Faster Family-wise Error Control for Neuroimaging with a Parametric Bootstrap

In neuroimaging, hundreds to hundreds of thousands of tests are performed across a set of brain regions or all locations in an image. Recent studies have shown that the most common family-wise error (FWE) controlling procedures in imaging, which rely on classical mathematical inequalities or Gaussian random field theory, yield FWE rates that are far from the nominal level. Depending on the approach used, the FWER can be exceedingly small or grossly inflated. Given the widespread use of neuroimaging as a tool for understanding neurological and psychiatric disorders, it is imperative that reliable multiple testing procedures are available. To our knowledge, only permutation joint testing procedures have been shown to reliably control the FWER at the nominal level. However, these procedures are computationally intensive due to the increasingly available large sample sizes and dimensionality of the images, and analyses can take days to complete. Here, we develop a parametric bootstrap joint testing procedure. The parametric bootstrap procedure works directly with the test statistics, which leads to much faster estimation of adjusted \emph{p}-values than resampling-based procedures while reliably controlling the FWER in sample sizes available in many neuroimaging studies. We demonstrate that the procedure controls the FWER in finite samples using simulations, and present region- and voxel-wise analyses to test for sex differences in developmental trajectories of cerebral blood flow

Infant behavioral reactivity predicts change in amygdala volume 12 years later

The current study examined the link between temperamental reactivity in infancy and amygdala development in middle childhood. A sample (n = 291) of four-month-old infants was assessed for infant temperament, and two groups were identified: those exhibiting negative reactivity (n = 116) and those exhibiting positive reactivity (n = 106). At 10 and 12 years of age structural imaging was completed on a subset of these participants (n = 75). Results indicate that, between 10 and 12 years of age, left amygdala volume increased more slowly in those with negative compared to positive reactive temperament. These results provide novel evidence linking early temperament to distinct patterns of brain development over middle childhood

Polygenic risk for Alzheimer's disease shapes hippocampal scene-selectivity

Preclinical models of Alzheimer’s disease (AD) suggest APOE modulates brain function in structures vulnerable to AD pathophysiology. However, genome-wide association studies now demonstrate that AD risk is shaped by a broader polygenic architecture, estimated via polygenic risk scoring (AD-PRS). Despite this breakthrough, the effect of AD-PRS on brain function in young individuals remains unknown. In a large sample (N = 608) of young, asymptomatic individuals, we measure the impact of both (i) APOE and (ii) AD-PRS on a vulnerable cortico-limbic scene-processing network heavily implicated in AD pathophysiology. Integrity of this network, which includes the hippocampus (HC), is fundamental for maintaining cognitive function during ageing. We show that AD-PRS, not APOE, selectively influences activity within the HC in response to scenes, while other perceptual nodes remained intact. This work highlights the impact of polygenic contributions to brain function beyond APOE, which could aid potential therapeutic/interventional strategies in the detection and prevention of AD

Neural activation in the ventromedial prefrontal cortex precedes conscious experience of being in or out of a transient hallucinatory state

Background and Hypotheses Auditory verbal hallucinations (AVHs) is not only a common symptom in schizophrenia but also observed in individuals in the general population. Despite extensive research, AVHs are poorly understood, especially their underlying neuronal architecture. Neuroimaging methods have been used to identify brain areas and networks that are activated during hallucinations. A characteristic feature of AVHs is, however, that they fluctuate over time, with varying frequencies of starts and stops. An unanswered question is, therefore, what neuronal events co-occur with the initiation and inhibition of an AVH episode. Study Design We investigated brain activation with fMRI in 66 individuals who experienced multiple AVH-episodes while in the scanner. We extracted time-series fMRI-data and monitored changes second-by-second from 10 s before to 15 s after participants indicated the start and stop of an episode, respectively, by pressing a hand-held response-button. Study Results We found a region in the ventromedial prefrontal cortex (VMPFC) which showed a significant increase in activation initiated a few seconds before participants indicated the start of an episode, and a corresponding decrease in activation initiated a few seconds before the end of an episode. Conclusions The consistent increase and decrease in activation in this area in advance of the consciously experienced presence or absence of the “voice” imply that this region may act as a switch in turning episodes on and off. The activation is unlikely to be confounded by motor responses. The findings could have clinical implications for brain stimulation treatments, like transcranial magnetic stimulation.publishedVersio

