Robust resting state fMRI processing for studies on typical brain development based on multi-echo EPI acquisition

Prantik Kundu, Brenda E. Benson, Katherine L. Baldwin, Dana Rosen, Wen Ming Luh, Peter A. Bandettini, Daniel S. Pine, Monique Ernst

Research output: Contribution to journalArticlepeer-review

31 Scopus citations


Several methodological challenges affect the study of typical brain development based on resting state blood oxygenation level dependent (BOLD) functional MRI (fMRI). One such challenge is mitigating artifacts such as those from head motion, known to be more substantial in younger subjects than older subjects. Other challenges include controlling for potential age-dependence in cerebrospinal fluid (CSF) volume affecting anatomical-functional coregistration; in vascular density affecting BOLD contrast-to-noise; and in CSF pulsation creating time series artifacts. Historically, these confounds have been approached through incorporating artifact-specific temporal and/or spatial filtering into preprocessing pipelines. However, such paths often come with new confounds or limitations. In this study we take the approach of a bottom-up revision of fMRI methodology based on acquisition of multi-echo fMRI and comprehensive utilization of the information in the TE-domain to enhance several aspects of fMRI analysis in the context of a developmental study. We show in a cohort of 25 healthy subjects, aged 9 to 43 years, that the analysis of multi-echo fMRI data eliminates a number of arbitrary processing steps such as bandpass filtering and spatial smoothing, while enabling procedures such as (Formula presented.) mapping, BOLD contrast normalization and signal dropout recovery, precise anatomical-functional coregistration based on T2 measurements, automatic denoising through removing subject motion, scanner-related signal drifts and physiology, as well as statistical inference for seed-based connectivity. These enhancements are of both theoretical significance and practical benefit in the study of typical brain development.

Original languageEnglish (US)
Pages (from-to)56-73
Number of pages18
JournalBrain Imaging and Behavior
Issue number1
StatePublished - Mar 11 2015


  • Aging
  • BOLD
  • Coregistration
  • Denoising
  • Functional connectivity
  • ICA
  • PCA
  • Seed-based
  • T

ASJC Scopus subject areas

  • Radiology Nuclear Medicine and imaging
  • Neurology
  • Clinical Neurology
  • Cognitive Neuroscience
  • Cellular and Molecular Neuroscience
  • Psychiatry and Mental health
  • Behavioral Neuroscience


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