A group model for stable multi-subject ICA on fMRI datasets

CalciSeg: A versatile approach for unsupervised segmentation of calcium imaging data

Recent advances in calcium imaging, including the development of fast and sensitive genetically encoded indicators, high-resolution camera chips for wide-field imaging, and resonant scanning mirrors in laser scanning microscopy, have notably improved the temporal and spatial resolution of functional imaging analysis. Nonetheless, the variability of imaging approaches and brain structures challenges the development of versatile and reliable segmentation methods. Standard techniques, such as manual selection of regions of interest or machine learning solutions, often fall short due to either user bias, non-transferability among systems, or computational demand. To overcome these issues, we developed CalciSeg, a data-driven and reproducible approach for unsupervised functional calcium imaging data segmentation. CalciSeg addresses the challenges associated with brain structure variability and user bias by offering a computationally efficient solution for automatic image segmentation based on two parameters: regions' size limits and number of refinement iterations. We evaluated CalciSeg efficacy on datasets of varied complexity, different insect species (locusts, bees, and cockroaches), and imaging systems (wide-field, confocal, and multiphoton), showing the robustness and generality of our approach. Finally, the user-friendly nature and open-source availability of CalciSeg facilitate the integration of this algorithm into existing analysis pipelines.

Energy in functional brain states correlates with cognition in adolescent-onset schizophrenia and healthy persons

Adolescent-onset schizophrenia (AOS) is a relatively rare and under-studied form of schizophrenia with more severe cognitive impairments and poorer outcome compared to adult-onset schizophrenia. Several neuroimaging studies have reported alterations in regional activations that account for activity in individual regions (first-order model) and functional connectivity that reveals pairwise co-activations (second-order model) in AOS compared to controls. The pairwise maximum entropy model, also called the Ising model, can integrate both first-order and second-order terms to elucidate a comprehensive picture of neural dynamics and captures both individual and pairwise activity measures into a single quantity known as energy, which is inversely related to the probability of state occurrence. We applied the MEM framework to task functional MRI data collected on 23 AOS individuals in comparison with 53 healthy control subjects while performing the Penn Conditional Exclusion Test (PCET), which measures executive function that has been repeatedly shown to be more impaired in AOS compared to adult-onset schizophrenia. Accuracy of PCET performance was significantly reduced among AOS compared to controls as expected. Average cumulative energy achieved for a participant over the course of the fMRI negatively correlated with task performance, and the association was stronger than any first-order associations. The AOS subjects spent more time in higher energy states that represent lower probability of occurrence and were associated with impaired executive function and greater severity of psychopathology suggesting that the neural dynamics may be less efficient compared to controls who spent more time in lower energy states occurring with higher probability and hence are more stable and efficient. The energy landscapes in both conditions featured attractors that corresponded to two distinct subnetworks, namely fronto-temporal and parieto-motor. Attractor basins were larger in the controls than in AOS; moreover, fronto-temporal basin size was significantly correlated with cognitive performance in controls but not among the AOS. The single trial trajectories for the AOS group also showed higher variability in concordance with shallow attractor basins among AOS. These findings suggest that the neural dynamics of AOS features more frequent occurrence of less probable states with shallower attractors, which lack the relation to executive function associated with attractors in control subjects suggesting a diminished capacity of AOS to generate task-effective brain states.

Spatial-temporal convolutional attention for discovering and characterizing functional brain networks in task fMRI

Functional brain networks (FBNs) are spatial patterns of brain function that play a critical role in understanding human brain function. There are many proposed methods for mapping the spatial patterns of brain function, however they oversimplify the underlying assumptions of brain function and have various limitations such as linearity and independence. Additionally, current methods fail to account for the dynamic nature of FBNs, which limits their effectiveness in accurately characterizing these networks. To address these limitations, we present a novel deep learning and spatial-wise attention based model called Spatial-Temporal Convolutional Attention (STCA) to accurately model dynamic FBNs. Specifically, we train STCA in a self-supervised manner by utilizing a Convolutional Autoencoder to guide the STCA module in assigning higher attention weights to regions of functional activity. To validate the reliability of the results, we evaluate our approach on the HCP-task motor behavior dataset, the experimental results demonstrate that the STCA derived FBNs have higher spatial similarity with the templates and that the spatial similarity between the templates and the FBNs derived by STCA fluctuates with the task design over time, suggesting that STCA can reflect the dynamic changes of brain function, providing a powerful tool to better understand human brain function. Code is available at https://github.com/SNNUBIAI/STCAE.

Graph Learning for Cortical Parcellation from Tensor Decompositions of Resting-State fMRI

Cortical parcellation has long been a cornerstone in the field of neuroscience, enabling the cerebral cortex to be partitioned into distinct, non-overlapping regions that facilitate the interpretation and comparison of complex neuroscientific data. In recent years, these parcellations have frequently been based on the use of resting-state fMRI (rsfMRI) data. In parallel, methods such as independent components analysis have long been used to identify large-scale functional networks with significant spatial overlap between networks. Despite the fact that both forms of decomposition make use of the same spontaneous brain activity measured with rsfMRI, a gap persists in establishing a clear relationship between disjoint cortical parcellations and brain-wide networks. To address this, we introduce a novel parcellation framework that integrates NASCAR, a three-dimensional tensor decomposition method that identifies a series of functional brain networks, with state-of-the-art graph representation learning to produce cortical parcellations that represent near-homogeneous functional regions that are consistent with these brain networks. Further, through the use of the tensor decomposition, we avoid the limitations of traditional approaches that assume statistical independence or orthogonality in defining the underlying networks. Our findings demonstrate that these parcellations are comparable or superior to established atlases in terms of homogeneity of the functional connectivity across parcels, task contrast alignment, and architectonic map alignment. Our methodological pipeline is highly automated, allowing for rapid adaptation to new datasets and the generation of custom parcellations in just minutes, a significant advancement over methods that require extensive manual input. We describe this integrated approach, which we refer to as Untamed, as a tool for use in the fields of cognitive and clinical neuroscientific research. Parcellations created from the Human Connectome Project dataset using Untamed, along with the code to generate atlases with custom parcel numbers, are publicly available at https://untamed-atlas.github.io.

Testing the triple network model of psychopathology in a transdiagnostic neurodevelopmental cohort

AIM

The triple network model of psychopathology posits that altered connectivity between the Salience (SN), Central Executive (CEN), and Default Mode Networks (DMN) may underlie neurodevelopmental conditions. However, this has yet to be tested in a transdiagnostic sample of young people.

METHOD

We investigated this in 175 children (60 girls) that represent a heterogeneous population who are experiencing neurodevelopmental difficulties in cognition and behavior, and 60 comparison children (33 girls). Hyperactivity/impulsivity and inattention were assessed by parent-report. Resting-state functional Magnetic Resonance Imaging data were acquired and functional connectivity was calculated between independent network components and regions of interest. We then examined whether connectivity between the SN, CEN and DMN was dimensionally related to hyperactivity/impulsivity and inattention, whilst controlling for age, gender, and motion.

RESULTS

Hyperactivity/impulsivity was associated with increased functional connectivity between the SN, CEN, and DMN in at-risk children, whereas it was associated with decreased functional connectivity between the CEN and DMN in comparison children. These effects replicated in an adult parcellation of brain function and when using increasingly stringent exclusion criteria for in-scanner motion.

CONCLUSION

Triple network connectivity characterizes transdiagnostic neurodevelopmental difficulties with hyperactivity/impulsivity. We suggest that this may arise from delayed network segregation, difficulties sustaining CEN activity to regulate behavior, and/or a heightened developmental mismatch between neural systems implicated in cognitive control relative to those implicated in reward/affect processing.

