Potential pitfalls when denoising resting state fMRI data using nuisance regression

In resting state fMRI, it is necessary to remove signal variance associated with noise sources, leaving cleaned fMRI time-series that more accurately reflect the underlying intrinsic brain fluctuations of interest. This is commonly achieved through nuisance regression, in which the fit is calculated of a noise model of head motion and physiological processes to the fMRI data in a General Linear Model, and the “cleaned” residuals of this fit are used in further analysis. We examine the statistical assumptions and requirements of the General Linear Model, and whether these are met during nuisance regression of resting state fMRI data. Using toy examples and real data we show how pre-whitening, temporal filtering and temporal shifting of regressors impact model fit. Based on our own observations, existing literature, and statistical theory, we make the following recommendations when employing nuisance regression: pre-whitening should be applied to achieve valid statistical inference of the noise model fit parameters; temporal filtering should be incorporated into the noise model to best account for changes in degrees of freedom; temporal shifting of regressors, although merited, should be achieved via optimisation and validation of a single temporal shift. We encourage all readers to make simple, practical changes to their fMRI denoising pipeline, and to regularly assess the appropriateness of the noise model used. By negotiating the potential pitfalls described in this paper, and by clearly reporting the details of nuisance regression in future manuscripts, we hope that the field will achieve more accurate and precise noise models for cleaning the resting state fMRI time-series

Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN

Neuroimaging research requires sophisticated tools for analyzing complex data, but efficiently leveraging these tools can be a major challenge, especially on large datasets. CBRAIN is a web-based platform designed to simplify the use and accessibility of neuroimaging research tools for large-scale, collaborative studies. In this paper, we describe how CBRAIN’s unique features and infrastructure were leveraged to integrate TAPAS PhysIO, an open-source MATLAB toolbox for physiological noise modeling in fMRI data. This case study highlights three key elements of CBRAIN’s infrastructure that enable streamlined, multimodal tool integration: a user-friendly GUI, a Brain Imaging Data Structure (BIDS) data-entry schema, and convenient in-browser visualization of results. By incorporating PhysIO into CBRAIN, we achieved significant improvements in the speed, ease of use, and scalability of physiological preprocessing. Researchers now have access to a uniform and intuitive interface for analyzing data, which facilitates remote and collaborative evaluation of results. With these improvements, CBRAIN aims to become an essential open-science tool for integrative neuroimaging research, supporting FAIR principles and enabling efficient workflows for complex analysis pipelines

Effect of prewhitening in resting-state functional near-infrared spectroscopy data

Published: 24 October 2018Near-infrared spectroscopy (NIRS) offers the potential to characterize resting-state functional connectivity (RSFC) in populations that are not easily assessed otherwise, such as young infants. In addition to the advantages of NIRS, one should also consider that the RS-NIRS signal requires specific data preprocessing and analysis. In particular, the RS-NIRS signal shows a colored frequency spectrum, which can be observed as temporal autocorrelation, thereby introducing spurious correlations. To address this issue, prewhitening of the RS-NIRS signal has been recently proposed as a necessary step to remove the signal temporal autocorrelation and therefore reduce false-discovery rates. However, the impact of this step on the analysis of experimental RS-NIRS data has not been thoroughly assessed prior to the present study. Here, the results of a standard preprocessing pipeline in a RS-NIRS dataset acquired in infants are compared with the results after incorporating two different prewhitening algorithms. Our results with a standard preprocessing replicated previous studies. Prewhitening altered RSFC patterns and disrupted the antiphase relationship between oxyhemoglobin and deoxyhemoglobin. We conclude that a better understanding of the effect of prewhitening on RS-NIRS data is still needed before directly considering its incorporation to the standard preprocessing pipeline.This research was possible due to the support of the Basque Government predoctoral grant PRE_2016_2_0188 to Borja Blanco, as well as the support of the Spanish Ministry of Economy and Competitiveness through the project PSI 2014-54512-P, Juan de la Cierva Fellowship (IJCI-2014-20821) and the “Severo Ochoa” Programme for Centres/Units of Excellence in R & D (SEV-2015-490)

