ALFF in the left posterior language reception area and bilateral non-speech motor areas. ROI-based FC analysis revealed decreased FC between the posterior language area involved in the perception and decoding of sensory information and anterior brain area involved in the initiation of speech motor function, as well as increased FC within anterior or posterior speech- and language-associated areas and between the prefrontal areas and default-mode network (DMN) in stuttering subjects. ICA showed that stuttering subjects had decreased FC in the DMN and increased FC in the sensorimotor network. Our findings support the concept that stuttering subjects have deficits in multiple functional systems (motor, language, auditory and DMN) and in the connections between them.
doi:10.1371/journal.pone.0030570
PMCID: PMC3262831  PMID: 22276215
17.  Broadband Local Field Potentials Correlate with Spontaneous Fluctuations in Functional Magnetic Resonance Imaging Signals in the Rat Somatosensory Cortex Under Isoflurane Anesthesia 
Brain Connectivity  2011;1(2):119-131.
Abstract
Resting-state functional magnetic resonance imaging (fMRI) is widely used for exploring spontaneous brain activity and large-scale networks; however, the neural processes underlying the observed resting-state fMRI signals are not fully understood. To investigate the neural correlates of spontaneous low-frequency fMRI fluctuations and functional connectivity, we developed a rat model of simultaneous fMRI and multiple-site intracortical neural recordings. This allowed a direct comparison to be made between the spontaneous signals and interhemispheric connectivity measured with the two modalities. Results show that low-frequency blood oxygen level-dependent (BOLD) fluctuations (<0.1 Hz) correlate significantly with slow power modulations (<0.1 Hz) of local field potentials (LFPs) in a broad frequency range (1–100 Hz) under isoflurane anesthesia (1%–1.8%). Peak correlation occurred between neural and hemodynamic activity when the BOLD signal was delayed by ∼4 sec relative to the LFP signal. The spatial location and extent of correlation was highly reproducible across studies, with the maximum correlation localized to a small area surrounding the site of microelectrode recording and to the homologous area in the contralateral hemisphere for most rats. Interhemispheric connectivity was calculated using BOLD correlation and band-limited LFP (1–4, 4–8, 8–14, 14–25, 25–40, and 40–100 Hz) coherence. Significant coherence was observed for the slow power changes of all LFP frequency bands as well as in the low-frequency BOLD data. A preliminary investigation of the effect of anesthesia on interhemispheric connectivity indicates that coherence in the high-frequency LFP bands declines with increasing doses of isoflurane, whereas coherence in the low-frequency LFP bands and the BOLD signal increases. These findings suggest that resting-state fMRI signals might be a reflection of broadband LFP power modulation, at least in isoflurane-anesthetized rats.
doi:10.1089/brain.2011.0014
PMCID: PMC3621847  PMID: 22433008
anesthetic effects; broadband LFP; functional connectivity; neural correlates; resting-state fMRI
18.  Altered baseline brain activity in children with bipolar disorder during mania state: a resting-state study 
Background
Previous functional magnetic resonance imaging (fMRI) studies have shown abnormal functional connectivity in regions involved in emotion processing and regulation in pediatric bipolar disorder (PBD). Recent studies indicate, however, that task-dependent neural changes only represent a small fraction of the brain’s total activity. How the brain allocates the majority of its resources at resting state is still unknown. We used the amplitude of low-frequency fluctuation (ALFF) method of fMRI to explore the spontaneous neuronal activity in resting state in PBD patients.
Methods
Eighteen PBD patients during the mania phase and 18 sex-, age- and education-matched healthy subjects were enrolled in this study and all patients underwent fMRI scanning. The ALFF method was used to compare the resting-state spontaneous neuronal activity between groups. Correlation analysis was performed between the ALFF values and Young Mania Rating Scale scores.
Results
Compared with healthy controls, PBD patients presented increased ALFF in bilateral caudate and left pallidum as well as decreased ALFF in left precuneus, left superior parietal lobule, and bilateral inferior occipital gyrus. Additionally, ALFF values in left pallidum were positively correlated with Young Mania Rating Scale score in PBD.
Conclusion
The abnormal resting-state neuronal activities of the basal ganglia, parietal cortex, and occipital cortex may play an important role in the pathophysiology in PBD patients.
doi:10.2147/NDT.S54663
PMCID: PMC3933715  PMID: 24570585
resting-state fMRI; amplitude of low-frequency fluctuation; child; bipolar disorder
19.  fMRI Resting Slow Fluctuations Correlate with the Activity of Fast Cortico-Cortical Physiological Connections 
PLoS ONE  2012;7(12):e52660.