Dynamic functional connectivity changes associated with psychiatric traits and cognitive deficits in Cushing's disease

Cushing's disease is a rare neuroendocrine disorder with excessive endogenous cortisol, impaired cognition, and psychiatric symptoms. Evidence from resting-state fMRI revealed the abnormalities of static brain connectivity in patients with Cushing's disease (CD patients). However, it is unknown whether the CD patients' dynamic functional connectivity would be abnormal and whether the dynamic features are associated with deficits in cognition and psychopathological symptoms. Here, we evaluated 50 patients with Cushing's disease and 57 healthy participants by using resting-state fMRI and dynamic functional connectivity (dFNC) approach. We focused on the dynamic features of default mode network (DMN), salience network (SN), and central executive network (CEN) because these are binding sites for the cognitive-affective process, as well as vital in understanding the pathophysiology of psychiatric disorders. The dFNC was further clustered into four states by k-mean clustering. CD patients showed more dwell time in State 1 but less time in State 4. Intriguingly, group differences in dwell time in these two states can explain the cognitive deficits of CD patients. Moreover, the inter-network connections between DMN and SN and the engagement time in State 4 negatively correlated with anxiety and depression but positively correlated with cognitive performance. Finally, the classifier trained by the dynamic features of these networks successfully classified CD patients from healthy participants. Together, our study revealed the dynamic features of CD patients' brains and found their associations with impaired cognition and emotional symptoms, which may open new avenues for understanding the cognitive and affective deficits induced by Cushing's disease.

Locally Low-Rank Denoising of Multi-Echo Functional MRI Data With Application in Resting-State Analysis

OBJECTIVES

Locally low-rank (LLR) denoising of functional magnetic resonance imaging (fMRI) time series image data is extended to multi-echo (ME) data. The proposed method extends the capabilities of non-physiologic noise suppression beyond single-echo applications with a dedicated ME algorithm.

MATERIALS AND METHODS

Following an institutional review board (IRB) approved protocol, resting-state fMRI data were acquired in 7 healthy subjects. A compact 3T scanner enabled whole-brain acquisition of multiband ME fMRI data at high spatial resolution (1.4 × 1.4 × 2.8 mm 3 ) with a 1810 ms repetition time (TR). Image data were denoised with ME-LLR preceding functional processing. The results of connectivity maps generated from denoised data were compared with maps generated with equivalent processing of non-denoised images. To assess ME-LLR as a method to reduce scan time, comparisons were made between maps computed from image data with full and retrospectively truncated durations. Assessments were completed with seed-based connectivity analyses using echo-combined image data. In a feasibility assessment, nondenoised and denoised full-duration echo-combined data were equivalently processed with independent component analysis (ICA) and compared.

RESULTS

ME-LLR denoising yielded strengthened resting-state network connectivity maps after nuisance regression and seed-based connectivity analysis. In assessing ME-LLR as a scan reduction mechanism, maps generated from denoised data at half scan time showed comparable quality with maps generated from full-duration, non-denoised data, at both single subject and group levels. ME-LLR substantially increased temporal signal-to-noise ratio (tSNR) for image data respective to each individual echo and for image data after nuisance regression. Among echo-specific image volumes, increases in tSNR yielded by ME-LLR were most pronounced for image data with the longest echo time and thereby lowest SNR. ICA showed resting-state networks consistently identified between non-denoised and denoised data, with clearer demarcation of networks for ME-LLR.

CONCLUSIONS

ME-LLR is demonstrated to suppress non-physiologic noise, enhance functional connectivity map quality, and could potentially facilitate scan time reduction in ME-fMRI.

Echoes from Intrinsic Connectivity Networks in the Subcortex

Decades of research have greatly improved our understanding of intrinsic human brain organization in terms of functional networks and the transmodal hubs within the cortex at which they converge. However, substrates of multinetwork integration in the human subcortex are relatively uncharted. Here, we leveraged recent advances in subcortical atlasing and ultra-high field (7 T) imaging optimized for the subcortex to investigate the functional architecture of 14 individual structures in healthy adult males and females with a fully data-driven approach. We revealed that spontaneous neural activity in subcortical regions can be decomposed into multiple independent subsignals that correlate with, or "echo," the activity in functional networks across the cortex. Distinct subregions of the thalamus, striatum, claustrum, and hippocampus showed a varied pattern of echoes from attention, control, visual, somatomotor, and default mode networks, demonstrating evidence for a heterogeneous organization supportive of functional integration. Multiple network activity furthermore converged within the globus pallidus externa, substantia nigra, and ventral tegmental area but was specific to one subregion, while the amygdala and pedunculopontine nucleus preferentially affiliated with a single network, showing a more homogeneous topography. Subregional connectivity of the globus pallidus interna, subthalamic nucleus, red nucleus, periaqueductal gray, and locus coeruleus did not resemble patterns of cortical network activity. Together, these finding describe potential mechanisms through which the subcortex participates in integrated and segregated information processing and shapes the spontaneous cognitive dynamics during rest.SIGNIFICANCE STATEMENT Despite the impact of subcortical dysfunction on brain health and cognition, large-scale functional mapping of subcortical structures severely lags behind that of the cortex. Recent developments in subcortical atlasing and imaging at ultra-high field provide new avenues for studying the intricate functional architecture of the human subcortex. With a fully data-driven analysis, we reveal subregional connectivity profiles of a large set of noncortical structures, including those rarely studied in fMRI research. The results have implications for understanding how the functional organization of the subcortex facilitates integrative processing through cross-network information convergence, paving the way for future work aimed at improving our knowledge of subcortical contributions to intrinsic brain dynamics and spontaneous cognition.

Altered Spinal Cord Functional Connectivity Associated with Parkinson's Disease Progression

BACKGROUND

Parkinson's disease (PD) has traditionally been viewed as an α-synucleinopathy brain pathology. Yet evidence based on postmortem human and animal experimental models indicates that the spinal cord may also be affected.

OBJECTIVE

Functional magnetic resonance imaging (fMRI) seems to be a promising candidate to better characterize spinal cord functional organization in PD patients.

METHODS

Resting-state spinal fMRI was performed in 70 PD patients and 24 age-matched healthy controls, the patients being divided into three groups based on their motor symptom severity: PD_low (n = 24), PD_med (n = 22), and PD_adv (n = 24) groups. A combination of independent component analysis (ICA) and a seed-based approach was applied.

RESULTS

When pooling all participants, the ICA revealed distinct ventral and dorsal components distributed along the rostro-caudal axis. This organization was highly reproducible within subgroups of patients and controls. PD severity, assessed by Unified Parkinson's Disease Rating Scale (UPDRS) scores, was associated with a decrease in spinal functional connectivity (FC). Notably, we observed a reduced intersegmental correlation in PD as compared to controls, the latter being negatively associated with patients' upper-limb UPDRS scores (P = 0.0085). This negative association between FC and upper-limb UPDRS scores was significant between adjacent C4-C5 (P = 0.015) and C5-C6 (P = 0.20) cervical segments, levels associated with upper-limb functions.

CONCLUSIONS

The present study provides the first evidence of spinal cord FC changes in PD and opens new avenues for the effective diagnosis and therapeutic strategies in PD. This underscores how spinal cord fMRI can serve as a powerful tool to characterize, in vivo, spinal circuits for a variety of neurological diseases. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

The expanding horizons of network neuroscience: From description to prediction and control

The field of network neuroscience has emerged as a natural framework for the study of the brain and has been increasingly applied across divergent problems in neuroscience. From a disciplinary perspective, network neuroscience originally emerged as a formal integration of graph theory (from mathematics) and neuroscience (from biology). This early integration afforded marked utility in describing the interconnected nature of neural units, both structurally and functionally, and underscored the relevance of that interconnection for cognition and behavior. But since its inception, the field has not remained static in its methodological composition. Instead, it has grown to use increasingly advanced graph-theoretic tools and to bring in several other disciplinary perspectives-including machine learning and systems engineering-that have proven complementary. In doing so, the problem space amenable to the discipline has expanded markedly. In this review, we discuss three distinct flavors of investigation in state-of-the-art network neuroscience: (i) descriptive network neuroscience, (ii) predictive network neuroscience, and (iii) a perturbative network neuroscience that draws on recent advances in network control theory. In considering each area, we provide a brief summary of the approaches, discuss the nature of the insights obtained, and highlight future directions.