Accelerating Permutation Testing in Voxel-wise Analysis through Subspace Tracking: A new plugin for SnPM

Permutation testing is a non-parametric method for obtaining the max null distribution used to compute corrected $p$-values that provide strong control of false positives. In neuroimaging, however, the computational burden of running such an algorithm can be significant. We find that by viewing the permutation testing procedure as the construction of a very large permutation testing matrix, $T$, one can exploit structural properties derived from the data and the test statistics to reduce the runtime under certain conditions. In particular, we see that $T$ is low-rank plus a low-variance residual. This makes $T$ a good candidate for low-rank matrix completion, where only a very small number of entries of $T$ ($\sim0.35\%$ of all entries in our experiments) have to be computed to obtain a good estimate. Based on this observation, we present RapidPT, an algorithm that efficiently recovers the max null distribution commonly obtained through regular permutation testing in voxel-wise analysis. We present an extensive validation on a synthetic dataset and four varying sized datasets against two baselines: Statistical NonParametric Mapping (SnPM13) and a standard permutation testing implementation (referred as NaivePT). We find that RapidPT achieves its best runtime performance on medium sized datasets ($50 \leq n \leq 200$), with speedups of 1.5x - 38x (vs. SnPM13) and 20x-1000x (vs. NaivePT). For larger datasets ($n \geq 200$) RapidPT outperforms NaivePT (6x - 200x) on all datasets, and provides large speedups over SnPM13 when more than 10000 permutations (2x - 15x) are needed. The implementation is a standalone toolbox and also integrated within SnPM13, able to leverage multi-core architectures when available.Comment: 36 pages, 16 figure

Machine learning-based identification of suicidal risk in patients with schizophrenia using multi-level resting-state fMRI features

Background: Some studies suggest that as much as 40% of all causes of death in a group of patients with schizophrenia can be attributed to suicides and compared with the general population, patients with schizophrenia have an 8.5-fold greater suicide risk (SR). There is a vital need for accurate and reliable methods to predict the SR among patients with schizophrenia based on biological measures. However, it is unknown whether the suicidal risk in schizophrenia can be related to alterations in spontaneous brain activity, or if the resting-state functional magnetic resonance imaging (rsfMRI) measures can be used alongside machine learning (ML) algorithms in order to identify patients with SR. Methods: Fifty-nine participants including patients with schizophrenia with and without SR as well as age and gender-matched healthy underwent 13 min resting-state functional magnetic resonance imaging. Both static and dynamic indexes of the amplitude of low-frequency fluctuation (ALFF), the fractional amplitude of low-frequency fluctuations (fALFF), regional homogeneity as well as functional connectivity (FC) were calculated and used as an input for five machine learning algorithms: Gradient boosting (GB), LASSO, Logistic Regression (LR), Random Forest and Support Vector Machine. Results: All groups revealed different intra-network functional connectivity in ventral DMN and anterior SN. The best performance was reached for the LASSO applied to FC with an accuracy of 70% and AUROC of 0.76 (p < 0.05). Significant classification ability was also reached for GB and LR using fALFF and ALFF measures. Conclusion Our findings suggest that SR in schizophrenia can be seen on the level of DMN and SN functional connectivity alterations. ML algorithms were able to significantly differentiate SR patients. Our results could be useful in developing neuromarkers of SR in schizophrenia based on non-invasive rsfMRI

Gray matter covariations and core symptoms of autism: the EU-AIMS Longitudinal European Autism Project.