Recording of slow spontaneous fluctuations at rest using functional magnetic resonance imaging (fMRI) allows distinct long-range cortical networks to be identified. The neuronal basis of connectivity as assessed by resting-state fMRI still needs to be fully clarified, considering that these signals are an indirect measure of neuronal activity, reflecting slow local variations in de-oxyhaemoglobin concentration. Here, we combined fMRI with multifocal transcranial magnetic stimulation (TMS), a technique that allows the investigation of the causal neurophysiological interactions occurring in specific cortico-cortical connections. We investigated whether the physiological properties of parieto-frontal circuits mapped with short-latency multifocal TMS at rest may have some relationship with the resting-state fMRI measures of specific resting-state functional networks (RSNs). Results showed that the activity of fast cortico-cortical physiological interactions occurring in the millisecond range correlated selectively with the coupling of fMRI slow oscillations within the same cortical areas that form part of the dorsal attention network, i.e., the attention system believed to be involved in reorientation of attention. We conclude that resting-state fMRI ongoing slow fluctuations likely reflect the interaction of underlying physiological cortico-cortical connections.
doi:10.1371/journal.pone.0052660
PMCID: PMC3527573  PMID: 23285136
20.  Investigation of long-term reproducibility of intrinsic connectivity network mapping: A resting-state fMRI study 
BACKGROUND AND PURPOSE
Connectivity mapping based on resting-state fMRI is rapidly developing and this methodology has great potential for clinical applications. However, before resting-state fMRI can be applied for diagnosis, prognosis, and monitoring treatment for an individual patient with neurologic or psychiatric diseases, it is essential to assess its long-term reproducibility and between-subject variations among healthy individuals. The purpose of the study is to (1) quantify the long-term test-retest reproducibility of intrinsic connectivity network (ICN) measures derived from resting-state fMRI, and (2) assess the between-subject variation of ICN measures across the whole brain.
MATERIALS AND METHODS
Longitudinal resting-state fMRI data of six healthy volunteers were acquired from nine scan sessions over a period of more than one year. The within-subject reproducibility and between-subject variation of ICN measures, across 1) the whole brain and 2) major nodes of the default mode network, were quantified with intraclass correlation coefficient (ICC) and coefficient of variance (COV).
RESULTS
Our data show that the long-term test-retest reproducibility of ICN measures is outstanding, with over 70% of the connectivity networks showing an ICC greater than 0.60. COV across six healthy volunteers in this sample was greater than 0.2, suggesting significant between-subject variation.
CONCLUSION
Our data indicate that resting-state ICN measures (e.g., the correlation coefficients between fMRI signal profiles from two different brain regions) are potentially suitable as biomarkers for monitoring disease progression and treatment effects in clinical trials and individual patients. Because between-subject variation is significant, it may be difficult to use quantitative ICN measures, in their current state, as a diagnostic tool.
doi:10.3174/ajnr.A2894
PMCID: PMC3584561  PMID: 22268094
21.  Characterization of resting state activity in MCI individuals 
PeerJ  2013;1:e135.
Objectives. Aging is the major risk factor for Alzheimer Disease (AD) and Mild Cognitive Impairment (MCI). The aim of this study was to identify novel modifications of brain functional connectivity in MCI patients. MCI individuals were compared to healthy elderly subjects.
Methods. We enrolled 37 subjects (age range 60–80 y.o.). Of these, 13 subjects were affected by MCI and 24 were age-matched healthy elderly control (HC). Subjects were evaluated with Mini Mental State Examination (MMSE), Frontal Assessment Battery (FAB), and prose memory (Babcock story) tests. In addition, with functional Magnetic Resonance Imaging (fMRI), we investigated resting state network (RSN) activities. Resting state (Rs) fMRI data were analyzed by means of Independent Component Analysis (ICA). Subjects were followed-up with neuropsychological evaluations for three years.
Results. Rs-fMRI of MCI subjects showed increased intrinsic connectivity in the Default Mode Network (DMN) and in the Somatomotor Network (SMN). Analysis of the DMN showed statistically significant increased activation in the posterior cingulate cortex (PCC) and left inferior parietal lobule (lIPL). During the three years follow-up, 4 MCI subjects converted to AD. The subset of MCI AD-converted patients showed increased connectivity in the right Inferior Parietal Lobule (rIPL). As for SMN activity, MCI and MCI-AD converted groups showed increased level of connectivity in correspondence of the right Supramarginal Gyrus (rSG).