Multisubject Task-Related fMRI Data Processing via a Two-Stage Generalized Canonical Correlation Analysis

Functional magnetic resonance imaging (fMRI) is one of the most popular methods for studying the human brain. Task-related fMRI data processing aims to determine which brain areas are activated when a specific task is performed and is usually based on the Blood Oxygen Level Dependent (BOLD) signal. The background BOLD signal also reflects systematic fluctuations in regional brain activity which are attributed to the existence of resting-state brain networks. We propose a new fMRI data generating model which takes into consideration the existence of common task-related and resting-state components. We first estimate the common task-related temporal component, via two successive stages of generalized canonical correlation analysis and, then, we estimate the common task-related spatial component, leading to a task-related activation map. The experimental tests of our method with synthetic data reveal that we are able to obtain very accurate temporal and spatial estimates even at very low Signal to Noise Ratio (SNR), which is usually the case in fMRI data processing. The tests with real-world fMRI data show significant advantages over standard procedures based on General Linear Models (GLMs).

Conflict- and error-related theta activities are coupled to BOLD signals in different brain regions

Both conflict and error processing have been linked to the midfrontal theta power (4-8 Hz) increase as indicated by EEG studies and greater hemodynamic activity in the anterior midcingulate cortex (aMCC) as indicated by fMRI studies. Conveniently, the source of the midfrontal theta power was estimated in or nearby aMCC. However, previous studies using concurrent EEG and fMRI recordings in resting-state or other cognitive tasks observed only a negative relationship between theta power and BOLD signal in the brain regions typically showing task-related deactivations. In this study, we used a simultaneous EEG-fMRI technique to investigate a trial-by-trial coupling between theta power and hemodynamic activity during the performance of two conflict tasks. Independent component analysis (ICA) was applied to denoise the EEG signal and select individual midfrontal EEG components, whereas group ICA was applied to fMRI data to obtain a functional parcellation of the frontal cortex. Using a linear mixed-effect model, theta power was coupled with the peak of hemodynamic responses from various frontal, cingulate, and insular cortical sites to unravel the potential brain sources that contribute to conflict- and error-related theta variability. Although several brain regions exhibited conflict-related increases in hemodynamic activity, the conflict pre-response theta showed only a negative correlation to BOLD signal in the midline area 9 (MA9), a region exhibiting conflict-sensitive deactivation. Conversely, and more expectedly, error-related theta showed a positive relationship to activity in the aMCC. Our results provide novel evidence suggesting that the amplitude of pre-response theta reflects the process of active inhibition that suppresses the MA9 activity. This process is affected independently by the stimulus congruency, reaction times variance, and is susceptible to the time-on-task effect. Finally, it predicts the commitment of an omission error. Together, our findings highlight that conflict- and error-related theta oscillations represent fundamentally different processes.

MRI biomarkers for Alzheimer's disease: the impact of functional connectivity in the default mode network and structural connectivity between lobes on diagnostic accuracy

Background

At present, clinical use of MRI in Alzheimer's disease (AD) is mostly focused on the assessment of brain atrophy, namely in the hippocampal region. Despite this, multiple biomarkers reflecting structural and functional brain connectivity changes have shown promising results in the assessment of AD. To help identify the most relevant ones that may stand a chance of being used in clinical practice, we compared multiple biomarker in terms of their value to discriminate AD from healthy controls and analyzed their age dependency.

Methods

20 AD patients and 20 matched controls underwent MRI-scanning (3T GE), including T1-weighted, diffusion-MRI, and resting-state-fMRI (rsfMRI). Whole brain, white matter, gray matter, cortical gray matter and hippocampi volumes were measured using icobrain. rsfMRI between regions of the default-mode-network (DMN) was assessed using group independent-component-analysis. Median diffusivity and kurtosis were determined in gray and white-matter. DTI data was used to evaluate pairwise structural connectivity between lobar regions and the hippocampi.

Logistic-Regression and Random-Forest models were trained to classify AD-status based on, respectively different isolated features and age, and feature-groups combined with age.

Results

Hippocampal features, features reflecting the functional connectivity between the medial-Pre-Frontal-Cortex (mPFC) and the posterior regions of the DMN, and structural interhemispheric frontal connectivity showed the strongest differences between AD-patients and controls. Structural interhemispheric parietal connectivity, structural connectivity between the parietal lobe and hippocampus in the right hemisphere, and mPFC-DMN-features, showed only an association with AD-status (p < 0.05) but not with age. Hippocampi volumes showed an association both with age and AD-status (p < 0.05).

Smallest-hippocampus-volume was the most discriminative feature. The best performance (accuracy:0.74, sensitivity:0.74, specificity:0.74) was obtained with an RF-model combining the best feature from each feature-group (smallest hippocampus volume, WM volume, median GM MD, lTPJ-mPFC connectivity and structural interhemispheric frontal connectivity) and age.

Conclusions

Brain connectivity changes caused by AD are reflected in multiple MRI-biomarkers. Decline in both the functional DMN-connectivity and the parietal interhemispheric structural connectivity may assist sepparating healthy-aging driven changes from AD, complementing hippocampal volumes which are affected by both aging and AD.

Association between aerobic fitness and the functional connectome in patients with schizophrenia

BACKGROUND

Schizophrenia is accompanied by widespread alterations in static functional connectivity associated with symptom severity and cognitive deficits. Improvements in aerobic fitness have been demonstrated to ameliorate symptomatology and cognition in people with schizophrenia, but the intermediary role of macroscale connectivity patterns remains unknown.

OBJECTIVE

Therefore, we aim to explore the relation between aerobic fitness and the functional connectome in individuals with schizophrenia. Further, we investigate clinical and cognitive relevance of the identified fitness-connectivity links.

METHODS

Patients diagnosed with schizophrenia were included in this cross-sectional resting-state fMRI analysis. Multilevel Bayesian partial correlations between aerobic fitness and functional connections across the whole brain as well as between static functional connectivity patterns and clinical and cognitive outcome were performed. Preliminary causal inferences were enabled based on mediation analyses.

RESULTS

Static functional connectivity between the subcortical nuclei and the cerebellum as well as between temporal seeds mediated the attenuating relation between aerobic fitness and total symptom severity. Functional connections between cerebellar seeds affected the positive link between aerobic fitness and global cognition, while the functional interplay between central and limbic seeds drove the beneficial association between aerobic fitness and emotion recognition.

CONCLUSION

The current study provides first insights into the interactions between aerobic fitness, the functional connectome and clinical and cognitive outcome in people with schizophrenia, but causal interpretations are preliminary. Further interventional aerobic exercise studies are needed to replicate the current findings and to enable conclusive causal inferences.

TRIAL REGISTRATION

The study which the manuscript is based on is registered in the International Clinical Trials Database (ClinicalTrials.gov identifier [NCT number]: NCT03466112) and in the German Clinical Trials Register (DRKS-ID: DRKS00009804).

Resting-State Functional Connectivity in Frontostriatal and Posterior Cortical Subtypes in Parkinson's Disease-Mild Cognitive Impairment

BACKGROUND

The "dual syndrome hypothesis" distinguished two subtypes in mild cognitive impairment (MCI) in Parkinson's disease: frontostriatal, characterized by attentional and executive deficits; and posterior cortical, characterized by visuospatial, memory, and language deficits.

OBJECTIVE

The aim was to identify resting-state functional modifications associated with these subtypes.

