Reduction of motion-related artifacts in resting state fMRI using aCompCor. - John Muschelli; Mary Beth Nebel; Brian S. Caffo; Anita D. Barber; James J. Pekar; Stewart H. Mostofsky (NeuroImage, 2014)

brainR: Interactive 3 and 4D Images of High Resolution Neuroimage Data. - John Muschelli; Elizabeth M. Sweeney; Ciprian M. Crainiceanu (R J., 2014)

Validated automatic brain extraction of head CT images. - John Muschelli; Natalie L. Ullman; W. Andrew Mould; Paul M. Vespa; Daniel F. Hanley; Ciprian M. Crainiceanu (NeuroImage, 2015)

fslr: Connecting the FSL Software with R. - John Muschelli; Elizabeth M. Sweeney; Martin A. Lindquist; Ciprian M. Crainiceanu (R J., 2015)

Removing inter-subject technical variability in magnetic resonance imaging studies. - Jean-Philippe Fortin; Elizabeth M. Sweeney; John Muschelli; Ciprian M. Crainiceanu; Russell T. Shinohara (NeuroImage, 2016)

MIMoSA: An Approach to Automatically Segment T2 Hyperintense and T1 Hypointense Lesions in Multiple Sclerosis. - Alessandra M. Valcarcel; Kristin A. Linn; Fariha Khalid; Simon N. Vandekar; Shahamat Tauhid; Theodore D. Satterthwaite; John Muschelli; Rohit Bakshi; Russell T. Shinohara (BrainLes@MICCAI (1), 2018)

freesurfer: Connecting the Freesurfer software with R. - John Muschelli; Elizabeth M. Sweeney; Ciprian M. Crainiceanu (F1000Research, 2018)

Recommendations for Processing Head CT Data. - John Muschelli (Frontiers Neuroinformatics, 2019)

Analysis of Student Behavior Using the R Package crsra. - Aboozar Hadavand; John Muschelli; Jeffrey T. Leek (J. Learn. Anal., 2019)

Statistical Methods for Processing Neuroimaging Data from Two Different Sites with a Down Syndrome Population Application. - Davneet S. Minhas; Zixi Yang; John Muschelli; Charles M. Laymon; Joseph M. Mettenburg; Matthew D. Zammit; Sterling C. Johnson; Chester A. Mathis; Ann D. Cohen; Benjamin L. Handen; William E. Klunk; Ciprian M. Crainiceanu; et al. (IPMU (3), 2020)

A Publicly Available, High Resolution, Unbiased CT Brain Template. - John Muschelli (IPMU (3), 2020)

ROC and AUC with a Binary Predictor: a Potentially Misleading Metric. - John Muschelli (J. Classif., 2020)

Rxnat: An Open-Source R Package for XNAT-Based Repositories. - Adrian Gherman; John Muschelli; Brian Caffo; Ciprian M. Crainiceanu (Frontiers Neuroinformatics, 2020)

ari: The Automated R Instructor. - Sean Kross; Jeffrey T. Leek; John Muschelli (R J., 2020)

A multi-scanner neuroimaging data harmonization using RAVEL and ComBat. - Mahbaneh Eshaghzadeh Torbati; Davneet S. Minhas; Ghasan Ahmad; Erin O'Connor; John Muschelli; Charles M. Laymon; Zixi Yang; Ann D. Cohen; Howard J. Aizenstein; William E. Klunk; Bradley T. Christian; Seong Jae Hwang; et al. (NeuroImage, 2021)

Moderated t-tests for group-level fMRI analysis. - Guoqing Wang; John Muschelli; Martin A. Lindquist (NeuroImage, 2021)

3D Deep Neural Network Segmentation of Intracerebral Hemorrhage: Development and Validation for Clinical Trials. - Matthew F. Sharrock; W. Andrew Mould; Hasan Ali; Meghan Hildreth; Issam A. Awad; Daniel F. Hanley; John Muschelli (Neuroinformatics, 2021)

Diurnal Physical Activity Patterns across Ages in a Large UK Based Cohort: The UK Biobank Study. - Julia Wrobel; John Muschelli; Andrew Leroux (Sensors, 2021)

Open-source Tools for Training Resources - OTTR. - Candace Savonen; Carrie Wright; Ava M. Hoffman; John Muschelli; Katherine E. L. Cox; Frederick J. Tan; Jeffrey T. Leek (CoRR, 2022)

ciftiTools: A package for reading, writing, visualizing, and manipulating CIFTI files in R. - Damon D. Pham; John Muschelli; Amanda F. Mejia (NeuroImage, 2022)

ModelArray: An R package for statistical analysis of fixel-wise data. - Chenying Zhao; Tinashe M. Tapera; Joëlle Bagautdinova; Josiane Bourque; Sydney Covitz; Raquel E. Gur; Ruben C. Gur; Bart Larsen; Kahini Mehta; Steven L. Meisler; Kristin Murtha; John Muschelli; et al. (NeuroImage, 2023)