Depth-Dependent Physiological Modulators of the BOLD Response in the Human Motor Cortex

This dissertation proposes a set of methods for improving spatial localization of cerebral metabolic changes using functional magnetic resonance imaging (fMRI). Blood oxygen level dependent (BOLD) fMRI estabilished itself as the most frequently used technique for mapping brain activity in humans. It is non-invasive and allows to obtain information about brain oxygenation changes in a few minutes. It was discovered in 1990 and, since then, it contributed enormously to the developments in neuroscientific research. Nevertheless, the BOLD contrast suffers from inherent limitations. This comes from the fact that the observed response is the result of a complex interplay between cerebral blood flow (CBF), cerebral blood volume (CBV) and cerebral metabolic rate of oxygen consumption (CMRO2) and has a strong dependency on baseline blood volume and oxygenation. Therefore, the observed response is mislocalized from the site where the metabolic activity takes place and it is subject to high variability across experiments due to normal brain physiology. Since the peak of BOLD changes can be as much as 4 mm apart from the site of metabolic changes, the problem of spatial mislocalization is particularly constraining at submillimeter resolution. Three methods are proposed in this work in order to overcome this limitation and make data more comparable. The first method involves a modification of an estabilished model for calibration of BOLD responses (the dilution model), in order to render it applicable at higher resolutions. The second method proposes a model-free scaling of the BOLD response, based on spatial normalization by a purely vascular response pattern. The third method takes into account the hypothesis that the cortical vasculature could act as a low-pass filter for BOLD fluctuations as the blood is carried downstream, and investigates differences in frequency composition of cortical laminae. All methods are described and tested on a depth-dependent scale in the human motor cortex

An Exploration of Ethnic Identity and Social Reorientation among Youth

Youths’ sense of connection to their ethnicity, or their ethnic identity, has been considered a culture asset in that this identification with one’s culture is thought to be protective and promotive for youth development, especially ethnic minority youth in the U.S. (Perez-Brena et al., 2018). Youths’ ethnic identity have been linked with lessened engagement in health compromising behaviors and behaviors that support their academic success (Rivas-Drake et al., 2014). However, the field continues to ask how ethnic identity serves as a cultural asset. This dissertation considered how ethnic identity translates into the cognitive and behavioral processes that support adjustment. This dissertation bridged ethnic identity developmental theories with other identity-relevant frameworks for adolescence that emphasize the neuroscience aspects that supports social reorientation and identity development (Dahl, 2016; Pfeifer & Peake, 2012; Steinberg, 2008; Telzer et al., 2018) as well as the role of social identities in decision-making (Berkman et al., 2017; Oyserman, 2007). In study 1, ethnic identity development was examined in relation to two important facets of adolescent adjustment; resisting peer influence and future orientation (Miller & Byrnes, 2001; Steinberg & Monahan, 2007; Steinberg et al., 2009). It was expected that youth who had explored their ethnicity and had greater clarity about their ethnic group membership would demonstrate greater resistance to peer influence and demonstrate tendencies to weigh decisions and their consequences with the future in mind. The findings showed that ethnic identity resolution was positively associated with resisting peer influence, relying more on their own perspective than that of their peers. This suggests the importance of resolution development in how youth appraise and discern socially salient information. In study 2 considered how, if at all, ethnic identity development is implicated in the brain. Despite burgeoning research demonstrating consequential associations of youth ethnic identity with cognition, behavior, and adjustment (Rivas-Drake et al., 2014), little is known about how ethnic identity may be reflected in the brain. I considered large-scale brain networks that are known to support human social interactions, social cognition, mentalizing, processing social norms, motivation, and self-referential thinking (Feng et al., 2021). These large-scale brain networks, from a domain-general perspective, are viewed as important for making sense of social interactions and relating such experiences into one’s self-concept (Buckner & DiNicola, 2019). It was hypothesized that ethnic identity exploration and resolution would be positively associated with the functional organization of the default mode network and the frontoparietal network (Andrews-Hanna et al., 2010; Vincent et al., 2008). A person-specific modeling approach (GIMME) was used to characterize brain connectivity amongst these networks (Beltz & Gates, 2017). Clarity about one’s ethnic group membership (e.g., resolution) was associated with greater frontoparietal network density (e.g., number of brain connections that comprised one’s personalized brain connectivity model) -- the network that supports cognitive control. Altogether, this dissertation offers a novel perspective for how ethnic identity functions as a cultural asset. These studies found that ethnic identity resolution development may be one way youths’ connection to their ethnicity translate to how they cognitively appraise socially salient information. This mechanism could be at work when youth navigate their social environments in ways that promote their adjustment. At the brain level, resolution was linked with connectivity within the cognitive control network during the resting state, potentially reflecting the everyday ways resolution supports behavioral adjustment.PHDPsychologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/169690/1/kconst_1.pd

