Feasibility of topological data analysis for event-related fMRI

Cameron T. Ellis, Michael Lesnick, Gregory Henselman-Petrusek, Bryn Keller, Jonathan D. Cohen

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Recent fMRI research shows that perceptual and cognitive representations are instantiated in high-dimensional multivoxel patterns in the brain. However, the methods for detecting these representations are limited. Topological data analysis (TDA) is a new approach, based on the mathematical field of topology, that can detect unique types of geometric features in patterns of data. Several recent studies have successfully applied TDA to study various forms of neural data; however, to our knowledge, TDA has not been successfully applied to data from event-related fMRI designs. Event-related fMRI is very common but limited in terms of the number of events that can be run within a practical time frame and the effect size that can be expected. Here, we investigate whether persistent homology—a popular TDA tool that identifies topological features in data and quantifies their robustness—can identify known signals given these constraints. We use fmrisim, a Python-based simulator of realistic fMRI data, to assess the plausibility of recovering a simple topological representation under a variety of conditions. Our results suggest that persistent homology can be used under certain circumstances to recover topological structure embedded in realistic fMRI data simulations.

Original languageEnglish (US)
Pages (from-to)695-706
Number of pages12
JournalNetwork Neuroscience
Issue number3
StatePublished - Jan 1 2019

All Science Journal Classification (ASJC) codes

  • Artificial Intelligence
  • Applied Mathematics
  • General Neuroscience
  • Computer Science Applications


  • Event-related design
  • FMRI
  • Persistent homology
  • Representation
  • Simulation
  • Topological data analysis


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