ModelArray is a scalable R package for statistical analysis of fixel-wise data derived from diffusion MRI (and beyond). It supports linear and nonlinear modeling and is extensible to more models. Full documentation: https://pennlinc.github.io/ModelArray/
Arielle Keller and Valerie Sydnor
Trends in Cognitive Sciences
Hierarchical functional system development supports executive function
How are developmental improvements in youth executive function supported by hierarchically organized maturational changes in functional brain systems? We highlight evidence that functional brain systems are embedded within a hierarchical sensorimotor-association axis and review evidence that functional system development varies along this axis. Developmental changes that strengthen the hierarchical organization of the cortex may support EF by facilitating top-down information flow and balancing within- and between-system communication.
Adam Richie-Halford & Matt Cieslak
Preprocessed HBN dMRI
We created a set of resources to enable research based on openly-available diffusion MRI (dMRI) data from the Healthy Brain Network (HBN) study. First, we curated the HBN dMRI data (N = 2747) into the Brain Imaging Data Structure and preprocessed it according to best-practices, including denoising and correcting for motion effects, susceptibility-related distortions, and eddy currents. Finally, we conducted extensive quality control. This work both delivers resources to advance transdiagnostic research in brain connectivity and pediatric mental health,
Sex Differences in Association Network Topography
We identified normative developmental sex differences in the functional topography of personalized association networks including the ventral attention network and default mode network. Furthermore, chromosomal enrichment analyses revealed that sex differences in multivariate patterns of functional topography were spatially coupled to the expression of X- linked genes as well as astrocytic and excitatory neuronal cell-type signatures. These results highlight the role of sex as a biological variable in shaping functional brain development in youth.
Arterial spin labeled (ASL) magnetic resonance imaging (MRI) is the primary method for non-invasively measuring regional brain perfusion in humans. We introduce ASLPrep, a suite of software pipelines that ensure the reproducible and generalizable processing of ASL MRI data.
Review: Neurodevelopment of the Association Cortices
We review how human brain maturation progresses along an evolutionarily rooted, sensorimotor-to-association axis of cortical organization. This spatiotemporal developmental program endows association cortices with a protracted period of plasticity, unique neurobiological properties, and heightened maturational variability linked to psychopathology.
Normative Modeling and Psychopathology
We examined how transdiagnostic dimensions of psychopathology tracked deviations from normative neurodevelopment of gray matter volume. We found that modeling cortical volume using normative models improved out-of-sample prediction of participants' psychopathology symptoms.
Developmental Cognitive Neuroscience
Leveraging multi-shell diffusion for studies of brain development in youth and young adulthood
We find key advantages of multi-shell diffusion metrics, including increased neurodevelopmental coupling and decreased spurious relationships with imaging data quality.
Biological Psychiatry: CNNI
Review: Network neuroscience and neuropsychiatric disorders
We aim to offer an accessible introduction to this emerging field and motivate further work that uses NN to better understand the normative development of brain networks and alterations in that development that accompany or foreshadow psychiatric disease.
Establishing the Validity of CS-DSI
If you're a neuroscientist who wants to use DSI to look at some cool microstructural details but can't afford to add the extra 20 minutes of scan time to your protocol, compressed sensing might be your new best friend!
We show that CS-DSI schemes can generate white matter derivatives comparable to those generated by a full DSI scheme, allowing up to a 60% decrease in scan time with minimal loss in accuracy or reliability! This could allow both researchers and even clinicians to harness the advantages of DSI sequences that were previously impractical to deploy.
Asymmetric Signaling Across the Hierarchy
We used network control theory to examine the amount of energy required to propagate dynamics across the sensory-fugal axis. Our results revealed an asymmetry in this energy indicating that bottom-up transitions were easier to complete compared to top-down transitions.
Curation of BIDS (CuBIDS)
CuBIDS is a neuroinformatics workflow and open-source Python-based software package designed to facilitate reproducible curation of neuroimaging data. CuBIDS also helps users summarize, categorize, and visualize the metadata heterogeneity present in their BIDS data, test pipelines on their dataset's entire parameter space, and perform metadata-based quality control.
Benchmarking dMRI Head Motion Correction
We report a comprehensive evaluation of both methods on realistic simulations of a software fiber phantom that provides known ground-truth head motion. We demonstrate that both FSL's Eddy and QSIPrep's SHOREline methods perform remarkably well. However, we show that performance can be impacted by sampling scheme, the pervasiveness of head motion, and the denoising strategy applied before head motion correction. Our study also provides an open and fully-reproducible workflow that could be used to accelerate evaluation studies of other dMRI processing methods in the future.