METHODS

Ninety-five nondemented patients categorized as having normal cognition (n = 31), frontostriatal (n = 14), posterior cortical (n = 20), or mixed (n = 30) cognitive subtype had a 3 T resting-state functional magnetic resonance imaging scan. Twenty-four age-matched healthy controls (HCs) were also included. A group-level independent component analysis was performed to identify resting-state networks, and the selected components were subdivided into 564 cortical regions in addition to 26 basal ganglia regions. Global intra- and inter-network connectivity along with global and local efficiencies was compared between groups. The network-based statistics approach was used to identify connections significantly different between groups.

RESULTS

Patients with posterior cortical deficits had increased intra-network functional connectivity (FC) within the basal ganglia network compared with patients with frontostriatal deficits. Patients with frontostriatal deficits had reduced inter-network FC between several networks, including the visual, default-mode, sensorimotor, salience, dorsal attentional, basal ganglia, and frontoparietal networks, compared with HCs, patients with normal cognition, and patients with a posterior cortical subtype. Similar results were also found between patients with a mixed subtype and HCs.

CONCLUSION

MCI subtypes are associated with specific changes in resting-state FC. Longitudinal studies are needed to determine the predictive potential of these markers regarding the risk of developing dementia. © 2021 International Parkinson and Movement Disorder Society.

Automatic parcellation of resting-state cortical dynamics by iterative community detection and similarity measurements

To investigate the properties of a large-scale brain network, it is a common practice to reduce the dimension of resting state functional magnetic resonance imaging (rs-fMRI) data to tens to hundreds of nodes. This study presents an analytic streamline that incorporates modular analysis and similarity measurements (MOSI) to fulfill functional parcellation (FP) of the cortex. MOSI is carried out by iteratively dividing a module into sub-modules (via the Louvain community detection method) and unifying similar neighboring sub-modules into a new module (adjacent sub-modules with a similarity index <0.05) until the brain modular structures of successive runs become constant. By adjusting the gamma value, a parameter in the Louvain algorithm, MOSI may segment the cortex with different resolutions. rs-fMRI scans of 33 healthy subjects were selected from the dataset of the Rockland sample. MOSI was applied to the rs-fMRI data after standardized pre-processing steps. The results indicate that the parcellated modules by MOSI are more homogeneous in content. After reducing the grouped voxels to representative neural nodes, the network structures were explored. The resultant network components were comparable with previous reports. The validity of MOSI in achieving data reduction has been confirmed. MOSI may provide a novel starting point for further investigation of the network properties of rs-fMRI data. Potential applications of MOSI are discussed.

Multivariate semi-blind deconvolution of fMRI time series

Whole brain estimation of the haemodynamic response function (HRF) in functional magnetic resonance imaging (fMRI) is critical to get insight on the global status of the neurovascular coupling of an individual in healthy or pathological condition. Most of existing approaches in the literature works on task-fMRI data and relies on the experimental paradigm as a surrogate of neural activity, hence remaining inoperative on resting-stage fMRI (rs-fMRI) data. To cope with this issue, recent works have performed either a two-step analysis to detect large neural events and then characterize the HRF shape or a joint estimation of both the neural and haemodynamic components in an univariate fashion. In this work, we express the neural activity signals as a combination of piece-wise constant temporal atoms associated with sparse spatial maps and introduce an haemodynamic parcellation of the brain featuring a temporally dilated version of a given HRF model in each parcel with unknown dilation parameters. We formulate the joint estimation of the HRF shapes and spatio-temporal neural representations as a multivariate semi-blind deconvolution problem in a paradigm-free setting and introduce constraints inspired from the dictionary learning literature to ease its identifiability. A fast alternating minimization algorithm, along with its efficient implementation, is proposed and validated on both synthetic and real rs-fMRI data at the subject level. To demonstrate its significance at the population level, we apply this new framework to the UK Biobank data set, first for the discrimination of haemodynamic territories between balanced groups (n=24 individuals in each) patients with an history of stroke and healthy controls and second, for the analysis of normal aging on the neurovascular coupling. Overall, we statistically demonstrate that a pathology like stroke or a condition like normal brain aging induce longer haemodynamic delays in certain brain areas (e.g. Willis polygon, occipital, temporal and frontal cortices) and that this haemodynamic feature may be predictive with an accuracy of 74 % of the individual's age in a supervised classification task performed on n=459 subjects.

Hemodynamic matrix factorization for functional magnetic resonance imaging

The General Linear Model (GLM) used in task-fMRI relates activated brain areas to extrinsic task conditions. The translation of resulting neural activation into a hemodynamic response is commonly approximated with a linear convolution model using a hemodynamic response function (HRF). There are two major limitations in GLM analysis. Firstly, the GLM assumes that neural activation is either on or off and matches the exact stimulus duration in the corresponding task timings. Secondly, brain networks observed in resting-state fMRI experiments present also during task experiments, but the GLM approach models these task-unrelated brain activity as noise. A novel kernel matrix factorization approach, called hemodynamic matrix factorization (HMF), is therefore proposed that addresses both limitations by assuming that task-related and task-unrelated brain activity can be modeled with the same convolution model as in GLM analysis. By contrast to the GLM, the proposed HMF is a blind source separation (BSS) technique, which decomposes fMRI data into modes. Each mode comprises of a neural activation time course and a spatial mapping. Two versions of HMF are proposed in which the neural activation time course of each mode is convolved with either the canonical HRF or predetermined subject-specific HRFs. Firstly, HMF with the canonical HRF is applied to two open-source cohorts. These cohorts comprise of several task experiments including motor, incidental memory, spatial coherence discrimination, verbal discrimination task and a very short localization task, engaging multiple parts of the eloquent cortex. HMF modes were obtained whose neural activation time course followed original task timings and whose corresponding spatial map matched cortical areas known to be involved in the respective task processing. Secondly, the alignment of these neural activation time courses to task timings were further improved by replacing the canonical HRF with subject-specific HRFs during HMF mode computation. In addition to task-related modes, HMF also produced seemingly task-unrelated modes whose spatial maps matched known resting-state networks. The validity of a fMRI task experiment relies on the assumption that the exposure to a stimulus for a given time causes an imminent increase in neural activation of equal duration. The proposed HMF is an attempt to falsify this assumption and allows to identify subject task participation that does not comply with the experiment instructions.

Jumping over baselines with new methods to predict activation maps from resting-state fMRI

Cognitive fMRI research primarily relies on task-averaged responses over many subjects to describe general principles of brain function. Nonetheless, there exists a large variability between subjects that is also reflected in spontaneous brain activity as measured by resting state fMRI (rsfMRI). Leveraging this fact, several recent studies have therefore aimed at predicting task activation from rsfMRI using various machine learning methods within a growing literature on 'connectome fingerprinting'. In reviewing these results, we found lack of an evaluation against robust baselines that reliably supports a novelty of predictions for this task. On closer examination to reported methods, we found most underperform against trivial baseline model performances based on massive group averaging when whole-cortex prediction is considered. Here we present a modification to published methods that remedies this problem to large extent. Our proposed modification is based on a single-vertex approach that replaces commonly used brain parcellations. We further provide a summary of this model evaluation by characterizing empirical properties of where prediction for this task appears possible, explaining why some predictions largely fail for certain targets. Finally, with these empirical observations we investigate whether individual prediction scores explain individual behavioral differences in a task.