Conclusions. Our findings indicate alterations of DMN and SMN activity in MCI subjects, thereby providing potential imaging-based markers that can be helpful for the early diagnosis and monitoring of these patients.
doi:10.7717/peerj.135
PMCID: PMC3757508  PMID: 24010015
rs-fMRI; MCI; Aging; AD; Alzheimer
22.  Reduced functional brain connectivity prior to and after disease onset in Huntington's disease☆☆☆ 
NeuroImage : Clinical  2013;2:377-384.
Background
Huntington's disease (HD) is characterised by both regional and generalised neuronal cell loss in the brain. Investigating functional brain connectivity patterns in rest in HD has the potential to broaden the understanding of brain functionality in relation to disease progression. This study aims to establish whether brain connectivity during rest is different in premanifest and manifest HD as compared to controls.
Methods
At the Leiden University Medical Centre study site of the TRACK-HD study, 20 early HD patients (disease stages 1 and 2), 28 premanifest gene carriers and 28 healthy controls underwent 3 T MRI scanning. Standard and high-resolution T1-weighted images and a resting state fMRI scan were acquired. Using FSL, group differences in resting state connectivity were examined for eight networks of interest using a dual regression method. With a voxelwise correction for localised atrophy, group differences in functional connectivity were examined.
Results
Brain connectivity of the left middle frontal and pre-central gyrus, and right post central gyrus with the medial visual network was reduced in premanifest and manifest HD as compared to controls (0.05 > p > 0.0001). In manifest HD connectivity of numerous widespread brain regions with the default mode network and the executive control network were reduced (0.05 > p > 0.0001).
Discussion
Brain regions that show reduced intrinsic functional connectivity are present in premanifest gene carriers and to a much larger extent in manifest HD patients. These differences are present even when the potential influence of atrophy is taken into account. Resting state fMRI could potentially be used for early disease detection in the premanifest phase of HD and for monitoring of disease modifying compounds.
Highlights
•We applied resting state fMRI in premanifest and manifest Huntington's disease.•Reduced functional brain connectivity was present in premanifest HD gene carriers.•Large regions demonstrate reduced functional brain connectivity in manifest HD.•Medial visual, default mode and executive control networks were affected.
doi:10.1016/j.nicl.2013.03.001
PMCID: PMC3778251  PMID: 24179791
Huntington's disease; Resting state fMRI; Premanifest gene carriers; Functional connectivity
23.  Effect of Acupuncture in Mild Cognitive Impairment and Alzheimer Disease: A Functional MRI Study 
PLoS ONE  2012;7(8):e42730.
We aim to clarify the mechanisms of acupuncture in treating mild cognitive impairment (MCI) and Alzheimer disease (AD) by using functional magnetic resonance imaging (fMRI). Thirty-six right-handed subjects (8 MCI patients, 14 AD patients, and 14 healthy elders) participated in this study. Clinical and neuropsychological examinations were performed on all the subjects. MRI data acquisition was performed on a SIEMENS verio 3-Tesla scanner. The fMRI study used a single block experimental design. We first acquired the baseline resting state data in the initial 3 minutes; we then acquired the fMRI data during the procession of acupuncture stimulation on the acupoints of Tai chong and Hegu for the following 3 minutes. Last, we acquired fMRI data for another 10 minutes after the needle was withdrawn. The preprocessing and data analysis were performed using the statistical parametric mapping (SPM8) software. Then the two-sample t-tests were performed between each two groups of different states. We found that during the resting state, brain activities in AD and MCI patients were different from those of control subjects. During the acupuncture and the second resting state after acupuncture, when comparing to resting state, there are several regions showing increased or decreased activities in MCI, AD subjects compared to normal subjects. Most of the regions were involved in the temporal lobe and the frontal lobe, which were closely related to the memory and cognition. In conclusion, we investigated the effect of acupuncture in AD and MCI patients by combing fMRI and traditional acupuncture. Our fMRI study confirmed that acupuncture at Tai chong (Liv3) and He gu (LI4) can activate certain cognitive-related regions in AD and MCI patients.
doi:10.1371/journal.pone.0042730
PMCID: PMC3423412  PMID: 22916152
24.  Identifying Neural Drivers with Functional MRI: An Electrophysiological Validation 
PLoS Biology  2008;6(12):e315.
