Parallel workflows for data-driven structural equation modeling in functional neuroimaging

Sarah Kenny, Michael Andric, Steven M. Boker, Michael C. Neale, Michael Wilde, Steven L. Small

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

We present a computational framework suitable for a data-driven approach to structural equation modeling (SEM) and describe several workflows for modeling functional magnetic resonance imaging (fMRI) data within this framework. The Computational Neuroscience Applications Research Infrastructure (CNARI) employs a high-level scripting language called Swift, which is capable of spawning hundreds of thousands of simultaneous R processes (R Development Core Team, 2008), consisting of self-contained SEMs, on a high performance computing system (HPC). These self-contained R processing jobs are data objects generated by OpenMx, a plug-in for R, which can generate a single model object containing the matrices and algebraic information necessary to estimate parameters of the model. With such an infrastructure in place a structural modeler may begin to investigate exhaustive searches of the model space. Specifi c applications of the infrastructure, statistics related to model fit, and limitations are discussed in relation to exhaustive SEM. In particular, we discuss how workfl ow management techniques can help to solve large computational problems in neuroimaging.

Original languageEnglish (US)
Article number34
JournalFrontiers in Neuroinformatics
Volume3
Issue numberOCT
DOIs
StatePublished - Oct 20 2009
Externally publishedYes

Fingerprint

Functional neuroimaging
Computing Methodologies
Space Simulation
Functional Neuroimaging
Workflow
Neurosciences
Neuroimaging
Language
Magnetic Resonance Imaging
Research
High level languages
Statistics
Scanning electron microscopy
Processing

Keywords

  • Exhaustive search
  • OpenMx
  • SEM
  • Swift
  • Workflows

ASJC Scopus subject areas

  • Neuroscience (miscellaneous)
  • Biomedical Engineering
  • Computer Science Applications

Cite this

Parallel workflows for data-driven structural equation modeling in functional neuroimaging. / Kenny, Sarah; Andric, Michael; Boker, Steven M.; Neale, Michael C.; Wilde, Michael; Small, Steven L.

In: Frontiers in Neuroinformatics, Vol. 3, No. OCT, 34, 20.10.2009.

Research output: Contribution to journalArticle

Kenny, Sarah ; Andric, Michael ; Boker, Steven M. ; Neale, Michael C. ; Wilde, Michael ; Small, Steven L. / Parallel workflows for data-driven structural equation modeling in functional neuroimaging. In: Frontiers in Neuroinformatics. 2009 ; Vol. 3, No. OCT.
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