Philip A. Cook

ComBat-Predict enhances generalizability of neuroimaging models to new sites

ComBat-Predict improves the generalizability of neuroimaging models to new sites by harmonizing site effects and reducing bias in cortical thickness predictions.

Deep Computational Anatomy via Latent-Aligned Multiview Normalizing Flows

The paper introduces LAMNr flows for multimodal data analysis, enabling shared latent subspaces and cross-view imputation, with applications in biological imaging.

Highly replicable multisite patterns of adolescent white matter maturation

The paper presents a curated dataset of processed diffusion MRI data from the ABCD Study, showing that specific diffusion metrics are sensitive to adolescent white matter development and robust to image quality variation.

Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications

The paper describes improvements in diffusion MRI processing for the HBCD study, introducing new software and observing developmental patterns in brain data.

Changes in brain connectivity and neurovascular dynamics during dexmedetomidine-induced loss of consciousness

This study examines changes in brain connectivity and neurovascular dynamics during dexmedetomidine-induced unconsciousness and recovery, finding widespread connectivity decreases and cerebellum-specific increases in structure-function coupling.

Parameter Efficient Fine-tuning of Transformer-based Masked Autoencoder Enhances Resource Constrained Neuroimage Analysis

This study evaluates parameter-efficient fine-tuning methods for vision transformers in neuroimaging, showing they outperform full fine-tuning and training from scratch with fewer parameters.

A sensorimotor-association axis of thalamocortical connection development

The paper shows thalamocortical connections develop along a sensorimotor-association gradient in youth, linking structural connectivity to cortical plasticity and environmental sensitivity.

Diffusion MRI Head Motion Correction Methods are Highly Accurate but Impacted by Denoising and Sampling Scheme

This study evaluates head motion correction methods in diffusion MRI, showing both Eddy and SHORELine perform well but are affected by denoising and sampling schemes.

Development of White Matter Fiber Covariance Networks Supports Executive Function in Youth

This study identifies white matter fiber covariance networks in youth, showing their development aligns with executive function and hierarchical cortical maturation patterns.

Comparison of Anatomical and Diffusion MRI for detecting Parkinson's Disease using Deep Convolutional Neural Network

This study compares anatomical and diffusion MRI for Parkinson's disease detection using deep convolutional neural networks, finding that dMRI-based models show promise for classification.

Establishing the Validity of Compressed Sensing Diffusion Spectrum Imaging

This study evaluates six compressed sensing diffusion spectrum imaging (CS-DSI) schemes, finding they provide accurate and reliable white matter structure measures with up to 80% reduced scan time compared to full DSI.

Removal of Scanner Effects in Covariance Improves Multivariate Pattern Analysis in Neuroimaging Data

This paper shows that removing scanner effects in mean and variance is insufficient for multivariate pattern analysis and proposes a method to harmonize covariance across scanners.

3D Convolutional Neural Networks for Classification of Alzheimer's and Parkinson's Disease with T1-Weighted Brain MRI

This paper proposes a 3D CNN for classifying Alzheimer's and Parkinson's disease using T1-weighted MRI, achieving higher ROC-AUC than random forest on multiple datasets.

FlywheelTools: Data Curation and Manipulation on the Flywheel Platform

FlywheelTools provides software for reproducible data curation and manipulation on the Flywheel platform, addressing challenges in converting neuroimaging data to BIDS format.

Transdiagnostic dimensions of psychopathology explain individuals' unique deviations from normative neurodevelopment in brain structure

The paper models cortical brain deviations from normative neurodevelopment to predict psychiatric symptoms, finding that transdiagnostic psychopathology dimensions better predict symptoms than specific disorder measures.

Differential impact of transdiagnostic, dimensional psychopathology on multiple scales of functional connectivity

The paper examines how different psychopathology dimensions affect various scales of brain functional connectivity using multiple modeling approaches.

QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI

QSIPrep is a software platform for preprocessing diffusion MRI data that supports multiple sampling schemes and ensures reproducibility through standardized workflows and quality measures.

Longitudinal ComBat: A Method for Harmonizing Longitudinal Multi-scanner Imaging Data

The paper introduces longitudinal ComBat to harmonize multi-scanner imaging data, showing it improves detection of longitudinal changes and controls type I error better than existing methods.

Development of structure-function coupling in human brain networks during youth

This study examines how structure-function coupling in brain networks develops during youth, finding it aligns with cortical hierarchies and supports cognitive improvements.

Advantages of Multi-shell Diffusion Models for Studies of Brain Development in Youth

This study evaluates DTI, NODDI, and MAPL in youth to assess their associations with age and motion, finding that multi-shell models offer advantages for neurodevelopmental studies despite motion sensitivity.

The ANTs Longitudinal Cortical Thickness Pipeline

The paper introduces an ANTs-based longitudinal cortical thickness pipeline and demonstrates its effectiveness in analyzing ADNI-1 data for detecting structural brain changes over time.

Linked dimensions of psychopathology and connectivity in functional brain networks

The paper identifies brain-based dimensions of psychopathology using sCCA in youths, finding four dimensions linked to functional dysconnectivity that replicate in an independent dataset.

Accelerated Cortical Thinning within Structural Brain Networks is Associated with Irritability in Youth

This study links accelerated cortical thinning in structural brain networks to irritability in youth, highlighting associations in emotion-related brain regions.

Diminished Cortical Thickness is Associated with Impulsive Choice in Adolescence

The paper examines the association between cortical thickness and impulsive choice in adolescents, finding reduced cortical thickness in specific brain regions linked to impulsive decision-making.

Data-driven Assessment of Structural Image Quality

The paper develops an automated method to assess structural brain image quality using Euler number and validates its effectiveness in identifying low-quality images and its relationship with cortical thickness and age-related associations.

Harmonization of cortical thickness measurements across scanners and sites

ComBat, an empirical Bayes location-and-scale model from genomics, removes additive and multiplicative scanner effects from regional cortical thickness across 11 scanners while preserving age associations.

The Impact of In-Scanner Head Motion on Structural Connectivity Derived from Diffusion Tensor Imaging

This paper evaluates how in-scanner head motion affects structural connectivity estimates from diffusion tractography in a developmental cohort, showing motion biases connectivity strength in a consistency and length-dependent manner.