Whether functional magnetic resonance imaging (fMRI) allows the identification of neural drivers remains an open question of particular importance to refine physiological and neuropsychological models of the brain, and/or to understand neurophysiopathology. Here, in a rat model of absence epilepsy showing spontaneous spike-and-wave discharges originating from the first somatosensory cortex (S1BF), we performed simultaneous electroencephalographic (EEG) and fMRI measurements, and subsequent intracerebral EEG (iEEG) recordings in regions strongly activated in fMRI (S1BF, thalamus, and striatum). fMRI connectivity was determined from fMRI time series directly and from hidden state variables using a measure of Granger causality and Dynamic Causal Modelling that relates synaptic activity to fMRI. fMRI connectivity was compared to directed functional coupling estimated from iEEG using asymmetry in generalised synchronisation metrics. The neural driver of spike-and-wave discharges was estimated in S1BF from iEEG, and from fMRI only when hemodynamic effects were explicitly removed. Functional connectivity analysis applied directly on fMRI signals failed because hemodynamics varied between regions, rendering temporal precedence irrelevant. This paper provides the first experimental substantiation of the theoretical possibility to improve interregional coupling estimation from hidden neural states of fMRI. As such, it has important implications for future studies on brain connectivity using functional neuroimaging.
Author Summary
Our understanding of how the brain works relies on the development of neuropsychological models, which describe how brain activity is coordinated among different regions during the execution of a given task. Knowing the directionality of information transfer between connected regions, and in particular distinguishing neural drivers, or the source of forward connections in the brain, from other brain regions, is critical to refine models of the brain. However, whether functional magnetic resonance imaging (fMRI), the most common technique for imaging brain function, allows one to identify neural drivers remains an open question. Here, we used a rat model of absence epilepsy, a form of nonconvulsive epilepsy that occurs during childhood in humans, showing spontaneous spike-and-wave discharges (nonconvulsive seizures) originating from the first somatosensory cortex, to validate several functional connectivity measures derived from fMRI. Standard techniques estimating interactions directly from fMRI data failed because blood flow dynamics varied between regions. However, we were able to identify the neural driver of spike-and-wave discharges when hemodynamic effects were explicitly removed using appropriate modelling. This study thus provides the first experimental substantiation of the theoretical possibility to improve interregional coupling estimation from hidden neural states of fMRI. As such, it has important implications for future studies on connectivity in the functional neuroimaging literature.
Neural long-range interactions can be distinguished from hemodynamic confounds in functional magnetic resonance imaging using new data analysis techniques that will allow experimental validation of models of brain function.
doi:10.1371/journal.pbio.0060315
PMCID: PMC2605917  PMID: 19108604
25.  Abnormal Resting-State Activities and Functional Connectivities of the Anterior and the Posterior Cortexes in Medication-Naïve Patients with Obsessive-Compulsive Disorder 
PLoS ONE  2013;8(6):e67478.
Background
Obsessive-compulsive disorder (OCD) is a mental illness characterized by the loss of control. Because the cingulate cortex is believed to be important in executive functions, such as inhibition, we used functional magnetic resonance imaging (fMRI) techniques to examine whether and how activity and functional connectivity (FC) of the cingulate cortex were altered in drug-naïve OCD patients.
Methods
Twenty-three medication-naïve OCD patients and 23 well-matched healthy controls received fMRI scans in a resting state. Functional connectivities of the anterior cingulate (ACC) and the posterior cingulate (PCC) to the whole brain were analyzed using correlation analyses based on regions of interest (ROI) identified by the fractional amplitude of low-frequency fluctuation (fALFF). Independent Component Analysis (ICA) was used to identify the resting-state sub-networks.
Results
fALFF analysis found that regional activity was increased in the ACC and decreased in the PCC in OCD patients when compared to controls. FC of the ACC and the PCC also showed different patterns. The ACC and the PCC were found to belong to different resting-state sub-networks in ICA analysis and showed abnormal FC, as well as contrasting correlations with the severity of OCD symptoms.
Conclusions
Activity of the ACC and the PCC were increased and decreased, respectively, in the medication-naïve OCD patients compared to controls. Different patterns in FC were also found between the ACC and the PCC with respect to these two groups. These findings implied that the cardinal feature of OCD, the loss of control, may be attributed to abnormal activities and FC of the ACC and the PCC.
doi:10.1371/journal.pone.0067478
PMCID: PMC3696097  PMID: 23840714

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