scholarly journals Using Temporal ICA to Selectively Remove Global Noise While Preserving Global Signal in Functional MRI Data

2017 ◽  
Author(s):  
Matthew F. Glasser ◽  
Timothy S. Coalson ◽  
Janine D. Bijsterbosch ◽  
Samuel J. Harrison ◽  
Michael P. Harms ◽  
...  
Keyword(s):  
Brain Activity ◽  
Resting State Fmri ◽  
Fmri Data ◽  
Physiological Noise ◽  
Temporal Noise ◽  
Global Signal ◽  
Human Connectome Project ◽  
Before And After ◽  
Components Analysis ◽  
Subject Motion

AbstractTemporal fluctuations in functional Magnetic Resonance Imaging (fMRI) have been profitably used to study brain activity and connectivity for over two decades. Unfortunately, fMRI data also contain structured temporal “noise” from a variety of sources, including subject motion, subject physiology, and the MRI equipment. Recently, methods have been developed to automatically and selectively remove spatially specific structured noise from fMRI data using spatial Independent Components Analysis (ICA) and machine learning classifiers. Spatial ICA is particularly effective at removing spatially specific structured noise from high temporal and spatial resolution fMRI data of the type acquired by the Human Connectome Project and similar studies. However, spatial ICA is mathematically, by design, unable to separate spatially widespread “global” structured noise from fMRI data (e.g., blood flow modulations from subject respiration). No methods currently exist to selectively and completely remove global structured noise while retaining the global signal from neural activity. This has left the field in a quandary—to do or not to do global signal regression—given that both choices have substantial downsides. Here we show that temporal ICA can selectively segregate and remove global structured noise while retaining global neural signal in both task-based and resting state fMRI data. We compare the results before and after temporal ICA cleanup to those from global signal regression and show that temporal ICA cleanup removes the global positive biases caused by global physiological noise without inducing the network-specific negative biases of global signal regression. We believe that temporal ICA cleanup provides a “best of both worlds” solution to the global signal and global noise dilemma and that temporal ICA itself unlocks interesting neurobiological insights from fMRI data.

scholarly journals Rest-task Modulation of fMRI-derived Global Signal Topography is Mediated by Transient Co-activation Patterns

2019 ◽  
Author(s):  
Jianfeng Zhang ◽  
Zirui Huang ◽  
Shankar Tumati ◽  
Georg Northoff
Keyword(s):  
Resting State ◽  
Resting State Fmri ◽  
Peak Period ◽  
Physiological Noise ◽  
Activation Patterns ◽  
Global Signal ◽  
Co Activation ◽  
Human Connectome Project ◽  
Partial Dissociation ◽  
Signal Correlation

AbstractRecent resting-state fMRI studies have revealed that the global signal (GS) exhibits a non-uniform spatial distribution across the gray matter. Whether this topography is informative remains largely unknown. We therefore tested rest-task modulation of global signal topography by analyzing static global signal correlation and dynamic co-activation patterns in a large sample of fMRI dataset (n=837) from the Human Connectome Project. The GS topography in the resting-state and in seven different tasks was first measured by correlating the global signal with the local timeseries (GSCORR). In the resting state, high GSCORR was observed mainly in the primary sensory and motor regions, while low GSCORR was seen in the association brain areas. This pattern changed during the seven tasks, with mainly decreased GSCORR in sensorimotor cortex. Importantly, this rest-task modulation of GSCORR could be traced to transient co-activation patterns at the peak period of global signal (GS-peak). By comparing the topography of GSCORR and respiration effects, we observed that the topography of respiration mimicked the topography of global signal in the resting-state whereas both differed during the task states; due to such partial dissociation, we assume that GSCORR could not be equated with a respiration effect. Finally, rest-task modulation of GS topography could not be exclusively explained by other sources of physiological noise. Together, we here demonstrate the informative nature of global signal topography by showing its rest-task modulation, the underlying dynamic co-activation patterns, and its partial dissociation from respiration effects during task states.

scholarly journals Quasi-Periodic Patterns of Intrinsic Brain Activity in Individuals and their Relationship to Global Signal

2017 ◽  
Author(s):  
Behnaz Yousefi ◽  
Jaemin Shin ◽  
Eric H. Schumacher ◽  
Shella D. Keilholz
Keyword(s):  
Large Scale ◽  
Brain Activity ◽  
Primary Source ◽  
Intrinsic Activity ◽  
Periodic Patterns ◽  
Physiological Noise ◽  
Global Signal ◽  
Human Connectome Project ◽  
Large Scale Networks ◽  
Induced Signal