Brain topography beyond parcellations: Local gradients of functional maps

Functional neuroimaging provides the unique opportunity to characterize brain regions based on their response to tasks or ongoing activity. As such, it holds the premise to capture brain spatial organization. Yet, the conceptual framework to describe this organization has remained elusive: on the one hand, parcellations build implicitly on a piecewise constant organization, i.e. flat regions separated by sharp boundaries; on the other hand, the recently popularized concept of functional gradient hints instead at a smooth structure. Noting that both views converge to a topographic scheme that pieces together local variations of functional features, we perform a quantitative assessment of local gradient-based models. Using as a driving case the prediction of functional Magnetic Resonance Imaging (fMRI) data -concretely, the prediction of task-fMRI from rest-fMRI maps across subjects- we develop a parcel-wise linear regression model based on a dictionary of reference topographies. Our method uses multiple random parcellations -as opposed to a single fixed parcellation- and aggregates estimates across these parcellations to predict functional features in left-out subjects. Our experiments demonstrate the existence of an optimal cardinality of the parcellation to capture local gradients of functional maps.

The integration of social and neural synchrony: a case for ecologically valid research using MEG neuroimaging

The recent decade has seen a shift from artificial and environmentally deprived experiments in neuroscience to real-life studies on multiple brains in interaction, coordination and synchrony. In these new interpersonal synchrony experiments, there has been a growing trend to employ naturalistic social interactions to evaluate mechanisms underlying synchronous neuronal communication. Here, we emphasize the importance of integrating the assessment of neural synchrony with measurement of nonverbal behavioral synchrony as expressed in various social contexts: relaxed social interactions, planning a joint pleasurable activity, conflict discussion, invocation of trauma, or support giving and assess the integration of neural and behavioral synchrony across developmental stages and psychopathological conditions. We also showcase the advantages of magnetoencephalography neuroimaging as a promising tool for studying interactive neural synchrony and consider the challenge of ecological validity at the expense of experimental rigor. We review recent evidence of rhythmic information flow between brains in interaction and conclude with addressing state-of-the-art developments that may contribute to advance research on brain-to-brain coordination to the next level.

Robust brain network identification from multi-subject asynchronous fMRI data

We describe a novel method for robust identification of common brain networks and their corresponding temporal dynamics across subjects from asynchronous functional MRI (fMRI) using tensor decomposition. We first temporally align asynchronous fMRI data using the orthogonal BrainSync transform, allowing us to study common brain networks across sessions and subjects. We then map the synchronized fMRI data into a 3D tensor (vertices × time × subject/session). Finally, we apply Nesterov-accelerated adaptive moment estimation (Nadam) within a scalable and robust sequential Canonical Polyadic (CP) decomposition framework to identify a low rank tensor approximation to the data. As a result of CP tensor decomposition, we successfully identified twelve known brain networks with their corresponding temporal dynamics from 40 subjects using the Human Connectome Project's language task fMRI data without any prior information regarding the specific task designs. Seven of these networks show distinct subjects' responses to the language task with differing temporal dynamics; two show sub-components of the default mode network that exhibit deactivation during the tasks; the remaining three components reflect non-task-related activities. We compare results to those found using group independent component analysis (ICA) and canonical ICA. Bootstrap analysis demonstrates increased robustness of networks found using the CP tensor approach relative to ICA-based methods.

Brain networks involved in place recognition based on personal and spatial semantics

Have you ever been to Krakow? If so, then you may recognize the Wawel Royal Castle from a picture due to your personal semantic memory, which stores all autobiographically significant concepts and repeated events of your past. If not, then you might still recognize the Wawel Royal Castle and be able to locate it on a map due to your spatial semantic memory. When recognizing a familiar landmark, how does neural activity depend on your memory related to that place? To address this question, we combined a novel task - the Krakow paradigm - with fMRI. In this task, participants are presented with a set of pictures showing various Krakow landmarks, each followed by two questions - one about its location, and the other about seeing the place in real-life, to trigger spatial and/or personal semantic memory, respectively. Group independent component analysis of fMRI data revealed several brain networks sensitive to the task conditions. Most sensitive was the medial temporal lobe network comprising bilateral hippocampus, parahippocampal, retrosplenial, and angular gyri, as well as distinct frontal areas. In agreement with the contextual continuum perspective, this network exhibited robust stimulus-related activity when the two memory types were combined, medium for spatial memory, and the weakest for baseline condition. The medial prefrontal network showed the same, pronounced deactivation for spatial memory and baseline conditions, yet far less deactivation for places seen in real-life. This effect was interpreted as self-referential processes counterbalancing the suppression of the brain's 'default mode.' In contrast, the motor, frontoparietal, and cingulo-opercular networks exhibited the strongest response-related activity for the spatial condition. These findings indicate that recognizing places based solely on general semantic knowledge requires more evidence accumulation, additional verbal semantics, and greater top-down control. Thus, the study imparts a novel insight into the neural mechanisms of place recognition. The Krakow paradigm has the potential to become a useful tool in future longitudinal or clinical studies.

Diagnosis of Autism Spectrum Disorder Based on Functional Brain Networks with Deep Learning

Autism spectrum disorder (ASD) is a neurological and developmental disorder. Traditional diagnosis of ASD is typically performed through the observation of behaviors and interview of a patient. However, these diagnosis methods are time-consuming and can be misleading sometimes. Integrating machine learning algorithms with neuroimages, a diagnosis method, can possibly be established to detect ASD subjects from typical control subjects. In this study, we develop deep learning methods for diagnosis of ASD from functional brain networks constructed with brain functional magnetic resonance imaging (fMRI) data. The entire Autism Brain Imaging Data Exchange 1 (ABIDE 1) data set is utilized to investigate the performance of our proposed methods. First, we construct the brain networks from brain fMRI images and define the raw features based on such brain networks. Second, we employ an autoencoder (AE) to learn the advanced features from the raw features. Third, we train a deep neural network (DNN) with the advanced features, which achieves the classification accuracy of 76.2% and the receiving operating characteristic curve (AUC) of 79.7%. As a comparison, we also apply the same advanced features to train several traditional machine learning algorithms to benchmark the classification performance. Finally, we combine the DNN with the pretrained AE and train it with the raw features, which achieves the classification accuracy of 79.2% and the AUC of 82.4%. These results show that our proposed deep learning methods outperform the state-of-the-art methods.

A technical review of canonical correlation analysis for neuroscience applications

Collecting comprehensive data sets of the same subject has become a standard in neuroscience research and uncovering multivariate relationships among collected data sets have gained significant attentions in recent years. Canonical correlation analysis (CCA) is one of the powerful multivariate tools to jointly investigate relationships among multiple data sets, which can uncover disease or environmental effects in various modalities simultaneously and characterize changes during development, aging, and disease progressions comprehensively. In the past 10 years, despite an increasing number of studies have utilized CCA in multivariate analysis, simple conventional CCA dominates these applications. Multiple CCA-variant techniques have been proposed to improve the model performance; however, the complicated multivariate formulations and not well-known capabilities have delayed their wide applications. Therefore, in this study, a comprehensive review of CCA and its variant techniques is provided. Detailed technical formulation with analytical and numerical solutions, current applications in neuroscience research, and advantages and limitations of each CCA-related technique are discussed. Finally, a general guideline in how to select the most appropriate CCA-related technique based on the properties of available data sets and particularly targeted neuroscience questions is provided.

Modelling subject variability in the spatial and temporal characteristics of functional modes

Recent work has highlighted the scale and ubiquity of subject variability in observations from functional MRI data (fMRI). Furthermore, it is highly likely that errors in the estimation of either the spatial presentation of, or the coupling between, functional regions can confound cross-subject analyses, making accurate and unbiased representations of functional data essential for interpreting any downstream analyses. Here, we extend the framework of probabilistic functional modes (PFMs) (Harrison et al., 2015) to capture cross-subject variability not only in the mode spatial maps, but also in the functional coupling between modes and in mode amplitudes. A new implementation of the inference now also allows for the analysis of modern, large-scale data sets, and the combined inference and analysis package, PROFUMO, is available from git.fmrib.ox.ac.uk/samh/profumo. A new implementation of the inference now also allows for the analysis of modern, large-scale data sets. Using simulated data, resting-state data from 1000 subjects collected as part of the Human Connectome Project (Van Essen et al., 2013), and an analysis of 14 subjects in a variety of continuous task-states (Kieliba et al., 2019), we demonstrate how PFMs are able to capture, within a single model, a rich description of how the spatio-temporal structure of resting-state fMRI activity varies across subjects. We also compare the new PFM model to the well established independent component analysis with dual regression (ICA-DR) pipeline. This reveals that, under PFM assumptions, much more of the (behaviorally relevant) cross-subject variability in fMRI activity should be attributed to the variability in spatial maps, and that, after accounting for this, functional coupling between modes primarily reflects current cognitive state. This has fundamental implications for the interpretation of cross-sectional studies of functional connectivity that do not capture cross-subject variability to the same extent as PFMs.

