bioRxiv

7/14/22

ModelArray

ModelArray is a scalable R package for statistical analysis of fixel data derived from diffusion MRI. It supports linear and nonlinear modeling and is extensible to more models. Full documentation: https://pennlinc.github.io/ModelArray/

Nature Methods

6/9/22

ASLPrep

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.

Biological Psychiatry

5/20/22

Personalized functional network topography and psychopathology in youth

Leveraging a large sample and advances in machine learning, we demonstrate that functional topography significantly predicts individual differences in diverse dimensions of psychopathology.

biorxiv

5/5/22

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.

Network Neuroscience

3/16/22

Efficient Coding

We develop and test a theory of how brain network architecture and biology perform lossy compression to support efficient communication among spatially distributed brain regions.

Neuron

9/15/21

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.

Translational Psychiatry

4/20/21

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.

JAMA Network Open

1/5/21

fMRI of Chronic Pain: A Meta Analysis

A comprehensive meta-analysis revealed that chronic pain does not appear to be associated with consistent alterations in the brain’s response to noxious stimuli.

Developmental Cognitive Neuroscience

6/1/20

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.

eLife

3/27/20

Control Energy of Executive Function in Youth

We leveraged advances in network control theory to describe how the structural connectome facilitates transitions to executive activation states

PNAS

12/4/19

Development of Structure Function Coupling

Coupling between structural and functional brain networks evolves in a hierarchy-dependent manner in youth

Neuropsychopharmacology

9/2/19

Irritability and Longitudinal Brain Development

Irritability is associated with accelerated cortical thinning in youth

Nature Communications

8/1/18

Dimensions of Psychopathology and Functional Brain Network

Machine-learning links dimensions of psychopathology to abnormalities of functional brain networks.

Biological Psychiatry: CNNI

4/5/18

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.

Human Brain Mapping

11/1/17

Review: Motion and functional connectivity

This review article provides an overview of the way in-scanner motion impacts functional connectivity data, as well as common approaches for mitigating this artifact.

NeuroImage

7/1/17

Benchmarking functional connectivity pipelines

We benchmark 14 of the most commonly used preprocessing pipelines for functional connectivity. This paper was one of the top 3 cited papers in 2017 published in NeuroImage.

PNAS

3/13/17

Developmental cortical networks and evolutionary expansion

In collaborative work with Christos Davatzikos, we define novel structural covariance networks, and show that their development during adolescence is associated with evolutionary expansion.

NeuroImage

6/1/16

Cortical coupling

Here we introduce a new measure --cortical coupling-- that describes the local association between brain measures.

American Journal of Psychiatry

1/22/16

Transdiagnostic Executive Dysfunction in Youth

We investigated executive system deficits in association with dimensions of psychiatric symptoms in youth using a working memory paradigm.

Journal of Neuroscience

1/14/15

Cortical topology and development

Here we show that cortical thinning in adolescence is partially governed by sulcal topology.

Journal of Neuroscience

10/9/13

Functional Maturation of the Executive System

Using fMRI and machine learning tools, we demonstrate that executive system activation is more strongly linked to individual differences in performance ability than chronological age.

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Science Advances

6/22/22

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.

PsyArXiv

6/7/22

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.

bioRxiv

5/12/22

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.

BioRxiv

5/1/22

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.

Science Advances

2/5/22

Reduction of the E:I Ratio during Adolescence

Using a combination of pharmacological fMRI data developmental fMRI data, we provide evidence for a developmental reduction of the excitation:inhibition ratio during adolescence that is specific to association cortex.

Frontiers in Neuroinformatics

6/22/21

FlywheelTools

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.

Cell Reports

3/29/21

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.

Neuropsychopharmacology

10/2/20

Neurocognitive and functional heterogeneity in depressed youth

We identified neurocognitive subtypes of depressed youth using semi-supervised machine learning.

Neuroscience & Biobehavioral Reviews

5/1/20

Convergent Neural Representation of Pain

Diverse experiments inducing acute pain in healthy volunteers recruit a convergent pattern of activation.

Human Brain Mapping

3/26/20

Multi‐scale network regression for brain‐phenotype associations

We designed, implemented, and deployed a multi-variate statistical tool to extract novel brain‐behavior relationships that are present on multiple scales.

American Journal of Psychiatry

12/1/19

Dimensions of Psychopathology and Brain Structure

Dissociable impact of dimensions of psychopathology on brain structure

Cerebral Cortex

8/23/19

Unifying Modular and Core-Periphery Networks

We a recently-developed stochastic block model that simultaneously uncovers modular and core–periphery structure

NeuroImage

6/1/18

Motion and Diffusion-Based Structural Networks

The impact of in-scanner head motion on structural connectivity derived from diffusion MRI.