Influence of Early Bilingual Exposure in the Developing Human Brain.

190 p.La adquisición del lenguaje es un proceso que ese encuentra determinado tanto por mecanismos de desarrollo cognitivo, como por la experiencia lingüística durante los primeros años de vida. Aunque se trata de un proceso relativamente complejo, los bebés muestran una gran habilidad para el aprendizaje del lenguaje. Un entorno de aprendizaje lingüístico bilingüe podría considerarse aun más complejo, ya que los bebés están expuestos a las características lingüísticas de dos lenguas simultáneamente. En primer lugar, los bebés que crecen en un entorno bilingüe tienen que ser capaces de darse cuenta de que están expuestos a dos lenguas diferentes, y posteriormente deben separar y aprender las características especificas de cada una de ellas; por ejemplo, los distintos fonemas, palabras o estructuras gramaticales. Aunque la exposición lingüística total de los bebés bilingües debería ser comparable a la de los bebés monolingües, es probable que la exposición a cada una de las lenguas de su entorno sea menor, ya que tienen que dividir su tiempo de exposición entre ambas. Si bien los bebés bilingües parecen no tener problemas para enfrentarse a un contexto de aprendizaje potencialmente más complejo, ya que alcanzan las distintas etapas de adquisición del lenguaje a un ritmo similar a los bebés monolingües, sí se han observado adaptaciones a nivel conductual y a nivel de funcionamiento cerebral que podrían producirse como consecuencia de este contexto.Basque Center on cognition, brain and languag

Influence of Early Bilingual Exposure in the Developing Human Brain.

190 p.La adquisición del lenguaje es un proceso que ese encuentra determinado tanto por mecanismos de desarrollo cognitivo, como por la experiencia lingüística durante los primeros años de vida. Aunque se trata de un proceso relativamente complejo, los bebés muestran una gran habilidad para el aprendizaje del lenguaje. Un entorno de aprendizaje lingüístico bilingüe podría considerarse aun más complejo, ya que los bebés están expuestos a las características lingüísticas de dos lenguas simultáneamente. En primer lugar, los bebés que crecen en un entorno bilingüe tienen que ser capaces de darse cuenta de que están expuestos a dos lenguas diferentes, y posteriormente deben separar y aprender las características especificas de cada una de ellas; por ejemplo, los distintos fonemas, palabras o estructuras gramaticales. Aunque la exposición lingüística total de los bebés bilingües debería ser comparable a la de los bebés monolingües, es probable que la exposición a cada una de las lenguas de su entorno sea menor, ya que tienen que dividir su tiempo de exposición entre ambas. Si bien los bebés bilingües parecen no tener problemas para enfrentarse a un contexto de aprendizaje potencialmente más complejo, ya que alcanzan las distintas etapas de adquisición del lenguaje a un ritmo similar a los bebés monolingües, sí se han observado adaptaciones a nivel conductual y a nivel de funcionamiento cerebral que podrían producirse como consecuencia de este contexto.Basque Center on cognition, brain and languag