Fine-grain atlases of functional modes for fMRI analysis

Population imaging markedly increased the size of functional-imaging datasets, shedding new light on the neural basis of inter-individual differences. Analyzing these large data entails new scalability challenges, computational and statistical. For this reason, brain images are typically summarized in a few signals, for instance reducing voxel-level measures with brain atlases or functional modes. A good choice of the corresponding brain networks is important, as most data analyses start from these reduced signals. We contribute finely-resolved atlases of functional modes, comprising from 64 to 1024 networks. These dictionaries of functional modes (DiFuMo) are trained on millions of fMRI functional brain volumes of total size 2.4 ​TB, spanned over 27 studies and many research groups. We demonstrate the benefits of extracting reduced signals on our fine-grain atlases for many classic functional data analysis pipelines: stimuli decoding from 12,334 brain responses, standard GLM analysis of fMRI across sessions and individuals, extraction of resting-state functional-connectomes biomarkers for 2500 individuals, data compression and meta-analysis over more than 15,000 statistical maps. In each of these analysis scenarii, we compare the performance of our functional atlases with that of other popular references, and to a simple voxel-level analysis. Results highlight the importance of using high-dimensional "soft" functional atlases, to represent and analyze brain activity while capturing its functional gradients. Analyses on high-dimensional modes achieve similar statistical performance as at the voxel level, but with much reduced computational cost and higher interpretability. In addition to making them available, we provide meaningful names for these modes, based on their anatomical location. It will facilitate reporting of results.

Sammba-MRI: A Library for Processing SmAll-MaMmal BrAin MRI Data in Python

Small-mammal neuroimaging offers incredible opportunities to investigate structural and functional aspects of the brain. Many tools have been developed in the last decade to analyse small animal data, but current softwares are less mature than the available tools that process human brain data. The Python package Sammba-MRI (SmAll-MaMmal BrAin MRI in Python; http://sammba-mri.github.io) allows flexible and efficient use of existing methods and enables fluent scriptable analysis workflows, from raw data conversion to multimodal processing.

Inter-Network High-Order Functional Connectivity (IN-HOFC) and its Alteration in Patients with Mild Cognitive Impairment

Little is known about the high-order interactions among brain regions measured by the similarity of higher-order features (other than the raw blood-oxygen-level-dependent signals) which can characterize higher-level brain functional connectivity (FC). Previously, we proposed FC topographical profile-based high-order FC (HOFC) and found that this metric could provide supplementary information to traditional FC for early Alzheimer's disease (AD) detection. However, whether such findings apply to network-level brain functional integration is unknown. In this paper, we propose an extended HOFC method, termed inter-network high-order FC (IN-HOFC), as a useful complement to the traditional inter-network FC methods, for characterizing more complex organizations among the large-scale brain networks. In the IN-HOFC, both network definition and inter-network FC are defined in a high-order manner. To test whether IN-HOFC is more sensitive to cognition decline due to brain diseases than traditional inter-network FC, 77 mild cognitive impairments (MCIs) and 89 controls are compared among the conventional methods and our IN-HOFC. The result shows that IN-HOFCs among three temporal lobe-related high-order networks are dampened in MCIs. The impairment of IN-HOFC is especially found between the anterior and posterior medial temporal lobe and could be a potential MCI biomarker at the network level. The competing network-level low-order FC methods, however, either revealing less or failing to detect any group difference. This work demonstrates the biological meaning and potential diagnostic value of the IN-HOFC in clinical neuroscience studies.

Reduced Modulation of Task-Related Connectivity Mediates Age-Related Declines in Bimanual Performance

Aging is accompanied by marked changes in motor behavior and its neural correlates. At the behavioral level, age-related declines in motor performance manifest, for example, as a reduced capacity to inhibit interference between hands during bimanual movements, particularly when task complexity increases. At the neural level, aging is associated with reduced differentiation between distinct functional systems. Functional connectivity (FC) dedifferentiation is characterized by more homogeneous connectivity patterns across various tasks or task conditions, reflecting a reduced ability of the aging adult to modulate brain activity according to changing task demands. It is currently unknown, however, how whole-brain dedifferentiation interacts with increasing task complexity. In the present study, we investigated age- and task-related FC in a group of 96 human adults across a wide age range (19.9-74.5 years of age) during the performance of a bimanual coordination task of varying complexity. Our findings indicated stronger task complexity-related differentiation between visuomotor- and nonvisuomotor-related networks, though modulation capability decreased with increasing age. Decreased FC modulation mediated larger complexity-related increases in between-hand interference, reflective of worse bimanual coordination. Thus, the ability to maintain high motor performance levels in older adults is related to the capability to properly segregate and modulate functional networks.

Dynamic Functional Network Analysis in Mild Traumatic Brain Injury

Mild traumatic brain injury (mTBI) is one of the most common neurological disorders for which a subset of patients develops persistent postconcussive symptoms. Previous studies discovered abnormalities and disruptions in the brain functional networks of mTBI patients principally using static functional connectivity measures which assume that neural communication across the brain is static during resting state conditions. In this study, we examine the differences in dynamic neural communication between mTBI and control participants through the application of a combination of dynamic functional analysis and graph theoretic algorithms. Resting state functional magnetic resonance imaging data was obtained on 47 mTBI patients at the acute stage of injury and 30 demographically matched healthy control participants. Results show unique alterations in both the static and dynamic functional connectivity at the acute stage in mTBI patients who suffer persistent symptoms (≥6 months after injury). In addition, mTBI patients with postconcussion syndrome demonstrated a unique allocation of time in various brain states compared to both control participants and mTBI patients with favorable outcomes. These findings suggest that global damage to the overall communication across the brain in the acute stage may contribute to chronic mTBI symptoms. Dynamic functional analysis is a powerful tool that provides insights into the brain states and the innovative analysis methodology utilized may hold the potential to delineate patients predisposed to poor outcomes upon early presentation following injury.

Machine learning in resting-state fMRI analysis

Machine learning techniques have gained prominence for the analysis of resting-state functional Magnetic Resonance Imaging (rs-fMRI) data. Here, we present an overview of various unsupervised and supervised machine learning applications to rs-fMRI. We offer a methodical taxonomy of machine learning methods in resting-state fMRI. We identify three major divisions of unsupervised learning methods with regard to their applications to rs-fMRI, based on whether they discover principal modes of variation across space, time or population. Next, we survey the algorithms and rs-fMRI feature representations that have driven the success of supervised subject-level predictions. The goal is to provide a high-level overview of the burgeoning field of rs-fMRI from the perspective of machine learning applications.