NeuroImage

4/1/18

Quantitative assessment of structural image quality

We assessed quantitative metrics of structural image quality, and described how image quality may impact inference about brain development.

Nature Communications

11/1/17

Network control in brain development

In collaborative work with Danielle Bassett, we show that brain networks become more controllable with development in adolescence.

Current Biology

6/5/17

Development of Structural Brain Networks

Structural brain networks grow more segregated during adolescent development, and support executive functioning.

American Journal of Psychiatry

1/31/17

Reward dysconnectivity in psychiatry

We delineate common functional connectivity abnormalities in the brain's reward system across mood and psychotic disorders.

Biological Psychiatry

5/9/16

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.

PNAS

10/19/15

Functional network development in adolescence

In collaborative work with Danielle Bassett, we track how the roles of functional sub-networks evolve in adolescence.

PNAS

5/27/14

Sex differences in cerebral blood flow in adolescence

We delineate fundamental normative sex differences in CBF evolution during adolescence.

NeuroImage

1/1/13

Preprocessing for motion artifact

We introduce a top-performing strategy for reducing motion artifact in functional connectivity data.

bioRxiv

6/14/22

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.

Neuropsychopharmacology

6/2/22

Mobility "Footprinting"

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.

Nature Communications

5/12/22

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.

Cerebral Cortex

3/28/22

Neighborhood SES and Executive System Function

In this study we found that lower neighborhood-level SES is associated with reduced activation of the executive system, even when controlling for other measures of developmental adversity.

Biological Psychiatry

9/15/21

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.

Nature Methods

6/21/21

QSIPrep

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.

Molecular Psychiatry

1/21/21

Glutamate and Reward Responsiveness

We used ultra-high field (7T) glutamate imaging to delineate associations between reward network neurochemistry and transdiagnostic reward responsiveness deficits.

Biological Psychiatry

7/1/20

Review: Parsing Heterogeneity in Psychopathology

This review provides an overview of methods for defining common and dissociable aspects of psychopathology

Neuron

4/22/20

Personalized Association Networks in Youth

Individual-specific association networks are refined in youth and predict cognition

Journal of Neuroscience

2/27/20

Longitudinal Development of Brain Iron

Diminished brain iron accumulation in the basal ganglia is associated with poorer cognitive performance during adolescence.

Biological Psychiatry

9/18/19

Neurostructural Heterogenity in Mood and Anxiety Disorders

We used a semi-supervised machine learning tool to parse heterogeneity in mood and anxiety disorders in youth

Nature Protocols

11/16/18

Protocol for mitigating motion artifact

We define a structured protocol for the evaluation and mitigation of motion artifact in functional connectivity MRI.

Cerebral Cortex

4/21/18

Prematurity and Structural Brain Development

Prematurity is associated with the deficit in executive function and abnormalities in structural covariance networks.

Journal of Neuroscience

3/7/18

Cortical thickness and adolescent impulsivity

In collaboration with Joe Kable, we demonstrate that impulsive choice during adolescence is associated with reduced cortical thickness in regions critical for reward valuation.

Molecular Psychiatry

9/19/17

Overall psychopathology and cerebral blood flow

Higher levels of overall psychopathology across disorders are associated with differences in cerebral blood flow in key brain regions such as the anterior cingulate cortex.

Human Brain Mapping

5/11/17

Hypergraphs in developing networks

In collaborative work with Danielle Bassett, we uncover novel developmental network features in high-resolution network hypergraphs.

Current Opinion in Behavioral Sciences

8/1/16

Review: Executive function and development

We review recent work investigating the neural basis for executive development during childhood and adolescence.

JAMA Psychiatry

5/1/16

Structural brain abnormalities in psychosis spectrum youth

We document structural brain abnormalities in youth with psychosis-spectrum symptoms, including medial temporal lobe regions such as the hippocampus.

Neuropsychopharmacology

3/13/15

Common reward deficits in unipolar and bipolar depression

Similar reward system deficits are dimensionally present in both unipolar and bipolar depression.

NeuroImage

2/1/14

Neuroimaging of the Philadelphia Neurodevelopmental Cohort

This provides an overview of the imaging procedures of the PNC, a large-scale NIMH-funded study (PI: Raquel E. Gur).

NeuroImage

3/1/12

Motion and functional connectivity

We provide one of the first descriptions of motion artifact's impact on functional connectivity.