Arielle S. Keller
Caregiver Monitoring and Cognition
Caregiving plays an important role in supporting cognitive development. We characterized replicable yet specific associations between caregiver monitoring, but not caregiver warmth, and cognition in two large sub-samples of 9-10 year olds. Caregiver monitoring partially mediated the association between household income and cognition, furthering our understanding of how socioeconomic disparities may contribute to disadvantages in cognitive development.
Network Development Supports the Emergence of Hierarchy and Cognition
Using multi-scale personalized functional networks in a large sample of youth, we demonstrate that developmental shifts in inter-network coupling systematically adhered to and strengthened a functional hierarchy of cortical organization. Furthermore, we demonstrate that network maturation had clear behavioral relevance: the development of coupling in unimodal and transmodal networks dissociably mediated the emergence of executive function.
Tinashe Michael Tapera
Frontiers in Neuroinformatics
Curating your imaging data into BIDS (Brain Imaging Data Structure) can be a time consuming, repetitive, and error prone task, particularly on large scale neuroimaging databases like Flywheel. We developed FlywheelTools, a toolkit of software packages, to accelerate the reproducible curation of imaging data on Flywheel.
Developmental coupling of cerebral blood flow and fMRI fluctuations in youth
We demonstrate that non-invasive imaging proxies of neurovascular coupling in children undergo substantial maturation in youth, with evidence of both prominent sex differences and functional relevance to executive function.
Amygala perfusion and anxiety
We demonstrate that normative developmental sex differences in perfusion of brain regions involved in emotion and social cognition -- such as the amygdala-- mediate established sex differences in mood and anxiety symptoms in youth.
Development of Top-Down Cortical Propagations in Youth
Hierarchical processing requires activity propagating between higher and lower-order cortical areas. Here, we leveraged advances in neuroimaging and computer vision to describe propagations robustly ascend and descend the cortical hierarchy. Notably, top-down propagations become both more prevalent with cognitive control demands and with development in youth.
Arielle S. Keller
Personalized Functional Brain Network Topography and Cognition
Individual differences in cognition during childhood are associated with important social, physical, and mental health outcomes in adolescence and adulthood. Quantifying variation in the total spatial representation of functional brain networks across the developing cortex may provide insight regarding individual differences in cognition. We test this idea by defining personalized functional networks that account for inter-individual heterogeneity in 9-10 year olds from the Adolescent Brain Cognitive Development Study. Across thousands of individuals, the total cortical representation of personalized networks could predict youth cognition. These results establish that heterogeneity in functional network topography is associated with individual differences in cognition before the critical transition into adolescence.
Characterizing the Spatiotemporal Sequence of Cortical Plasticity
Leveraging intrinsic activity amplitude as a functional marker of plasticity, we find evidence for a cortical gradient of neurodevelopmental plasticity in youth. Declines in the amplitude of intrinsic activity were initiated heterochronously across regions, coupled to the maturation of a plasticity breaking factor, impacted by children’s developmental environments, and temporally staggered along a sensorimotor-association axis from ages 8 to 18.
A Pathway for Amygdala TMS Neuromodulation
Connectivity-guided transcranial magnetic stimulation applied to the ventrolateral prefrontal cortex elicited acute modulations of amygdala fMRI activity, demonstrating therapeutic potential for emotion-related psychopathology.
We demonstrate that statistical patterns of smartphone-based mobility features represent unique “footprints” that allow individual identification. Critically, mobility footprints exhibit varying levels of person-specific distinctiveness and are associated with individual differences in affective instability, circadian variability, and brain functional connectivity.
Average Controllability and Psychosis
We found that average controllability better predicted the symptoms of psychosis spectrum than commonly used graph-theoretic summaries of regional structural connectivity. We found that this improved prediction was driven by regions located in the transmodal cortex.
Diffusion-weighted magnetic resonance imaging (dMRI) is the primary method for noninvasively studying the organization of white matter in the human brain. Here we introduce QSIPrep, an integrative software platform for the processing of diffusion images that is compatible with nearly all dMRI sampling schemes. Drawing on a diverse set of software suites to capitalize on their complementary strengths, QSIPrep facilitates the implementation of best practices for processing of diffusion images.