Beyond consensus: Embracing heterogeneity in curated neuroimaging meta-analysis

Coordinate-based meta-analysis can provide important insights into mind-brain relationships. A popular approach for curated small-scale meta-analysis is activation likelihood estimation (ALE), which identifies brain regions consistently activated across a selected set of experiments, such as within a functional domain or mental disorder. ALE can also be utilized in meta-analytic co-activation modeling (MACM) to identify brain regions consistently co-activated with a seed region. Therefore, ALE aims to find consensus across experiments, treating heterogeneity across experiments as noise. However, heterogeneity within an ALE analysis of a functional domain might indicate the presence of functional sub-domains. Similarly, heterogeneity within a MACM analysis might indicate the involvement of a seed region in multiple co-activation patterns that are dependent on task contexts. Here, we demonstrate the use of the author-topic model to automatically determine if heterogeneities within ALE-type meta-analyses can be robustly explained by a small number of latent patterns. In the first application, the author-topic modeling of experiments involving self-generated thought (N = 179) revealed cognitive components fractionating the default network. In the second application, the author-topic model revealed that the left inferior frontal junction (IFJ) participated in multiple task-dependent co-activation patterns (N = 323). Furthermore, the author-topic model estimates compared favorably with spatial independent component analysis in both simulation and real data. Overall, the results suggest that the author-topic model is a flexible tool for exploring heterogeneity in ALE-type meta-analyses that might arise from functional sub-domains, mental disorder subtypes or task-dependent co-activation patterns. Code for this study is publicly available (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/meta-analysis/Ngo2019_AuthorTopic).

Spatial and Temporal Characteristics of Visual Field Progression in Glaucoma Assessed by Parallel Factor Analysis

Purpose

To explore spatial and temporal characteristics of glaucomatous visual field (VF) progression through multi-way decomposition of data.

Methods

Six serial VF exams with intervals of 6.0 ± 1.0 months in 121 pre-perimetric glaucoma eyes and 80 perimetric glaucoma eyes were arranged into a three-dimensional cube. The data were decomposed using parallel factor analysis.

Results

Three tri-linear components (i.e., spatial scores, temporal loadings, and subject-specific loadings) were identified. Component 1 clearly showed differences between superior and inferior hemispheres, linear trends over time, and wide variability in perimetric glaucoma. Findings were compatible with well-known characteristics of glaucomatous VF defects. Component 2 showed nasal and central areas in contrast with superior, inferior, and temporal peripheral locations, whereas component 3 showed a contrast between nasal and temporal hemispheres. Both components 2 and 3 failed to show clear temporal trends.

Conclusions

Identification of spatio-temporal patterns shows new possibilities for a multi-way decomposition methodology for earlier diagnosis and prediction of glaucomatous VF progression.

Diagnostic neuroimaging markers of obsessive-compulsive disorder: Initial evidence from structural and functional MRI studies

As of yet, no diagnostic biomarkers are available for obsessive-compulsive disorder (OCD), and its diagnosis relies entirely upon the recognition of behavioural features assessed through clinical interview. Neuroimaging studies have shown that various brain structures are abnormal in OCD patients compared to healthy controls. However, the majority of these results are based on average differences between groups, which limits diagnostic usage in clinical practice. In recent years, a growing number of studies have applied multivariate pattern analysis (MVPA) techniques on neuroimaging data to extract patterns of altered brain structure, function and connectivity typical for OCD. MVPA techniques can be used to develop predictive models that extract regularities in data to classify individual subjects based on their diagnosis. In the present paper, we reviewed the literature of MVPA studies using data from different imaging modalities to distinguish OCD patients from controls. A systematic search retrieved twelve articles that fulfilled the inclusion and exclusion criteria. Reviewed studies have been able to classify OCD diagnosis with accuracies ranging from 66% up to 100%. Features important for classification were different across imaging modalities and widespread throughout the brain. Although studies have shown promising results, sample sizes used are typically small which can lead to high variance of the estimated model accuracy, cohort-specific solutions and lack of generalizability of findings. Some of the challenges are discussed that need to be overcome in order to move forward toward clinical applications.

Benchmarking functional connectome-based predictive models for resting-state fMRI

Functional connectomes reveal biomarkers of individual psychological or clinical traits. However, there is great variability in the analytic pipelines typically used to derive them from rest-fMRI cohorts. Here, we consider a specific type of studies, using predictive models on the edge weights of functional connectomes, for which we highlight the best modeling choices. We systematically study the prediction performances of models in 6 different cohorts and a total of 2000 individuals, encompassing neuro-degenerative (Alzheimer's, Post-traumatic stress disorder), neuro-psychiatric (Schizophrenia, Autism), drug impact (Cannabis use) clinical settings and psychological trait (fluid intelligence). The typical prediction procedure from rest-fMRI consists of three main steps: defining brain regions, representing the interactions, and supervised learning. For each step we benchmark typical choices: 8 different ways of defining regions -either pre-defined or generated from the rest-fMRI data- 3 measures to build functional connectomes from the extracted time-series, and 10 classification models to compare functional interactions across subjects. Our benchmarks summarize more than 240 different pipelines and outline modeling choices that show consistent prediction performances in spite of variations in the populations and sites. We find that regions defined from functional data work best; that it is beneficial to capture between-region interactions with tangent-based parametrization of covariances, a midway between correlations and partial correlation; and that simple linear predictors such as a logistic regression give the best predictions. Our work is a step forward to establishing reproducible imaging-based biomarkers for clinical settings.

The effects of serotonin modulation on medial prefrontal connectivity strength and stability: A pharmacological fMRI study with citalopram

BACKGROUND

Static and dynamic functional connectivity are being increasingly used to measure the effects of disease and a range of different interventions on brain networks. While preliminary evidence suggests that static connectivity can be modulated by chronic antidepressants administration in healthy individuals and in major depression, much less is known about the acute effects of antidepressants especially on dynamic functional connectivity changes. Here we examine acute effects of antidepressants on dynamic functional connectivity within the default mode network. The default mode network is a well described network with many functions in which the role of serotonin is not clear.

METHODS

In this work we measured acute pharmacological effects of an infusion of the selective serotonin reuptake inhibitor (SSRI) citalopram (10 mg) in a sample of thirteen healthy volunteers randomised to receive on two occasions the active compound or placebo in a cross over dosing.

RESULTS

Acute citalopram administration relative to placebo increased static connectivity between the medial prefrontal cortex and right dorsolateral prefrontal cortex and posterior cingulate cortex. The SSRI also induced a reduction in variability of connectivity with the medial prefrontal cortex in the precuneus and posterior cingulate cortex.

DISCUSSION

The measured changes are compatible with modified serotonin cortical availability.

LEICA: Laplacian eigenmaps for group ICA decomposition of fMRI data

Independent component analysis (ICA) is a data-driven method that has been increasingly used for analyzing functional Magnetic Resonance Imaging (fMRI) data. However, generalizing ICA to multi-subject studies is non-trivial due to the high-dimensionality of the data, the complexity of the underlying neuronal processes, the presence of various noise sources, and inter-subject variability. Current group ICA based approaches typically use several forms of the Principal Component Analysis (PCA) method to extend ICA for generating group inferences. However, linear dimensionality reduction techniques have serious limitations including the fact that the underlying BOLD signal is a complex function of several nonlinear processes. In this paper, we propose an effective non-linear ICA-based model for extracting group-level spatial maps from multi-subject fMRI datasets. We use a non-linear dimensionality reduction algorithm based on Laplacian eigenmaps to identify a manifold subspace common to the group, such that this mapping preserves the correlation among voxels' time series as much as possible. These eigenmaps are modeled as linear mixtures of a set of group-level spatial features, which are then extracted using ICA. The resulting algorithm is called LEICA (Laplacian Eigenmaps for group ICA decomposition). We introduce a number of methods to evaluate LEICA using 100-subject resting state and 100-subject working memory task fMRI datasets from the Human Connectome Project (HCP). The test results show that the extracted spatial maps from LEICA are meaningful functional networks similar to those produced by some of the best known methods. Importantly, relative to state-of-the-art methods, our algorithm compares favorably in terms of the functional cohesiveness of the spatial maps generated, as well as in terms of the reproducibility of the results.