AbstractQuasiperiodic patterns (QPPs) as reported by Majeed et al., 2011 are prominent features of the brain’s intrinsic activity that involve important large-scale networks (default mode, DMN; task positive, TPN) and are likely to be major contributors to widely used measures of functional connectivity. We examined the variability of these patterns in 470 individuals from the Human Connectome Project resting state functional MRI dataset. The QPPs from individuals can be coarsely categorized into two types: one where strong anti-correlation between the DMN and TPN is present, and another where most areas are strongly correlated. QPP type could be predicted by an individual’s global signal, with lower global signal corresponding to QPPs with strong anti-correlation. After regression of global signal, all QPPs showed strong anti-correlation between DMN and TPN. QPP occurrence and type was similar between a subgroup of individuals with extremely low motion (or even high motion) and the rest of the sample, which shows that motion is not a major contributor to the QPPs. After regression of estimates of slow respiratory and cardiac induced signal fluctuations, more QPPs showed strong anti-correlation between DMN and TPN, an indication that while physiological noise influences the QPP type, it is not the primary source of the QPP itself. QPPs were more similar for the same subjects scanned on different days than for different subjects. These results provide the first assessment of the variability in individual QPPs and their relationship to physiological parameters.

scholarly journals Resting-state brain activity can predict target-independent aptitude in fMRI-neurofeedback training

2021 ◽  
Author(s):  
Takashi Nakano ◽  
Masahiro Takamura ◽  
Haruki Nishimura ◽  
Maro Machizawa ◽  
Naho Ichikawa ◽  
...  
Keyword(s):  
Resting State ◽  
Brain Connectivity ◽  
Brain Activity ◽  
Resting State Fmri ◽  
Brain Regions ◽  
Posterior Cingulate Cortex ◽  
Fmri Data ◽  
Independent Test ◽  
The Individual ◽  
The Brain

AbstractNeurofeedback (NF) aptitude, which refers to an individual’s ability to change its brain activity through NF training, has been reported to vary significantly from person to person. The prediction of individual NF aptitudes is critical in clinical NF applications. In the present study, we extracted the resting-state functional brain connectivity (FC) markers of NF aptitude independent of NF-targeting brain regions. We combined the data in fMRI-NF studies targeting four different brain regions at two independent sites (obtained from 59 healthy adults and six patients with major depressive disorder) to collect the resting-state fMRI data associated with aptitude scores in subsequent fMRI-NF training. We then trained the regression models to predict the individual NF aptitude scores from the resting-state fMRI data using a discovery dataset from one site and identified six resting-state FCs that predicted NF aptitude. Next we validated the prediction model using independent test data from another site. The result showed that the posterior cingulate cortex was the functional hub among the brain regions and formed predictive resting-state FCs, suggesting NF aptitude may be involved in the attentional mode-orientation modulation system’s characteristics in task-free resting-state brain activity.

scholarly journals Evaluating the sensitivity of functional connectivity measures to motion artifact in resting-state fMRI data

2020 ◽  
Author(s):  
Arun S. Mahadevan ◽  
Ursula A. Tooley ◽  
Maxwell A. Bertolero ◽  
Allyson P. Mackey ◽  
Danielle S. Bassett
Keyword(s):  
Functional Connectivity ◽  
Resting State ◽  
Partial Correlation ◽  
Motion Artifact ◽  
Resting State Fmri ◽  
Alternative Methods ◽  
Fmri Data ◽  
Retest Reliability ◽  
Human Connectome Project ◽  
Test Retest Reliability

AbstractFunctional connectivity (FC) networks are typically inferred from resting-state fMRI data using the Pearson correlation between BOLD time series from pairs of brain regions. However, alternative methods of estimating functional connectivity have not been systematically tested for their sensitivity or robustness to head motion artifact. Here, we evaluate the sensitivity of six different functional connectivity measures to motion artifact using resting-state data from the Human Connectome Project. We report that FC estimated using full correlation has a relatively high residual distance-dependent relationship with motion compared to partial correlation, coherence and information theory-based measures, even after implementing rigorous methods for motion artifact mitigation. This disadvantage of full correlation, however, may be offset by higher test-retest reliability and system identifiability. FC estimated by partial correlation offers the best of both worlds, with low sensitivity to motion artifact and intermediate system identifiability, with the caveat of low test-retest reliability. We highlight spatial differences in the sub-networks affected by motion with different FC metrics. Further, we report that intra-network edges in the default mode and retrosplenial temporal sub-networks are highly correlated with motion in all FC methods. Our findings indicate that the method of estimating functional connectivity is an important consideration in resting-state fMRI studies and must be chosen carefully based on the parameters of the study.

scholarly journals Template-based prediction of vigilance fluctuations in resting-state fMRI

