Visualizing temporal brain-state changes for fMRI using t-distributed stochastic neighbor embedding

Harshit Parmar, Brian Nutter, Rodney Long, Sameer Antani, Sunanda Mitra

Research output: Contribution to journalArticlepeer-review


Purpose: Currently, functional magnetic resonance imaging (fMRI) is the most commonly used technique for obtaining dynamic information about the brain. However, because of the complexity of the data, it is often difficult to directly visualize the temporal aspect of the fMRI data. Approach: We outline a t-distributed stochastic neighbor embedding (t-SNE)-based postprocessing technique that can be used for visualization of temporal information from a 4D fMRI data. Apart from visualization, we also show its utility in detection of major changes in the brain meta-states during the scan duration. Results: The t-SNE approach is able to detect brain-state changes from task to rest and vice versa for single- and multitask fMRI data. A temporal visualization can also be obtained for task and resting state fMRI data for assessing the temporal dynamics during the scan duration. Additionally, hemodynamic delay can be quantified by comparison of the detected brain-state changes with the experiment paradigm for task fMRI data. Conclusion: The t-SNE visualization can visualize help identify major brain-state changes from fMRI data. Such visualization can provide information about the degree of involvement and attentiveness of the subject during the scan and can be potentially utilized as a quality control for subject's performance during the scan.

Original languageEnglish
Article number046001
JournalJournal of Medical Imaging
Issue number4
StatePublished - Jul 1 2021


  • brain-state changes
  • dimensionality reduction
  • functional MRI visualization
  • t -distributed stochastic neighbor embedding


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