BACKGROUND: Voxel-based morphometry (VBM) studies in autism spectrum disorder (autism) have yielded diverging results. This might partly be attributed to structural alterations being associating with the combined influence of several regions rather than with a single region. Further, these structural covariation differences may relate to continuous measures of autism rather than with categorical case-control contrasts. The current study aimed to identify structural covariation alterations in autism, and assessed canonical correlations between brain covariation patterns and core autism symptoms. METHODS: We studied 347 individuals with autism and 252 typically developing individuals, aged between 6 and 30 years, who have been deeply phenotyped in the Longitudinal European Autism Project. All participants' VBM maps were decomposed into spatially independent components using independent component analysis. A generalized linear model (GLM) was used to examine case-control differences. Next, canonical correlation analysis (CCA) was performed to separately explore the integrated effects between all the brain sources of gray matter variation and two sets of core autism symptoms. RESULTS: GLM analyses showed significant case-control differences for two independent components. The first component was primarily associated with decreased density of bilateral insula, inferior frontal gyrus, orbitofrontal cortex, and increased density of caudate nucleus in the autism group relative to typically developing individuals. The second component was related to decreased densities of the bilateral amygdala, hippocampus, and parahippocampal gyrus in the autism group relative to typically developing individuals. The CCA results showed significant correlations between components that involved variation of thalamus, putamen, precentral gyrus, frontal, parietal, and occipital lobes, and the cerebellum, and repetitive, rigid and stereotyped behaviors and abnormal sensory behaviors in autism individuals. LIMITATIONS: Only 55.9% of the participants with autism had complete questionnaire data on continuous parent-reported symptom measures. CONCLUSIONS: Covaried areas associated with autism diagnosis and/or symptoms are scattered across the whole brain and include the limbic system, basal ganglia, thalamus, cerebellum, precentral gyrus, and parts of the frontal, parietal, and occipital lobes. Some of these areas potentially subserve social-communicative behavior, whereas others may underpin sensory processing and integration, and motor behavior

Differences in the link between social trait judgment and socio-emotional experience in neurotypical and autistic individuals

Neurotypical (NT) individuals and individuals with autism spectrum disorder (ASD) make different judgments of social traits from others\u27 faces; they also exhibit different social emotional responses in social interactions. A common hypothesis is that the differences in face perception in ASD compared with NT is related to distinct social behaviors. To test this hypothesis, we combined a face trait judgment task with a novel interpersonal transgression task that induces measures social emotions and behaviors. ASD and neurotypical participants viewed a large set of naturalistic facial stimuli while judging them on a comprehensive set of social traits (e.g., warm, charismatic, critical). They also completed an interpersonal transgression task where their responsibility in causing an unpleasant outcome to a social partner was manipulated. The purpose of the latter task was to measure participants\u27 emotional (e.g., guilt) and behavioral (e.g., compensation) responses to interpersonal transgression. We found that, compared with neurotypical participants, ASD participants\u27 self-reported guilt and compensation tendency was less sensitive to our responsibility manipulation. Importantly, ASD participants and neurotypical participants showed distinct associations between self-reported guilt and judgments of criticalness from others\u27 faces. These findings reveal a novel link between perception of social traits and social emotional responses in ASD

Eight weddings and six funerals: An fMRI study on autobiographical memories

\u201cAutobiographical memory\u201d (AM) refers to remote memories from one's own life. Previous neuroimaging studies have highlighted that voluntary retrieval processes from AM involve different forms of memory and cognitive functions. Thus, a complex and widespread brain functional network has been found to support AM. The present functional magnetic resonance imaging (fMRI) study used a multivariate approach to determine whether neural activity within the AM circuit would recognize memories of real autobiographical events, and to evaluate individual differences in the recruitment of this network. Fourteen right-handed females took part in the study. During scanning, subjects were presented with sentences representing a detail of a highly emotional real event (positive or negative) and were asked to indicate whether the sentence described something that had or had not really happened to them. Group analysis showed a set of cortical areas able to discriminate the truthfulness of the recalled events: medial prefrontal cortex, posterior cingulate/retrosplenial cortex, precuneus, bilateral angular, superior frontal gyri, and early visual cortical areas. Single-subject results showed that the decoding occurred at different time points. No differences were found between recalling a positive or a negative event. Our results show that the entire AM network is engaged in monitoring the veracity of AMs. This process is not affected by the emotional valence of the experience but rather by individual differences in cognitive strategies used to retrieve AMs