2017 ◽  
Author(s):  
Maryam Falahpour ◽  
Catie Chang ◽  
Chi Wah Wong ◽  
Thomas T. Liu
Keyword(s):  
Resting State ◽  
Brain Connectivity ◽  
Resting State Fmri ◽  
Fmri Data ◽  
Eyes Closed ◽  
Vigilance State ◽  
Global Signal ◽  
Significant Difference ◽  
Eyes Open ◽  
Positive Correlations

AbstractChanges in vigilance or alertness during a typical resting state fMRI scan are inevitable and have been found to affect measures of functional brain connectivity. Since it is not often feasible to monitor vigilance with EEG during fMRI scans, it would be of great value to have methods for estimating vigilance levels from fMRI data alone. A recent study, conducted in macaque monkeys, proposed a template-based approach for fMRI-based estimation of vigilance fluctuations. Here, we use simultaneously acquired EEG/fMRI data to investigate whether the same template-based approach can be employed to estimate vigilance fluctuations of awake humans across different resting-state conditions. We first demonstrate that the spatial pattern of correlations between EEG-defined vigilance and fMRI in our data is consistent with the previous literature. Notably, however, we observed a significant difference between the eyes-closed (EC) and eyes-open (EO) conditions finding stronger negative correlations with vigilance in regions forming the default mode network and higher positive correlations in thalamus and insula in the EC condition when compared to the EO condition. Taking these correlation maps as “templates” for vigilance estimation, we found that the template-based approach produced fMRI-based vigilance estimates that were significantly correlated with EEG-based vigilance measures, indicating its generalizability from macaques to humans. We also demonstrate that the performance of this method was related to the overall amount of variability in a subject’s vigilance state, and that the template-based approach outperformed the use of the global signal as a vigilance estimator. In addition, we show that the template-based approach can be used to estimate the variability across scans in the amplitude of the vigilance fluctuations. We discuss the benefits and tradeoffs of using the template-based approach in future fMRI studies.

scholarly journals Resting state connectivity during total sleep deprivation: A functional magnetic resonance study

2020 ◽  
Author(s):  
Vivianne Jakobsson
Keyword(s):  
Magnetic Resonance ◽  
Sleep Deprivation ◽  
Resting State ◽  
Resting State Fmri ◽  
Head Motion ◽  
Functional Magnetic Resonance ◽  
Global Signal ◽  
Significant Difference ◽  
Before And After ◽  
Eyes Open

Introduction: Sleep deprivation is a common problem that may have serious consequences. In this study, functional magnetic resonance imaging (fMRI), a technique frequently used to study networks in the brain, was used to investigate the resting state of the sleep deprived brain, in order to discover whether this state affects the intrinsic connectivity and the global signal variability (GSV). Aims: To investigate whether GSV increases with sleep deprivation. Material and Methods: In this cross over study 18 healthy participants, age 20 – 30, underwent in randomized order resting-state fMRI for 20min before and after 24h sleep deprivation. We extracted the global signal, calculated the standard deviation per participant, and analysed it with respect to sleep depraved yes/no, head motion, eyes open/closed and self-evaluation of sleepiness using Karolinska Sleepiness Score (KSS). Results: We found that GSV was higher during sleep deprivation (0.3362 ± 0.0241, p<0.0001) without KSS data. With KSS, sleep deprivation was not significant (0.0619 ± 0.1145, p=0.5889). High KSS rating had a significant effect on GSV (0.1497 ± 0.0409, p=0.0003), as had head motion (1.7974 ± 0.1539, p<0.0001). There was no significant difference between having eyes open or closed (0.0126 ± 0.0578, p=0.8278), and no significant increase for each time period of 20s in the scanner (0.0065 ± 0.0021, p=0.0029). Conclusions: We found that the global signal variation is increased by sleep deprivation and sleepiness. More specific conclusions cannot be made from our data so far.

scholarly journals Decreased Intrinsic Neural Timescales in Mesial Temporal Lobe Epilepsy

2021 ◽  
Vol 15 ◽  
Author(s):  
Kefan Wang ◽  
Xiaonan Zhang ◽  
Chengru Song ◽  
Keran Ma ◽  
Man Bai ◽  
...  
Keyword(s):  
Temporal Lobe Epilepsy ◽  
Resting State ◽  
Brain Activity ◽  
Resting State Fmri ◽  
Mesial Temporal Lobe Epilepsy ◽  
Fmri Data ◽  
Healthy Controls ◽  
Neural Signals ◽  
Mesial Temporal Lobe ◽  
The Brain