Instability of default mode network connectivity in major depression: a two-sample confirmation study

Major depression is associated with altered static functional connectivity in various brain networks, particularly the default mode network (DMN). Dynamic functional connectivity is a novel tool with little application in affective disorders to date, and holds the potential to unravel fluctuations in connectivity strength over time in major depression. We assessed stability of connectivity in major depression between the medial prefrontal cortex (mPFC) and posterior cingulate cortex (PCC), key nodes in the DMN that are implicated in ruminative cognitions. Functional connectivity stability between the mPFC and PCC over the course of a resting-state functional magnetic resonance imaging (fMRI) scan was compared between medication-free patients with major depression and healthy controls matched for age, sex and handedness. We tested replicability of the results in an independent sample using multi-echo resting-state fMRI. The primary sample included 20 patients and 19 controls, while the validation sample included 19 patients and 19 controls. Greater connectivity variability was detected in major depression between mPFC and PCC. This was demonstrated in both samples indicating that the results were reliable and were not influenced by the fMRI acquisition approach used. Our results demonstrate that alterations within the DMN in major depression go beyond changes in connectivity strength and extend to reduced connectivity stability within key DMN regions. Findings were robustly replicated across two independent samples. Further research is necessary to better understand the nature of these fluctuations in connectivity and their relationship to the aetiology of major depression.

Inferring Individual-Level Variations in the Functional Parcellation of the Cerebral Cortex

OBJECTIVE

Functional parcellation of the cerebral cortex is variable across different subjects or between cognitive states. Ignoring individual-or state-dependent variations in the functional parcellation may lead to inaccurate representations of individual functional connectivity, limiting the precision of interpretations of differences in individual connectivity profiles. However, it is difficult to infer the individual-level variations due to the relatively low robustness of methods for parcellation of individual subjects.

METHODS

We propose a method called "joint K-means" to robustly parcellate the cerebral cortex using functional magnetic resonance imaging (fMRI) data for contrasts between two states or subjects that intended to characterize variance in individual functional parcellations. The key idea of the proposed method is to jointly infer parcellations in contrasted datasets by iterative descent, while constraining the similarity of the two pathways in searches for local minima to reduce spurious variations.

RESULTS

Parcellations of resting-state fMRI datasets from the Human Connectome Project show that the similarity of parcellations for an individual subject studied on two sessions is greater than that between different subjects. Differences in parcellations between subjects are nonuniformly distributed across the cerebral cortex, with clusters of higher variance in the prefrontal, lateral temporal, and occipito-parietal cortices. This pattern is reproducible across sessions, between groups, and using different numbers of parcels.

CONCLUSION

The individual-level variations inferred by the proposed method are plausible and consistent with the previously reported functional connectivity variability.

SIGNIFICANCE

The proposed method is a promising tool for investigating relationships between the cerebral functional organization and behavioral differences.

Pyrcca: Regularized Kernel Canonical Correlation Analysis in Python and Its Applications to Neuroimaging

In this article we introduce Pyrcca, an open-source Python package for performing canonical correlation analysis (CCA). CCA is a multivariate analysis method for identifying relationships between sets of variables. Pyrcca supports CCA with or without regularization, and with or without linear, polynomial, or Gaussian kernelization. We first use an abstract example to describe Pyrcca functionality. We then demonstrate how Pyrcca can be used to analyze neuroimaging data. Specifically, we use Pyrcca to implement cross-subject comparison in a natural movie functional magnetic resonance imaging (fMRI) experiment by finding a data-driven set of functional response patterns that are similar across individuals. We validate this cross-subject comparison method in Pyrcca by predicting responses to novel natural movies across subjects. Finally, we show how Pyrcca can reveal retinotopic organization in brain responses to natural movies without the need for an explicit model.

Deriving reproducible biomarkers from multi-site resting-state data: An Autism-based example

Resting-state functional Magnetic Resonance Imaging (R-fMRI) holds the promise to reveal functional biomarkers of neuropsychiatric disorders. However, extracting such biomarkers is challenging for complex multi-faceted neuropathologies, such as autism spectrum disorders. Large multi-site datasets increase sample sizes to compensate for this complexity, at the cost of uncontrolled heterogeneity. This heterogeneity raises new challenges, akin to those face in realistic diagnostic applications. Here, we demonstrate the feasibility of inter-site classification of neuropsychiatric status, with an application to the Autism Brain Imaging Data Exchange (ABIDE) database, a large (N=871) multi-site autism dataset. For this purpose, we investigate pipelines that extract the most predictive biomarkers from the data. These R-fMRI pipelines build participant-specific connectomes from functionally-defined brain areas. Connectomes are then compared across participants to learn patterns of connectivity that differentiate typical controls from individuals with autism. We predict this neuropsychiatric status for participants from the same acquisition sites or different, unseen, ones. Good choices of methods for the various steps of the pipeline lead to 67% prediction accuracy on the full ABIDE data, which is significantly better than previously reported results. We perform extensive validation on multiple subsets of the data defined by different inclusion criteria. These enables detailed analysis of the factors contributing to successful connectome-based prediction. First, prediction accuracy improves as we include more subjects, up to the maximum amount of subjects available. Second, the definition of functional brain areas is of paramount importance for biomarker discovery: brain areas extracted from large R-fMRI datasets outperform reference atlases in the classification tasks.

Detecting Spatio-Temporal Modes in Multivariate Data by Entropy Field Decomposition

A new data analysis method that addresses a general problem of detecting spatio-temporal variations in multivariate data is presented. The method utilizes two recent and complimentary general approaches to data analysis, information field theory (IFT) and entropy spectrum pathways (ESP). Both methods reformulate and incorporate Bayesian theory, thus use prior information to uncover underlying structure of the unknown signal. Unification of ESP and IFT creates an approach that is non-Gaussian and non-linear by construction and is found to produce unique spatio-temporal modes of signal behavior that can be ranked according to their significance, from which space-time trajectories of parameter variations can be constructed and quantified. Two brief examples of real world applications of the theory to the analysis of data bearing completely different, unrelated nature, lacking any underlying similarity, are also presented. The first example provides an analysis of resting state functional magnetic resonance imaging (rsFMRI) data that allowed us to create an efficient and accurate computational method for assessing and categorizing brain activity. The second example demonstrates the potential of the method in the application to the analysis of a strong atmospheric storm circulation system during the complicated stage of tornado development and formation using data recorded by a mobile Doppler radar. Reference implementation of the method will be made available as a part of the QUEST toolkit that is currently under development at the Center for Scientific Computation in Imaging.

Validation of Shared and Specific Independent Component Analysis (SSICA) for Between-Group Comparisons in fMRI

Independent component analysis (ICA) has been widely used to study functional magnetic resonance imaging (fMRI) connectivity. However, the application of ICA in multi-group designs is not straightforward. We have recently developed a new method named “shared and specific independent component analysis” (SSICA) to perform between-group comparisons in the ICA framework. SSICA is sensitive to extract those components which represent a significant difference in functional connectivity between groups or conditions, i.e., components that could be considered “specific” for a group or condition. Here, we investigated the performance of SSICA on realistic simulations, and task fMRI data and compared the results with one of the state-of-the-art group ICA approaches to infer between-group differences. We examined SSICA robustness with respect to the number of allowable extracted specific components and between-group orthogonality assumptions. Furthermore, we proposed a modified formulation of the back-reconstruction method to generate group-level t-statistics maps based on SSICA results. We also evaluated the consistency and specificity of the extracted specific components by SSICA. The results on realistic simulated and real fMRI data showed that SSICA outperforms the regular group ICA approach in terms of reconstruction and classification performance. We demonstrated that SSICA is a powerful data-driven approach to detect patterns of differences in functional connectivity across groups/conditions, particularly in model-free designs such as resting-state fMRI. Our findings in task fMRI show that SSICA confirms results of the general linear model (GLM) analysis and when combined with clustering analysis, it complements GLM findings by providing additional information regarding the reliability and specificity of networks.