It is well established that epilepsy is characterized by the destruction of the information capacity of brain network and the interference with information processing in regions outside the epileptogenic focus. However, the potential mechanism remains poorly understood. In the current study, we applied a recently proposed approach on the basis of resting-state fMRI data to measure altered local neural dynamics in mesial temporal lobe epilepsy (mTLE), which represents how long neural information is stored in a local brain area and reflect an ability of information integration. Using resting-state-fMRI data recorded from 36 subjects with mTLE and 36 healthy controls, we calculated the intrinsic neural timescales (INT) of neural signals by summing the positive magnitude of the autocorrelation of the resting-state brain activity. Compared to healthy controls, the INT values were significantly lower in patients in the right orbitofrontal cortices, right insula, and right posterior lobe of cerebellum. Whereas, we observed no statistically significant changes between patients with long- and short-term epilepsy duration or between left-mTLE and right-mTLE. Our study provides distinct insight into the brain abnormalities of mTLE from the perspective of the dynamics of the brain activity, highlighting the significant role of intrinsic timescale in understanding neurophysiological mechanisms. And we postulate that altered intrinsic timescales of neural signals in specific cortical brain areas may be the neurodynamic basis of cognitive impairment and emotional comorbidities in mTLE patients.

scholarly journals Physiological noise modeling in fMRI based on the pulsatile component of photoplethysmograph

2020 ◽  
Author(s):  
Michalis Kassinopoulos ◽  
Georgios D. Mitsis
Keyword(s):  
Heart Rate ◽  
Brain Activity ◽  
Low Frequency ◽  
Blood Oxygenation ◽  
Breathing Patterns ◽  
Physiological Noise ◽  
Model Based ◽  
Human Connectome Project ◽  
Contrast Mechanism ◽  
Noise Correction

AbstractThe blood oxygenation level-dependent (BOLD) contrast mechanism allows the noninvasive monitoring of changes in deoxyhemoglobin content. As such, it is commonly used in functional magnetic resonance imaging (fMRI) to study brain activity since levels of deoxyhemoglobin are indirectly related to local neuronal activity through neurovascular coupling mechanisms. However, the BOLD signal is severely affected by physiological processes as well as motion. Due to this, several noise correction techniques have been developed to correct for the associated confounds. The present study focuses on cardiac pulsatility fMRI confounds, aiming to refine model-based techniques that utilize the photoplethysmograph (PPG) signal. Specifically, we propose a new technique based on convolution filtering, termed cardiac pulsatility model (CPM) and compare its performance with RETROICOR, which is a technique commonly used to model fMRI fluctuations due to cardiac pulsatility. Further, we investigate whether variations in the amplitude of the PPG pulses (PPG-Amp) covary with variations in amplitude of pulse-related fMRI fluctuations, as well as with the systemic low frequency oscillations (SLFOs) component of the fMRI global signal (GS – defined as the mean signal across all gray matter voxels). Capitalizing on 3T fMRI data from the Human Connectome Project, CPM was found to explain a significantly larger fraction of the fMRI signal variance compared to RETROICOR, particularly for subjects with larger heart rate variability during the scan. The amplitude of the fMRI pulse-related fluctuations did not covary with PPG-Amp; however, PPG-Amp explained significant variance in the GS that was not attributed to variations in heart rate or breathing patterns. Our results suggest that the proposed approach can model high-frequency fluctuations due to pulsation as well as low-frequency physiological fluctuations more accurately compared to model-based techniques commonly employed in fMRI studies.

scholarly journals Computing personalized brain functional networks from fMRI using self-supervised deep learning

2021 ◽  
Author(s):  
Hongming Li ◽  
Srinivasan Dhivya ◽  
Zaixu Cui ◽  
Chuanjun Zhuo ◽  
Raquel E. Gur ◽  
...  
Keyword(s):  
Deep Learning ◽  
Resting State ◽  
Brain Function ◽  
Resting State Fmri ◽  
Fmri Data ◽  
Functional Networks ◽  
Brain Functional Networks ◽  
Human Connectome Project ◽  
Functional Homogeneity ◽  
Decoder Architecture

ABSTRACTA novel self-supervised deep learning (DL) method is developed for computing bias-free, personalized brain functional networks (FNs) that provide unique opportunities to better understand brain function, behavior, and disease. Specifically, convolutional neural networks with an encoder-decoder architecture are employed to compute personalized FNs from resting-state fMRI data without utilizing any external supervision by optimizing functional homogeneity of personalized FNs in a self-supervised setting. We demonstrate that a DL model trained on fMRI scans from the Human Connectome Project can identify canonical FNs and generalizes well across four different datasets. We further demonstrate that the identified personalized FNs are informative for predicting individual differences in behavior, brain development, and schizophrenia status. Taken together, self-supervised DL allows for rapid, generalizable computation of personalized FNs.

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